Coronavirus vaccines
Designed coronavirus polypeptide sequences are described, and their use as vaccines against viruses of the coronavirus family. The designed sequences include designed coronavirus spike(S) proteins and fragments thereof, including designed S protein receptor binding domain (RBD) sequence SEQ ID NO:17, designed truncated S protein sequence SEQ ID NO:15, and designed full length S protein sequence SEQ ID NO:13. Designed coronavirus envelope (E), membrane (M), and nucleocapsid (N) protein sequences are also described, and their use as vaccines. Nucleic acid molecules encoding the polypeptides, vectors, fusion proteins, pharmaceutical compositions, cells, and their use as vaccines against viruses of the coronavirus family are also described.
1 . An isolated polypeptide, which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO:31.
2 . A polypeptide according to claim 1 , which comprises at least one, or all of the amino acid residues, optionally at least five, at least ten, or at least fifteen of the amino acid residues, at the following positions: A at a position corresponding to residue position 3 of SEQ ID NO:11; K at a position corresponding to residue position 6 of SEQ ID NO:11; E at a position corresponding to residue position 7 of SEQ ID NO:11, V at a position corresponding to residue position 8 of SEQ ID NO:11; P at a position corresponding to residue position 30 of SEQ ID NO: 11; E at a position corresponding to residue position 36 of SEQ ID NO:11; T at a position corresponding to residue position 54 of SEQ ID NO: 11; T at a position corresponding to residue position 120 of SEQ ID NO: 11; T at a position corresponding to residue position 126 of SEQ ID NO: 11; T at a position corresponding to residue position 127 of SEQ ID NO:11; S at a position corresponding to residue position 152 of SEQ ID NO: 11; D at a position corresponding to residue position 153 of SEQ ID NO:11; S at a position corresponding to residue position 163 of SEQ ID NO:11; N at a position corresponding to residue position 201 of SEQ ID NO:11; L at a position corresponding to residue position 211 of SEQ ID NO:11; and D at a position corresponding to residue position 214 of SEQ ID NO:11.
3 . A polypeptide according to claim 1 , which comprises at least one, or all of the amino acid residues at the following positions: V at a position corresponding to residue position 99 of SEQ ID NO:11; S at a position corresponding to residue position 137 of SEQ ID NO: 11; L at a position corresponding to residue position 138 of SEQ ID NO:11; K at a position corresponding to residue position 142 of SEQ ID NO:11; S at a position corresponding to residue position 156 of SEQ ID NO: 11; P at a position corresponding to residue position 157 of SEQ ID NO: 11; G at a position corresponding to residue position 159 of SEQ ID NO:11; K at a position corresponding to residue position 160 of SEQ ID NO:11; Y at a position corresponding to residue position 172 of SEQ ID NO:11; R at a position corresponding to residue position 175 of SEQ ID NO: 11; and F at a position corresponding to residue position 180 of SEQ ID NO: 11.
4 . A polypeptide according to claim 1 , which comprises at least one, or all of the amino acid residues at the following positions: K at a position corresponding to residue position 28 of SEQ ID NO: 11; K at a position corresponding to residue position 39 of SEQ ID NO: 11; and I at a position corresponding to residue position 123 of SEQ ID NO:11.
5 . A polypeptide according to claim 1 , which comprises amino acid residue T at the position corresponding to the amino acid residue position 185 of SEQ ID NO:11.
6 . A polypeptide according to claim 1 , which comprises the following discontinuous amino acid sequences:
a)
(i)
(SEQ ID NO: 57)
NITNLCPFGEVENATK;
(ii)
(SEQ ID NO: 58)
KKISN;
(iii)
(SEQ ID NO: 59)
NI;
b)
(i)
(SEQ ID NO: 71)
YNSTSFSTFKCYGVSPTKLNDLCFT;
(ii)
(SEQ ID NO: 72)
DDFT;
iii)
(SEQ ID NO: 62)
FELLN;
or
c)
(i)
(SEQ ID NO: 63)
RGDEVRQ;
(SEQ ID NO: 73
TGVIADY
iii)
(SEQ ID NO: 74)
YRSLRKSK;
(iv)
(SEQ ID NO: 75)
YSPGGK;
(v)
(SEQ ID NO: 77)
FNCYYPLRSYGFFPTNGTGY;
wherein the discontinuous amino acid sequences of (a) (i)-(iii) are present in the order recited, the discontinuous amino acid sequences of (b) (i)-(iii) are present in the order recited, and the discontinuous amino acid sequences of (c) (i)-(v) are present in the order recited.
7 . An isolated nucleic acid molecule encoding a polypeptide according to claim 1 , or the complement thereof.
8 . A vector comprising a nucleic acid molecule of claim 7 , optionally which further comprises a promoter operably linked to the nucleic acid.
9 . A vector according to claim 8 , wherein the promoter is for expression of a polypeptide encoded by the nucleic acid in mammalian cells.
10 . A vector according to claim 8 , which is a vaccine vector.
11 . An isolated cell comprising a vector of claim 8 .
12 . A fusion protein comprising a polypeptide according to claim 1 .
13 . A pharmaceutical composition comprising:
a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO:31;
a nucleic acid molecule encoding a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO:31, or the complement thereof, or
a vector comprising a nucleic acid molecule encoding a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO:31, or the complement thereof, optionally which further comprises a promoter operably linked to the nucleic acid;
and a pharmaceutically acceptable carrier, excipient, or diluent.
14 . A pharmaceutical composition according to claim 13 , which further comprises an adjuvant for enhancing an immune response in a subject to the polypeptide, or to a polypeptide encoded by the nucleic acid, of the composition.
15 . A pseudotyped virus comprising a polypeptide according to claim 1 .
16 . A method of inducing an immune response to a coronavirus in a subject, which comprises administering to the subject an effective amount of:
i) a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO:31;
ii) a nucleic acid molecule encoding a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO:31, or the complement thereof;
iii) a vector comprising a nucleic acid molecule encoding a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO:31, or the complement thereof; or
iv) a pharmaceutical composition comprising:
a) a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO:31, and a pharmaceutically acceptable carrier, excipient, or diluent;
b) a nucleic acid molecule encoding a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO:31, or the complement thereof, and a pharmaceutically acceptable carrier, excipient, or diluent; or
c) a vector comprising a nucleic acid molecule encoding a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO: 31, or the complement thereof, and a pharmaceutically acceptable carrier, excipient, or diluent.
17 . A method of immunizing a subject against a coronavirus, which comprises administering to the subject an effective amount of:
i) a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO:31;
ii) a nucleic acid molecule encoding a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO:31, or the complement thereof;
iii) a vector comprising a nucleic acid molecule encoding a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO:31, or the complement thereof, optionally which further comprises a promoter operably linked to the nucleic acid; or
iv) a pharmaceutical composition comprising:
a) a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO:31, and a pharmaceutically acceptable carrier, excipient, or diluent;
b) a nucleic acid molecule encoding a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO:31, or the complement thereof, and a pharmaceutically acceptable carrier, excipient, or diluent; or
c) a vector comprising a nucleic acid molecule encoding a polypeptide which comprises an amino acid sequence of SEQ ID NO: 31 (COV_S_T2_17), or an amino acid sequence which has at least 95%, 96%, 97%, 98%, or 99% amino acid identity over its entire length with the amino acid sequence of SEQ ID NO: 31, or the complement thereof, and a pharmaceutically acceptable carrier, excipient, or diluent.
18 . A method according to claim 16 , wherein the coronavirus is a β-coronavirus.
19 . A method according to claim 18 , wherein the β-coronavirus is a lineage B β-coronavirus.
20 . A vector according to claim 10 , wherein the vaccine vector is a viral vaccine vector, a bacterial vaccine vector, an RNA vaccine vector, or a DNA vaccine vector.
21 . A method according to claim 18 , wherein the β-coronavirus is a lineage B or C β-coronavirus.
22 . A method according to claim 19 , wherein lineage B β-coronavirus is SARS-COV or SARS-COV-2.