US20200030432A1 - Zoonotic disease rna vaccines - Google Patents

Zoonotic disease rna vaccines Download PDF

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US20200030432A1
US20200030432A1 US16/494,988 US201816494988A US2020030432A1 US 20200030432 A1 US20200030432 A1 US 20200030432A1 US 201816494988 A US201816494988 A US 201816494988A US 2020030432 A1 US2020030432 A1 US 2020030432A1
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vaccine
zoonotic disease
antigen
disease vaccine
rna
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Giuseppe Ciaramella
Sunny Himansu
Vladimir Presnyak
Kerry Benenato
Ellalahewage Sathyajith Kumarasinghe
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ModernaTx Inc
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ModernaTx Inc
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Assigned to MODERNATX, INC. reassignment MODERNATX, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: PRESNYAK, Vladimir, HIMANSU, Sunny, KUMARASINGHE, ELLALAHEWAGE SATHYAJITH, CIARAMELLA, GIUSEPPE, BENENATO, Kerry
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    • A—HUMAN NECESSITIES
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    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
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    • A—HUMAN NECESSITIES
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    • A61K31/7115—Nucleic acids or oligonucleotides having modified bases, i.e. other than adenine, guanine, cytosine, uracil or thymine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • A61P31/16—Antivirals for RNA viruses for influenza or rhinoviruses
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/86—Viral vectors
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/53—DNA (RNA) vaccination
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/545—Medicinal preparations containing antigens or antibodies characterised by the dose, timing or administration schedule
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    • C12N2760/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses negative-sense
    • C12N2760/00011—Details
    • C12N2760/14011—Filoviridae
    • C12N2760/14111—Ebolavirus, e.g. Zaire ebolavirus
    • C12N2760/14134—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
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    • C12N2760/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses negative-sense
    • C12N2760/00011—Details
    • C12N2760/18011—Paramyxoviridae
    • C12N2760/18211—Henipavirus, e.g. hendra virus
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    • C12N2760/00011—Details
    • C12N2760/18011—Paramyxoviridae
    • C12N2760/18211—Henipavirus, e.g. hendra virus
    • C12N2760/18234—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
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    • C12N2760/00011—Details
    • C12N2760/18011—Paramyxoviridae
    • C12N2760/18611—Respirovirus, e.g. Bovine, human parainfluenza 1,3
    • C12N2760/18634—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2770/00011—Details
    • C12N2770/20011—Coronaviridae
    • C12N2770/20034—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein

Definitions

  • Zoonotic diseases are infectious diseases that are naturally transmitted from vertebrate animals to humans and vice versa. They are caused by all types of pathogenic agents, including bacteria, parasites, fungi, viruses and prions. In regions densely populated with both people and livestock, zoonotic diseases can spread very quickly. With changes in the environment, human behavior and habitat, increasingly these infections are emerging from wildlife species. Specific examples of zoonotic viruses include Lassa virus, Nipah virus, and betacoronaviruses.
  • Lassa virus a segmented negative-sense RNA virus that belongs to the family Arenaviridae, is endemic to West Africa. Transmission typically occurs through contact with infected rodents or virus-contaminated rodent excreta, and person-to-person transmission.
  • the LASV expresses just one protein on its surface, termed GPC, which mediates both attachment to and entry of host cells.
  • GPC is a class I viral fusion protein that forms trimers on the viral surface. Each monomer in the trimer is assembled by distinct GP1 and GP2 subunits that mediate receptor binding and membrane fusion, respectively.
  • GP2 is coiled about the base of GP1 in a structure that is only metastable.
  • the complex is prone to rapid disassembly of GP1 from GP2 and rearrangement of the GP2 into a much more stable six-helix bundle.
  • the release of energy achieved by collapsing of the metastable viral-surface conformation to the much more stable six-helix bundle conformation drives fusion of viral and host membranes during infection.
  • Because of its metastability it is difficult to maintain GPC on its trimeric pre-fusion configuration when expressed recombinantly or even when expressed on some particle surfaces.
  • Antibodies against the resulting separated subunits are not potently neutralizing.
  • prior vaccine approaches that included natural GPC failed to elicit an effective antibody response, leading vaccine manufacturers to instead focus on induction of cell-mediated immunity as the most likely correlate of protection. Further, in the absence of knowledge about how to create or purify stabilized Lassa virus GPC trimeric, vaccine makers did not have the necessary reagents to evaluate the most ideal antibody responses.
  • the structure of the viral surface GP trimer remained unknown for Lassa and all other arenaviruses until this year.
  • Nipah virus of the genus henipahvirus (which includes Hendra virus) is part of the paramyxovirus family (see FIG. 7 ). Nipah first emerged in Malaysia in 1998, initially in domestic pigs and subsequently causing severe disease in humans, eventually killing over 1000 people. New outbreaks have occurred every year since, with fatality rates ranging from 40-70%. Nipah virus is classified as a BSL-4 agent and as a Category C priority pathogen by the CDC and NIAID. The primary reservoir is Pteropus bats; however, the virus is able to infect and replicate in many mammals (Luby et al 2013; Angeletti et al 2016).
  • MERS-CoV Middle Eastern Respiratory Syndrome Coronavirus
  • RNA ribonucleic acid
  • ORF open reading frame
  • IM intramuscular
  • the ORF encodes a Lassa virus antigen.
  • the Lassa virus antigen comprises a glycoprotein.
  • the Lassa virus antigen comprises a Lassa virus glycoprotein precursor (GPC), a structurally stabilized Lassa virus GPC, an ectodomain of Lassa virus glycoprotein 1 (GP1), or a Lassa virus glycoprotein 2 (GP2).
  • GPC Lassa virus glycoprotein precursor
  • GP1 a Lassa virus glycoprotein precursor
  • GP2 a Lassa virus glycoprotein 1
  • GP2 a Lassa virus glycoprotein 2
  • the Lassa virus antigen comprises amino acid residues 59-259 of a Lassa virus GPC.
  • the Lassa virus antigen comprises a nucleocapsid protein (NP).
  • NP nucleocapsid protein
  • the Lassa virus antigen has an amino acid sequence that has at least 90%, at least 95%, or at least 99% identity to an amino acid sequence identified by any one of SEQ ID NO: 1-3, but does not include wild-type protein sequence.
  • the Lassa virus antigen has an amino acid sequence of any one of SEQ ID NO: 1-3.
  • the RNA comprising an ORF sequence has at least 90%, at least 95%, or at least 99% identity to a nucleic acid sequence identified by any one of SEQ ID NO: 6, 7 or 9, but does not include wild-type protein sequence.
  • the RNA comprising an ORF sequence comprises a nucleic acid sequence of any one of SEQ ID NO: 6, 7 or 9.
  • the ORF encodes a Nipah virus antigen and/or a Hendra virus antigen.
  • the Nipah virus antigen and/or a Hendra virus antigen comprises a hemagglutinin-neuraminidase protein (HN), a hemagglutinin protein (H), or a glycoprotein (G).
  • HN hemagglutinin-neuraminidase protein
  • H hemagglutinin protein
  • G glycoprotein
  • the Nipah virus antigen and/or a Hendra virus antigen comprises an attachment glycoprotein, optionally a type II membrane protein.
  • the Nipah virus antigen and/or a Hendra virus antigen comprises a fusion (F) glycoprotein.
  • the F glycoprotein comprises a trimeric class I fusogenic envelope glycoprotein containing two heptad repeat (HR) regions and a hydrophobic fusion peptide.
  • the Nipah virus antigen and/or a Hendra virus antigen is a Nipah virus antigen.
  • the Nipah virus antigen and/or a Hendra virus antigen is a Hendra virus antigen.
  • the Nipah virus antigen and/or a Hendra virus antigen has an amino acid sequence that has at least 90%, at least 95%, or at least 99% identity to an amino acid sequence identified by any one of SEQ ID NO: 10-13 but does not include wild-type protein sequence.
  • the Nipah virus antigen and/or a Hendra virus antigen has an amino acid sequence of any one of SEQ ID NO: 10-13.
  • the RNA comprising an ORF sequence has at least 90%, at least 95%, or at least 99% identity to a nucleic acid sequence identified by SEQ ID NO: 16 or 17, but does not include wild-type protein sequence.
  • the RNA comprising an ORF sequence comprises a nucleic acid sequence of SEQ ID NO: 16 or 17.
  • the ORF encodes a middle east respiratory syndrome coronavirus (MERS-CoV) antigen and/or a severe acute respiratory syndrome-like coronavirus WIV1 (SL-CoV-WIV1) antigen.
  • MERS-CoV middle east respiratory syndrome coronavirus
  • SL-CoV-WIV1 severe acute respiratory syndrome-like coronavirus WIV1
  • the MERS-CoV antigen and/or a SL-CoV-WIV1 antigen comprises a betacoronavirus structural protein.
  • the betacoronavirus structural protein is spike protein, envelope protein, nucleocapsid protein, or membrane protein.
  • rein the betacoronavirus structural protein is spike protein.
  • the betacoronavirus structural protein a S1 subunit of the spike protein or a S2 subunit of the spike protein.
  • the MERS-CoV antigen and/or a SL-CoV-WIV1 antigen is a MERS-CoV antigen.
  • the MERS-CoV antigen and/or a SL-CoV-WIV1 antigen is a SL-CoV-WIV1 antigen.
  • the MERS-CoV antigen and/or a SL-CoV-WIV1 antigen has an amino acid sequence that has at least 90%, at least 95%, or at least 99% identity to an amino acid sequence identified SEQ ID NO: 18 but does not include wild-type protein sequence.
  • the MERS-CoV antigen and/or a SL-CoV-WIV1 antigen has an amino acid sequence of SEQ ID NO: 18.
  • the RNA comprising an ORF sequence has at least 90%, at least 95%, or at least 99% identity to a nucleic acid sequence identified by SEQ ID NO: 18, but does not include wild-type protein sequence.
  • the RNA comprising an ORF sequence comprises a nucleic acid sequence of SEQ ID NO: 18.
  • IM administration of a therapeutically effective amount of the vaccine to a subject induces a neutralizing antibody titer in the subject.
  • the neutralizing antibody titer is at least 100 neutralizing units per milliliter (NU/mL), at least 500 NU/mL, or at least 1000 NU/mL.
  • the neutralizing antibody titer is sufficient to reduce viral infection of B cells by at least 50% relative to a neutralizing antibody titer of an unvaccinated control subject or relative to a neutralizing antibody titer of a subject vaccinated with a live attenuated viral vaccine, an inactivated viral vaccine, or a protein subunit viral vaccine.
  • the neutralizing antibody titer is induced in the subject following fewer than three doses of the vaccine.
  • a single dose is of 10 ⁇ g-100 ⁇ g.
  • the neutralizing antibody titer and/or a T cell immune response is sufficient to reduce the rate of asymptomatic viral infection relative to the neutralizing antibody titer of unvaccinated control subjects.
  • the neutralizing antibody titer and/or a T cell immune response is sufficient to prevent viral latency the subject.
  • the neutralizing antibody titer is sufficient to block fusion of virus with epithelial cells and/or B cells of the subject.
  • the neutralizing antibody titer is induced within 20 days following a single 10-100 ⁇ g of the vaccine, or within 40 days following a second 10-100 ⁇ g dose of the vaccine.
  • IM administration of a therapeutically effective amount of the vaccine to a subject induces a T cell immune response in the subject.
  • the T cell immune response comprises a CD4 + T cell immune response and/or a CD8 + T cell immune response.
  • the antigen is expressed on the surface of cells of the subject.
  • the vaccine comprises
  • RNA ribonucleic acid
  • ORF open reading frame
  • the vaccine comprises a RNA having an ORF encoding two antigens formulated in a lipid nanoparticle.
  • the vaccine comprises two RNAs, each having an ORF encoding an antigen, wherein the two RNAs are formulated in a single lipid nanoparticle or wherein the each RNAs is formulated in a single lipid nanoparticle.
  • the vaccine further comprises at least one additional RNA having an ORF encoding at least one additional antigen.
  • the lipid nanoparticle comprises a molar ratio of 20-60% ionizable cationic lipid, 5-25% non-cationic lipid, 25-55% sterol, and 0.5-15% PEG-modified lipid
  • the antigen is fused to a signal peptide.
  • the antigen is fused to a scaffold moiety.
  • the scaffold moiety is selected from the group consisting of: ferritin, encapsulin, lumazine synthase, hepatitis B surface antigen, and hepatitis B core antigen.
  • the RNA comprises messenger RNA (mRNA).
  • mRNA messenger RNA
  • the RNA further comprises a 5′UTR and/or a 3′UTR.
  • the RNA is unmodified.
  • the RNA comprise a modified nucleotide.
  • At least 80% of the uracil in the ORF comprise 1-methyl-pseudouridine modification.
  • Some aspects of the present disclosure provide methods comprising administering to a subject the zoonotic disease vaccine in a therapeutically effective amount to induce an immune response in the subject.
  • the therapeutically effective amount induces a neutralizing antibody titer and/or a T cell immune response in the subject.
  • the vaccine is at least 80% relative to unvaccinated control subjects.
  • detectable levels of the antigen are produced in the serum of the subject at 1-72 hours post administration of the vaccine.
  • a neutralizing antibody titer of at least 100 NU/ml, at least 500 NU/ml, or at least 1000 NU/ml is produced in the serum of the subject at 1-72 hours post administration of the vaccine.
  • the therapeutically effective amount is a total dose of 20 ⁇ g-200 ⁇ g or a total dose of 50 ⁇ g-100 ⁇ g.
  • FIG. 1 shows the crystal structure of Lassa virus GPC in its trimeric, pre-fusion viral surface conformation.
  • the three monomers are colored purple, orange and green, respectively, with the GP1 subunits in a light shade and GP2 subunits in a darker shade of each color.
  • These structures illustrate the assembly surfaces of the trimer and quaternary epitopes at the base and apex that are formed only when the subunits assemble together in the trimer.
  • FIG. 2 shows anti-Ebola virus glycoprotein mouse IgG titers on 7 and 19 days post dose 2.
  • FIG. 3 shows the Ebola lethal challenge model study design.
  • AG1 represents the designated Ebola GP mRNA vaccine, and
  • AG2 represents the mRNA vaccine expressing wild type GP.
  • FIG. 4 shows mortality analysis of Guinea pigs in the Ebola challenge model.
  • FIG. 5 shows the average group weight loss post Ebola challenge.
  • FIG. 6 shows morbidity scores for individual animals.
  • FIG. 7 shows the paramyxovirus family.
  • FIG. 8 shows experimental design for the cotton rat challenge study.
  • FIG. 9 shows viral titers (top panel) and serum PIV3 neutralizing antibody titers (bottom panel) in cotton rats.
  • FIG. 10 shows viral titers (top panel) and serum PIV3 neutralizing antibody titers (bottom panel) in African green monkeys.
  • FIG. 11 shows VN titers in Balb/C mice after 2-dose immunization with MERS-CoV spike protein mRNA vaccine.
  • FIG. 12 shows VN titers against MERS-CoV after prime only (left), prime-boost (middle) or placebo (right) treatment. Individual values are shown as well as the geometric mean titer.
  • FIG. 13 shows MERS-CoV PCR and titration levels in nose swabs after challenge in prime only (left), prime-boost (middle) or placebo (right) treated animals.
  • Panels A-C Individual PCR values are shown as well as the lower limit of detection (1.2 log 10 CDU/mL). Samples below the lower limit of detection are plotted as 1.1 log 10 CDU/mL.
  • Panels D-F Individual viral titration values are shown as well as the lower limit of detection (0.8 log 10 TCID50/mL). Samples below the lower limit of detection are plotted as 0.7 log 10 TCID50/mL.
  • FIG. 14 shows MERS-CoV PCR and titration levels in throat swabs after challenge in prime only (left), prime-boost (middle) or placebo (right) treated animals.
  • Panels A-C Individual PCR values are shown as well as the lower limit of detection (1.2 log 10 CDU/mL). Samples below the lower limit of detection are plotted as 1.1 log 10 CDU/mL.
  • Panels D-F Individual titration values are shown as well as the lower limit of detection (0.8 log 10 TCID50/mL). Samples below the lower limit of detection are plotted as 0.7 log 10 TCID50/mL.
  • FIG. 15 shows MERS-CoV PCR (left panel) and titration (right panel) results in pooled lung samples after challenge in prime only (1a), prime-boost (1b) or placebo (2) treated groups. Individual values are shown as well as the (range of the) lower limit of detection of PCR (2.8 log 10 CDU/g) and virus titration (1.2-1.4 log 10 TCID50/g).
  • LASV is an arenavirus (negative ssRNA) that represents a significant unmet global health care need.
  • LASV expresses just one protein on its surface, termed GPC, which mediates both attachment to and entry of host cells.
  • GPC is a class I viral fusion protein that forms trimers on the viral surface. Each monomer in the trimer is assembled by distinct GP1 and GP2 subunits that mediate receptor binding and membrane fusion, respectively.
  • GP2 is coiled about the base of GP1 in structure that is only metastable. The complex is prone to rapid disassembly of GP1 from GP2 and rearrangement of the GP2 into a much more stable six-helix bundle.
  • the mRNA vaccines of the disclosure have been designed to express viral membrane bound proteins (B cell antigens) as well as intracellular proteins (T cell antigens).
  • Arenaviruses including LASV are pleomorphic enveloped viruses with membrane GP glycoprotein as the major surface antigen.
  • the Lassa glycoprotein is a potent vaccine antigen with structural similarities to Ebola glycoproteins.
  • the disclosure in some aspects includes, a mRNA vaccine expressing full length-membrane bound Lassa glycoprotein precursor GPC.
  • the GPC precursor mRNA once translated will be matured through a natural process by the cellular proteases into the fully matured GP glycoprotein.
  • the membrane anchored version of this protein will form trimers on cell surfaces and recognized by the immune system to generate humoral and cellular responses.
  • the most effective anti LASV antibodies are directed against a quaternary epitopes on GPC (those only formed when both GP1 and GP2 are intertwined, and three GP1-GP2 monomers form the proper trimer).
  • Engineering and stabilization of GPC to firmly remain in this assembly allows recognition by the most potent human antibodies, and that the potent antibodies themselves are sufficient to provide post-exposure protection, even late in the disease course.
  • the properly stabilized GPC trimer displays key quaternary epitopes that lead to broadly reactive, potent, and protective antibodies.
  • the mRNA vaccines of the disclosure in some embodiments are designed to produce these unique stabilized GPCs in order to provoke production of the type and quality of neutralizing antibody necessary for eliminating the virus in the host.
  • Nipah virus (NiV) and Hendra virus (HeV) are part of the paramyxovirus family.
  • Virus-cell fusion by the paramyxoviruses is mediated by both an attachment protein (which can vary by genus) and a fusion (F) protein, which is well conserved throughout the family.
  • attachment protein which can vary by genus
  • F fusion
  • Parainfluenza virus 3 (PIV3, genus respirovirus), is closely related to Nipah virus.
  • a mRNA vaccine against PIV3 encoding the PIV3 F protein which exists functionally as a membrane bound trimer of two disulfide-linked subunits has been developed. Applicants have demonstrated that this PIV3 mRNA vaccine drives the efficient expression of this protein in its biologically relevant conformation, thus generating a robust neutralizing response.
  • Paramyxoviruses such as HeV and NiV possess two major membrane-anchored glycoproteins in the envelope of the viral particle.
  • One glycoprotein is required for virion attachment to receptors on host cells and is designated as either hemagglutinin-neuraminidase protein (HN) or hemagglutinin protein (H), and the other is glycoprotein (G), which has neither hemagglutination nor neuraminidase activities.
  • the attachment glycoproteins are type II membrane proteins, where the molecule's amino (N) terminus is oriented toward the cytoplasm and the protein's carboxy (C) terminus is extracellular.
  • the other major glycoprotein is the fusion (F) glycoprotein, which is a trimeric class I fusogenic envelope glycoprotein containing two heptad repeat (HR) regions and a hydrophobic fusion peptide.
  • F fusion glycoprotein
  • HeV and NiV infect cells though a pH-independent membrane fusion process into receptive host cells through the concerted action of their attachment G glycoprotein and F glycoprotein following receptor binding.
  • the primary function of the HeV and NiV attachment G glycoprotein is to engage appropriate receptors on the surfaces of host cells, which for the majority of well-characterized paramyxoviruses are sialic acid moieties.
  • the HeV and NiV G glycoproteins utilize the host cell protein receptors ephrin B2 and/or ephrin B3 and antibodies have been developed which block viral attachment by the G glycoprotein.
  • mRNA vaccines based on Nipah and Hendra F proteins have been developed. Additionally, soluble Nipah glycoprotein (G) vaccines and Hendra glycoprotein (G) vaccines are encompassed by the disclosure. In some aspects the vaccines may include F and G alone and/or in combination at different ratios.
  • Nipah F The fusion glycoprotein (F) of Nipah virus mediates membrane fusion and is required for viral entry.
  • Nipah F like RSV F, is a class I fusion protein and they have similar structures and functions.
  • the vaccines of the disclosure include stabilizing mutations to maintain the prefusion structure of Nipah F. Ideally stabilized mutants will maintain biophysical properties including structure and antigenicity.
  • RNA vaccines that include polynucleotide encoding a Middle East respiratory syndrome coronavirus (MERS-CoV) antigen and/or Bat SARS-like coronavirus WIV1, (SL-CoV-WIV1).
  • MERS-CoV Middle East respiratory syndrome coronavirus
  • SL-CoV-WIV1 Bat SARS-like coronavirus WIV1,
  • MERS-CoV is a positive-sense, single-stranded RNA virus of the genus Betacoronavirus.
  • the genomes are phylogenetically classified into two clades, clade A and clade B. It has a strong tropism for non-ciliated bronchial epithelial cells, evades the innate immune response and antagonizes interferon (IFN) production in infected cells.
  • Dipeptyl peptidase 4 (DDP4, also known as CD26) has been identified as a functional cellular receptor for MERS-CoV. Its enzymatic activity is not required for infection, although its amino acid sequence is highly conserved across species and is expressed in the human bronchial epithelium and kidneys. Most infected individuals develop severe acute respiratory illnesses, including fever, cough, and shortness of breath, and the virus can be fatal. The disease may be transmitted among humans, generally among those in close contact.
  • Bat SARS-like coronavirus WIV1, (SL-CoV-WIV1) or SARS-like coronavirus WIV1 (WIV1) was isolated recently from Chinese rufous horseshoe bats. It is a single-stranded, enveloped, positive-sense RNA betacoronavirus. It has been demonstrated by phylogenetic analysis direct transmission of SARS from bats to humans may occur without intermediary Chinese civets.
  • MERS-CoV encodes at least four unique accessory proteins, such as 3, 4a, 4b and 5, two replicase proteins (open reading frame 1a and 1b), and four major structural proteins, including spike (S), envelope (E), nucleocapsid (N), and membrane (M) proteins (Almazan F et al. MBio 2013; 4(5):e00650-13).
  • the accessory proteins play nonessential roles in MERS-CoV replication, but they are likely structural proteins or interferon antagonists, modulating in vivo replication efficiency and/or pathogenesis, as in the case of SARS-CoV (Almazan F et al. MBio 2013; 4(5):e00650-13; Totura A L et al.
  • the other proteins of MERS-CoV maintain different functions in virus replication.
  • the E protein involves in virulence, and deleting the E-coding gene results in replication-competent and propagation-defective viruses or attenuated viruses (Almazan F et al. MBio 2013; 4(5):e00650-13).
  • the S protein is particularly essential in mediating virus binding to cells expressing receptor dipeptidyl peptidase-4 (DPP4) through receptor-binding domain (RBD) in the S1 subunit, whereas the S2 subunit subsequently mediates virus entry via fusion of the virus and target cell membranes (Li F. J Virol 2015; 89(4):1954-64; Raj V S et al. Nature 2013; 495(7440):251-4).
  • DPP4 receptor dipeptidyl peptidase-4
  • RBD receptor-binding domain
  • the vaccine encodes the major antigenic component for MERS-CoV or SL-CoV-WIV1, the spike (S) glycoprotein.
  • Spike protein is a typical type I viral fusion protein that exists as trimer on the viral surface with each monomer consisting of a Head (S1) and stem (S2) domain similar to influenza Hemagglutinin (HA).
  • the S1 domain of the spike glycoprotein includes the receptor binding domain (RBD) that engages with the dipeptidyl peptidase-4 (DPP4) receptor and mediates viral fusion into the host cell, an N-terminal domain that may make initial contact with target cells, and 2 subdomains, all of which are susceptible to neutralizing antibodies.
  • S2 domain consists of a six helix bundle fusion core involved in membrane fusion with the host endosomal membrane and is also a target for neutralization.
  • Spike protein for betacoronaviruses has been shown to be an effective target for vaccines as antibodies against this protein are generated during natural infection and are protective in a passive transfer animal model (REF). It has been demonstrated that mRNA vaccine for MERS-CoV elicits high levels of neutralizing antibodies and significantly reduces viral load in infected animals (see Examples).
  • pre-S prefusion conformation
  • RNA vaccines described herein are superior to current vaccines in several ways.
  • the lipid nanoparticle (LNP) delivery system used herein increases the efficacy of RNA vaccines in comparison to other formulations, including a protamine-based approach described in the literature.
  • the use of this LNP delivery system enables the effective delivery of chemically-modified RNA vaccines or unmodified RNA vaccines, without requiring additional adjuvant to produce a therapeutic result (e.g., production neutralizing antibody titer and/or a T cell response).
  • the zoonotic disease RNA vaccines disclosed herein are superior to conventional vaccines by a factor of at least 10 fold, 20, fold, 40, fold, 50 fold, 100 fold, 500 fold, or 1,000 fold when administered intramuscularly (IM) or intradermally (ID). These results can be achieved even when significantly lower doses of the RNA (e.g., mRNA) are administered in comparison with RNA doses used in other classes of lipid based formulations.
  • IM intramuscularly
  • ID intradermally
  • LNP used in the studies described herein has been used previously to deliver siRNA in various animal models as well as in humans.
  • the fact that LNP is useful in vaccines is quite surprising, particularly when immunity to an antigen has been hard to generate. It has been observed that therapeutic delivery of siRNA formulated in LNP causes an undesirable inflammatory response associated with a transient IgM response, typically leading to a reduction in antigen production and a compromised immune response.
  • the LNP-mRNA formulations of the present disclosure are demonstrated herein to generate enhanced IgG levels, sufficient for prophylactic and therapeutic methods rather than transient IgM responses.
  • Antigens are proteins capable of inducing an immune response (e.g., causing an immune system to produce antibodies against the antigens).
  • use of the term antigen encompasses immunogenic proteins and immunogenic fragments (an immunogenic fragment that induces (or is capable of inducing) an immune response to a zoonotic disease antigen), unless otherwise stated.
  • protein encompasses peptides and the term “antigen” encompasses antigenic fragments.
  • Zoonotic disease vaccines comprise at least one (one or more) ribonucleic acid (RNA, e.g., mRNA) having an open reading frame encoding at least one Lassa virus, Nipah virus, or betacoronavirus antigen.
  • RNA ribonucleic acid
  • Non-limiting examples of zoonotic disease antigens are provided below.
  • the antigens may be encoded by (thus the RNA may comprise or consist of) any one of sequences set forth in SEQ ID NO: 6, 7, 9, 16, 17, or 20.
  • the antigens comprise a sequence set forth in SEQ ID NO: 1, 2, 3, 10, 11, 12, 13, or 18.
  • the aforementioned sequences may further comprise a 5′ cap (e.g., 7mG(5′)ppp(5′)NlmpNp), a polyA tail, or a 5′ cap and a polyA tail.
  • the zoonotic disease vaccines of the present disclosure may comprise any of the RNA open reading frames (ORFs), or encode any of the protein ORFs, described herein, with or without a signal sequence. It should also be understood that the zoonotic disease vaccines of the present disclosure may include any 5′ untranslated region (UTR) and/or any 3′ UTR. Any UTR sequence (e.g., of the prior art) may be used or exchanged for any of the UTR sequences described herein. UTRs may also be omitted from the vaccine constructs provided herein.
  • ORFs RNA open reading frames
  • the zoonotic disease vaccines of the present disclosure may include any 5′ untranslated region (UTR) and/or any 3′ UTR. Any UTR sequence (e.g., of the prior art) may be used or exchanged for any of the UTR sequences described herein. UTRs may also be omitted from the vaccine constructs provided herein.
  • the zoonotic disease vaccines of the present disclosure comprise at least one (one or more) ribonucleic acid (RNA) having an open reading frame encoding at least one zoonotic disease antigen.
  • the zoonotic disease antigen is a Lassa virus antigen.
  • the zoonotic disease antigen is a Nipah virus antigen.
  • the zoonotic disease antigen is a betcoronavirus antigen.
  • the RNA is a messenger RNA (mRNA) having an open reading frame encoding at least one zoonotic disease antigen.
  • the RNA e.g., mRNA
  • the RNA further comprises a (at least one) 5′UTR, 3′UTR, a polyA tail and/or a 5′ cap.
  • Nucleic acids comprise a polymer of nucleotides (nucleotide monomers), also referred to as polynucleotides. Nucleic acids may be or may include, for example, deoxyribonucleic acids (DNAs), ribonucleic acids (RNAs), threose nucleic acids (TNAs), glycol nucleic acids (GNAs), peptide nucleic acids (PNAs), locked nucleic acids (LNAs, including LNA having a ⁇ -D-ribo configuration, ⁇ -LNA having an ⁇ -L-ribo configuration (a diastereomer of LNA), 2′-amino-LNA having a 2′-amino functionalization, and 2′-amino- ⁇ -LNA having a 2′-amino functionalization), ethylene nucleic acids (ENA), cyclohexenyl nucleic acids (CeNA) and/or chimeras and/or combinations thereof.
  • DNAs deoxy
  • Messenger RNA is any ribonucleic acid that encodes a (at least one) protein (a naturally-occurring, non-naturally-occurring, or modified polymer of amino acids) and can be translated to produce the encoded protein in vitro, in vivo, in situ or ex vivo.
  • RNA messenger RNA
  • nucleic acid sequences set forth in the instant application may recite “T”s in a representative DNA sequence but where the sequence represents RNA (e.g., mRNA), the “T”s would be substituted for “U”s.
  • any of the DNAs disclosed and identified by a particular sequence identification number herein also disclose the corresponding RNA (e.g., mRNA) sequence complementary to the DNA, where each “T” of the DNA sequence is substituted with “U.”
  • the mRNA polynucleotides of the vaccines as provided herein are synthetic molecules, i.e., they are not naturally-occurring molecules. That is, the mRNA polynucleotides of the present disclosure are isolated mRNA polynucleotides.
  • isolated polynucleotides refer to polynucleotides that are substantially physically separated from other cellular material (e.g., separated from cells and/or systems that produce the polynucleotides) or from other material that hinders their use in the vaccines of the present disclosure. Isolated polynucleotides are substantially pure in that they have been substantially separated from the substances with which they may be associated in living or viral systems.
  • mRNA polynucleotide vaccines are not associated with living or viral systems, such as cells or viruses.
  • the mRNA polynucleotide vaccines do not include viral components (e.g., viral capsids, viral enzymes, or other viral proteins, for example, those needed for viral-based replication), and the mRNA polynucleotide vaccines are not packaged within, encapsulated within, linked to, or otherwise associated with a virus or viral particle.
  • the mRNA vaccines comprise a lipid nanoparticle that consists of, or consists essentially of, one or more mRNA polynucleotides (e.g., mRNA polynucleotides encoding one or more zoonotic viral antigen(s)).
  • mRNA polynucleotides e.g., mRNA polynucleotides encoding one or more zoonotic viral antigen(s)
  • An open reading frame is a continuous stretch of DNA or RNA beginning with a start codon (e.g., methionine (ATG or AUG)) and ending with a stop codon (e.g., TAA, TAG or TGA, or UAA, UAG or UGA).
  • An ORF typically encodes a protein. It will be understood that the sequences disclosed herein may further comprise additional elements, e.g., 5′ and 3′ UTRs, but that those elements, unlike the ORF, need not necessarily be present in a vaccine of the present disclosure.
  • an RNA of the present disclosure encodes a zoonotic disease antigen variant.
  • Antigen or other polypeptide variants refers to molecules that differ in their amino acid sequence from a wild-type, native or reference sequence.
  • the antigen/polypeptide variants may possess substitutions, deletions, and/or insertions at certain positions within the amino acid sequence, as compared to a native or reference sequence.
  • variants possess at least 50% identity to a wild-type, native or reference sequence.
  • variants share at least 80%, or at least 90% identity with a wild-type, native or reference sequence.
  • Variant antigens/polypeptides encoded by nucleic acids of the disclosure may contain amino acid changes that confer any of a number of desirable properties, e.g., that enhance their immunogenicity, enhance their expression, and/or improve their stability or PK/PD properties in a subject.
  • Variant antigens/polypeptides can be made using routine mutagenesis techniques and assayed as appropriate to determine whether they possess the desired property. Assays to determine expression levels and immunogenicity are well known in the art and exemplary such assays are set forth in the Examples section.
  • PK/PD properties of a protein variant can be measured using art recognized techniques, e.g., by determining expression of antigens in a vaccinated subject over time and/or by looking at the durability of the induced immune response.
  • the stability of protein(s) encoded by a variant nucleic acid may be measured by assaying thermal stability or stability upon urea denaturation or may be measured using in silico prediction. Methods for such experiments and in silico determinations are known in the art.
  • a zoonotic disease vaccine comprises an mRNA ORF having a nucleotide sequence identified by any one of the sequences provided herein (see e.g., Sequence Listing), or having a nucleotide sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a nucleotide sequence identified by any one of the sequence provided herein.
  • identity refers to a relationship between the sequences of two or more polypeptides (e.g. antigens) or polynucleotides (nucleic acids), as determined by comparing the sequences. Identity also refers to the degree of sequence relatedness between or among sequences as determined by the number of matches between strings of two or more amino acid residues or nucleic acid residues. Identity measures the percent of identical matches between the smaller of two or more sequences with gap alignments (if any) addressed by a particular mathematical model or computer program (e.g., “algorithms”). Identity of related antigens or nucleic acids can be readily calculated by known methods.
  • Percent (%) identity as it applies to polypeptide or polynucleotide sequences is defined as the percentage of residues (amino acid residues or nucleic acid residues) in the candidate amino acid or nucleic acid sequence that are identical with the residues in the amino acid sequence or nucleic acid sequence of a second sequence after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent identity. Methods and computer programs for the alignment are well known in the art. It is understood that identity depends on a calculation of percent identity but may differ in value due to gaps and penalties introduced in the calculation.
  • variants of a particular polynucleotide or polypeptide have at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% but less than 100% sequence identity to that particular reference polynucleotide or polypeptide as determined by sequence alignment programs and parameters described herein and known to those skilled in the art.
  • tools for alignment include those of the BLAST suite (Stephen F. Altschul, et al (1997), “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs”, Nucleic Acids Res.
  • sequence tags or amino acids such as one or more lysines
  • Sequence tags can be used for peptide detection, purification or localization.
  • Lysines can be used to increase peptide solubility or to allow for biotinylation.
  • amino acid residues located at the carboxy and amino terminal regions of the amino acid sequence of a peptide or protein may optionally be deleted providing for truncated sequences.
  • Certain amino acids e.g., C-terminal or N-terminal residues
  • sequences for (or encoding) signal sequences, termination sequences, transmembrane domains, linkers, multimerization domains (such as, e.g., foldon regions) and the like may be substituted with alternative sequences that achieve the same or a similar function.
  • cavities in the core of proteins can be filled to improve stability, e.g., by introducing larger amino acids.
  • buried hydrogen bond networks may be replaced with hydrophobic resides to improve stability.
  • glycosylation sites may be removed and replaced with appropriate residues.
  • sequences are readily identifiable to one of skill in the art. It should also be understood that some of the sequences provided herein contain sequence tags or terminal peptide sequences (e.g., at the N-terminal or C-terminal ends) that may be deleted, for example, prior to use in the preparation of an RNA (e.g., mRNA) vaccine.
  • RNA e.g., mRNA
  • protein fragments, functional protein domains, and homologous proteins are also considered to be within the scope of zoonotic disease antigens of interest.
  • any protein fragment meaning a polypeptide sequence at least one amino acid residue shorter than a reference antigen sequence but otherwise identical
  • an antigen includes 2, 3, 4, 5, 6, 7, 8, 9, 10, or more mutations, as shown in any of the sequences provided or referenced herein.
  • Antigens/antigenic polypeptides can range in length from about 4, 6, or 8 amino acids to full length proteins.
  • Naturally-occurring eukaryotic mRNA molecules can contain stabilizing elements, including, but not limited to untranslated regions (UTR) at their 5′-end (5′ UTR) and/or at their 3′-end (3′ UTR), in addition to other structural features, such as a 5′-cap structure or a 3′-poly(A) tail.
  • UTR untranslated regions
  • Both the 5′ UTR and the 3′ UTR are typically transcribed from the genomic DNA and are elements of the premature mRNA. Characteristic structural features of mature mRNA, such as the 5′-cap and the 3′-poly(A) tail are usually added to the transcribed (premature) mRNA during mRNA processing.
  • a vaccine includes at least one RNA polynucleotide having an open reading frame encoding at least one antigenic polypeptide having at least one modification, at least one 5′ terminal cap, and is formulated within a lipid nanoparticle.
  • 5′-capping of polynucleotides may be completed concomitantly during the in vitro-transcription reaction using the following chemical RNA cap analogs to generate the 5′-guanosine cap structure according to manufacturer protocols: 3′-O-Me-m7G(5′)ppp(5′) G [the ARCA cap]; G(5′)ppp(5′)A; G(5′)ppp(5′)G; m7G(5′)ppp(5′)A; m7G(5′)ppp(5′)G (New England BioLabs, Ipswich, Mass.).
  • 5′-capping of modified RNA may be completed post-transcriptionally using a Vaccinia Virus Capping Enzyme to generate the “Cap 0” structure: m7G(5′)ppp(5′)G (New England BioLabs, Ipswich, Mass.).
  • Cap 1 structure may be generated using both Vaccinia Virus Capping Enzyme and a 2′-O methyl-transferase to generate: m7G(5′)ppp(5′)G-2′-O-methyl.
  • Cap 2 structure may be generated from the Cap 1 structure followed by the 2′-O-methylation of the 5′-antepenultimate nucleotide using a 2′-O methyl-transferase.
  • Cap 3 structure may be generated from the Cap 2 structure followed by the 2′-O-methylation of the 5′-preantepenultimate nucleotide using a 2′-O methyl-transferase.
  • Enzymes may be derived from a recombinant source.
  • the 3′-poly(A) tail is typically a stretch of adenine nucleotides added to the 3′-end of the transcribed mRNA. It can, in some instances, comprise up to about 400 adenine nucleotides. In some embodiments, the length of the 3′-poly(A) tail may be an essential element with respect to the stability of the individual mRNA.
  • zoonotic disease RNA vaccines may include one or more stabilizing elements.
  • Stabilizing elements may include for instance a histone stem-loop.
  • a stem-loop binding protein (SLBP) a 32 kDa protein has been identified. It is associated with the histone stem-loop at the 3′-end of the histone messages in both the nucleus and the cytoplasm. Its expression level is regulated by the cell cycle; it peaks during the S-phase, when histone mRNA levels are also elevated. The protein has been shown to be essential for efficient 3′-end processing of histone pre-mRNA by the U7 snRNP.
  • SLBP continues to be associated with the stem-loop after processing, and then stimulates the translation of mature histone mRNAs into histone proteins in the cytoplasm.
  • the RNA binding domain of SLBP is conserved through metazoa and protozoa; its binding to the histone stem-loop depends on the structure of the loop.
  • the minimum binding site includes at least three nucleotides 5′ and two nucleotides 3′ relative to the stem-loop.
  • zoonotic disease RNA vaccines include a coding region, at least one histone stem-loop, and optionally, a poly(A) sequence or polyadenylation signal.
  • the poly(A) sequence or polyadenylation signal generally should enhance the expression level of the encoded protein.
  • the encoded protein in some embodiments, is not a histone protein, a reporter protein (e.g. Luciferase, GFP, EGFP, ⁇ -Galactosidase, EGFP), or a marker or selection protein (e.g. alpha-Globin, Galactokinase and Xanthine:guanine phosphoribosyl transferase (GPT)).
  • a reporter protein e.g. Luciferase, GFP, EGFP, ⁇ -Galactosidase, EGFP
  • a marker or selection protein e.g. alpha-Globin, Galactokinase and Xanthine
  • the combination of a poly(A) sequence or polyadenylation signal and at least one histone stem-loop acts synergistically to increase the protein expression beyond the level observed with either of the individual elements.
  • the synergistic effect of the combination of poly(A) and at least one histone stem-loop does not depend on the order of the elements or the length of the poly(A) sequence.
  • zoonotic disease RNA vaccines do not comprise a histone downstream element (HDE).
  • Histone downstream element includes a purine-rich polynucleotide stretch of approximately 15 to 20 nucleotides 3′ of naturally occurring stem-loops, representing the binding site for the U7 snRNA, which is involved in processing of histone pre-mRNA into mature histone mRNA.
  • the nucleic acid does not include an intron.
  • zoonotic disease RNA vaccines may or may not contain an enhancer and/or promoter sequence, which may be modified or unmodified or which may be activated or inactivated.
  • the histone stem-loop is generally derived from histone genes, and includes an intramolecular base pairing of two neighbored partially or entirely reverse complementary sequences separated by a spacer, consisting of a short sequence, which forms the loop of the structure.
  • the unpaired loop region is typically unable to base pair with either of the stem loop elements. It occurs more often in RNA, as is a key component of many RNA secondary structures, but may be present in single-stranded DNA as well.
  • the Stability of the stem-loop structure generally depends on the length, number of mismatches or bulges, and base composition of the paired region.
  • wobble base pairing non-Watson-Crick base pairing
  • the at least one histone stem-loop sequence comprises a length of 15 to 45 nucleotides.
  • zoonotic disease RNA vaccines may have one or more AU-rich sequences removed. These sequences, sometimes referred to as AURES are destabilizing sequences found in the 3′UTR. The AURES may be removed from the RNA vaccines. Alternatively the AURES may remain in the RNA vaccine.
  • a zoonotic disease vaccine comprises a RNA having an ORF that encodes a signal peptide fused to the zoonotic disease antigen.
  • Signal peptides comprising the N-terminal 15-60 amino acids of proteins, are typically needed for the translocation across the membrane on the secretory pathway and, thus, universally control the entry of most proteins both in eukaryotes and prokaryotes to the secretory pathway.
  • the signal peptide of a nascent precursor protein (pre-protein) directs the ribosome to the rough endoplasmic reticulum (ER) membrane and initiates the transport of the growing peptide chain across it for processing.
  • pre-protein nascent precursor protein
  • ER processing produces mature proteins, wherein the signal peptide is cleaved from precursor proteins, typically by a ER-resident signal peptidase of the host cell, or they remain uncleaved and function as a membrane anchor.
  • a signal peptide may also facilitate the targeting of the protein to the cell membrane.
  • a signal peptide may have a length of 15-60 amino acids.
  • a signal peptide may have a length of 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 amino acids.
  • a signal peptide has a length of 20-60, 25-60, 30-60, 35-60, 40-60, 45-60, 50-60, 55-60, 15-55, 20-55, 25-55, 30-55, 35-55, 40-55, 45-55, 50-55, 15-50, 20-50, 25-50, 30-50, 35-50, 40-50, 45-50, 15-45, 20-45, 25-45, 30-45, 35-45, 40-45, 15-40, 20-40, 25-40, 30-40, 35-40, 15-35, 20-35, 25-35, 30-35, 15-30, 20-30, 25-30, 15-25, 20-25, or 15-20 amino acids.
  • the signal peptide may comprise one of the following sequences:
  • a zoonotic disease RNA vaccine of the present disclosure includes an RNA encoding an antigenic fusion protein.
  • the encoded antigen or antigens may include two or more proteins (e.g., protein and/or protein fragment) joined together.
  • the protein to which a protein antigen is fused does not promote a strong immune response to itself, but rather to the zoonotic disease antigen.
  • Antigenic fusion proteins in some embodiments, retain the functional property from each original protein.
  • RNA vaccines as provided herein encode fusion proteins which comprise zoonotic disease antigens linked to scaffold moieties.
  • scaffold moieties impart desired properties to an antigen encoded by a nucleic acid of the disclosure.
  • scaffold proteins may improve the immunogenicity of an antigen, e.g., by altering the structure of the antigen, altering the uptake and processing of the antigen, and/or causing the antigen to bind to a binding partner.
  • the scaffold moiety is protein that can self-assemble into protein nanoparticles that are highly symmetric, stable, and structurally organized, with diameters of 10-150 nm, a highly suitable size range for optimal interactions with various cells of the immune system.
  • viral proteins or virus-like particles can be used to form stable nanoparticle structures. Examples of such viral proteins are known in the art.
  • the scaffold moiety is a hepatitis B surface antigen (HBsAg). HBsAg forms spherical particles with an average diameter of ⁇ 22 nm and which lacked nucleic acid and hence are non-infectious (Lopez-Sagaseta, J. et al.
  • the scaffold moiety is a hepatitis B core antigen (HBcAg) self-assembles into particles of 24-31 nm diameter, which resembled the viral cores obtained from HBV-infected human liver.
  • HBcAg produced in self-assembles into two classes of differently sized nanoparticles of 300 ⁇ and 360 ⁇ diameter, corresponding to 180 or 240 protomers.
  • a zoonotic disease antigen is fused to HBsAG or HBcAG to facilitate self-assembly of nanoparticles displaying the zoonotic disease antigen.
  • bacterial protein platforms may be used.
  • these self-assembling proteins include ferritin, lumazine and encapsulin.
  • Ferritin is a protein whose main function is intracellular iron storage. Ferritin is made of 24 subunits, each composed of a four-alpha-helix bundle, that self-assemble in a quaternary structure with octahedral symmetry (Cho K. J. et al. J Mol Biol. 2009; 390:83-98). Several high-resolution structures of ferritin have been determined, confirming that Helicobacter pylori ferritin is made of 24 identical protomers, whereas in animals, there are ferritin light and heavy chains that can assemble alone or combine with different ratios into particles of 24 subunits (Granier T. et al. J Biol Inorg Chem. 2003; 8:105-111; Lawson D. M. et al. Nature. 1991; 349:541-544). Ferritin self-assembles into nanoparticles with robust thermal and chemical stability. Thus, the ferritin nanoparticle is well-suited to carry and expose antigens.
  • Lumazine synthase is also well-suited as a nanoparticle platform for antigen display.
  • LS which is responsible for the penultimate catalytic step in the biosynthesis of riboflavin, is an enzyme present in a broad variety of organisms, including archaea, bacteria, fungi, plants, and eubacteria (Weber S. E. Flavins andFlavoproteins . Methods and Protocols, Series: Methods in Molecular Biology. 2014).
  • the LS monomer is 150 amino acids long, and consists of beta-sheets along with tandem alpha-helices flanking its sides.
  • Encapsulin a novel protein cage nanoparticle isolated from thermophile Thermotoga maritima , may also be used as a platform to present antigens on the surface of self-assembling nanoparticles.
  • the mRNAs of the disclosure encode more than one polypeptide, referred to herein as fusion proteins.
  • the mRNA further encodes a linker located between at least one or each domain of the fusion protein.
  • the linker can be, for example, a cleavable linker or protease-sensitive linker.
  • the linker is selected from the group consisting of F2A linker, P2A linker, T2A linker, E2A linker, and combinations thereof. This family of self-cleaving peptide linkers, referred to as 2A peptides, has been described in the art (see for example, Kim, J. H. et al.
  • the linker is an F2A linker. In some embodiments, the linker is a GGGS linker. In some embodiments, the fusion protein contains three domains with intervening linkers, having the structure: domain-linker-domain-linker-domain.
  • Cleavable linkers known in the art may be used in connection with the disclosure.
  • Exemplary such linkers include: F2A linkers, T2A linkers, P2A linkers, E2A linkers (See, e.g., WO2017/127750).
  • linkers include: F2A linkers, T2A linkers, P2A linkers, E2A linkers (See, e.g., WO2017/127750).
  • linkers include: F2A linkers, T2A linkers, P2A linkers, E2A linkers (See, e.g., WO2017/127750).
  • linkers include: F2A linkers, T2A linkers, P2A linkers, E2A linkers (See, e.g., WO2017/127750).
  • other art-recognized linkers may be suitable for use in the constructs of the disclosure (e.g., encoded by the nucleic acids of the disclosure).
  • polycistronic constructs
  • an ORF encoding an antigen of the disclosure is codon optimized. Codon optimization methods are known in the art. For example, an ORF of any one or more of the sequences provided herein may be codon optimized. Codon optimization, in some embodiments, may be used to match codon frequencies in target and host organisms to ensure proper folding; bias GC content to increase mRNA stability or reduce secondary structures; minimize tandem repeat codons or base runs that may impair gene construction or expression; customize transcriptional and translational control regions; insert or remove protein trafficking sequences; remove/add post translation modification sites in encoded protein (e.g., glycosylation sites); add, remove or shuffle protein domains; insert or delete restriction sites; modify ribosome binding sites and mRNA degradation sites; adjust translational rates to allow the various domains of the protein to fold properly; or reduce or eliminate problem secondary structures within the polynucleotide.
  • Codon optimization may be used to match codon frequencies in target and host organisms to ensure proper folding; bias GC content to increase mRNA stability or reduce
  • Codon optimization tools, algorithms and services are known in the art—non-limiting examples include services from GeneArt (Life Technologies), DNA2.0 (Menlo Park Calif.) and/or proprietary methods.
  • the open reading frame (ORF) sequence is optimized using optimization algorithms.
  • a codon optimized sequence shares less than 95% sequence identity to a naturally-occurring or wild-type sequence ORF (e.g., a naturally-occurring or wild-type mRNA sequence encoding a zoonotic disease antigen). In some embodiments, a codon optimized sequence shares less than 90% sequence identity to a naturally-occurring or wild-type sequence (e.g., a naturally-occurring or wild-type mRNA sequence encoding a zoonotic disease antigen).
  • a codon optimized sequence shares less than 85% sequence identity to a naturally-occurring or wild-type sequence (e.g., a naturally-occurring or wild-type mRNA sequence encoding a zoonotic disease antigen). In some embodiments, a codon optimized sequence shares less than 80% sequence identity to a naturally-occurring or wild-type sequence (e.g., a naturally-occurring or wild-type mRNA sequence encoding a zoonotic disease antigen).
  • a codon optimized sequence shares less than 75% sequence identity to a naturally-occurring or wild-type sequence (e.g., a naturally-occurring or wild-type mRNA sequence encoding a zoonotic disease antigen).
  • a codon optimized sequence shares between 65% and 85% (e.g., between about 67% and about 85% or between about 67% and about 80%) sequence identity to a naturally-occurring or wild-type sequence (e.g., a naturally-occurring or wild-type mRNA sequence encoding a zoonotic disease antigen). In some embodiments, a codon optimized sequence shares between 65% and 75% or about 80% sequence identity to a naturally-occurring or wild-type sequence (e.g., a naturally-occurring or wild-type mRNA sequence encoding a zoonotic disease antigen).
  • a codon-optimized sequence encodes an antigen that is as immunogenic as, or more immunogenic than (e.g., at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 100%, or at least 200% more), than a zoonotic disease antigen encoded by a non-codon-optimized sequence.
  • a codon-optimized sequence shares between 65% and 85% (e.g., between about 67% and about 85%, or between about 67% and about 80%) sequence identity to a naturally-occurring sequence or a wild-type sequence (e.g., a naturally-occurring or wild-type mRNA sequence encoding a polypeptide or protein of interest (e.g., an antigenic protein or polypeptide)).
  • a naturally-occurring sequence or a wild-type sequence e.g., a naturally-occurring or wild-type mRNA sequence encoding a polypeptide or protein of interest (e.g., an antigenic protein or polypeptide)
  • a codon-optimized sequence shares between 65% and 75%, or about 80% sequence identity to a naturally-occurring sequence or wild-type sequence (e.g., a naturally-occurring or wild-type mRNA sequence encoding a polypeptide or protein of interest (e.g., an antigenic protein or polypeptide)).
  • a naturally-occurring sequence or wild-type sequence e.g., a naturally-occurring or wild-type mRNA sequence encoding a polypeptide or protein of interest (e.g., an antigenic protein or polypeptide)
  • the modified mRNAs When transfected into mammalian host cells, the modified mRNAs have a stability of between 12-18 hours, or greater than 18 hours, e.g., 24, 36, 48, 60, 72, or greater than 72 hours and are capable of being expressed by the mammalian host cells.
  • a codon optimized RNA may be one in which the levels of G/C are enhanced.
  • the G/C-content of nucleic acid molecules may influence the stability of the RNA.
  • RNA having an increased amount of guanine (G) and/or cytosine (C) residues may be functionally more stable than RNA containing a large amount of adenine (A) and thymine (T) or uracil (U) nucleotides.
  • WO02/098443 discloses a pharmaceutical composition containing an mRNA stabilized by sequence modifications in the translated region. Due to the degeneracy of the genetic code, the modifications work by substituting existing codons for those that promote greater RNA stability without changing the resulting amino acid. The approach is limited to coding regions of the RNA.
  • RNA e.g., mRNA
  • nucleotides and nucleosides of the present disclosure comprise standard nucleoside residues such as those present in transcribed RNA (e.g. A, G, C, or U).
  • nucleotides and nucleosides of the present disclosure comprise standard deoxyribonucleosides such as those present in DNA (e.g. dA, dG, dC, or dT).
  • Zoonotic disease RNA vaccines of the present disclosure comprise, in some embodiments, at least one nucleic acid (e.g., RNA) having an open reading frame encoding at least one zoonotic disease antigen, wherein the nucleic acid comprises nucleotides and/or nucleosides that can be standard (unmodified) or modified as is known in the art.
  • nucleotides and nucleosides of the present disclosure comprise modified nucleotides or nucleosides.
  • modified nucleotides and nucleosides can be naturally-occurring modified nucleotides and nucleosides or non-naturally occurring modified nucleotides and nucleosides.
  • modifications can include those at the sugar, backbone, or nucleobase portion of the nucleotide and/or nucleoside as are recognized in the art.
  • a naturally-occurring modified nucleotide or nucleotide of the disclosure is one as is generally known or recognized in the art.
  • Non-limiting examples of such naturally occurring modified nucleotides and nucleotides can be found, inter alia, in the widely recognized MODOMICS database.
  • a non-naturally occurring modified nucleotide or nucleoside of the disclosure is one as is generally known or recognized in the art.
  • Non-limiting examples of such non-naturally occurring modified nucleotides and nucleosides can be found, inter alia, in published US application Nos. PCT/US2012/058519; PCT/US2013/075177; PCT/US2014/058897; PCT/US2014/058891; PCT/US2014/070413; PCT/US2015/36773; PCT/US2015/36759; PCT/US2015/36771; or PCT/IB2017/051367 all of which are incorporated by reference herein.
  • nucleic acids of the disclosure can comprise standard nucleotides and nucleosides, naturally-occurring nucleotides and nucleosides, non-naturally-occurring nucleotides and nucleosides, or any combination thereof.
  • Nucleic acids of the disclosure e.g., DNA nucleic acids and RNA nucleic acids, such as mRNA nucleic acids
  • Nucleic acids of the disclosure comprise various (more than one) different types of standard and/or modified nucleotides and nucleosides.
  • a particular region of a nucleic acid contains one, two or more (optionally different) types of standard and/or modified nucleotides and nucleosides.
  • a modified RNA nucleic acid e.g., a modified mRNA nucleic acid
  • introduced to a cell or organism exhibits reduced degradation in the cell or organism, respectively, relative to an unmodified nucleic acid comprising standard nucleotides and nucleosides.
  • a modified RNA nucleic acid (e.g., a modified mRNA nucleic acid), introduced into a cell or organism, may exhibit reduced immunogenicity in the cell or organism, respectively (e.g., a reduced innate response) relative to an unmodified nucleic acid comprising standard nucleotides and nucleosides.
  • Nucleic acids e.g., RNA nucleic acids, such as mRNA nucleic acids
  • Nucleic acids in some embodiments, comprise non-natural modified nucleotides that are introduced during synthesis or post-synthesis of the nucleic acids to achieve desired functions or properties.
  • the modifications may be present on internucleotide linkages, purine or pyrimidine bases, or sugars.
  • the modification may be introduced with chemical synthesis or with a polymerase enzyme at the terminal of a chain or anywhere else in the chain. Any of the regions of a nucleic acid may be chemically modified.
  • nucleic acid e.g., RNA nucleic acids, such as mRNA nucleic acids.
  • a “nucleoside” refers to a compound containing a sugar molecule (e.g., a pentose or ribose) or a derivative thereof in combination with an organic base (e.g., a purine or pyrimidine) or a derivative thereof (also referred to herein as “nucleobase”).
  • nucleotide refers to a nucleoside, including a phosphate group.
  • Modified nucleotides may by synthesized by any useful method, such as, for example, chemically, enzymatically, or recombinantly, to include one or more modified or non-natural nucleosides.
  • Nucleic acids can comprise a region or regions of linked nucleosides. Such regions may have variable backbone linkages. The linkages can be standard phosphodiester linkages, in which case the nucleic acids would comprise regions of nucleotides.
  • Modified nucleotide base pairing encompasses not only the standard adenosine-thymine, adenosine-uracil, or guanosine-cytosine base pairs, but also base pairs formed between nucleotides and/or modified nucleotides comprising non-standard or modified bases, wherein the arrangement of hydrogen bond donors and hydrogen bond acceptors permits hydrogen bonding between a non-standard base and a standard base or between two complementary non-standard base structures, such as, for example, in those nucleic acids having at least one chemical modification.
  • non-standard base pairing is the base pairing between the modified nucleotide inosine and adenine, cytosine or uracil. Any combination of base/sugar or linker may be incorporated into nucleic acids of the present disclosure.
  • modified nucleobases in nucleic acids comprise 1-methyl-pseudouridine (m1 ⁇ ), 1-ethyl-pseudouridine (e1 ⁇ ), 5-methoxy-uridine (mo5U), 5-methyl-cytidine (m5C), and/or pseudouridine (v).
  • modified nucleobases in nucleic acids comprise 5-methoxymethyl uridine, 5-methylthio uridine, 1-methoxymethyl pseudouridine, 5-methyl cytidine, and/or 5-methoxy cytidine.
  • the polyribonucleotide includes a combination of at least two (e.g., 2, 3, 4 or more) of any of the aforementioned modified nucleobases, including but not limited to chemical modifications.
  • a RNA nucleic acid of the disclosure comprises 1-methyl-pseudouridine (m1 ⁇ ) substitutions at one or more or all uridine positions of the nucleic acid.
  • a RNA nucleic acid of the disclosure comprises 1-methyl-pseudouridine (m1 ⁇ ) substitutions at one or more or all uridine positions of the nucleic acid and 5-methyl cytidine substitutions at one or more or all cytidine positions of the nucleic acid.
  • a RNA nucleic acid of the disclosure comprises pseudouridine ( ⁇ ) substitutions at one or more or all uridine positions of the nucleic acid.
  • a RNA nucleic acid of the disclosure comprises pseudouridine ( ⁇ ) substitutions at one or more or all uridine positions of the nucleic acid and 5-methyl cytidine substitutions at one or more or all cytidine positions of the nucleic acid.
  • a RNA nucleic acid of the disclosure comprises uridine at one or more or all uridine positions of the nucleic acid.
  • nucleic acids e.g., RNA nucleic acids, such as mRNA nucleic acids
  • RNA nucleic acids are uniformly modified (e.g., fully modified, modified throughout the entire sequence) for a particular modification.
  • a nucleic acid can be uniformly modified with 1-methyl-pseudouridine, meaning that all uridine residues in the mRNA sequence are replaced with 1-methyl-pseudouridine.
  • a nucleic acid can be uniformly modified for any type of nucleoside residue present in the sequence by replacement with a modified residue such as those set forth above.
  • nucleic acids of the present disclosure may be partially or fully modified along the entire length of the molecule.
  • one or more or all or a given type of nucleotide e.g., purine or pyrimidine, or any one or more or all of A, G, U, C
  • nucleotides X in a nucleic acid of the present disclosure are modified nucleotides, wherein X may be any one of nucleotides A, G, U, C, or any one of the combinations A+G, A+U, A+C, G+U, G+C, U+C, A+G+U, A+G+C, G+U+C or A+G+C.
  • the nucleic acid may contain from about 1% to about 100% modified nucleotides (either in relation to overall nucleotide content, or in relation to one or more types of nucleotide, i.e., any one or more of A, G, U or C) or any intervening percentage (e.g., from 1% to 20%, from 1% to 25%, from 1% to 50%, from 1% to 60%, from 1% to 70%, from 1% to 80%, from 1% to 90%, from 1% to 95%, from 10% to 20%, from 10% to 25%, from 10% to 50%, from 10% to 60%, from 10% to 70%, from 10% to 80%, from 10% to 90%, from 10% to 95%, from 10% to 100%, from 20% to 25%, from 20% to 50%, from 20% to 60%, from 20% to 70%, from 20% to 80%, from 20% to 90%, from 20% to 95%, from 20% to 100%, from 50% to 60%, from 50% to 70%, from 50% to 80%, from 50% to 90%, from 50% to 95%, from 50% to 100%, from 70% to
  • the nucleic acids may contain at a minimum 1% and at maximum 100% modified nucleotides, or any intervening percentage, such as at least 5% modified nucleotides, at least 10% modified nucleotides, at least 25% modified nucleotides, at least 50% modified nucleotides, at least 80% modified nucleotides, or at least 90% modified nucleotides.
  • the nucleic acids may contain a modified pyrimidine such as a modified uracil or cytosine.
  • At least 5%, at least 10%, at least 25%, at least 50%, at least 80%, at least 90% or 100% of the uracil in the nucleic acid is replaced with a modified uracil (e.g., a 5-substituted uracil).
  • the modified uracil can be replaced by a compound having a single unique structure, or can be replaced by a plurality of compounds having different structures (e.g., 2, 3, 4 or more unique structures).
  • cytosine in the nucleic acid is replaced with a modified cytosine (e.g., a 5-substituted cytosine).
  • the modified cytosine can be replaced by a compound having a single unique structure, or can be replaced by a plurality of compounds having different structures (e.g., 2, 3, 4 or more unique structures).
  • the nucleic acids of the present disclosure may comprise one or more regions or parts which act or function as an untranslated region. Where nucleic acids are designed to encode at least one antigen of interest, the nucleic may comprise one or more of these untranslated regions (UTRs). Wild-type untranslated regions of a nucleic acid are transcribed but not translated. In mRNA, the 5′ UTR starts at the transcription start site and continues to the start codon but does not include the start codon; whereas, the 3′ UTR starts immediately following the stop codon and continues until the transcriptional termination signal. There is growing body of evidence about the regulatory roles played by the UTRs in terms of stability of the nucleic acid molecule and translation.
  • the regulatory features of a UTR can be incorporated into the polynucleotides of the present disclosure to, among other things, enhance the stability of the molecule.
  • the specific features can also be incorporated to ensure controlled down-regulation of the transcript in case they are misdirected to undesired organs sites.
  • a variety of 5′UTR and 3′UTR sequences are known and available in the art.
  • a 5′ UTR is region of an mRNA that is directly upstream (5′) from the start codon (the first codon of an mRNA transcript translated by a ribosome).
  • a 5′ UTR does not encode a protein (is non-coding).
  • Natural 5′UTRs have features that play roles in translation initiation. They harbor signatures like Kozak sequences which are commonly known to be involved in the process by which the ribosome initiates translation of many genes.
  • Kozak sequences have the consensus CCR(A/G)CCAUGG (SEQ ID NO: 27), where R is a purine (adenine or guanine) three bases upstream of the start codon (AUG), which is followed by another ‘G’0.5′UTR also have been known to form secondary structures which are involved in elongation factor binding.
  • a 5′ UTR is a heterologous UTR, i.e., is a UTR found in nature associated with a different ORF.
  • a 5′ UTR is a synthetic UTR, i.e., does not occur in nature.
  • Synthetic UTRs include UTRs that have been mutated to improve their properties, e.g., which increase gene expression as well as those which are completely synthetic.
  • Exemplary 5′ UTRs include Xenopus or human derived a-globin or b-globin (U.S. Pat. Nos.
  • CMV immediate-early 1 (IE1) gene (US2014/0206753, WO2013/185069), the sequence GGGAUCCUACC (SEQ ID NO: 28) (WO2014/144196) may also be used.
  • 5′ UTR of a TOP gene is a 5′ UTR of a TOP gene lacking the 5′ TOP motif (the oligopyrimidine tract) (e.g., WO2015/101414, WO2015/101415, WO2015/062738, WO2015/024667, WO2015/024667; 5′ UTR element derived from ribosomal protein Large 32 (L32) gene (WO2015/101414, WO2015/101415, WO2015/062738), 5′ UTR element derived from the 5′UTR of an hydroxysteroid (17- ⁇ ) dehydrogenase 4 gene (HSD17B4) (WO2015/024667), or a 5′ UTR element derived from the 5′ UTR of ATP5A1 (WO2015/024667) can be used.
  • an internal ribosome entry site is used instead of a 5′ UTR.
  • a 3′ UTR is region of an mRNA that is directly downstream (3′) from the stop codon (the codon of an mRNA transcript that signals a termination of translation).
  • a 3′ UTR does not encode a protein (is non-coding).
  • Natural or wild type 3′ UTRs are known to have stretches of adenosines and uridines embedded in them. These AU rich signatures are particularly prevalent in genes with high rates of turnover. Based on their sequence features and functional properties, the AU rich elements (AREs) can be separated into three classes (Chen et al, 1995): Class I AREs contain several dispersed copies of an AUUUA motif within U-rich regions. C-Myc and MyoD contain class I AREs.
  • Class II AREs possess two or more overlapping UUAUUUA(U/A)(U/A) (SEQ ID NO: 29) nonamers. Molecules containing this type of AREs include GM-CSF and TNF-a. Class III ARES are less well defined. These U rich regions do not contain an AUUUA motif. c-Jun and Myogenin are two well-studied examples of this class. Most proteins binding to the AREs are known to destabilize the messenger, whereas members of the ELAV family, most notably HuR, have been documented to increase the stability of mRNA. HuR binds to AREs of all the three classes. Engineering the HuR specific binding sites into the 3′ UTR of nucleic acid molecules will lead to HuR binding and thus, stabilization of the message in vivo.
  • AREs 3′ UTR AU rich elements
  • nucleic acids e.g., RNA
  • AREs can be used to modulate the stability of nucleic acids (e.g., RNA) of the disclosure.
  • nucleic acids e.g., RNA
  • one or more copies of an ARE can be introduced to make nucleic acids of the disclosure less stable and thereby curtail translation and decrease production of the resultant protein.
  • AREs can be identified and removed or mutated to increase the intracellular stability and thus increase translation and production of the resultant protein.
  • Transfection experiments can be conducted in relevant cell lines, using nucleic acids of the disclosure and protein production can be assayed at various time points post-transfection. For example, cells can be transfected with different ARE-engineering molecules and by using an ELISA kit to the relevant protein and assaying protein produced at 6 hour, 12 hour, 24 hour, 48 hour, and 7 days post-transfection.
  • 3′ UTRs may be heterologous or synthetic.
  • globin UTRs including Xenopus ⁇ -globin UTRs and human ⁇ -globin UTRs are known in the art (U.S. Pat. Nos. 8,278,063, 9,012,219, US2011/0086907).
  • a modified ⁇ -globin construct with enhanced stability in some cell types by cloning two sequential human ⁇ -globin 3′UTRs head to tail has been developed and is well known in the art (US2012/0195936, WO2014/071963).
  • a2-globin, al-globin, UTRs and mutants thereof are also known in the art (WO2015/101415, WO2015/024667).
  • 3′ UTRs described in the mRNA constructs in the non-patent literature include CYBA (Ferizi et al., 2015) and albumin (Thess et al., 2015).
  • Other exemplary 3′ UTRs include that of bovine or human growth hormone (wild type or modified) (WO2013/185069, US2014/0206753, WO2014/152774), rabbit ⁇ globin and hepatitis B virus (HBV), ⁇ -globin 3′ UTR and Viral VEEV 3′ UTR sequences are also known in the art.
  • the sequence UUUGAAUU (WO2014/144196) is used.
  • 3′ UTRs of human and mouse ribosomal protein are used.
  • Other examples include rps9 3′UTR (WO2015/101414), FIG. 4 (WO2015/101415), and human albumin 7 (WO2015/101415).
  • 5′UTRs that are heterologous or synthetic may be used with any desired 3′ UTR sequence.
  • a heterologous 5′UTR may be used with a synthetic 3′UTR with a heterologous 3′′ UTR.
  • Non-UTR sequences may also be used as regions or subregions within a nucleic acid.
  • introns or portions of introns sequences may be incorporated into regions of nucleic acid of the disclosure. Incorporation of intronic sequences may increase protein production as well as nucleic acid levels.
  • the ORF may be flanked by a 5′ UTR which may contain a strong Kozak translational initiation signal and/or a 3′ UTR which may include an oligo(dT) sequence for templated addition of a poly-A tail.
  • 5′ UTR may comprise a first polynucleotide fragment and a second polynucleotide fragment from the same and/or different genes such as the 5′ UTRs described in US Patent Application Publication No. 2010/0293625 and PCT/US2014/069155, herein incorporated by reference in its entirety.
  • any UTR from any gene may be incorporated into the regions of a nucleic acid.
  • multiple wild-type UTRs of any known gene may be utilized. It is also within the scope of the present disclosure to provide artificial UTRs which are not variants of wild type regions. These UTRs or portions thereof may be placed in the same orientation as in the transcript from which they were selected or may be altered in orientation or location. Hence a 5′ or 3′ UTR may be inverted, shortened, lengthened, made with one or more other 5′ UTRs or 3′ UTRs.
  • the term “altered” as it relates to a UTR sequence means that the UTR has been changed in some way in relation to a reference sequence.
  • a 3′ UTR or 5′ UTR may be altered relative to a wild-type or native UTR by the change in orientation or location as taught above or may be altered by the inclusion of additional nucleotides, deletion of nucleotides, swapping or transposition of nucleotides. Any of these changes producing an “altered” UTR (whether 3′ or 5′) comprise a variant UTR.
  • a double, triple or quadruple UTR such as a 5′ UTR or 3′ UTR may be used.
  • a “double” UTR is one in which two copies of the same UTR are encoded either in series or substantially in series.
  • a double beta-globin 3′ UTR may be used as described in US Patent publication 20100129877, the contents of which are incorporated herein by reference in its entirety.
  • patterned UTRs are those UTRs which reflect a repeating or alternating pattern, such as ABABAB or AABBAABBAABB or ABCABCABC or variants thereof repeated once, twice, or more than 3 times. In these patterns, each letter, A, B, or C represent a different UTR at the nucleotide level.
  • flanking regions are selected from a family of transcripts whose proteins share a common function, structure, feature or property.
  • polypeptides of interest may belong to a family of proteins which are expressed in a particular cell, tissue or at some time during development.
  • the UTRs from any of these genes may be swapped for any other UTR of the same or different family of proteins to create a new polynucleotide.
  • a “family of proteins” is used in the broadest sense to refer to a group of two or more polypeptides of interest which share at least one function, structure, feature, localization, origin, or expression pattern.
  • the untranslated region may also include translation enhancer elements (TEE).
  • TEE translation enhancer elements
  • the TEE may include those described in US Application No. 2009/0226470, herein incorporated by reference in its entirety, and those known in the art.
  • cDNA encoding the polynucleotides described herein may be transcribed using an in vitro transcription (IVT) system.
  • IVT in vitro transcription
  • IVTT in vitro transcription of RNA is known in the art and is described in International Publication WO2014/152027, which is incorporated by reference herein in its entirety.
  • the RNA transcript is generated using a non-amplified, linearized DNA template in an in vitro transcription reaction to generate the RNA transcript.
  • the template DNA is isolated DNA.
  • the template DNA is cDNA.
  • the cDNA is formed by reverse transcription of a RNA polynucleotide, for example, but not limited to Lassa virus, Nipah virus, or betacoronavirus RNA, e.g. mRNA.
  • cells e.g., bacterial cells, e.g., E. coli , e.g., DH-1 cells are transfected with the plasmid DNA template.
  • the transfected cells are cultured to replicate the plasmid DNA which is then isolated and purified.
  • the DNA template includes a RNA polymerase promoter, e.g., a T7 promoter located 5′ to and operably linked to the gene of interest.
  • an in vitro transcription template encodes a 5′ untranslated (UTR) region, contains an open reading frame, and encodes a 3′ UTR and a polyA tail.
  • UTR 5′ untranslated
  • the particular nucleic acid sequence composition and length of an in vitro transcription template will depend on the mRNA encoded by the template.
  • a “5′ untranslated region” refers to a region of an mRNA that is directly upstream (i.e., 5′) from the start codon (i.e., the first codon of an mRNA transcript translated by a ribosome) that does not encode a polypeptide.
  • the 5′ UTR may comprise a promoter sequence. Such promoter sequences are known in the art. It should be understood that such promoter sequences will not be present in a vaccine of the disclosure.
  • a “3′ untranslated region” refers to a region of an mRNA that is directly downstream (i.e., 3′) from the stop codon (i.e., the codon of an mRNA transcript that signals a termination of translation) that does not encode a polypeptide.
  • An “open reading frame” is a continuous stretch of DNA beginning with a start codon (e.g., methionine (ATG)), and ending with a stop codon (e.g., TAA, TAG or TGA) and encodes a polypeptide.
  • a start codon e.g., methionine (ATG)
  • a stop codon e.g., TAA, TAG or TGA
  • a “polyA tail” is a region of mRNA that is downstream, e.g., directly downstream (i.e., 3′), from the 3′ UTR that contains multiple, consecutive adenosine monophosphates.
  • a polyA tail may contain 10 to 300 adenosine monophosphates.
  • a polyA tail may contain 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290 or 300 adenosine monophosphates.
  • a polyA tail contains 50 to 250 adenosine monophosphates.
  • the poly(A) tail functions to protect mRNA from enzymatic degradation, e.g., in the cytoplasm, and aids in transcription termination, and/or export of the mRNA from the nucleus and translation.
  • a nucleic acid includes 200 to 3,000 nucleotides.
  • a nucleic acid may include 200 to 500, 200 to 1000, 200 to 1500, 200 to 3000, 500 to 1000, 500 to 1500, 500 to 2000, 500 to 3000, 1000 to 1500, 1000 to 2000, 1000 to 3000, 1500 to 3000, or 2000 to 3000 nucleotides).
  • An in vitro transcription system typically comprises a transcription buffer, nucleotide triphosphates (NTPs), an RNase inhibitor and a polymerase.
  • NTPs nucleotide triphosphates
  • RNase inhibitor an RNase inhibitor
  • the NTPs may be manufactured in house, may be selected from a supplier, or may be synthesized as described herein.
  • the NTPs may be selected from, but are not limited to, those described herein including natural and unnatural (modified) NTPs.
  • RNA polymerases or variants may be used in the method of the present disclosure.
  • the polymerase may be selected from, but is not limited to, a phage RNA polymerase, e.g., a T7 RNA polymerase, a T3 RNA polymerase, a SP6 RNA polymerase, and/or mutant polymerases such as, but not limited to, polymerases able to incorporate modified nucleic acids and/or modified nucleotides, including chemically modified nucleic acids and/or nucleotides. Some embodiments exclude the use of DNase.
  • the RNA transcript is capped via enzymatic capping.
  • the RNA comprises 5′ terminal cap, for example, 7mG(5′)ppp(5′)NlmpNp.
  • Nucleic acids the present disclosure may be manufactured in whole or in part using solid phase techniques.
  • Solid-phase chemical synthesis of nucleic acids is an automated method wherein molecules are immobilized on a solid support and synthesized step by step in a reactant solution. Solid-phase synthesis is useful in site-specific introduction of chemical modifications in the nucleic acid sequences.
  • nucleic acids of the present disclosure by the sequential addition of monomer building blocks may be carried out in a liquid phase.
  • DNA or RNA ligases promote intermolecular ligation of the 5′ and 3′ ends of polynucleotide chains through the formation of a phosphodiester bond.
  • Nucleic acids such as chimeric polynucleotides and/or circular nucleic acids may be prepared by ligation of one or more regions or subregions. DNA fragments can be joined by a ligase catalyzed reaction to create recombinant DNA with different functions. Two oligodeoxynucleotides, one with a 5′ phosphoryl group and another with a free 3′ hydroxyl group, serve as substrates for a DNA ligase.
  • nucleic acid clean-up may include, but is not limited to, nucleic acid clean-up, quality assurance and quality control. Clean-up may be performed by methods known in the arts such as, but not limited to, AGENCOURT® beads (Beckman Coulter Genomics, Danvers, Mass.), poly-T beads, LNATM oligo-T capture probes (EXIQON® Inc, Vedbaek, Denmark) or HPLC based purification methods such as, but not limited to, strong anion exchange HPLC, weak anion exchange HPLC, reverse phase HPLC (RP-HPLC), and hydrophobic interaction HPLC (HIC-HPLC).
  • AGENCOURT® beads Beckman Coulter Genomics, Danvers, Mass.
  • poly-T beads poly-T beads
  • LNATM oligo-T capture probes EXIQON® Inc, Vedbaek, Denmark
  • HPLC based purification methods such as, but not limited to, strong anion exchange HPLC, weak anion exchange HPLC, reverse phase HP
  • purified when used in relation to a nucleic acid such as a “purified nucleic acid” refers to one that is separated from at least one contaminant.
  • a “contaminant” is any substance that makes another unfit, impure or inferior.
  • a purified nucleic acid e.g., DNA and RNA
  • a purified nucleic acid is present in a form or setting different from that in which it is found in nature, or a form or setting different from that which existed prior to subjecting it to a treatment or purification method.
  • a quality assurance and/or quality control check may be conducted using methods such as, but not limited to, gel electrophoresis, UV absorbance, or analytical HPLC.
  • the nucleic acids may be sequenced by methods including, but not limited to reverse-transcriptase-PCR.
  • the nucleic acids of the present disclosure may be quantified in exosomes or when derived from one or more bodily fluid.
  • Bodily fluids include peripheral blood, serum, plasma, ascites, urine, cerebrospinal fluid (CSF), sputum, saliva, bone marrow, synovial fluid, aqueous humor, amniotic fluid, cerumen, breast milk, broncheoalveolar lavage fluid, semen, prostatic fluid, cowper's fluid or pre-ejaculatory fluid, sweat, fecal matter, hair, tears, cyst fluid, pleural and peritoneal fluid, pericardial fluid, lymph, chyme, chyle, bile, interstitial fluid, menses, pus, sebum, vomit, vaginal secretions, mucosal secretion, stool water, pancreatic juice, lavage fluids from sinus cavities, bronchopulmonary aspirates, blastocyl cavity fluid, and umbilical cord blood.
  • CSF cerebrospinal fluid
  • exosomes may be retrieved from an organ selected from the group consisting of lung, heart, pancreas, stomach, intestine, bladder, kidney, ovary, testis, skin, colon, breast, prostate, brain, esophagus, liver, and placenta.
  • Assays may be performed using construct specific probes, cytometry, qRT-PCR, real-time PCR, PCR, flow cytometry, electrophoresis, mass spectrometry, or combinations thereof while the exosomes may be isolated using immunohistochemical methods such as enzyme linked immunosorbent assay (ELISA) methods. Exosomes may also be isolated by size exclusion chromatography, density gradient centrifugation, differential centrifugation, nanomembrane ultrafiltration, immunoabsorbent capture, affinity purification, microfluidic separation, or combinations thereof.
  • immunohistochemical methods such as enzyme linked immunosorbent assay (ELISA) methods.
  • Exosomes may also be isolated by size exclusion chromatography, density gradient centrifugation, differential centrifugation, nanomembrane ultrafiltration, immunoabsorbent capture, affinity purification, microfluidic separation, or combinations thereof.
  • nucleic acids of the present disclosure in some embodiments, differ from the endogenous forms due to the structural or chemical modifications.
  • the nucleic acid may be quantified using methods such as, but not limited to, ultraviolet visible spectroscopy (UV/Vis).
  • UV/Vis ultraviolet visible spectroscopy
  • a non-limiting example of a UV/Vis spectrometer is a NANODROP® spectrometer (ThermoFisher, Waltham, Mass.).
  • the quantified nucleic acid may be analyzed in order to determine if the nucleic acid may be of proper size, check that no degradation of the nucleic acid has occurred.
  • Degradation of the nucleic acid may be checked by methods such as, but not limited to, agarose gel electrophoresis, HPLC based purification methods such as, but not limited to, strong anion exchange HPLC, weak anion exchange HPLC, reverse phase HPLC (RP-HPLC), and hydrophobic interaction HPLC (HIC-HPLC), liquid chromatography-mass spectrometry (LCMS), capillary electrophoresis (CE) and capillary gel electrophoresis (CGE).
  • HPLC based purification methods such as, but not limited to, strong anion exchange HPLC, weak anion exchange HPLC, reverse phase HPLC (RP-HPLC), and hydrophobic interaction HPLC (HIC-HPLC), liquid chromatography-mass spectrometry (LCMS), capillary electrophoresis (CE) and capillary gel electrophoresis (CGE).
  • LNPs Lipid Nanoparticles
  • zoonotic disease RNA e.g., mRNA
  • vaccines of the disclosure are formulated in a lipid nanoparticle (LNP).
  • Lipid nanoparticles typically comprise ionizable cationic lipid, non-cationic lipid, sterol and PEG lipid components along with the nucleic acid cargo of interest.
  • the lipid nanoparticles of the disclosure can be generated using components, compositions, and methods as are generally known in the art, see for example PCT/US2016/052352; PCT/US2016/068300; PCT/US2017/037551; PCT/US2015/027400; PCT/US2016/047406; PCT/US2016000129; PCT/US2016/014280; PCT/US2016/014280; PCT/US2017/038426; PCT/US2014/027077; PCT/US2014/055394; PCT/US2016/52117; PCT/US2012/069610; PCT/US2017/027492; PCT/US2016/059575 and PCT/US2016/069491, all of which are incorporated by reference herein in their entirety.
  • Vaccines of the present disclosure are typically formulated in lipid nanoparticle.
  • the lipid nanoparticle comprises at least one ionizable cationic lipid, at least one non-cationic lipid, at least one sterol, and/or at least one polyethylene glycol (PEG)-modified lipid.
  • PEG polyethylene glycol
  • the lipid nanoparticle comprises a molar ratio of 20-60% ionizable cationic lipid.
  • the lipid nanoparticle may comprise a molar ratio of 20-50%, 20-40%, 20-30%, 30-60%, 30-50%, 30-40%, 40-60%, 40-50%, or 50-60% ionizable cationic lipid.
  • the lipid nanoparticle comprises a molar ratio of 20%, 30%, 40%, 50, or 60% ionizable cationic lipid.
  • the lipid nanoparticle comprises a molar ratio of 5-25% non-cationic lipid.
  • the lipid nanoparticle may comprise a molar ratio of 5-20%, 5-15%, 5-10%, 10-25%, 10-20%, 10-25%, 15-25%, 15-20%, or 20-25% non-cationic lipid.
  • the lipid nanoparticle comprises a molar ratio of 5%, 10%, 15%, 20%, or 25% non-cationic lipid.
  • the lipid nanoparticle comprises a molar ratio of 25-55% sterol.
  • the lipid nanoparticle may comprise a molar ratio of 25-50%, 25-45%, 25-40%, 25-35%, 25-30%, 30-55%, 30-50%, 30-45%, 30-40%, 30-35%, 35-55%, 35-50%, 35-45%, 35-40%, 40-55%, 40-50%, 40-45%, 45-55%, 45-50%, or 50-55% sterol.
  • the lipid nanoparticle comprises a molar ratio of 25%, 30%, 35%, 40%, 45%, 50%, or 55% sterol.
  • the lipid nanoparticle comprises a molar ratio of 0.5-15% PEG-modified lipid.
  • the lipid nanoparticle may comprise a molar ratio of 0.5-10%, 0.5-5%, 1-15%, 1-10%, 1-5%, 2-15%, 2-10%, 2-5%, 5-15%, 5-10%, or 10-15%.
  • the lipid nanoparticle comprises a molar ratio of 0.5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, or 15% PEG-modified lipid.
  • the lipid nanoparticle comprises a molar ratio of 20-60% ionizable cationic lipid, 5-25% non-cationic lipid, 25-55% sterol, and 0.5-15% PEG-modified lipid.
  • an ionizable cationic lipid of the disclosure comprises a compound of Formula (I):
  • R 1 is selected from the group consisting of C 5-30 alkyl, C 5-20 alkenyl, —R*YR′′, —YR′′, and —R′′M′R′;
  • R 2 and R 3 are independently selected from the group consisting of H, C 1-14 alkyl, C 2-14 alkenyl, —R*YR′′, —YR′′, and —R*OR′′, or R 2 and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle;
  • R 4 is selected from the group consisting of a C 3-6 carbocycle, —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, —CQ(R) 2 , and unsubstituted C 1-6 alkyl, where Q is selected from a carbocycle, heterocycle, —OR, —O(CH 2 ) n N(R) 2 , —C(O)OR, —OC(O)R, —CX 3 , —CX 2 H, —CXH 2 , —CN, —N(R) 2 , —C(O)N(R) 2 , —N(R)C(O)R, —N(R)S(O) 2 R, —N(R)C(O)N(R) 2 , —N(R)C(S)N(R) 2 , —N(R)R 8 , —O(CH 2 ) n OR,
  • each R 5 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • each R 6 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • M and M′ are independently selected from —C(O)O—, —OC(O)—, —C(O)N(R′)—, —N(R′)C(O)—, —C(O)—, —C(S)—, —C(S)S—, —SC(S)—, —CH(OH)—, —P(O)(OR′)O—, —S(O) 2 —, —S—S—, an aryl group, and a heteroaryl group;
  • R 7 is selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • R 8 is selected from the group consisting of C 3-6 carbocycle and heterocycle
  • R 9 is selected from the group consisting of H, CN, NO 2 , C 1-6 alkyl, —OR, —S(O) 2 R, —S(O) 2 N(R) 2 , C 2-6 alkenyl, C 3-6 carbocycle and heterocycle;
  • each R is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • each R′ is independently selected from the group consisting of C 1-18 alkyl, C 2-18 alkenyl, —R*YR′′, —YR′′, and H;
  • each R′′ is independently selected from the group consisting of C 3-14 alkyl and C 3-14 alkenyl
  • each R* is independently selected from the group consisting of C 1-12 alkyl and C 2-12 alkenyl;
  • each Y is independently a C 3-6 carbocycle
  • each X is independently selected from the group consisting of F, Cl, Br, and I;
  • n is selected from 5, 6, 7, 8, 9, 10, 11, 12, and 13.
  • a subset of compounds of Formula (I) includes those in which when R 4 is —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, or —CQ(R) 2 , then (i) Q is not —N(R) 2 when n is 1, 2, 3, 4 or 5, or (ii) Q is not 5, 6, or 7-membered heterocycloalkyl when n is 1 or 2.
  • another subset of compounds of Formula (I) includes those in which
  • R 1 is selected from the group consisting of C 5-30 alkyl, C 5-20 alkenyl, —R*YR′′, —YR′′, and —R′′M′R′;
  • R 2 and R 3 are independently selected from the group consisting of H, C 1-14 alkyl, C 2-14 alkenyl, —R*YR′′, —YR′′, and —R*OR′′, or R 2 and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle;
  • R 4 is selected from the group consisting of a C 3-6 carbocycle, —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, —CQ(R) 2 , and unsubstituted C 1-6 alkyl, where Q is selected from a C 3-6 carbocycle, a 5- to 14-membered heteroaryl having one or more heteroatoms selected from N, O, and S, —OR, —O(CH 2 ) n N(R) 2 , —C(O)OR, —OC(O)R, —CX 3 , —CX 2 H, —CXH 2 , —CN, —C(O)N(R) 2 , —N(R)C(O)R, —N(R)S(O) 2 R, —N(R)C(O)N(R) 2 , —N(R)C(S)N(R) 2 , —CRN
  • each R 5 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • each R 6 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • M and M′ are independently selected from —C(O)O—, —OC(O)—, —C(O)N(R′)—, —N(R′)C(O)—, —C(O)—, —C(S)—, —C(S)S—, —SC(S)—, —CH(OH)—, —P(O)(OR′)O—, —S(O) 2 —, —S—S—, an aryl group, and a heteroaryl group;
  • R 7 is selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • R 8 is selected from the group consisting of C 3-6 carbocycle and heterocycle
  • R 9 is selected from the group consisting of H, CN, NO 2 , C 1-6 alkyl, —OR, —S(O) 2 R, —S(O) 2 N(R) 2 , C 2-6 alkenyl, C 3-6 carbocycle and heterocycle;
  • each R is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • each R′ is independently selected from the group consisting of C 1-18 alkyl, C 2-18 alkenyl, —R*YR′′, —YR′′, and H;
  • each R′′ is independently selected from the group consisting of C 3-14 alkyl and C 3-14 alkenyl
  • each R* is independently selected from the group consisting of C 1-12 alkyl and C 2-12 alkenyl;
  • each Y is independently a C 3-6 carbocycle
  • each X is independently selected from the group consisting of F, Cl, Br, and I;
  • n is selected from 5, 6, 7, 8, 9, 10, 11, 12, and 13,
  • another subset of compounds of Formula (I) includes those in which
  • R 1 is selected from the group consisting of C 5-30 alkyl, C 5-20 alkenyl, —R*YR′′, —YR′′, and —R′′M′R′;
  • R 2 and R 3 are independently selected from the group consisting of H, C 1-14 alkyl, C 2-14 alkenyl, —R*YR′′, —YR′′, and —R*OR′′, or R 2 and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle;
  • R 4 is selected from the group consisting of a C 3-6 carbocycle, —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, —CQ(R) 2 , and unsubstituted C 1-6 alkyl, where Q is selected from a C 3-6 carbocycle, a 5- to 14-membered heterocycle having one or more heteroatoms selected from N, O, and S, —OR, —O(CH 2 ) n N(R) 2 , —C(O)OR, —OC(O)R, —CX 3 , —CX 2 H, —CXH 2 , —CN, —C(O)N(R) 2 , —N(R)C(O)R, —N(R)S(O) 2 R, —N(R)C(O)N(R) 2 , —N(R)C(S)N(R) 2 , —CRN(
  • each R 5 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • each R 6 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • M and M′ are independently selected from —C(O)O—, —OC(O)—, —C(O)N(R′)—, —N(R′)C(O)—, —C(O)—, —C(S)—, —C(S)S—, —SC(S)—, —CH(OH)—, —P(O)(OR′)O—, —S(O) 2 —, —S—S—, an aryl group, and a heteroaryl group;
  • R 7 is selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • R 8 is selected from the group consisting of C 3-6 carbocycle and heterocycle
  • R 9 is selected from the group consisting of H, CN, NO 2 , C 1-6 alkyl, —OR, —S(O) 2 R, —S(O) 2 N(R) 2 , C 2-6 alkenyl, C 3-6 carbocycle and heterocycle;
  • each R is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • each R′ is independently selected from the group consisting of C 1-18 alkyl, C 2-18 alkenyl, —R*YR′′, —YR′′, and H;
  • each R′′ is independently selected from the group consisting of C 3-14 alkyl and C 3-14 alkenyl
  • each R* is independently selected from the group consisting of C 1-12 alkyl and C 2-12 alkenyl;
  • each Y is independently a C 3-6 carbocycle
  • each X is independently selected from the group consisting of F, Cl, Br, and I;
  • n is selected from 5, 6, 7, 8, 9, 10, 11, 12, and 13,
  • another subset of compounds of Formula (I) includes those in which
  • R 1 is selected from the group consisting of C 5-30 alkyl, C 5-20 alkenyl, —R*YR′′, —YR′′, and —R′′M′R′;
  • R 2 and R 3 are independently selected from the group consisting of H, C 1-14 alkyl, C 2-14 alkenyl, —R*YR′′, —YR′′, and —R*OR′′, or R 2 and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle;
  • R 4 is selected from the group consisting of a C 3-6 carbocycle, —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, —CQ(R) 2 , and unsubstituted C 1-6 alkyl, where Q is selected from a C 3-6 carbocycle, a 5- to 14-membered heteroaryl having one or more heteroatoms selected from N, O, and S, —OR, —O(CH 2 ) n N(R) 2 , —C(O)OR, —OC(O)R, —CX 3 , —CX 2 H, —CXH 2 , —CN, —C(O)N(R) 2 , —N(R)C(O)R, —N(R)S(O) 2 R, —N(R)C(O)N(R) 2 , —N(R)C(S)N(R) 2 , —CRN
  • each R 5 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • each R 6 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • M and M′ are independently selected from —C(O)O—, —OC(O)—, —C(O)N(R′)—, —N(R′)C(O)—, —C(O)—, —C(S)—, —C(S)S—, —SC(S)—, —CH(OH)—, —P(O)(OR′)O—, —S(O) 2 —, —S—S—, an aryl group, and a heteroaryl group;
  • R 7 is selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • R 8 is selected from the group consisting of C 3-6 carbocycle and heterocycle
  • R 9 is selected from the group consisting of H, CN, NO 2 , C 1-6 alkyl, —OR, —S(O) 2 R, —S(O) 2 N(R) 2 , C 2-6 alkenyl, C 3-6 carbocycle and heterocycle;
  • each R is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • each R′ is independently selected from the group consisting of C 1-18 alkyl, C 2-18 alkenyl, —R*YR′′, —YR′′, and H;
  • each R′′ is independently selected from the group consisting of C 3-14 alkyl and C 3-14 alkenyl
  • each R* is independently selected from the group consisting of C 1-12 alkyl and C 2-12 alkenyl;
  • each Y is independently a C 3-6 carbocycle
  • each X is independently selected from the group consisting of F, Cl, Br, and I;
  • n is selected from 5, 6, 7, 8, 9, 10, 11, 12, and 13,
  • another subset of compounds of Formula (I) includes those in which
  • R 1 is selected from the group consisting of C 5-30 alkyl, C 5-20 alkenyl, —R*YR′′, —YR′′, and —R′′M′R′;
  • R 2 and R 3 are independently selected from the group consisting of H, C 2-14 alkyl, C 2-14 alkenyl, —R*YR′′, —YR′′, and —R*OR′′, or R 2 and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle;
  • R 4 is —(CH 2 ) n Q or —(CH 2 ) n CHQR, where Q is —N(R) 2 , and n is selected from 3, 4, and 5;
  • each R 5 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • each R 6 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • M and M′ are independently selected from —C(O)O—, —OC(O)—, —C(O)N(R′)—, —N(R′)C(O)—, —C(O)—, —C(S)—, —C(S)S—, —SC(S)—, —CH(OH)—, —P(O)(OR′)O—, —S(O) 2 —, —S—S—, an aryl group, and a heteroaryl group;
  • R 7 is selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • each R is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • each R′ is independently selected from the group consisting of C 1-18 alkyl, C 2-18 alkenyl, —R*YR′′, —YR′′, and H;
  • each R′′ is independently selected from the group consisting of C 3-14 alkyl and C 3-14 alkenyl
  • each R* is independently selected from the group consisting of C 1-12 alkyl and C 1-12 alkenyl;
  • each Y is independently a C 3-6 carbocycle
  • each X is independently selected from the group consisting of F, Cl, Br, and I;
  • n is selected from 5, 6, 7, 8, 9, 10, 11, 12, and 13,
  • another subset of compounds of Formula (I) includes those in which
  • R 1 is selected from the group consisting of C 5-30 alkyl, C 5-20 alkenyl, —R*YR′′, —YR′′, and —R′′M′R′;
  • R 2 and R 3 are independently selected from the group consisting of C 1-14 alkyl, C 2-14 alkenyl, —R*YR′′, —YR′′, and —R*OR′′, or R 2 and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle;
  • R 4 is selected from the group consisting of —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, and —CQ(R) 2 , where Q is —N(R) 2 , and n is selected from 1, 2, 3, 4, and 5;
  • each R 5 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • each R 6 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • M and M′ are independently selected from —C(O)O—, —OC(O)—, —C(O)N(R′)—, —N(R′)C(O)—, —C(O)—, —C(S)—, —C(S)S—, —SC(S)—, —CH(OH)—, —P(O)(OR′)O—, —S(O) 2 —, —S—S—, an aryl group, and a heteroaryl group;
  • R 7 is selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • each R is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H;
  • each R′ is independently selected from the group consisting of C 1-18 alkyl, C 2-18 alkenyl, —R*YR′′, —YR′′, and H;
  • each R′′ is independently selected from the group consisting of C 3-14 alkyl and C 3-14 alkenyl
  • each R* is independently selected from the group consisting of C 1-12 alkyl and C 1-12 alkenyl;
  • each Y is independently a C 3-6 carbocycle
  • each X is independently selected from the group consisting of F, Cl, Br, and I;
  • n is selected from 5, 6, 7, 8, 9, 10, 11, 12, and 13,
  • a subset of compounds of Formula (I) includes those of Formula (IA):
  • M 1 is a bond or M′;
  • a subset of compounds of Formula (I) includes those of Formula (II):
  • M 1 is a bond or M′
  • a subset of compounds of Formula (I) includes those of Formula (IIa), (IIb), (IIc), or (lie):
  • R 4 is as described herein.
  • a subset of compounds of Formula (I) includes those of Formula (IId):
  • each of R 2 and R 3 may be independently selected from the group consisting of C 5-14 alkyl and C 5-14 alkenyl.
  • an ionizable cationic lipid of the disclosure comprises a compound having structure:
  • an ionizable cationic lipid of the disclosure comprises a compound having structure:
  • a non-cationic lipid of the disclosure comprises 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-gly cero-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-diundecanoyl-sn-glycero-phosphocholine (DUPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-di-O-octadecenyl-sn-glycero-3-phosphocholine
  • a PEG modified lipid of the disclosure comprises a PEG-modified phosphatidylethanolamine, a PEG-modified phosphatidic acid, a PEG-modified ceramide, a PEG-modified dialkylamine, a PEG-modified diacylglycerol, a PEG-modified dialkylglycerol, and mixtures thereof.
  • the PEG-modified lipid is PEG-DMG, PEG-c-DOMG (also referred to as PEG-DOMG), PEG-DSG and/or PEG-DPG.
  • a sterol of the disclosure comprises cholesterol, fecosterol, sitosterol, ergosterol, campesterol, stigmasterol, brassicasterol, tomatidine, ursolic acid, alpha-tocopherol, and mixtures thereof.
  • a LNP of the disclosure comprises an ionizable cationic lipid of Compound 1, wherein the non-cationic lipid is DSPC, the structural lipid that is cholesterol, and the PEG lipid is PEG-DMG.
  • a LNP of the disclosure comprises an N:P ratio of from about 2:1 to about 30:1.
  • a LNP of the disclosure comprises an N:P ratio of about 6:1.
  • a LNP of the disclosure comprises an N:P ratio of about 3:1.
  • a LNP of the disclosure comprises a wt/wt ratio of the ionizable cationic lipid component to the RNA of from about 10:1 to about 100:1.
  • a LNP of the disclosure comprises a wt/wt ratio of the ionizable cationic lipid component to the RNA of about 20:1.
  • a LNP of the disclosure comprises a wt/wt ratio of the ionizable cationic lipid component to the RNA of about 10:1.
  • a LNP of the disclosure has a mean diameter from about 50 nm to about 150 nm.
  • a LNP of the disclosure has a mean diameter from about 70 nm to about 120 nm.
  • the zoonotic disease vaccines may include an RNA (e.g. mRNA) or multiple RNAs encoding two or more antigens of the same or different zoonotic disease species.
  • a zoonotic disease vaccine includes an RNA or multiple RNAs encoding two or more antigens.
  • the RNA (at least one RNA) of a zoonotic disease vaccine may encode 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more antigens.
  • two or more different RNA (e.g., mRNA) encoding antigens may be formulated in the same lipid nanoparticle.
  • two or more different RNA encoding antigens may be formulated in separate lipid nanoparticles (each RNA formulated in a single lipid nanoparticle).
  • the lipid nanoparticles may then be combined and administered as a single vaccine composition (e.g., comprising multiple RNA encoding multiple antigens) or may be administered separately.
  • RNA e.g., mRNA
  • RNA e.g., mRNA
  • therapeutic vaccines are particularly amenable to combination vaccination approaches due to a number of factors including, but not limited to, speed of manufacture, ability to rapidly tailor vaccines to accommodate perceived geographical threat, and the like.
  • the vaccines utilize the human body to produce the antigenic protein, the vaccines are amenable to the production of larger, more complex antigenic proteins, allowing for proper folding, surface expression, antigen presentation, etc. in the human subject.
  • a combination vaccine can be administered that includes RNA (e.g., mRNA) encoding at least one antigenic polypeptide protein (or antigenic portion thereof) of a first virus and further includes RNA encoding at least one antigenic polypeptide protein (or antigenic portion thereof) of a second virus.
  • RNA e.g., mRNA
  • LNP lipid nanoparticle
  • the zoonotic disease vaccines may include an RNA or multiple RNAs encoding two or more antigens of the same or different viral strains. Also provided herein are combination vaccines that include RNA encoding one or more zoonotic disease antigen(s) and one or more antigen(s) of a different organisms (e.g., bacterial and/or viral organism).
  • the vaccines of the present disclosure may be combination vaccines that target one or more antigens of the same strain/species, or one or more antigens of different strains/species, e.g., antigens which induce immunity to organisms which are found in the same geographic areas where the risk of Lassa virus, Nipah virus, or betacoronavirus infection is high or organisms to which an individual is likely to be exposed to when exposed to the virus.
  • Flagellin is an approximately 500 amino acid monomeric protein that polymerizes to form the flagella associated with bacterial motion. Flagellin is expressed by a variety of flagellated bacteria ( Salmonella typhimurium for example) as well as non-flagellated bacteria (such as Escherichia coli ). Sensing of flagellin by cells of the innate immune system (dendritic cells, macrophages, etc.) is mediated by the Toll-like receptor 5 (TLR5) as well as by Nod-like receptors (NLRs) Ipaf and Naip5. TLRs and NLRs have been identified as playing a role in the activation of innate immune response and adaptive immune response. As such, flagellin provides an adjuvant effect in a vaccine.
  • TLR5 Toll-like receptor 5
  • NLRs Nod-like receptors
  • the nucleotide and amino acid sequences encoding known flagellin polypeptides are publicly available in the NCBI GenBank database.
  • a flagellin polypeptide refers to a full length flagellin protein, immunogenic fragments thereof, and peptides having at least 50% sequence identify to a flagellin protein or immunogenic fragments thereof.
  • Exemplary flagellin proteins include flagellin from Salmonella typhi (UniPro Entry number: Q56086), Salmonella typhimurium (AOAOC9DG09), Salmonella enteritidis (AOAOC9BAB7), and Salmonella choleraesuis (Q6V2X8).
  • the flagellin polypeptide has at least 60%, 70%, 75%, 80%, 90%, 95%, 97%, 98%, or 99% sequence identify to a flagellin protein or immunogenic fragments thereof.
  • the flagellin polypeptide is an immunogenic fragment.
  • An immunogenic fragment is a portion of a flagellin protein that provokes an immune response.
  • the immune response is a TLR5 immune response.
  • An example of an immunogenic fragment is a flagellin protein in which all or a portion of a hinge region has been deleted or replaced with other amino acids.
  • an antigenic polypeptide may be inserted in the hinge region. Hinge regions are the hypervariable regions of a flagellin.
  • Hinge regions of a flagellin are also referred to as “D3 domain or region, “propeller domain or region,” “hypervariable domain or region” and “variable domain or region.” “At least a portion of a hinge region,” as used herein, refers to any part of the hinge region of the flagellin, or the entirety of the hinge region. In other embodiments an immunogenic fragment of flagellin is a 20, 25, 30, 35, or 40 amino acid C-terminal fragment of flagellin.
  • the flagellin monomer is formed by domains D0 through D3.
  • D0 and D1 which form the stem, are composed of tandem long alpha helices and are highly conserved among different bacteria.
  • the D1 domain includes several stretches of amino acids that are useful for TLR5 activation.
  • the entire D1 domain or one or more of the active regions within the domain are immunogenic fragments of flagellin. Examples of immunogenic regions within the D1 domain include residues 88-114 and residues 411-431 (in Salmonella typhimurium FliC flagellin). Within the 13 amino acids in the 88-100 region, at least 6 substitutions are permitted between Salmonella flagellin and other flagellins that still preserve TLR5 activation.
  • immunogenic fragments of flagellin include flagellin like sequences that activate TLR5 and contain a 13 amino acid motif that is 53% or more identical to the Salmonella sequence in 88-100 of FliC (LQRVRELAVQSAN; SEQ ID NO: 31).
  • compositions e.g., pharmaceutical compositions
  • methods, kits and reagents for prevention or treatment of zoonotic disease in humans and other mammals for example.
  • zoonotic disease RNA e.g., mRNA
  • vaccines can be used as therapeutic or prophylactic agents. They may be used in medicine to prevent and/or treat infectious disease.
  • a zoonotic disease vaccine containing RNA polynucleotides as described herein can be administered to a subject (e.g., a mammalian subject, such as a human subject), and the RNA polynucleotides are translated in vivo to produce an antigenic polypeptide (antigen).
  • a subject e.g., a mammalian subject, such as a human subject
  • the RNA polynucleotides are translated in vivo to produce an antigenic polypeptide (antigen).
  • an “effective amount” of a zoonotic disease vaccine is based, at least in part, on the target tissue, target cell type, means of administration, physical characteristics of the RNA (e.g., length, nucleotide composition, and/or extent of modified nucleosides), other components of the vaccine, and other determinants, such as age, body weight, height, sex and general health of the subject.
  • an effective amount of a zoonotic disease vaccine provides an induced or boosted immune response as a function of antigen production in the cells of the subject.
  • an effective amount of the zoonotic disease RNA vaccine containing RNA polynucleotides having at least one chemical modifications are more efficient than a composition containing a corresponding unmodified polynucleotide encoding the same antigen or a peptide antigen.
  • Increased antigen production may be demonstrated by increased cell transfection (the percentage of cells transfected with the RNA vaccine), increased protein translation and/or expression from the polynucleotide, decreased nucleic acid degradation (as demonstrated, for example, by increased duration of protein translation from a modified polynucleotide), or altered antigen specific immune response of the host cell.
  • composition refers to the combination of an active agent with a carrier, inert or active, making the composition especially suitable for diagnostic or therapeutic use in vivo or ex vivo.
  • a “pharmaceutically acceptable carrier,” after administered to or upon a subject, does not cause undesirable physiological effects.
  • the carrier in the pharmaceutical composition must be “acceptable” also in the sense that it is compatible with the active ingredient and can be capable of stabilizing it.
  • One or more solubilizing agents can be utilized as pharmaceutical carriers for delivery of an active agent.
  • a pharmaceutically acceptable carrier include, but are not limited to, biocompatible vehicles, adjuvants, additives, and diluents to achieve a composition usable as a dosage form.
  • examples of other carriers include colloidal silicon oxide, magnesium stearate, cellulose, and sodium lauryl sulfate. Additional suitable pharmaceutical carriers and diluents, as well as pharmaceutical necessities for their use, are described in Remington's Pharmaceutical Sciences.
  • RNA vaccines in accordance with the present disclosure may be used for treatment or prevention of zoonotic disease.
  • Zoonotic disease RNA vaccines may be administered prophylactically or therapeutically as part of an active immunization scheme to healthy individuals or early in infection during the incubation phase or during active infection after onset of symptoms.
  • the amount of RNA vaccines of the present disclosure provided to a cell, a tissue or a subject may be an amount effective for immune prophylaxis.
  • Zoonotic disease RNA (e.g., mRNA) vaccines may be administered with other prophylactic or therapeutic compounds.
  • a prophylactic or therapeutic compound may be an adjuvant or a booster.
  • the term “booster” refers to an extra administration of the prophylactic (vaccine) composition.
  • a booster or booster vaccine may be given after an earlier administration of the prophylactic composition.
  • the time of administration between the initial administration of the prophylactic composition and the booster may be, but is not limited to, 1 minute, 2 minutes, 3 minutes, 4 minutes, 5 minutes, 6 minutes, 7 minutes, 8 minutes, 9 minutes, 10 minutes, 15 minutes, 20 minutes 35 minutes, 40 minutes, 45 minutes, 50 minutes, 55 minutes, 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours, 22 hours, 23 hours, 1 day, 36 hours, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 10 days, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 1 year, 18 months, 2 years, 3 years, 4 years, 5 years, 6 years, 7 years, 8 years, 9 years, 10 years, 11 years, 12 years, 13 years, 14
  • zoonotic disease RNA vaccines may be administered intramuscularly, intranasally or intradermally, similarly to the administration of inactivated vaccines known in the art.
  • RNA vaccines may be utilized in various settings depending on the prevalence of the infection or the degree or level of unmet medical need. As a non-limiting example, the RNA vaccines may be utilized to treat and/or prevent a variety of infectious disease. RNA vaccines have superior properties in that they produce much larger antibody titers, better neutralizing immunity, produce more durable immune responses, and/or produce responses earlier than commercially available vaccines.
  • compositions including zoonotic disease RNA vaccines and RNA vaccine compositions and/or complexes optionally in combination with one or more pharmaceutically acceptable excipients.
  • Zoonotic disease RNA e.g., mRNA
  • vaccines may be formulated or administered alone or in conjunction with one or more other components.
  • zoonotic disease RNA vaccines may comprise other components including, but not limited to, adjuvants.
  • zoonotic disease RNA vaccines do not include an adjuvant (they are adjuvant free).
  • Zoonotic disease RNA e.g., mRNA
  • vaccines may be formulated or administered in combination with one or more pharmaceutically-acceptable excipients.
  • vaccine compositions comprise at least one additional active substances, such as, for example, a therapeutically-active substance, a prophylactically-active substance, or a combination of both.
  • Vaccine compositions may be sterile, pyrogen-free or both sterile and pyrogen-free.
  • General considerations in the formulation and/or manufacture of pharmaceutical agents, such as vaccine compositions, may be found, for example, in Remington: The Science and Practice of Pharmacy 21st ed., Lippincott Williams & Wilkins, 2005 (incorporated herein by reference in its entirety).
  • RNA vaccines are administered to humans, human patients or subjects.
  • active ingredient generally refers to the RNA vaccines or the polynucleotides contained therein, for example, RNA polynucleotides (e.g., mRNA polynucleotides) encoding antigens.
  • Formulations of the vaccine compositions described herein may be prepared by any method known or hereafter developed in the art of pharmacology.
  • preparatory methods include the step of bringing the active ingredient (e.g., mRNA polynucleotide) into association with an excipient and/or one or more other accessory ingredients, and then, if necessary and/or desirable, dividing, shaping and/or packaging the product into a desired single- or multi-dose unit.
  • compositions in accordance with the disclosure will vary, depending upon the identity, size, and/or condition of the subject treated and further depending upon the route by which the composition is to be administered.
  • the composition may comprise between 0.1% and 100%, e.g., between 0.5 and 50%, between 1-30%, between 5-80%, at least 80% (w/w) active ingredient.
  • zoonotic disease RNA vaccines are formulated using one or more excipients to: (1) increase stability; (2) increase cell transfection; (3) permit the sustained or delayed release (e.g., from a depot formulation); (4) alter the biodistribution (e.g., target to specific tissues or cell types); (5) increase the translation of encoded protein in vivo; and/or (6) alter the release profile of encoded protein (antigen) in vivo.
  • excipients can include, without limitation, lipidoids, liposomes, lipid nanoparticles, polymers, lipoplexes, core-shell nanoparticles, peptides, proteins, cells transfected with zoonotic disease RNA vaccines (e.g., for transplantation into a subject), hyaluronidase, nanoparticle mimics and combinations thereof.
  • compositions e.g., pharmaceutical compositions
  • zoonotic disease RNA vaccines can be used as therapeutic or prophylactic agents.
  • the RNA vaccines of the disclosure are used to provide prophylactic protection from zoonotic disease.
  • the RNA vaccines of the disclosure are used to treat a zoonotic disease infection.
  • the zoonotic disease vaccines of the present disclosure are used in the priming of immune effector cells, for example, to activate peripheral blood mononuclear cells (PBMCs) ex vivo, which are then infused (re-infused) into a subject.
  • PBMCs peripheral blood mononuclear cells
  • a subject may be any mammal, including non-human primate and human subjects.
  • a subject is a human subject.
  • the zoonotic disease vaccines are administered to a subject (e.g., a mammalian subject, such as a human subject) in an effective amount to induce an antigen-specific immune response.
  • a subject e.g., a mammalian subject, such as a human subject
  • the RNA encoding the zoonotic disease antigen is expressed and translated in vivo to produce the antigen, which then stimulates an immune response in the subject.
  • Prophylactic protection from zoonotic disease can be achieved following administration of a zoonotic disease RNA vaccine of the present disclosure.
  • Vaccines can be administered once, twice, three times, four times or more but it is likely sufficient to administer the vaccine once (optionally followed by a single booster). It is possible, although less desirable, to administer the vaccine to an infected individual to achieve a therapeutic response. Dosing may need to be adjusted accordingly.
  • a method of eliciting an immune response in a subject against zoonotic disease involves administering to the subject a zoonotic disease RNA vaccine comprising at least one RNA (e.g., mRNA) having an open reading frame encoding at least one zoonotic disease antigen, thereby inducing in the subject an immune response specific to zoonotic disease antigen, wherein anti-antigen antibody titer in the subject is increased following vaccination relative to anti-antigen antibody titer in a subject vaccinated with a prophylactically effective dose of a traditional vaccine against the zoonotic disease.
  • An “anti-antigen antibody” is a serum antibody the binds specifically to the antigen.
  • a prophylactically effective dose is an effective dose that prevents infection with the virus at a clinically acceptable level.
  • the effective dose is a dose listed in a package insert for the vaccine.
  • a traditional vaccine refers to a vaccine other than the mRNA vaccines of the present disclosure.
  • a traditional vaccine includes, but is not limited, to live microorganism vaccines, killed microorganism vaccines, subunit vaccines, protein antigen vaccines, DNA vaccines, virus like particle (VLP) vaccines, etc.
  • a traditional vaccine is a vaccine that has achieved regulatory approval and/or is registered by a national drug regulatory body, for example the Food and Drug Administration (FDA) in the United States or the European Medicines Agency (EMA).
  • FDA Food and Drug Administration
  • EMA European Medicines Agency
  • the anti-antigen antibody titer in the subject is increased 1 log to 10 log following vaccination relative to anti-antigen antibody titer in a subject vaccinated with a prophylactically effective dose of a traditional vaccine against the zoonotic disease or an unvaccinated subject. In some embodiments, the anti-antigen antibody titer in the subject is increased 1 log, 2 log, 3 log, 4 log, 5 log, or 10 log following vaccination relative to anti-antigen antibody titer in a subject vaccinated with a prophylactically effective dose of a traditional vaccine against the zoonotic disease or an unvaccinated subject.
  • a method of eliciting an immune response in a subject against a zoonotic disease involves administering to the subject a zoonotic disease RNA vaccine comprising at least one RNA polynucleotide having an open reading frame encoding at least one zoonotic disease antigen, thereby inducing in the subject an immune response specific to zoonotic disease antigen, wherein the immune response in the subject is equivalent to an immune response in a subject vaccinated with a traditional vaccine against the zoonotic disease at 2 times to 100 times the dosage level relative to the RNA vaccine.
  • the immune response in the subject is equivalent to an immune response in a subject vaccinated with a traditional vaccine at twice the dosage level relative to the zoonotic disease RNA vaccine. In some embodiments, the immune response in the subject is equivalent to an immune response in a subject vaccinated with a traditional vaccine at three times the dosage level relative to the zoonotic disease RNA vaccine. In some embodiments, the immune response in the subject is equivalent to an immune response in a subject vaccinated with a traditional vaccine at 4 times, 5 times, 10 times, 50 times, or 100 times the dosage level relative to the zoonotic disease RNA vaccine.
  • the immune response in the subject is equivalent to an immune response in a subject vaccinated with a traditional vaccine at 10 times to 1000 times the dosage level relative to the zoonotic disease RNA vaccine. In some embodiments, the immune response in the subject is equivalent to an immune response in a subject vaccinated with a traditional vaccine at 100 times to 1000 times the dosage level relative to the zoonotic disease RNA vaccine.
  • the immune response is assessed by determining [protein] antibody titer in the subject.
  • the ability of serum or antibody from an immunized subject is tested for its ability to neutralize viral uptake or reduce zoonotic disease transformation of human B lymphocytes.
  • the ability to promote a robust T cell response(s) is measured using art recognized techniques.
  • the disclosure provide methods of eliciting an immune response in a subject against a zoonotic disease by administering to the subject a zoonotic disease RNA vaccine comprising at least one RNA polynucleotide having an open reading frame encoding at least one zoonotic disease antigen, thereby inducing in the subject an immune response specific to zoonotic disease antigen, wherein the immune response in the subject is induced 2 days to 10 weeks earlier relative to an immune response induced in a subject vaccinated with a prophylactically effective dose of a traditional vaccine against the zoonotic disease.
  • the immune response in the subject is induced in a subject vaccinated with a prophylactically effective dose of a traditional vaccine at 2 times to 100 times the dosage level relative to the RNA vaccine.
  • the immune response in the subject is induced 2 days, 3 days, 1 week, 2 weeks, 3 weeks, 5 weeks, or 10 weeks earlier relative to an immune response induced in a subject vaccinated with a prophylactically effective dose of a traditional vaccine.
  • Zoonotic disease RNA (e.g., mRNA) vaccines may be administered by any route which results in a therapeutically effective outcome. These include, but are not limited, to intradermal, intramuscular, intranasal, and/or subcutaneous administration.
  • the present disclosure provides methods comprising administering RNA vaccines to a subject in need thereof. The exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the disease, the particular composition, its mode of administration, its mode of activity, and the like.
  • zoonotic disease RNA (e.g., mRNA) vaccines compositions are typically formulated in dosage unit form for ease of administration and uniformity of dosage.
  • RNA e.g., mRNA
  • the specific therapeutically effective, prophylactically effective, or appropriate imaging dose level for any particular patient will depend upon a variety of factors including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed; and like factors well known in the medical arts.
  • the effective amount of a zoonotic disease vaccine may be as low as 20 rig, administered for example as a single dose or as two 10 ⁇ g doses. In some embodiments, the effective amount is a total dose of 20 ⁇ g-200 ⁇ g.
  • the effective amount may be a total dose of 20 ⁇ g, 25 ⁇ g, 30 ⁇ g, 35 ⁇ g, 40 ⁇ g, 45 ⁇ g, 50 ⁇ g, 55 ⁇ g, 60 ⁇ g, 65 ⁇ g, 70 ⁇ g, 75 ⁇ g, 80 ⁇ g, 85 ⁇ g, 90 ⁇ g, 95 ⁇ g, 100 ⁇ g, 110 ⁇ g, 120 ⁇ g, 130 ⁇ g, 140 ⁇ g, 150 ⁇ g, 160 ⁇ g, 170 ⁇ g, 180 ⁇ g, 190 ⁇ g or 200 ⁇ g.
  • the effective amount is a total dose of 25 ⁇ g-200 ⁇ g.
  • the effective amount is a total dose of 50 ⁇ g-200 ⁇ g.
  • zoonotic disease RNA (e.g., mRNA) vaccines compositions may be administered at dosage levels sufficient to deliver 0.0001 mg/kg to 100 mg/kg, 0.001 mg/kg to 0.05 mg/kg, 0.005 mg/kg to 0.05 mg/kg, 0.001 mg/kg to 0.005 mg/kg, 0.05 mg/kg to 0.5 mg/kg, 0.01 mg/kg to 50 mg/kg, 0.1 mg/kg to 40 mg/kg, 0.5 mg/kg to 30 mg/kg, 0.01 mg/kg to 10 mg/kg, 0.1 mg/kg to 10 mg/kg, or 1 mg/kg to 25 mg/kg, of subject body weight per day, one or more times a day, per week, per month, etc.
  • the desired dosage may be delivered three times a day, two times a day, once a day, every other day, every third day, every week, every two weeks, every three weeks, every four weeks, every 2 months, every three months, every 6 months, etc.
  • the desired dosage may be delivered using multiple administrations (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or more administrations). When multiple administrations are employed, split dosing regimens such as those described herein may be used.
  • zoonotic disease RNA (e.g., mRNA) vaccines compositions may be administered at dosage levels sufficient to deliver 0.0005 mg/kg to 0.01 mg/kg, e.g., about 0.0005 mg/kg to about 0.0075 mg/kg, e.g., about 0.0005 mg/kg, about 0.001 mg/kg, about 0.002 mg/kg, about 0.003 mg/kg, about 0.004 mg/kg or about 0.005 mg/kg.
  • zoonotic disease RNA e.g., mRNA
  • vaccine compositions may be administered once or twice (or more) at dosage levels sufficient to deliver 0.025 mg/kg to 0.250 mg/kg, 0.025 mg/kg to 0.500 mg/kg, 0.025 mg/kg to 0.750 mg/kg, or 0.025 mg/kg to 1.0 mg/kg.
  • zoonotic disease RNA (e.g., mRNA) vaccine compositions may be administered twice (e.g., Day 0 and Day 7, Day 0 and Day 14, Day 0 and Day 21, Day 0 and Day 28, Day 0 and Day 60, Day 0 and Day 90, Day 0 and Day 120, Day 0 and Day 150, Day 0 and Day 180, Day 0 and 3 months later, Day 0 and 6 months later, Day 0 and 9 months later, Day 0 and 12 months later, Day 0 and 18 months later, Day 0 and 2 years later, Day 0 and 5 years later, or Day 0 and 10 years later) at a total dose of or at dosage levels sufficient to deliver a total dose of 0.0100 mg, 0.025 mg, 0.050 mg, 0.075 mg, 0.100 mg, 0.125 mg, 0.150 mg, 0.175 mg, 0.200 mg, 0.225 mg, 0.250 mg, 0.275 mg, 0.300 mg, 0.325 mg, 0.350 mg, 0.375 mg, 0.400 mg, 0.425
  • zoonotic disease RNA (e.g., mRNA) vaccine compositions may be administered twice (e.g., Day 0 and Day 7, Day 0 and Day 14, Day 0 and Day 21, Day 0 and Day 28, Day 0 and Day 60, Day 0 and Day 90, Day 0 and Day 120, Day 0 and Day 150, Day 0 and Day 180, Day 0 and 3 months later, Day 0 and 6 months later, Day 0 and 9 months later, Day 0 and 12 months later, Day 0 and 18 months later, Day 0 and 2 years later, Day 0 and 5 years later, or Day 0 and 10 years later) at a total dose of or at dosage levels sufficient to deliver a total dose of 0.010 mg, 0.025 mg, 0.100 mg or 0.400 mg.
  • twice e.g., Day 0 and Day 7, Day 0 and Day 14, Day 0 and Day 21, Day 0 and Day 28, Day 0 and Day 60, Day 0 and Day 90, Day 0 and Day 120, Day 0 and Day 150, Day
  • the zoonotic disease RNA (e.g., mRNA) vaccine for use in a method of vaccinating a subject is administered the subject a single dosage of between 10 ⁇ g/kg and 400 ⁇ g/kg of the nucleic acid vaccine in an effective amount to vaccinate the subject.
  • the RNA vaccine for use in a method of vaccinating a subject is administered the subject a single dosage of between 10 ⁇ g and 400 ⁇ g of the nucleic acid vaccine in an effective amount to vaccinate the subject.
  • a zoonotic disease RNA (e.g., mRNA) vaccine for use in a method of vaccinating a subject is administered to the subject as a single dosage of 25-1000 ⁇ g (e.g., a single dosage of mRNA encoding a zoonotic disease antigen).
  • a zoonotic disease RNA vaccine is administered to the subject as a single dosage of 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950 or 1000 ⁇ g.
  • a zoonotic disease RNA vaccine may be administered to a subject as a single dose of 25-100, 25-500, 50-100, 50-500, 50-1000, 100-500, 100-1000, 250-500, 250-1000, or 500-1000 ⁇ g.
  • a zoonotic disease RNA (e.g., mRNA) vaccine for use in a method of vaccinating a subject is administered to the subject as two dosages, the combination of which equals 25-1000 ⁇ g of the zoonotic disease RNA (e.g., mRNA) vaccine.
  • AN zoonotic disease RNA (e.g., mRNA) vaccine pharmaceutical composition described herein can be formulated into a dosage form described herein, such as an intranasal, intratracheal, or injectable (e.g., intravenous, intraocular, intravitreal, intramuscular, intradermal, intracardiac, intraperitoneal, and subcutaneous).
  • injectable e.g., intravenous, intraocular, intravitreal, intramuscular, intradermal, intracardiac, intraperitoneal, and subcutaneous.
  • Some aspects of the present disclosure provide formulations of the zoonotic disease RNA (e.g., mRNA) vaccine, wherein the zoonotic disease RNA vaccine is formulated in an effective amount to produce an antigen specific immune response in a subject (e.g., production of antibodies specific to an anti-zoonotic disease antigen).
  • an effective amount is a dose of an zoonotic disease RNA (e.g., mRNA) vaccine effective to produce an antigen-specific immune response.
  • methods of inducing an antigen-specific immune response in a subject are also provided herein.
  • an immune response to a vaccine or LNP of the present disclosure is the development in a subject of a humoral and/or a cellular immune response to a (one or more) zoonotic disease protein(s) present in the vaccine.
  • a “humoral” immune response refers to an immune response mediated by antibody molecules, including, e.g., secretory (IgA) or IgG molecules, while a “cellular” immune response is one mediated by T-lymphocytes (e.g., CD4+ helper and/or CD8+ T cells (e.g., CTLs) and/or other white blood cells.
  • CTLs cytolytic T-cells
  • MHC major histocompatibility complex
  • helper T-cells act to help stimulate the function, and focus the activity nonspecific effector cells against cells displaying peptide antigens in association with MHC molecules on their surface.
  • a cellular immune response also leads to the production of cytokines, chemokines, and other such molecules produced by activated T-cells and/or other white blood cells including those derived from CD4+ and CD8+ T-cells.
  • the antigen-specific immune response is characterized by measuring an anti-zoonotic disease antigen antibody titer produced in a subject administered an zoonotic disease RNA (e.g., mRNA) vaccine as provided herein.
  • An antibody titer is a measurement of the amount of antibodies within a subject, for example, antibodies that are specific to a particular antigen (e.g., an anti-zoonotic disease antigen) or epitope of an antigen.
  • Antibody titer is typically expressed as the inverse of the greatest dilution that provides a positive result.
  • Enzyme-linked immunosorbent assay is a common assay for determining antibody titers, for example.
  • an antibody titer is used to assess whether a subject has had an infection or to determine whether immunizations are required. In some embodiments, an antibody titer is used to determine the strength of an autoimmune response, to determine whether a booster immunization is needed, to determine whether a previous vaccine was effective, and to identify any recent or prior infections. In accordance with the present disclosure, an antibody titer may be used to determine the strength of an immune response induced in a subject by the zoonotic disease RNA (e.g., mRNA) vaccine.
  • RNA e.g., mRNA
  • an anti-zoonotic disease antigen antibody titer produced in a subject is increased by at least 1 log relative to a control.
  • anti-zoonotic disease antigen antibody titer produced in a subject may be increased by at least 1.5, at least 2, at least 2.5, or at least 3 log relative to a control.
  • the anti-zoonotic disease antigen antibody titer produced in the subject is increased by 1, 1.5, 2, 2.5 or 3 log relative to a control.
  • the anti-zoonotic disease antigen antibody titer produced in the subject is increased by 1-3 log relative to a control.
  • the anti-zoonotic disease antigen antibody titer produced in a subject may be increased by 1-1.5, 1-2, 1-2.5, 1-3, 1.5-2, 1.5-2.5, 1.5-3, 2-2.5, 2-3, or 2.5-3 log relative to a control.
  • the anti-zoonotic disease antigen antibody titer produced in a subject is increased at least 2 times relative to a control.
  • the anti-zoonotic disease antigen antibody titer produced in a subject may be increased at least 3 times, at least 4 times, at least 5 times, at least 6 times, at least 7 times, at least 8 times, at least 9 times, or at least 10 times relative to a control.
  • the anti-zoonotic disease antigen antibody titer produced in the subject is increased 2, 3, 4, 5, 6, 7, 8, 9, or 10 times relative to a control.
  • the anti-zoonotic disease antigen antibody titer produced in a subject is increased 2-10 times relative to a control.
  • the anti-zoonotic disease antigen antibody titer produced in a subject may be increased 2-10, 2-9, 2-8, 2-7, 2-6, 2-5, 2-4, 2-3, 3-10, 3-9, 3-8, 3-7, 3-6, 3-5, 3-4, 4-10, 4-9, 4-8, 4-7, 4-6, 4-5, 5-10, 5-9, 5-8, 5-7, 5-6, 6-10, 6-9, 6-8, 6-7, 7-10, 7-9, 7-8, 8-10, 8-9, or 9-10 times relative to a control.
  • a control in some embodiments, is the anti-zoonotic disease antigen antibody titer produced in a subject who has not been administered an zoonotic disease RNA (e.g., mRNA) vaccine.
  • a control is an anti-zoonotic disease antigen antibody titer produced in a subject administered a recombinant or purified zoonotic disease protein vaccine.
  • Recombinant protein vaccines typically include protein antigens that either have been produced in a heterologous expression system (e.g., bacteria or yeast) or purified from large amounts of the pathogenic organism.
  • the ability of an zoonotic disease vaccine to be effective is measured in a murine model.
  • the zoonotic disease vaccines may be administered to a murine model and the murine model assayed for induction of neutralizing antibody titers.
  • Viral challenge studies may also be used to assess the efficacy of a vaccine of the present disclosure.
  • the zoonotic disease vaccines may be administered to a murine model, the murine model challenged with zoonotic disease antigen, and the murine model assayed for survival and/or immune response (e.g., neutralizing antibody response, T cell response (e.g., cytokine response)).
  • an effective amount of an zoonotic disease RNA (e.g., mRNA) vaccine is a dose that is reduced compared to the standard of care dose of a recombinant zoonotic disease protein vaccine.
  • a “standard of care,” as provided herein, refers to a medical or psychological treatment guideline and can be general or specific. “Standard of care” specifies appropriate treatment based on scientific evidence and collaboration between medical professionals involved in the treatment of a given condition. It is the diagnostic and treatment process that a physician/clinician should follow for a certain type of patient, illness or clinical circumstance.
  • a “standard of care dose,” as provided herein, refers to the dose of a recombinant or purified zoonotic disease protein vaccine, or a live attenuated or inactivated zoonotic disease vaccine, or an zoonotic disease VLP vaccine, that a physician/clinician or other medical professional would administer to a subject to treat or prevent a zoonotic disease, or a zoonotic disease-related condition, while following the standard of care guideline for treating or preventing a zoonotic disease, or a zoonotic disease related condition.
  • the anti-zoonotic disease antigen antibody titer produced in a subject administered an effective amount of a zoonotic disease RNA vaccine is equivalent to an anti-zoonotic disease antigen antibody titer produced in a control subject administered a standard of care dose of a recombinant or purified zoonotic disease protein vaccine, or a live attenuated or inactivated zoonotic disease vaccine, or a zoonotic disease VLP vaccine.
  • an effective amount of a zoonotic disease RNA (e.g., mRNA) vaccine is a dose equivalent to an at least 2-fold reduction in a standard of care dose of a recombinant or purified zoonotic disease protein vaccine.
  • an effective amount of a zoonotic disease RNA vaccine may be a dose equivalent to an at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, or at least 10-fold reduction in a standard of care dose of a recombinant or purified zoonotic disease protein vaccine.
  • an effective amount of a zoonotic disease RNA vaccine is a dose equivalent to an at least at least 100-fold, at least 500-fold, or at least 1000-fold reduction in a standard of care dose of a recombinant or purified zoonotic disease protein vaccine.
  • an effective amount of a zoonotic disease RNA vaccine is a dose equivalent to a 2-, 3-, 4-, 5-, 6-, 7-, 8-, 9-, 10-, 20-, 50-, 100-, 250-, 500-, or 1000-fold reduction in a standard of care dose of a recombinant or purified zoonotic disease protein vaccine.
  • the anti-zoonotic disease antigen antibody titer produced in a subject administered an effective amount of a zoonotic disease RNA vaccine is equivalent to an anti-zoonotic disease antigen antibody titer produced in a control subject administered the standard of care dose of a recombinant or protein zoonotic disease protein vaccine, or a live attenuated or inactivated zoonotic disease vaccine, or a zoonotic disease VLP vaccine.
  • an effective amount of a zoonotic disease RNA (e.g., mRNA) vaccine is a dose equivalent to a 2-fold to 1000-fold (e.g., 2-fold to 100-fold, 10-fold to 1000-fold) reduction in the standard of care dose of a recombinant or purified zoonotic disease protein vaccine, wherein the anti-zoonotic disease antigen antibody titer produced in the subject is equivalent to an anti-zoonotic disease antigen antibody titer produced in a control subject administered the standard of care dose of a recombinant or purified zoonotic disease protein vaccine, or a live attenuated or inactivated zoonotic disease vaccine, or a zoonotic disease VLP vaccine.
  • a 2-fold to 1000-fold e.g., 2-fold to 100-fold, 10-fold to 1000-fold
  • the anti-zoonotic disease antigen antibody titer produced in the subject is equivalent to an anti-zoonotic disease antigen antibody
  • the effective amount of a zoonotic disease RNA (e.g., mRNA) vaccine is a dose equivalent to a 2 to 1000-, 2 to 900-, 2 to 800-, 2 to 700-, 2 to 600-, 2 to 500-, 2 to 400-, 2 to 300-, 2 to 200-, 2 to 100-, 2 to 90-, 2 to 80-, 2 to 70-, 2 to 60-, 2 to 50-, 2 to 40-, 2 to 30-, 2 to 20-, 2 to 10-, 2 to 9-, 2 to 8-, 2 to 7-, 2 to 6-, 2 to 5-, 2 to 4-, 2 to 3-, 3 to 1000-, 3 to 900-, 3 to 800-, 3 to 700-, 3 to 600-, 3 to 500-, 3 to 400-, 3 to 3 to 00-, 3 to 200-, 3 to 100-, 3 to 90-, 3 to 80-, 3 to 70-, 3 to 60-, 3 to 50-, 3 to 40-, 3 to 30-, 3 to 20-, 3
  • the anti-zoonotic disease antigen antibody titer produced in the subject is equivalent to an anti-zoonotic disease antigen antibody titer produced in a control subject administered the standard of care dose of a recombinant or purified zoonotic disease protein vaccine, or a live attenuated or inactivated zoonotic disease vaccine, or a zoonotic disease VLP vaccine.
  • the effective amount is a dose equivalent to (or equivalent to an at least) 2-, 3-, 4-, 5-, 6-, 7-, 8-, 9-, 10-, 20-, 30-, 40-, 50-, 60-, 70-, 80-, 90-, 100-, 110-, 120-, 130-, 140-, 150-, 160-, 170-, 1280-, 190-, 200-, 210-, 220-, 230-, 240-, 250-, 260-, 270-, 280-, 290-, 300-, 310-, 320-, 330-, 340-, 350-, 360-, 370-, 380-, 390-, 400-, 410-, 420-, 430-, 440-, 450-, 4360-, 470-, 480-, 490-, 500-, 510-, 520-, 530-, 540-, 550-, 560-, 5760-, 580-, 590-, 600-, 610-,
  • an anti-zoonotic disease antigen antibody titer produced in the subject is equivalent to an anti-zoonotic disease antigen antibody titer produced in a control subject administered the standard of care dose of a recombinant or purified zoonotic disease protein vaccine, or a live attenuated or inactivated zoonotic disease vaccine, or a zoonotic disease VLP vaccine.
  • the effective amount of a zoonotic disease RNA (e.g., mRNA) vaccine is a total dose of 50-1000 ⁇ g. In some embodiments, the effective amount of a zoonotic disease RNA (e.g., mRNA) vaccine is a total dose of 50-1000, 50-900, 50-800, 50-700, 50-600, 50-500, 50-400, 50-300, 50-200, 50-100, 50-90, 50-80, 50-70, 50-60, 60-1000, 60-900, 60-800, 60-700, 60-600, 60-500, 60-400, 60-300, 60-200, 60-100, 60-90, 60-80, 60-70, 70-1000, 70-900, 70-800, 70-700, 70-600, 70-500, 70-400, 70-300, 70-200, 70-100, 70-90, 70-80, 80-1000, 80-900, 80-800, 80-700, 80-600, 80
  • the effective amount of a zoonotic disease RNA (e.g., mRNA) vaccine is a total dose of 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950 or 1000 ⁇ g. In some embodiments, the effective amount is a dose of 25-500 ⁇ g administered to the subject a total of two times.
  • the effective amount of a zoonotic disease RNA (e.g., mRNA) vaccine is a dose of 25-500, 25-400, 25-300, 25-200, 25-100, 25-50, 50-500, 50-400, 50-300, 50-200, 50-100, 100-500, 100-400, 100-300, 100-200, 150-500, 150-400, 150-300, 150-200, 200-500, 200-400, 200-300, 250-500, 250-400, 250-300, 300-500, 300-400, 350-500, 350-400, 400-500 or 450-500 ⁇ g administered to the subject a total of two times.
  • a zoonotic disease RNA (e.g., mRNA) vaccine is a dose of 25-500, 25-400, 25-300, 25-200, 25-100, 25-50, 50-500, 50-400, 50-300, 50-200, 50-100, 100-500, 100-400, 100-300, 100-200,
  • the effective amount of a zoonotic disease RNA (e.g., mRNA) vaccine is a total dose of 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, or 500 ⁇ g administered to the subject a total of two times.
  • Vaccine efficacy may be assessed using standard analyses (see, e.g., Weinberg et al., J Infect Dis. 2010 Jun. 1; 201(11):1607-10). For example, vaccine efficacy may be measured by double-blind, randomized, clinical controlled trials. Vaccine efficacy may be expressed as a proportionate reduction in disease attack rate (AR) between the unvaccinated (ARU) and vaccinated (ARV) study cohorts and can be calculated from the relative risk (RR) of disease among the vaccinated group with use of the following formulas:
  • AR disease attack rate
  • vaccine effectiveness may be assessed using standard analyses (see, e.g., Weinberg et al., J Infect Dis. 2010 Jun. 1; 201(11):1607-10).
  • Vaccine effectiveness is an assessment of how a vaccine (which may have already proven to have high vaccine efficacy) reduces disease in a population. This measure can assess the net balance of benefits and adverse effects of a vaccination program, not just the vaccine itself, under natural field conditions rather than in a controlled clinical trial.
  • Vaccine effectiveness is proportional to vaccine efficacy (potency) but is also affected by how well target groups in the population are immunized, as well as by other non-vaccine-related factors that influence the ‘real-world’ outcomes of hospitalizations, ambulatory visits, or costs.
  • a retrospective case control analysis may be used, in which the rates of vaccination among a set of infected cases and appropriate controls are compared.
  • Vaccine effectiveness may be expressed as a rate difference, with use of the odds ratio (OR) for developing infection despite vaccination:
  • efficacy of the zoonotic disease vaccine is at least 60% relative to unvaccinated control subjects.
  • efficacy of the zoonotic disease vaccine may be at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 95%, at least 98%, or 100% relative to unvaccinated control subjects.
  • Sterilizing immunity refers to a unique immune status that prevents effective pathogen infection into the host.
  • the effective amount of a zoonotic disease vaccine of the present disclosure is sufficient to provide sterilizing immunity in the subject for at least 1 year.
  • the effective amount of a zoonotic disease vaccine of the present disclosure is sufficient to provide sterilizing immunity in the subject for at least 2 years, at least 3 years, at least 4 years, or at least 5 years.
  • the effective amount of a zoonotic disease vaccine of the present disclosure is sufficient to provide sterilizing immunity in the subject at an at least 5-fold lower dose relative to control.
  • the effective amount may be sufficient to provide sterilizing immunity in the subject at an at least 10-fold lower, 15-fold, or 20-fold lower dose relative to a control.
  • the effective amount of a zoonotic disease vaccine of the present disclosure is sufficient to produce detectable levels of zoonotic disease antigen as measured in serum of the subject at 1-72 hours post administration.
  • An antibody titer is a measurement of the amount of antibodies within a subject, for example, antibodies that are specific to a particular antigen (e.g., an anti-zoonotic disease antigen).
  • Antibody titer is typically expressed as the inverse of the greatest dilution that provides a positive result.
  • Enzyme-linked immunosorbent assay (ELISA) is a common assay for determining antibody titers, for example.
  • the effective amount of a zoonotic disease vaccine of the present disclosure is sufficient to produce a 1,000-10,000 neutralizing antibody titer produced by neutralizing antibody against the zoonotic disease antigen as measured in serum of the subject at 1-72 hours post administration. In some embodiments, the effective amount is sufficient to produce a 1,000-5,000 neutralizing antibody titer produced by neutralizing antibody against the zoonotic disease antigen as measured in serum of the subject at 1-72 hours post administration. In some embodiments, the effective amount is sufficient to produce a 5,000-10,000 neutralizing antibody titer produced by neutralizing antibody against the zoonotic disease antigen as measured in serum of the subject at 1-72 hours post administration.
  • the neutralizing antibody titer is at least 100 NT 50 .
  • the neutralizing antibody titer may be at least 200, 300, 400, 500, 600, 700, 800, 900 or 1000 NT 50 .
  • the neutralizing antibody titer is at least 10,000 NT 50 .
  • the neutralizing antibody titer is at least 100 neutralizing units per milliliter (NU/mL).
  • the neutralizing antibody titer may be at least 200, 300, 400, 500, 600, 700, 800, 900 or 1000 NU/mL.
  • the neutralizing antibody titer is at least 10,000 NU/mL.
  • an anti-zoonotic disease antigen antibody titer produced in the subject is increased by at least 1 log relative to a control.
  • an anti-zoonotic disease antigen antibody titer produced in the subject may be increased by at least 2, 3, 4, 5, 6, 7, 8, 9 or 10 log relative to a control.
  • an anti-zoonotic disease antigen antibody titer produced in the subject is increased at least 2 times relative to a control.
  • an anti-zoonotic disease antigen antibody titer produced in the subject is increased by at least 3, 4, 5, 6, 7, 8, 9 or 10 times relative to a control.
  • a geometric mean which is the nth root of the product of n numbers, is generally used to describe proportional growth.
  • Geometric mean in some embodiments, is used to characterize antibody titer produced in a subject.
  • a control may be, for example, an unvaccinated subject, or a subject administered a live attenuated zoonotic disease vaccine, an inactivated zoonotic disease vaccine, or a protein subunit zoonotic disease vaccine.
  • a Lassa virus (LASV) vaccine comprising at least one RNA polynucleotide having an open reading frame encoding at least one LASV antigenic polypeptide.
  • the LASV antigenic polypeptide is a Lassa glycoprotein precursor GPC.
  • the LASV antigenic polypeptide is a structurally stabilized GPC.
  • the LASV antigenic polypeptide is a ectodomain of LASV glycoprotein 1 (GP1).
  • the LASV antigenic polypeptide is a glycoprotein.
  • the glycoprotein comprises amino acid residues 59-259 of the LASV glycoprotein precursor (GPC).
  • the LASV antigenic polypeptide is glycoprotein 2 (GP2). In some embodiments, the LASV antigenic polypeptide is a nucleocapsid protein (NP). In some embodiments, the LASV antigenic polypeptide is fused to a signal peptide.
  • GP2 glycoprotein 2
  • NP nucleocapsid protein
  • the LASV antigenic has an amino acid sequence that has at least 90% identity to an amino acid sequence identified by any one of SEQ ID NO: 1-3, but does not include wild-type protein sequence. In some embodiments, the LASV antigenic has an amino acid sequence that has at least 95% identity to an amino acid sequence identified by any one of SEQ ID NO: 1-3, but does not include wild-type protein sequence. In some embodiments, the LASV antigenic has an amino acid sequence that has at least 99% identity to an amino acid sequence identified by any one of SEQ ID NO: 1-3, but does not include wild-type protein sequence. In some embodiments, the LASV antigenic polypeptide has an amino acid sequence of any one of SEQ ID NO: 1-3.
  • the at least one RNA polynucleotide has a nucleic acid sequence that has at least 80% identity to any one of SEQ ID NO: 6, 7, or 9, but does not include wild-type mRNA sequence. In some embodiments, the at least one RNA polynucleotide has a nucleic acid sequence that has at least 85% identity to any one of SEQ ID NO: 6, 7, or 9, but does not include wild-type mRNA sequence. In some embodiments, the at least one RNA polynucleotide has a nucleic acid sequence that has at least 90% identity to any one of SEQ ID NO: 6, 7, or 9, but does not include wild-type mRNA sequence. In some embodiments, the at least one RNA polynucleotide has a nucleic acid sequence that has at least 95% identity to any one of SEQ ID NO: 6, 7, or 9, but does not include wild-type mRNA sequence.
  • the at least one RNA polynucleotide has a nucleic acid sequence that has at least 98% identity to any one of SEQ ID NO: 4-9, but does not include wild-type mRNA sequence. In some embodiments, the at least one RNA polynucleotide has a nucleic acid sequence of any one of SEQ ID NO: 6, 7, or 9. In some embodiments, the LASV antigenic polypeptide has membrane fusion activity, attaches to cell receptors, causes fusion of viral and cellular membranes, and/or is responsible for binding of the virus to a cell being infected.
  • the at least one RNA polynucleotide having an open reading frame encoding at least one LASV antigenic polypeptide comprises at least one chemical modification.
  • the chemical modification is selected from pseudouridine, N1-methylpseudouridine, N1-ethylpseudouridine, 2-thiouridine, 4′-thiouridine, 5-methylcytosine, 5-methyluridine, 2-thio-1-methyl-1-deaza-pseudouridine, 2-thio-1-methyl-pseudouridine, 2-thio-5-aza-uridine, 2-thio-dihydropseudouridine, 2-thio-dihydrouridine, 2-thio-pseudouridine, 4-methoxy-2-thio-pseudouridine, 4-methoxy-pseudouridine, 4-thio-1-methyl-pseudouridine, 4-thio-pseudouridine, 5-aza-uridine, dihydropse
  • the chemical modification is in the carbon 5-position of the uracil. In some embodiments, the chemical modification is a N1-methylpseudouridine or N1-ethylpseudouridine. In some embodiments, at least 80% of the uracil in the open reading frame have a chemical modification. In some embodiments, at least 90% of the uracil in the open reading frame have a chemical modification. In some embodiments, 100% of the uracil in the open reading frame have a chemical modification. In some embodiments, 100% of the uracil in the open reading frame is modified to include N1-methyl pseudouridine at the 5-position of the uracil.
  • At least one RNA polynucleotide having an open reading frame encoding at least one LASV antigenic polypeptide further encodes at least one 5′ terminal cap.
  • the 5′ terminal cap is 7mG(5′)ppp(5′)NlmpNp.
  • the RNA polynucleotide having an open reading frame encoding at least one LASV antigenic polypeptide is formulated in a cationic lipid nanoparticle.
  • the cationic lipid nanoparticle has a mean diameter of 50-200 nm.
  • the cationic lipid nanoparticle comprises a cationic lipid, a PEG-modified lipid, a sterol and a non-cationic lipid.
  • the cationic lipid nanoparticle comprises a molar ratio of about 20-60% cationic lipid, 0.5-15% PEG-modified lipid, 25-55% sterol, and 5-25% non-cationic lipid.
  • the cationic lipid is an ionizable cationic lipid and the non-cationic lipid is a neutral lipid, and the sterol is a cholesterol.
  • the cationic lipid is selected from 2,2-dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane (DLin-KC2-DMA), dilinoleyl-methyl-4-dimethylaminobutyrate (DLin-MC3-DMA), and di((Z)-non-2-en-1-yl) 9-((4-(dimethylamino)butanoyl)oxy)heptadecanedioate (L319).
  • the cationic lipid nanoparticle comprises a compound of Formula (I), optionally Compound 3, 18, 20, 25, 26, 29, 30, 60, 108-112, or 122. In some embodiments, the cationic lipid nanoparticle comprises a compound of Formula (II). In some embodiments, the cationic lipid nanoparticle has a polydispersity value of less than 0.4. In some embodiments, the cationic lipid nanoparticle has a net neutral charge at a neutral pH value. In some embodiments, further comprising an adjuvant.
  • the open reading frame encoding at least one LASV antigenic polypeptide is codon-optimized.
  • the LASV vaccine is multivalent.
  • the LASV vaccine is formulated in an effective amount to produce an antigen-specific immune response.
  • the LASV vaccine is for use in a method of inducing an antigen specific immune response in a subject, the method comprising administering to the subject the LASV vaccine in an amount effective to produce an antigen specific immune response in the subject.
  • One aspect of the disclosure is a pharmaceutical composition for use in vaccination of a subject comprising an effective dose of the LASV vaccine as described herein, wherein the effective dose is sufficient to produce detectable levels of antigen as measured in serum of the subject at 1-72 hours post administration.
  • the cut off index of the antigen is 1-2.
  • One aspect of the disclosure is a pharmaceutical composition for use in vaccination of a subject comprising an effective dose of the LASV vaccine as described herein, wherein the effective dose is sufficient to produce a 1,000-10,000 neutralization titer produced by neutralizing antibody against said antigen as measured in serum of the subject at 1-72 hours post administration.
  • compositions comprising the LASV vaccine as described herein formulated in a lipid nanoparticle comprising compounds of Formula (I), (IA) and/or Formula (II), discussed below.
  • One aspect of the disclosure is a method of inducing an immune response in a subject, the method comprising administering to the subject the LASV vaccine as described herein in an amount effective to produce an antigen-specific immune response in the subject.
  • the antigen specific immune response comprises a T cell response or a B cell response.
  • the subject is administered a single dose of the vaccine.
  • the subject is administered a booster dose of the vaccine.
  • the vaccine is administered to the subject by intradermal injection or intramuscular injection.
  • an anti-antigenic polypeptide antibody titer produced in the subject is increased by at least 1 log relative to a control.
  • an anti-antigenic polypeptide antibody titer produced in the subject is increased by 1-3 log relative to a control. In some embodiments, the anti-antigenic polypeptide antibody titer produced in the subject is increased at least 2 times relative to a control. In some embodiments, the anti-antigenic polypeptide antibody titer produced in the subject is increased 2-10 times relative to a control. In some embodiments, the control is an anti-antigenic polypeptide antibody titer produced in a subject who has not been administered a vaccine against the virus.
  • a paramyxovirus vaccine comprising: at least one RNA polynucleotide having an open reading frame encoding at least one Nipah virus (NiV) and/or Hendra virus (HeV) antigenic polypeptide.
  • the NiV and/or HeV antigenic polypeptide is a hemagglutinin-neuraminidase protein (HN) or hemagglutinin protein (H).
  • the NiV and/or HeV antigenic polypeptide is a glycoprotein (G).
  • the NiV and/or HeV antigenic polypeptide is an attachment glycoproteins which is a type II membrane protein.
  • the NiV and/or HeV antigenic polypeptide is a fusion (F) glycoprotein.
  • the F glycoprotein comprises a trimeric class I fusogenic envelope glycoprotein containing two heptad repeat (HR) regions and a hydrophobic fusion peptide.
  • the NiV and/or HeV antigenic polypeptide is NiV antigenic polypeptide. In some embodiments, the NiV and/or HeV antigenic polypeptide is HeV antigenic polypeptide. In some embodiments, the NiV and/or HeV antigenic polypeptide is fused to a signal peptide. In some embodiments, the NiV and/or HeV antigenic has an amino acid sequence that has at least 90% identity to an amino acid sequence identified by any one of SEQ ID NO: 10-13, but does not include wild-type protein sequence. In some embodiments, the NiV and/or HeV antigenic has an amino acid sequence that has at least 95% identity to an amino acid sequence identified by any one of SEQ ID NO: 10-13, but does not include wild-type protein sequence.
  • the NiV and/or HeV antigenic has an amino acid sequence that has at least 99% identity to an amino acid sequence identified by any one of SEQ ID NO: 10-13, but does not include wild-type protein sequence.
  • the NiV and/or HeV antigenic polypeptide has an amino acid sequence of any one of SEQ ID NO: 10-13.
  • the at least one RNA polynucleotide has a nucleic acid sequence that has at least 80% identity to any one of SEQ ID NO: 16 or 17, but does not include wild-type mRNA sequence.
  • At least one RNA polynucleotide has a nucleic acid sequence that has at least 85% identity to SEQ ID NO: 16 or 17, but does not include wild-type mRNA sequence. In some embodiments, at least one RNA polynucleotide has a nucleic acid sequence that has at least 90% identity to SEQ ID NO: 16 or 17, but does not include wild-type mRNA sequence. In some embodiments, at least one RNA polynucleotide has a nucleic acid sequence that has at least 95% identity to SEQ ID NO: 16 or 17, but does not include wild-type mRNA sequence.
  • At least one RNA polynucleotide has a nucleic acid sequence that has at least 98% identity to SEQ ID NO: 16 or 17, but does not include wild-type mRNA sequence. In some embodiments, at least one RNA polynucleotide has a nucleic acid sequence of SEQ ID NO: 16 or 17.
  • the antigenic polypeptide has membrane fusion activity, attaches to cell receptors, causes fusion of viral and cellular membranes, and/or is responsible for binding of the virus to a cell being infected.
  • at least one RNA polynucleotide comprises at least one chemical modification.
  • the chemical modification is selected from pseudouridine, N1-methylpseudouridine, N1-ethylpseudouridine, 2-thiouridine, 4′-thiouridine, 5-methylcytosine, 5-methyluridine, 2-thio-1-methyl-1-deaza-pseudouridine, 2-thio-1-methyl-pseudouridine, 2-thio-5-aza-uridine, 2-thio-dihydropseudouridine, 2-thio-dihydrouridine, 2-thio-pseudouridine, 4-methoxy-2-thio-pseudouridine, 4-methoxy-pseudouridine, 4-thio-1-methyl-pseudouridine, 4-thio-pseudouridine, 5-aza-uridine, dihydropseudouridine, 5-methoxyuridine and 2′-O-methyl uridine.
  • the chemical modification is in the 5-position of the uracil.
  • the chemical modification is a N1-methylpseudouridine or N1-ethylpseudouridine.
  • at least 80% of the uracil in the open reading frame have a chemical modification.
  • at least 90% of the uracil in the open reading frame have a chemical modification.
  • 100% of the uracil in the open reading frame have a chemical modification.
  • 100% of the uracil in the open reading frame is modified to include N1-methyl pseudouridine at the 5-position of the uracil.
  • at least one RNA polynucleotide further encodes at least one 5′ terminal cap.
  • the 5′ terminal cap is 7mG(5′)ppp(5′)NlmpNp.
  • the RNA polynucleotide is formulated in a cationic lipid nanoparticle.
  • the cationic lipid nanoparticle has a mean diameter of 50-200 nm.
  • the cationic lipid nanoparticle comprises a cationic lipid, a PEG-modified lipid, a sterol and a non-cationic lipid.
  • the cationic lipid nanoparticle comprises a molar ratio of about 20-60% cationic lipid, 0.5-15% PEG-modified lipid, 25-55% sterol, and 5-25% non-cationic lipid.
  • the cationic lipid is an ionizable cationic lipid and the non-cationic lipid is a neutral lipid, and the sterol is a cholesterol.
  • the cationic lipid is selected from 2,2-dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane (DLin-KC2-DMA), dilinoleyl-methyl-4-dimethylaminobutyrate (DLin-MC3-DMA), and di((Z)-non-2-en-1-yl) 9-((4-(dimethylamino)butanoyl)oxy)heptadecanedioate (L319).
  • the cationic lipid nanoparticle comprises a compound of Formula (I), optionally Compound 3, 18, 20, 25, 26, 29, 30, 60, 108-112, or 122.
  • the cationic lipid nanoparticle comprises a compound of Formula (II). In some embodiments, the cationic lipid nanoparticle has a polydispersity value of less than 0.4. In some embodiments, the cationic lipid nanoparticle has a net neutral charge at a neutral pH value. Some embodiments further comprise an adjuvant. In some embodiments, the open reading frame is codon-optimized. In some embodiments, the vaccine is multivalent. Some embodiments are formulated in an effective amount to produce an antigen-specific immune response. Some embodiments are for use in a method of inducing an antigen specific immune response in a subject, the method comprising administering to the subject the vaccine in an amount effective to produce an antigen specific immune response in the subject.
  • One aspect of the disclosure is a pharmaceutical composition for use in vaccination of a subject comprising an effective dose of the paramyxovirus vaccine as described herein, wherein the effective dose is sufficient to produce detectable levels of antigen as measured in serum of the subject at 1-72 hours post administration.
  • the cut off index of the antigen is 1-2.
  • One aspect of the disclosure is a pharmaceutical composition for use in vaccination of a subject comprising an effective dose of the paramyxovirus vaccine as described herein, wherein the effective dose is sufficient to produce a 1,000-10,000 neutralization titer produced by neutralizing antibody against said antigen as measured in serum of the subject at 1-72 hours post administration.
  • compositions comprising the paramyxovirus vaccine as described herein formulated in a lipid nanoparticle comprising compounds of Formula (I), (IA), and/or Formula (II), discussed below.
  • One aspect of the disclosure is a method of inducing an immune response in a subject, the method comprising administering to the subject the paramyxovirus vaccine as described herein in an amount effective to produce an antigen-specific immune response in the subject.
  • the antigen specific immune response comprises a T cell response or a B cell response.
  • the subject is administered a single dose of the vaccine.
  • the subject is administered a booster dose of the vaccine.
  • the vaccine is administered to the subject by intradermal injection or intramuscular injection.
  • an anti-antigenic polypeptide antibody titer produced in the subject is increased by at least 1 log relative to a control.
  • an anti-antigenic polypeptide antibody titer produced in the subject is increased by 1-3 log relative to a control. In some embodiments, the anti-antigenic polypeptide antibody titer produced in the subject is increased at least 2 times relative to a control. In some embodiments, the anti-antigenic polypeptide antibody titer produced in the subject is increased 2-10 times relative to a control. In some embodiments, the control is an anti-antigenic polypeptide antibody titer produced in a subject who has not been administered a vaccine against the virus.
  • RNA ribonucleic acid
  • SARS-like coronavirus WIV1 SARS-like coronavirus WIV1
  • the antigenic polypeptide is a betacoronavirus structural protein.
  • the betacoronavirus structural protein is spike protein (S), envelope protein (E), nucleocapsid protein (N) or membrane protein (M).
  • the betacoronavirus structural protein is spike protein (S).
  • the antigenic polypeptide is a S1 subunit of the spike protein (S).
  • the antigenic polypeptide is a S2 subunit of the spike protein (S). In some embodiments, the antigenic polypeptide is an SL-CoV-WIV1 antigenic polypeptide. In some embodiments, the antigenic polypeptide is a MERS-CoV antigenic polypeptide. In some embodiments, the open reading from is codon-optimized. In some embodiments, the vaccine is multivalent. In some embodiments, at least one RNA polynucleotide encodes at least 2 antigenic polypeptides. In some embodiments, at least one RNA polynucleotide encodes at least 10 antigenic polypeptides. In some embodiments, at least one RNA polynucleotide encodes at least 100 antigenic polypeptides. In some embodiments, at least one RNA polynucleotide encodes 2-100 antigenic polypeptides.
  • the MERS-CoV or SL-CoV-WIV1 antigenic polypeptide has an amino acid sequence that has at least 90% identity to an amino acid sequence identified by SEQ ID NO: 18, but does not include wild-type protein sequence. In some embodiments, the MERS-CoV or SL-CoV-WIV1 antigenic polypeptide has an amino acid sequence that has at least 95% identity to an amino acid sequence identified by SEQ ID NO: 18, but does not include wild-type protein sequence. In some embodiments, the MERS-CoV or SL-CoV-WIV1 antigenic polypeptide has an amino acid sequence of SEQ ID NO: 18.
  • At least one RNA polynucleotide has a nucleic acid sequence that has at least 80% identity to SEQ ID NO: 19 or 20, but does not include wild-type mRNA sequence. In some embodiments, at least one RNA polynucleotide has a nucleic acid sequence that has at least 90% identity to SEQ ID NO: 19 or 20, but does not include wild-type mRNA sequence. In some embodiments, at least one RNA polynucleotide has a nucleic acid sequence of SEQ ID NO: 19 or 20.
  • At least one RNA polynucleotide comprises at least one chemical modification.
  • the chemical modification is selected from pseudouridine, N1-methylpseudouridine, N1-ethylpseudouridine, 2-thiouridine, 4′-thiouridine, 5-methylcytosine, 5-methyluridine, 2-thio-1-methyl-1-deaza-pseudouridine, 2-thio-1-methyl-pseudouridine, 2-thio-5-aza-uridine, 2-thio-dihydropseudouridine, 2-thio-dihydrouridine, 2-thio-pseudouridine, 4-methoxy-2-thio-pseudouridine, 4-methoxy-pseudouridine, 4-thio-1-methyl-pseudouridine, 4-thio-pseudouridine, 5-aza-uridine, dihydropseudouridine, 5-methoxyuridine and 2′-O-methyl
  • the chemical modification is in the 5-position of the uracil. In some embodiments, the chemical modification is a N1-methylpseudouridine or N1-ethylpseudouridine. In some embodiments, at least 80% of the uracil in the open reading frame have a chemical modification. In some embodiments, at least 90% of the uracil in the open reading frame have a chemical modification. In some embodiments, 100% of the uracil in the open reading frame have a chemical modification. In some embodiments, 100% of the uracil in the open reading frame is modified to include N1-methyl pseudouridine at the 5-position of the uracil. In some embodiments, at least one RNA polynucleotide further encodes at least one 5′ terminal cap. In some embodiments, the 5′ terminal cap is 7mG(5′)ppp(5′)NlmpNp.
  • the RNA polynucleotide is formulated in a cationic lipid nanoparticle.
  • the cationic lipid nanoparticle has a mean diameter of 50-200 nm.
  • the cationic lipid nanoparticle comprises a cationic lipid, a PEG-modified lipid, a sterol and a non-cationic lipid.
  • the cationic lipid nanoparticle comprises a molar ratio of about 20-60% cationic lipid, 0.5-15% PEG-modified lipid, 25-55% sterol, and 5-25% non-cationic lipid.
  • the cationic lipid is an ionizable cationic lipid and the non-cationic lipid is a neutral lipid, and the sterol is a cholesterol.
  • the cationic lipid is selected from 2,2-dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane (DLin-KC2-DMA), dilinoleyl-methyl-4-dimethylaminobutyrate (DLin-MC3-DMA), and di((Z)-non-2-en-1-yl) 9-((4-(dimethylamino)butanoyl)oxy)heptadecanedioate (L319).
  • the cationic lipid nanoparticle comprises a compound of Formula (I), optionally Compound 3, 18, 20, 25, 26, 29, 30, 60, 108-112, or 122. In some embodiments, the cationic lipid nanoparticle comprises a compound of Formula (II). In some embodiments, the cationic lipid nanoparticle has a polydispersity value of less than 0.4. In some embodiments, the cationic lipid nanoparticle has a net neutral charge at a neutral pH value. Some embodiments further comprise an adjuvant. In some embodiments, the open reading frame is codon-optimized. In some embodiments, the vaccine is multivalent. Some embodiments are formulated in an effective amount to produce an antigen-specific immune response. Some embodiments are for use in a method of inducing an antigen specific immune response in a subject, the method comprising administering to the subject the vaccine in an amount effective to produce an antigen specific immune response in the subject.
  • One aspect of the invention is a pharmaceutical composition for use in vaccination of a subject comprising an effective dose of the betacoronavirus vaccine as described herein, wherein the effective dose is sufficient to produce detectable levels of antigen as measured in serum of the subject at 1-72 hours post administration.
  • the cut off index of the antigen is 1-2.
  • One aspect of the invention is a pharmaceutical composition for use in vaccination of a subject comprising an effective dose of the betacoronavirus vaccine as described herein, wherein the effective dose is sufficient to produce a 1,000-10,000 neutralization titer produced by neutralizing antibody against said antigen as measured in serum of the subject at 1-72 hours post administration.
  • composition comprising the betacoronavirus vaccine as described herein formulated in a lipid nanoparticle comprising compounds of Formula (I):
  • R 1 is selected from the group consisting of C 5-30 alkyl, C 5-20 alkenyl, —R*YR′′, —YR′′, and —R′′M′R′;
  • R 2 and R 3 are independently selected from the group consisting of H, C 1-14 alkyl, C 2-14 alkenyl, —R*YR′′, —YR′′, and —R*OR′′, or R 2 and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle;
  • R 4 is selected from the group consisting of a C 3-6 carbocycle, —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, —CQ(R) 2 , and unsubstituted C 1-6 alkyl, where Q is selected from a carbocycle, heterocycle, —OR, —O(CH 2 ) n N(R) 2 , —C
  • a subset of compounds of Formula (I) includes those in which when R 4 is —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, or —CQ(R) 2 , then (i) Q is not —N(R) 2 when n is 1, 2, 3, 4 or 5, or (ii) Q is not 5, 6, or 7-membered heterocycloalkyl when n is 1 or 2.
  • a subset of compounds of Formula (I) includes those in which R 1 is selected from the group consisting of C 5-30 alkyl, C 5-20 alkenyl, —R*YR′′, —YR′′, and —R′′M′R′; R 2 and R 3 are independently selected from the group consisting of H, C 1-14 alkyl, C 2-14 alkenyl, —R*YR′′, —YR′′, and —R*OR′′, or R 2 and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle; R 4 is selected from the group consisting of a C 3-6 carbocycle, —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, —CQ(R) 2 , and unsubstituted C 1-6 alkyl, where Q is selected from a C 3-6 carbocycle, a 5- to 14-membered heteroaryl having one or more hetero
  • a subset of compounds of Formula (I) includes those in which R 1 is selected from the group consisting of C 5-30 alkyl, C 5-20 alkenyl, —R*YR′′, —YR′′, and —R′′M′R′; R 2 and R 3 are independently selected from the group consisting of H, C 1-14 alkyl, C 2-14 alkenyl, —R*YR′′, —YR′′, and —R*OR′′, or R 2 and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle; R 4 is selected from the group consisting of a C 3-6 carbocycle, —(CH 2 ) n Q, —(CH 2 ) n CHQR, —CHQR, —CQ(R) 2 , and unsubstituted C 1-6 alkyl, where Q is selected from a C 3-6 carbocycle, a 5- to 14-membered heterocycle having one or more heteroatom
  • the subset of compounds of Formula (I) includes those in which R 1 is selected from the group consisting of C 5-30 alkyl, C 5-20 alkenyl, —R*YR′′, —YR′′, and —R′′M′R′; R 2 and R 3 are independently selected from the group consisting of H, C 2-14 alkyl, C 2-14 alkenyl, —R*YR′′, —YR′′, and —R*OR′′, or R 2 and R 3 , together with the atom to which they are attached, form a heterocycle or carbocycle; R 4 is —(CH 2 ) n Q or —(CH 2 ) n CHQR, where Q is —N(R) 2 , and n is selected from 3, 4, and 5; each R 5 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl, and H; each R 6 is independently selected from the group consisting of C 1-3 alkyl, C 2-3 alkenyl,
  • a subset of compounds of Formula (I) includes those of Formula (IA): (IA), or a salt or isomer thereof, wherein 1 is selected from 1, 2, 3, 4, and 5; m is selected from 5, 6, 7, 8, and 9; M 1 is a bond or M′; R 4 is unsubstituted C 1-3 alkyl, or —(CH 2 ) n Q, in which Q is OH, —NHC(S)N(R) 2 , —NHC(O)N(R) 2 , —N(R)C(O)R, —N(R)S(O) 2 R, —N(R)R 8 , —NHC( ⁇ NR 9 )N(R) 2 , —NHC( ⁇ CHR 9 )N(R) 2 , —OC(O)N(R) 2 , —N(R)C(O)OR, heteroaryl or heterocycloalkyl; M and M′ are independently selected from —C(S)N(
  • One aspect of the invention is a method of inducing an immune response in a subject, the method comprising administering to the subject the betacoronavirus vaccine as described herein in an amount effective to produce an antigen-specific immune response in the subject.
  • the antigen specific immune response comprises a T cell response or a B cell response.
  • the subject is administered a single dose of the vaccine.
  • the subject is administered a booster dose of the vaccine.
  • the vaccine is administered to the subject by intradermal injection or intramuscular injection.
  • an anti-antigenic polypeptide antibody titer produced in the subject is increased by at least 1 log relative to a control. In some embodiments, an anti-antigenic polypeptide antibody titer produced in the subject is increased by 1-3 log relative to a control. In some embodiments, the anti-antigenic polypeptide antibody titer produced in the subject is increased at least 2 times relative to a control. In some embodiments, the anti-antigenic polypeptide antibody titer produced in the subject is increased 2-10 times relative to a control. In some embodiments, the control is an anti-antigenic polypeptide antibody titer produced in a subject who has not been administered a vaccine against the virus.
  • mice 8-10 week old female Balb/c mice were immunized intramuscularly with 10 ⁇ g of Ebola mRNA vaccines or recombinant Zaire ebolavirus Glycoprotein on day 0 and 14. Serum samples were collected on day 21, 33, 52 and 77 to measure antibody response.
  • the first clinical study (FIH) will be initiated in the US and will include approximately 90 subjects. Three dose levels of investigational vaccine will be tested compared to placebo in a staggered manner. To mitigate risk of different immunogenicity in subjects from endemic and non-endemic setting, the second clinical study in endemic setting will be initiated in collaboration with a local clinical study site. Following evaluation of immunogenicity and safety data from both clinical studies (at 1 month post-vaccination), a dose of vaccine for further development will be selected.
  • An mRNA vaccine was designed based on the PIV3 fusion protein and tested in two animal models, cotton rat and African green monkey, for immunogenicity and protection from viral challenge.
  • cotton rats were dosed 10 ⁇ g, or 25 ⁇ g of the mRNA PIV3 vaccine, placebo, or formalin inactivated (FI) PIV3 vaccine at days 0 and 28. Blood was collected pre-dose and on days 27 and 56 (28 days post dose 2) for immunogenicity testing by viral neutralization assay. On day 57 the animals were challenged with PIV3 and viral titer measured 5 days post challenge on lung and nose samples.
  • FI formalin inactivated
  • both the 10 ⁇ g and 25 ⁇ g doses of mRNA vaccine completely protected cotton rats from a challenge that results in viral loads of 4 to 5 logs in lung and nose respectively, while FI vaccine showed no significant protection.
  • the right panel shows that this protection was the result of neutralizing titers in the range of 7 to 9 logs.
  • the second model used to assess our mRNA PIV3 vaccine was African green monkey, which were screened as PIV3 seronegative before the experiment.
  • the design was similar to the cotton rat study, but with animals dosed at 5, 25, or 50 ug of the vaccine.
  • absolute neutralizing titers in serum were lower than in the cotton rat model, however the 25 and 50 ⁇ g doses still conferred complete protection from detectable viral load.
  • the 5 ug dose resulted in a reduction in viral load at 5 days post challenge of approximately 1.5 to 2 logs in nose and lung, respectively, relative to placebo.
  • VN Virus neutralizing antibody titers in the mouse sera in response to MERS spike protein mRNA vaccine measured on Day 0, 21, 42 and 56 using an in vitro neutralization assay. All animals were confirmed to be seronegative at the beginning of the study.
  • a single dose of the mRNA vaccine induced neutralizing antibodies with an average serum titer of 1:320 on day 21.
  • the VN antibody titers were boosted to 1:3000 by day 42 and further boosted up to 1:4800 by day 56.
  • placebo treated mice had no detectable VN antibody titer throughout the study.
  • Oryctolagus cuniculus has been recently identified as a suitable animal model for MERS-CoV infection.
  • the sequence homology for the receptor gene for MERS-CoV, DPP4(dipeptidyl peptidase 4), between humans and rabbits is such that it allows proficient infection of rabbits with MERS-CoV (Ra et al., J Virol 2014; Haagmans et al., J Virol, 2015). Nevertheless, replication of MERS-CoV in rabbits require a very high viral inoculum administered through the intra-nasal and intra-tracheal route.
  • MERS-CoV spike protein mRNA vaccine In order to assess the efficacy of MERS-CoV spike protein mRNA vaccine, 6 month old New Zealand white rabbits were challenged 6 weeks after prime with EMC/2012 MERS-CoV. The vaccine was tested in a one or two dose regimen, with the boost spaced 3 weeks apart on day 21 for group 2, and each dose was 20 ⁇ g. Nasal and Throat swabs were collected from one day prior to challenge; to the end of study, 4 days post challenge. Serum from animals was collected on Day 0, 21, 35, 42 and 47 for measuring virus neutralizing antibody titers.
  • virus could be detected by PCR on day 1 after challenge in all animals. Three animals remained PCR positive until the end of follow up, while 3 animals became PCR negative in within 2 to 4 days post challenge ( FIG. 13 , Panel A). None of the PCR positive signals detected after challenge could be confirmed by virus titration ( FIG. 13 , Panel D).
  • virus could be detected by PCR on day 1 after challenge in three out of six animals, which remained positive on day 2 after challenge and were PCR negative by day 3 post challenge ( FIG. 13 , Panel B). None of the PCR positive signals detected after challenge could be confirmed by virus titration ( FIG. 13 , Panel E).
  • virus could be detected by PCR on day 1 after challenge in all animals.
  • One animal remained PCR positive until day 3 after challenge, however all animals were PCR negative day 4 post challenge ( FIG. 14 , Panel A). None of the PCR positive signals detected after challenge could be confirmed by virus titration ( FIG. 14 , Panel D).
  • virus could be detected by PCR day 1 after challenge in three out of six animals and all were PCR negative the following day. Additionally, two of these animals were PCR positive on the last day of follow up ( FIG. 14 , Panel B). PCR signals could not be detected in any of the other three animals. None of the PCR positive signals detected after challenge could be confirmed by virus titration ( FIG. 14 , Panel E).
  • Viral loads were also measured in the right nasal turbinates post mortem at the day of scheduled euthanasia (4 dpi).
  • Levels of viral RNA were measured using a MERS-CoV-specific TaqMan PCR and levels of infectious (replication competent) virus using Vero cell culture.
  • Rabbit lungs were dissected into 9 separated regions post mortem for individual for assessment of viral load by region of the lung.
  • the different sections of the lungs were pooled (equal amount of material for each section) and these samples were tested by both PCR and titration ( FIG. 15 ).
  • Results by PCR showed that only one animal in the prime-boost group was PCR negative in the lungs.
  • PCR positive signals could be detected in almost all animals
  • virus titration on the total lung samples resulted in only two positive animals, both in the placebo group.
  • the patterns of viral load observed by PCR and by titration observed in each of the sample types in the rabbit challenge model are suggestive of a high level of protection from viral replication.
  • the lack of any replicating virus in most of the vaccinated animal samples indicates that any PCR signal found in those same samples is likely due to the detection of residual nucleic acid sequences from input virus during the challenge itself.
  • the body of the immunogenicity and viral challenge data indicate that the vaccines of the invention generate robust immunologic responses with high neutralizing titers that are protective from viral replication upon challenge.
  • any of the mRNA sequences described herein may include a 5′ UTR and/or a 3′ UTR.
  • the UTR sequences may be selected from the following sequences, or other known UTR sequences may be used.
  • any of the mRNA constructs described herein may further comprise a polyA tail and/or cap (e.g., 7mG(5′)ppp(5′)NlmpNp).
  • RNAs and encoded antigen sequences described herein include a signal peptide and/or a peptide tag (e.g., C-terminal His tag), it should be understood that the indicated signal peptide and/or peptide tag may be substituted for a different signal peptide and/or peptide tag, or the signal peptide and/or peptide tag may be omitted.
  • a signal peptide and/or a peptide tag e.g., C-terminal His tag
  • Lassa_GPC protein (SEQ ID NO: 1) MGQIVTFFQEVPHVIEEVMNIVLIALSLLAILKGIYNVATCGLFGLVSFLLLCGRSCSTTYKGVYELQTLELD MASLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNLSDAHKKDLYDHALMSIISTFHLSIPN FNQYEAMSCDFNGGKISVQYNLSHTYAVDAANHCGTIANGVLQTFMRMAWGGSYIALDSGKGSWDCIM TSYQYLIIQNTTWEDHCQFSRPSPIGYLGLLSQRTRDIYISRRLLGTFTWTLSDSEGNETPGGYCLTRWMLIE AELKCFGNTAVAKCNEKHDEEFCDMLRLFDFNKQAIMRLKTEAQMSIQLINKAVNALINDQLIMKNHLRD IMGIPYCNYSKYWYLNHTVTGKTSLPRCWLVSNGSYLNETRFSDDIEQQADNMITEMLQKEYLDR

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