INFLUENZA-CORONAVIRUS COMBINATION VACCINES
The disclosure provides combination miRNA vaccines for respiratory viruses, such as influenza and coronaviruses (e.g., SARS-CoV-2) as well as methods of using the vaccines.
1 . A combination vaccine, comprising
a first messenger ribonucleic acid (mRNA) polynucleotide comprising an open reading frame (ORF) encoding a first respiratory virus antigenic polypeptide, wherein the first respiratory virus antigenic polypeptide is an influenza virus antigen; and
a second mRNA polynucleotide comprising an ORF encoding a second respiratory virus antigenic polypeptide from a coronavirus;
and a lipid nanoparticle.
2 . A combination vaccine, comprising a first messenger ribonucleic acid (mRNA) polynucleotide comprising an open reading frame (ORF) encoding a first respiratory virus antigenic polypeptide, wherein the first respiratory virus antigenic polypeptide is an influenza virus antigen;
a second mRNA polynucleotide comprising an ORF encoding a second respiratory virus antigenic polypeptide from a second influenza virus;
a third mRNA polynucleotide comprising an ORF encoding a third respiratory virus antigenic polypeptide from a third influenza virus;
a fourth mRNA polynucleotide comprising an ORF encoding a fourth respiratory virus antigenic polypeptide from a fourth influenza virus;
a fifth mRNA polynucleotide comprising an ORF encoding a fifth respiratory virus antigenic polypeptide from a first coronavirus;
a sixth mRNA polynucleotide comprising an ORF encoding a sixth respiratory virus antigenic polypeptide from a second coronavirus;
and a lipid nanoparticle.
3 . The combination vaccine of claim 2 , wherein the first, second, third and fourth viruses are selected from influenza A viruses and influenza B viruses.
4 . The combination vaccine of claim 1 or 2 , wherein the coronavirus, first coronavirus, and/or second coronavirus is a betacoronavirus.
5 . The combination vaccine of claim 1 or 2 , wherein the coronavirus, first coronavirus, and/or second coronavirus is selected from the group consisting of MERS-CoV, SARS-CoV, SARS-CoV-2, HCoV-OC43, HCoV-229E, HCoV-NL63, HCoV-NL, HCoV-NH and HCoV-HKU1.
6 . The combination vaccine of claim 1 or 2 , wherein the first respiratory virus antigenic polypeptide is from an influenza virus B.
7 . The combination vaccine of claim 1 or 2 , wherein the first respiratory virus antigenic polypeptide is from an influenza virus A.
8 . The combination vaccine of claim 1 or 2 , wherein the first respiratory virus antigenic polypeptide is hemagglutinin antigen (HA) or a neuraminidase antigen (NA).
9 . The combination vaccine of claim 1 or 2 , wherein the second respiratory virus antigenic polypeptide is from a SARS-CoV.
10 . The combination vaccine of claim 1 or 2 , wherein the second respiratory virus antigenic polypeptide is from SARS-CoV-2.
11 . The combination vaccine of claim 1 or 2 , wherein the second respiratory virus antigenic polypeptide is from a non-SARS human coronavirus (HCoV).
12 . The combination vaccine of any one of claims 1-11 , wherein the vaccine comprises at least 2 mRNA polynucleotides comprising an ORF encoding an influenza virus antigen.
13 . The combination vaccine of any one of claims 1-12 , wherein the vaccine comprises 2-4 mRNA polynucleotides comprising an ORF encoding an influenza virus antigen.
14 . The combination vaccine of any one of claims 1-12 , wherein the vaccine comprises at least 2 mRNA polynucleotides comprising an ORF encoding a respiratory virus antigenic polypeptide from a coronavirus.
15 . The combination vaccine of any one of claims 1-14 , wherein the vaccine comprises less than 15 mRNA polynucleotides.
16 . The combination vaccine of claim 15 , wherein the vaccine comprises 3-10 mRNA polynucleotides.
17 . The combination vaccine of claim 15 , wherein the vaccine comprises 4-10 mRNA polynucleotides.
18 . The combination vaccine of claim 15 , wherein the vaccine comprises 5-10 mRNA polynucleotides.
19 . The combination vaccine of claim 15 , wherein the vaccine comprises 8-9 mRNA polynucleotides.
20 . The combination vaccine of any one of claims 1-19 , wherein the vaccine comprises at least three mRNA polynucleotides encoding influenza virus antigenic polypeptides.
21 . The combination vaccine of claim 20 , wherein the vaccine comprises at least eight mRNA polynucleotides encoding influenza virus antigenic polypeptides.
22 . The combination vaccine of claim 20 , wherein the vaccine comprises at least two mRNA polynucleotides encoding coronavirus antigenic polypeptides.
23 . The combination vaccine of any one of claims 1-22 , wherein the first and second mRNA polynucleotides are present in the combination vaccine in a ratio of 1:1.
24 . The combination vaccine of any one of claims 1-22 , wherein the combination vaccine comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 4:1 from the influenza virus to the coronavirus.
25 . The combination vaccine of any one of claims 1-22 , wherein the combination vaccine comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 3:1 from the influenza virus to the coronavirus.
26 . The combination vaccine of any one of claims 1-22 , wherein the combination vaccine comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 2:1 from the influenza virus to the coronavirus.
27 . The combination vaccine of any one of claims 1-22 , wherein the combination vaccine comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 5:1 from the influenza virus to the coronavirus.
28 . The combination vaccine of any one of claims 1-22 , wherein the combination vaccine comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 4:2 from the influenza virus to the coronavirus.
29 . The combination vaccine of any one of claims 1-22 , wherein the combination vaccine comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 1:2 from the influenza virus to the coronavirus.
30 . The combination vaccine of any one of claims 1-22 , wherein the combination vaccine comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 8:2 from the first virus to the second virus.
31 . The combination vaccine of any one of claims 1-22 , wherein the combination vaccine comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 8:1 from the first virus to the second virus.
32 . The combination vaccine claim 31 , wherein the respiratory virus antigenic polypeptides of the first virus comprise HAs and NAs, in a ratio of 4:4.
33 . The combination vaccine of any one of claims 1-32 , wherein each of the mRNA polynucleotides in the combination vaccine is complementary with and does not interfere with each other mRNA polynucleotide in the combination vaccine.
34 . The combination vaccine of any one of claims 1-32 , wherein at least one of the respiratory virus antigenic polypeptides is derived from a naturally occurring antigen.
35 . The combination vaccine of any one of claims 1-32 , wherein at least one of the respiratory virus antigenic polypeptides is a stabilized version of a naturally occurring antigen.
36 . The combination vaccine of any one of claims 1-32 , wherein at least one of the respiratory virus antigenic polypeptides is a non-naturally occurring antigen.
37 . The combination vaccine of any one of claims 1-36 , wherein the vaccine further comprises an mRNA polynucleotide encoding a structurally altered variant respiratory virus antigenic polypeptide, wherein the structurally altered variant is a structurally altered variant of any one of the first or second respiratory virus antigenic polypeptides.
38 . The combination vaccine of any one of claims 1-36 , wherein at least one of the first and second mRNA polynucleotides is polycistronic.
39 . The combination vaccine of any one of claims 1-36 , wherein each of the first and second mRNA polynucleotides is polycistronic.
40 . A multivalent RNA composition, comprising a first messenger ribonucleic acid (mRNA) polynucleotide comprising an open reading frame (ORF) encoding a first respiratory virus antigenic polypeptide, from a first virus; and
a second mRNA polynucleotide comprising an ORF encoding a second respiratory virus antigenic polypeptide from a coronavirus;
wherein the multivalent RNA composition comprises greater than 40% polyA-tailed RNAs and/or the first and/or second mRNA polynucleotides is different in length from one another by at least 100 nucleotides.
41 . The multivalent RNA composition of claim 40 , wherein the composition is produced by a method comprising:
(a) combining a linearized first DNA molecule encoding the first mRNA polynucleotide and a linearized second DNA molecule encoding the second mRNA polynucleotide into a single reaction vessel, wherein the first DNA molecule and the second DNA molecule are obtained from different sources; and
(b) simultaneously in vitro transcribing the linearized first DNA molecule and the linearized second DNA molecule to obtain a multivalent RNA composition.
42 . The multivalent RNA composition of claim 41 , wherein the different sources are a first and second bacterial cell culture and wherein the first and second bacterial cell culture are not co-cultured.
43 . The multivalent RNA composition of claim 42 , wherein the amounts of the first and second DNA molecules present in the reaction mixture prior to the start of the IVT have been normalized.
44 . The multivalent RNA composition of claim 40 , wherein the coronavirus is selected from the group consisting of MERS-CoV, SARS-CoV, SARS-CoV-2, HCoV-OC43, HCoV-229E, HCoV-NL63, HCoV-NL, HCoV-NH and HCoV-HKU1.
45 . A multivalent RNA composition, comprising 2-15 mRNA polynucleotides, each comprising a distinct open reading frame (ORF) encoding a respiratory virus antigenic polypeptide, wherein at least one respiratory virus antigenic polypeptide is an influenza virus and at least one respiratory virus antigenic polypeptide is a coronavirus, and wherein each mRNA polynucleotide comprises one or more non-coding sequence in an untranslated region (UTR), optionally a 5′ UTR or 3′ UTR.
46 . The multivalent RNA composition of claim 45 , wherein the non-coding sequence is positioned in a 3′ UTR of an mRNA, upstream of the polyA tail of the mRNA.
47 . The multivalent RNA composition of claim 45 , wherein the non-coding sequence is positioned in a 3′ UTR of an mRNA, downstream of the polyA tail of the mRNA.
48 . The multivalent RNA composition of claim 45 , wherein the non-coding sequence is positioned in a 3′ UTR of an mRNA between the last codon of the ORF of the mRNA and the first “A” of the polyA tail of the mRNA.
49 . The multivalent RNA composition of claim 45 , wherein the non-coding sequence comprises between 1 and 10 nucleotides.
50 . The multivalent RNA composition of any one of claims 45-49 , wherein the non-coding sequence comprises one or more RNAse cleavage sites.
51 . The multivalent RNA composition of claim 50 , wherein the RNAse cleavage site is an RNase H cleavage site.
52 . The multivalent RNA composition of claim 45 , wherein the coronavirus antigen is selected from the group consisting of MERS-CoV, SARS-CoV, SARS-CoV-2, HCoV-OC43, HCoV-229E, HCoV-NL63, HCoV-NL, HCoV-NH and HCoV-HKU1.
53 . A multivalent RNA composition, comprising a first messenger ribonucleic acid (mRNA) polynucleotide comprising an open reading frame (ORF) encoding a first respiratory virus antigenic polypeptide, from an influenza virus;
a second mRNA polynucleotide comprising an ORF encoding a second respiratory virus antigenic polypeptide from a coronavirus; and
wherein at least one of the respiratory virus antigenic polypeptides is derived from a naturally occurring antigen or a stabilized version of a naturally occurring antigen and further comprising an mRNA polynucleotide encoding a structurally altered variant respiratory virus antigenic polypeptide, wherein the structurally altered variant is a structurally altered variant of any one of the first or second respiratory virus antigenic polypeptides.
54 . The multivalent RNA composition of claim 53 , wherein the coronavirus is selected from the group consisting of MERS-CoV, SARS-CoV, SARS-CoV-2, HCoV-OC43, HCoV-229E, HCoV-NL63, HCoV-NL, HCoV-NH and HCoV-HKU1.
55 . The multivalent RNA composition of any one of claims 53-54 , wherein the structurally altered variant is a structurally altered variant of the first respiratory virus antigenic polypeptide.
56 . The multivalent RNA composition of any one of claims 53-55 , wherein the structurally altered variant is a structurally altered variant of the second respiratory virus antigenic polypeptide.
57 . A multivalent RNA composition, comprising 5 to 15 messenger ribonucleic acid (mRNA) polynucleotides, each comprising an open reading frame (ORF) encoding a distinct respiratory virus antigenic polypeptide, wherein the respiratory virus antigenic polypeptides are derived from two different viral families, wherein the two viral families comprise influenza viruses and coronaviruses; and a lipid nanoparticle.
58 . The multivalent RNA composition of claim 57 , wherein the composition has 3-6 mRNA polynucleotides comprising an ORF encoding an influenza antigen.
59 . The multivalent RNA composition of any one of claim 57-58 , wherein the composition has 1-5 mRNA polynucleotides comprising an ORF encoding a coronavirus antigen.
60 . A multivalent RNA composition, comprising a set of at least 6 messenger ribonucleic acid (mRNA) polynucleotides, each comprising an open reading frame (ORF) encoding a respiratory virus antigenic polypeptide from a first or second virus; wherein the first virus is an influenza virus, wherein the second virus is a coronavirus, and wherein the composition comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 4:1, 4:2, or 4:3 from the first virus to the second virus.
61 . The multivalent RNA composition of any one of claims 40-60 , wherein the first and second mRNA polynucleotides are present in the combination vaccine in a ratio of 1:1.
62 . The multivalent RNA composition of any one of claims 40-60 , wherein the multivalent RNA composition comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 4:1 from the first virus to the second virus.
63 . The multivalent RNA composition of any one of claims 40-60 , wherein the multivalent RNA composition comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 3:1 from the first virus to the second virus.
64 . The multivalent RNA composition of any one of claims 40-60 , wherein the multivalent RNA composition comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 2:1 from the first virus to the second virus.
65 . The multivalent RNA composition of any one of claims 40-60 , wherein the multivalent RNA composition comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 5:1 from the first virus to the second virus.
66 . The multivalent RNA composition of any one of claims 40-60 , wherein the multivalent RNA composition comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 4:2 from the first virus to the second virus.
67 . The multivalent RNA composition of any one of claims 40-60 , wherein the multivalent RNA composition comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 1:2 from the first virus to the second virus.
68 . The multivalent RNA composition of any one of claims 40-60 , wherein the multivalent RNA composition comprises a ratio of mRNA polynucleotides encoding respiratory virus antigenic polypeptides of 8:1 or 8:2 from the first virus to the second virus.
69 . The multivalent RNA composition of any one of claims 40-68 , wherein the antigenic polypeptides include a Fusion (F) protein, a spike (S) protein, and a hemagglutinin antigen (HA).
70 . The multivalent RNA composition of claim 69 , further comprising a neuraminidase (NA) antigen.
71 . The multivalent RNA composition of any one of claims 40-70 , further comprising at least one lipid nanoparticle (LNP).
72 . The multivalent RNA composition 71, wherein the LNP comprises a molar ratio of 20-60% ionizable amino lipid, 5-25% non-cationic lipid, 25-55% sterol, and 0.5-15% PEG-modified lipid.
73 . The multivalent RNA composition of claim 72 , wherein the ionizable amino lipid comprises the structure of Compound 1:
74 . The combination vaccine of any one of claims 1-39 or the multivalent RNA composition of any one of claims 40-73 , wherein the respiratory virus antigenic polypeptide comprises a cell surface glycoprotein.
75 . A method for vaccinating a subject, comprising:
administering to the subject a combination vaccine, wherein the combination vaccine comprises a first messenger ribonucleic acid (mRNA) polynucleotide comprising an open reading frame (ORF) encoding a first respiratory virus antigenic polypeptide from an influenza virus; and a second mRNA polynucleotide comprising an ORF encoding a second respiratory virus antigenic polypeptide from a coronavirus.
76 . The method of claim 75 , wherein the subject is 65 years of age or older.
77 . The method of claim 75 , wherein the subject is under 18 years of age.
78 . The method of claim 75 , wherein the method prevents a respiratory infection in the subject.
79 . The method of claim 75 , wherein the method reduces the severity of a respiratory infection in the subject.
80 . The method of claim 75 , wherein the subject is seronegative for at least one of the antigenic polypeptides.
81 . The method of claim 75 , wherein the subject is seronegative for all of the antigenic polypeptides.
82 . The method of claim 75 , wherein the subject is seropositive for at least one of the antigenic polypeptides.
83 . The method of claim 75 , wherein the subject is seropositive for all of the antigenic polypeptides.
84 . The method of any one of claims 75-83 , further comprising administering a booster vaccine.
85 . The method of claim 84 , wherein the booster vaccine is administered between 3 weeks and 1 year after the combination vaccine.
86 . The method of claim 84 or 85 , wherein the booster vaccine comprises at least one mRNA polynucleotide comprising an ORF encoding the first or second respiratory virus antigenic polypeptides.
87 . The method of claim 84 or 85 , wherein the booster vaccine comprises at least one mRNA polynucleotide comprising an ORF encoding the first and second respiratory virus antigenic polypeptides.
88 . The method of claim 84 or 85 , wherein the booster vaccine comprises at least one mRNA polynucleotide comprising an ORF encoding a structurally altered variant of the first or second respiratory virus antigenic polypeptides.
89 . The method of any one of claims 84-88 , wherein the combination vaccine is a seasonal booster vaccine.
90 . The method of any one of claims 75-89 , wherein the combination vaccine is a vaccine of any one of claims 1-74 .
91 . A method of preventing or reducing the severity of a respiratory infection by administering the combination/multivalent vaccine of any one of claims 1-74 to a subject in an effective amount to prevent infection or reduce the severity of a respiratory infection in the subject based on a single dose or single dose with a booster.
92 . The method of any one of claims 75-91 , wherein the combination vaccine is administered to the subject in a dose of 25 μg, 50 μg, or 100 μg.
93 . The method of any one of claims 75-92 , wherein each RNA polynucleotide of the vaccine is formulated in a separate LNP.
94 . The method of any one of claims 75-93 , wherein the RNA polynucleotides of the vaccine are co-formulated in an LNP.
95 . The combination vaccine of any one of claims 1-39 or the multivalent RNA composition of any one of claims 40-74 , comprising mRNA polynucleotides encoding four HA antigens.
96 . The combination vaccine or multivalent RNA composition of claim 95 , wherein the four HA antigens are present in a 1:1:1:1 ratio.
97 . The combination vaccine or multivalent RNA composition of claim 95 or 96 , further comprising mRNA polynucleotides encoding four NA antigens.
98 . The combination vaccine or the multivalent RNA composition of claim 97 , wherein the four NA antigens are present in a 1:1:1:1 ratio.
99 . The combination vaccine or the multivalent RNA composition of claim 98 , wherein the ratio of HA antigens to NA antigens is 1:1.
100 . The combination vaccine or the multivalent RNA composition of claim 98 , wherein the ratio of HA antigens to NA antigens is 3:1.
101 . The method of any one of claims 75-94 , wherein the combination vaccine comprises mRNA polynucleotides encoding four HA antigens.
102 . The method of claim 101 , wherein the four HA antigens are present in a 1:1:1:1 ratio.
103 . The method of claim 101 or 102 , further comprising mRNA polynucleotides encoding four NA antigens.
104 . The method of claim 103 , wherein the four NA antigens are present in a 1:1:1:1 ratio.
105 . The method of claim 104 , wherein the ratio of HA antigens to NA antigens is 1:1.
106 . The method of claim 104 , wherein the ratio of HA antigens to NA antigens is 3:1.
107 . The combination vaccine of any one of claims 1-39 , the multivalent RNA composition of any one of claims 40-74 and 95-100 , and the method of any one of claims 75-94 and 101-106 , wherein the coronavirus is a betacoronavirus.