Methods and compositions for chimeric coronavirus spike proteins

1. A chimeric coronavirus spike protein comprising, in orientation from amino to carboxy terminus:

a) a first region comprising a portion of a coronavirus spike protein ectodomain that precedes a coronavirus spike protein receptor binding domain (RBD) as located in a nonchimeric coronavirus spike protein, of a first coronavirus;

b) a second region comprising a coronavirus spike protein receptor binding domain (RBD) of a second coronavirus that is different from said first coronavirus;

c) a third region comprising a portion of a coronavirus spike protein S1 domain as located in a nonchimeric coronavirus spike protein immediately downstream of the RBD, contiguous with a portion of a coronavirus spike protein S2 domain as located immediately upstream of a fusion protein domain in a nonchimeric coronavirus spike protein, wherein said third region is of said first coronavirus; and

d) a fourth region comprising a portion of a coronavirus spike protein from the start of the fusion protein domain through the carboxy terminal end as located in a nonchimeric coronavirus spike protein of a third coronavirus that is different from said first coronavirus and said second coronavirus.

2. The chimeric coronavirus spike protein of claim 1 , wherein the chimeric coronavirus spike protein is derived from subgroup 1a coronaviruses, subgroup 1b coronaviruses, subgroup 2a coronaviruses, subgroup 2b coronaviruses, subgroup 2c coronaviruses, subgroup 2d coronaviruses or subgroup 3 coronaviruses.

3. The chimeric coronavirus of claim 2 , derived from subgroup 2b coronaviruses wherein said first, second and third subgroup 2b coronaviruses are different from one another and wherein the subgroup 2b coronaviruses are selected from the group consisting of Bat SARS CoV (GenBank Accession No. FJ211859), SARS CoV (GenBank Accession No. FJ211860), BtSARS.HKU3.1 (GenBank Accession No. DQ022305), BtSARS.HKU3.2 (GenBank Accession No. DQ084199), BtSARS.HKU3.3 (GenBank Accession No. DQ084200), BtSARS.Rm1 (GenBank Accession No. DQ412043), BtCoV.279.2005 (GenBank Accession No. DQ648857), BtSARS.Rf1 (GenBank Accession No. DQ412042), BtCoV.273.2005 (GenBank Accession No. DQ648856), BtSARS.Rp3 (GenBank Accession No. DQ071615), SARS CoV.A022 (GenBank Accession No. AY686863), SARSCoV.CUHK-W1 (GenBank Accession No. AY278554), SARSCoV.GD01 (GenBank Accession No. AY278489), SARSCoV.HC.SZ.61.03 (GenBank Accession No. AY515512), SARSCoV.SZ16 (GenBank Accession No. AY304488), SARSCoV.Urbani (GenBank Accession No. AY278741), SARSCoV.civet010 (GenBank Accession No. AY572035), and SARSCoV.MA.15 (GenBank Accession No. DQ497008).

4. The chimeric subgroup 2b coronavirus spike protein of claim 3 , wherein said first subgroup 2b coronavirus is Bat SARS CoV-HKU3 (GenBank Accession No. FJ211859), said second subgroup 2b coronavirus is SARSCoV.Urbani (GenBank Accession No. AY278741.1), and said third subgroup 2b coronavirus is BtCoV 279.2005 (DQ648857).

5. The chimeric coronavirus spike protein of claim 1 , comprising the amino acid sequence:

(SEQ ID NO: 1)

1

MKILIFAFLA NLAKAQEGCG IISRKPQPKM AQVSSSRRGV YYNDDIFRSD VLHLTQDYFL

61

PFDSNLTQYF SLNVDSDRYT YFDNPILDFG DGVYFAATEK SNVIRGWIFG SSFDNTTQSA

121

VIVNNSTHII IRVCNFNLCK EPMYTVSRGT QQNAWVYQSA FNCTYDRVEK SFQLDTTPKT

181

GNFKDLREYV FKNRDGFLSV YQTYTAVNLP RGLPTGFSVL KPILKLPFGI NITSYRVVMA

241

MFSQTTSNFL PESAAYYVGN LKYSTFMLRF NENGTITDAV DCSQNPLAEL KCTIKNFNVD

301

KGIYQTSNFR VSPTQEVIRF PNITN LCPFG EVFNATKFPS VYAWERKKIS NCVADYSVLY

361

NSTFFSTFKC YGVSATKLND LCFSNVYADS FVVKGDDVRQ IAPGQTGVIA DYNYKLPDDF

421

MGCVLAWNTR NIDATSTGNY NYKYRYLRHG KLRPFERDIS NVPFSPDGKP CTPPALNCYW

481

PLNDYGFYTT TGIGYQPYRV VVLS FELLNA PATVCGPKLS TDLVKNQCVN FNFNGLKGTG

541

VLTSSSKRFQ SFQQFGRDTS DFTDSVRDPQ TLEILDISPC SFGGVSVITP GTNASSEVAV

601

LYQDVNCTDV PTAIRADQLT PAWRVYSTGV NVFQTQAGCL IGAEHVNASY ECDIPIGAGI

661

CASYHTASVL RSTGQKSIVA YTMSLGAENS IAYANNSIAI PTNFSISVTT EVMPVSMAKT

721

AVDCTMYICG DSLECSNLLL QYGSFCTQLN RALTGIAIEQ DKNTQEVFAQ VKQMYKTPAI

781

KDFGGFNFSQ ILPDPSKPTK RSFIEDLLFN KVTLADAGFM KQYGDCLGDV SARDLICAQK

841

FNGLTVLPPL LTDEMVAAY T AALVSGTATA GWTFGAGSAL QIPFAMQMAY RFNGIGVTQN

901

VLYENQKQIA NQFNKAISQI QESLTTTSTA LGKLQDVVND NAQALNTLVK QLSSNFGAIS

961

SVLNDILSRL DKVEAEVQID RLITGRLQSL QTYVTQQLIR AAEIRASANL AATKMSECVL

1021

GQSKRVDFCG KGYHLMSFPQ AAPHGVVFLH VTYVPSQERN FTTAPAICHE GKAYFPREGV

1081

FVSNGTSWFI TQRNFYSPQI ITTDNTFVAG NCDVVIGIIN NTVYDPLQPE LDSFKEELDK

1141

YFKNHTSPDV DLGDISGINA SVVNIQKEID RLNEVAKNLN ESLIDLQELG KYEQYIKWPW

1201

YVWLGFIAGL IAIVMVTILL CCMTSCCSCL KGACSCGSCC KFDEDDSEPV LKGVKLHYT .

6. The chimeric coronavirus of claim 2 , derived from subgroup 2c coronaviruses wherein said first, second and third subgroup 2c coronaviruses are different from one another and wherein the subgroup 2c coronaviruses are selected from the group consisting of Middle East respiratory syndrome coronavirus isolate Riyadh_2_2012 (GenBank Accession No. KF600652.1), Middle East respiratory syndrome coronavirus isolate Al-Hasa_18_2013 (GenBank Accession No. KF600651.1), Middle East respiratory syndrome coronavirus isolate Al-Hasa_17_2013 (GenBank Accession No. KF600647.1), Middle East respiratory syndrome coronavirus isolate Al-Hasa_15_2013 (GenBank Accession No. KF600645.1), Middle East respiratory syndrome coronavirus isolate Al-Hasa_16_2013 (GenBank Accession No. KF600644.1), Middle East respiratory syndrome coronavirus isolate Al-Hasa_21_2013 (GenBank Accession No. KF600634), Middle East respiratory syndrome coronavirus isolate Al-Hasa_19_2013 (GenBank Accession No. KF600632), Middle East respiratory syndrome coronavirus isolate Buraidah_1_2013 (GenBank Accession No. KF600630.1), Middle East respiratory syndrome coronavirus isolate Hafr-Al-Batin_1_2013 (GenBank Accession No. KF600628.1), Middle East respiratory syndrome coronavirus isolate Al-Hasa_12_2013 (GenBank Accession No. KF600627.1), Middle East respiratory syndrome coronavirus isolate Bisha_1_2012 (GenBank Accession No. KF600620.1), Middle East respiratory syndrome coronavirus isolate Riyadh_3_2013 (GenBank Accession No. KF600613.1), Middle East respiratory syndrome coronavirus isolate Riyadh_1_2012 (GenBank Accession No. KF600612.1), Middle East respiratory syndrome coronavirus isolate Al-Hasa_3_2013 (GenBank Accession No. KF186565.1), Middle East respiratory syndrome coronavirus isolate Al-Hasa_1_2013 (GenBank Accession No. KF186567.1), Middle East respiratory syndrome coronavirus isolate Al-Hasa_2_2013 (GenBank Accession No. KF186566.1), Middle East respiratory syndrome coronavirus isolate Al-Hasa_4_2013 (GenBank Accession No. KF186564.1), Middle East respiratory syndrome coronavirus (GenBank Accession No. KF192507.1), Betacoronavirus England 1-N1 (GenBank Accession No. NC_019843), MERS-CoV_SA-N1 (GenBank Accession No. KC667074), an isolate of Middle East Respiratory Syndrome Coronavirus having GenBank Accession No: KF600656.1, GenBank Accession No: KF600655.1, GenBank Accession No: KF600654.1, GenBank Accession No: KF600649.1, GenBank Accession No: KF600648.1, GenBank Accession No: KF600646.1, GenBank Accession No: KF600643.1, GenBank Accession No: KF600642.1, GenBank Accession No: KF600640.1, GenBank Accession No: KF600639.1, GenBank Accession No: KF600638.1, GenBank Accession No: KF600637.1, GenBank Accession No: KF600636.1, GenBank Accession No: KF600635.1, GenBank Accession No: KF600631.1, GenBank Accession No: KF600626.1, GenBank Accession No: KF600625.1, GenBank Accession No: KF600624.1, GenBank Accession No: KF600623.1, GenBank Accession No: KF600622.1, GenBank Accession No: KF600621.1, GenBank Accession No: KF600619.1, GenBank Accession No: KF600618.1, GenBank Accession No: KF600616.1, GenBank Accession No: KF600615.1, GenBank Accession No: KF600614.1, GenBank Accession No: KF600641.1, GenBank Accession No: KF600633.1, GenBank Accession No: KF600629.1, or GenBank Accession No: KF600617.1, Coronavirus Neoromicia/PML-PHE1/RSA/2011 GenBank Accession: KC869678.2, Bat Coronavirus Taper/CILKSA_287/Bisha/Saudi Arabia/GenBank Accession No: KF493885.1, Bat coronavirus Rhhar/CII_KSA_003/Bisha/Saudi Arabia/2013 GenBank Accession No: KF493888.1, Bat coronavirus Pikuh/CII_KSA_001/Riyadh/Saudi Arabia/2013 GenBank Accession No: KF493887.1, Bat coronavirus Rhhar/CII_KSA_002/Bisha/Saudi Arabia/2013 GenBank Accession No: KF493886.1, Bat Coronavirus Rhhar/CII_KSA_004/Bisha/Saudi Arabia/2013 GenBank Accession No: KF493884.1, BtCoV.HKU4.2 (GenBank Accession No. EF065506), BtCoV.HKU4.1 (GenBank Accession No. NC_009019), BtCoV.HKU4.3 (GenBank Accession No. EF065507), BtCoV.HKU4.4 (GenBank Accession No. EF065508), BtCoV133.2005 (GenBank Accession No. NC_008315), BtCoV.HKU5.5 (GenBank Accession No. EF065512); BtCoV.HKU5.1 (GenBank Accession No. NC_009020), BtCoV.HKU5.2 (GenBank Accession No. EF065510), BtCoV.HKU5.3 (GenBank Accession No. EF065511), human betacoronavirus 2c Jordan-N3/2012 (GenBank Accession No. KC776174.11; human betacoronavirus 2c EMC/2012 (GenBank Accession No. JX869059.2), and a Pipistrellus bat coronavirus HKU5 isolate having GenBank Accession No:KC522089.1, GenBank Accession No:KC522088.1, GenBank Accession No:KC522087.1, GenBank Accession No:KC522086.1, GenBank Accession No: KC522085.1, GenBank Accession No:KC522084.1, GenBank Accession No:KC522083.1, GenBank Accession No:KC522082.1, GenBank Accession No:KC522081.1, GenBank Accession No:KC522080.1, GenBank Accession No:KC522079.1, GenBank Accession No: KC522078.1, GenBank Accession No:KC522077.1, GenBank Accession No:KC522076.1, GenBank Accession No:KC522075.1, GenBank Accession No:KC522104.1, GenBank Accession No:KC522104.1, GenBank Accession No:KC522103.1, GenBank Accession No: KC522102.1, GenBank Accession No:KC522101.1, GenBank Accession No:KC522100.1, GenBank Accession No:KC522099.1, GenBank Accession No:KC522098.1, GenBank Accession No:KC522097.1, GenBank Accession No:KC522096.1, GenBank Accession No: KC522095.1, GenBank Accession No:KC522094.1, GenBank Accession No:KC522093.1, GenBank Accession No:KC522092.1, GenBank Accession No:KC522091.1, GenBank Accession No:KC522090.1, GenBank Accession No:KC522119.1 GenBank Accession No: KC522118.1 GenBank Accession No:KC522117.1 GenBank Accession No:KC522116.1 GenBank Accession No:KC522115.1 GenBank Accession No:KC522114.1 GenBank Accession No:KC522113.1 GenBank Accession No:KC522112.1 GenBank Accession No: KC522111.1 GenBank Accession No:KC522110.1 GenBank Accession No:KC522109.1 GenBank Accession No:KC522108.1, GenBank Accession No:KC522107.1, GenBank Accession No:KC522106.1, GenBank Accession No:KC522105.1) Pipistrellus bat coronavirus HKU4 isolates (GenBank Accession No:KC522048.1, GenBank Accession No:KC522047.1, GenBank Accession No:KC522046.1, GenBank Accession No:KC522045.1, GenBank Accession No:KC522044.1, GenBank Accession No:KC522043.1, GenBank Accession No: KC522042.1, GenBank Accession No:KC522041.1, GenBank Accession No:KC522040.1 GenBank Accession No:KC522039.1, GenBank Accession No:KC522038.1, GenBank Accession No:KC522037.1, GenBank Accession No:KC522036.1, GenBank Accession No:KC522048.1 GenBank Accession No:KC522047.1, GenBank Accession No:KC522046.1 GenBank Accession No:KC522045.1 GenBank Accession No:KC522044.1 GenBank Accession No:KC522043.1 GenBank Accession No:KC522042.1 GenBank Accession No:KC522041.1 GenBank Accession No:KC522040.1, GenBank Accession No:KC522039.1 GenBank Accession No:KC522038.1 GenBank Accession No:KC522037.1 GenBank Accession No:KC522036.1, GenBank Accession No:KC522061.1 GenBank Accession No:KC522060.1 GenBank Accession No:KC522059.1 GenBank Accession No:KC522058.1 GenBank Accession No:KC522057.1 GenBank Accession No:KC522056.1 GenBank Accession No:KC522055.1 GenBank Accession No:KC522054.1 GenBank Accession No:KC522053.1 GenBank Accession No:KC522052.1 GenBank Accession No:KC522051.1 GenBank Accession No:KC522050.1 GenBank Accession No:KC522049.1 GenBank Accession No:KC522074.1, GenBank Accession No:KC522073.1 GenBank Accession No:KC522072.1 GenBank Accession No:KC522071.1 GenBank Accession No:KC522070.1 GenBank Accession No:KC522069.1 GenBank Accession No:KC522068.1 GenBank Accession No:KC522067.1, GenBank Accession No:KC522066.1 GenBank Accession No:KC522065.1 GenBank Accession No:KC522064.1, GenBank Accession No:KC522063.1, or GenBank Accession No:KC522062.1.

7. The chimeric subgroup 2c coronavirus spike protein of claim 6 , wherein said first subgroup 2c coronavirus is BtCoV HKU4.2 (GenBank Accession No. EF065506.1); said second subgroup 2c coronavirus is MERS-CoV (GenBank Accession No. JX869059.2), and said third subgroup 2c coronavirus is BtCoV HKU5.5 (EF065512.1).

8. The chimeric coronavirus spike protein of claim 1 , comprising the amino acid sequence:

(SEQ ID NO: 5)

1

MTLLMCLLMS LLIFVRGCDS QFVDMSPASN TSECLESQVD AAAFSKLMWP YPIDPSKVDG

61

IIYPLGRTYS NITLAYTGLF PLQGDLGSQY LYSVSHAVGH DGDPTKAYIS NYSLLVNDFD

121

NGFVVRIGAA ANSTGTIVIS PSVNTKIKKA YPAFILGSSL TNTSAGQPLY ANYSLTIIPD

181

GCGTVLHAFY CILKPRTVNR CPSGTGYVSY FIYETVHNDC QSTINRNASL NSFKSFFDLV

241

NCTFFNSWDI TADETKEWFG ITQDTQGVHL YSSRKGDLYG GNMFRFATLP VYEGIKYYTV

301

IPRSFRSKAN KREAWAAFYV YKLHQLTYLL DFSVDGYIRR AIDCGHDDLS QLHCSYTSFE

361

VDTGVYSVSS Y EAKPSGSVV EQAEGVECDF SPLLSGTPPQ VYNFKRLVFT NCNYNLTKLL

421

SLFSVNDFTC SQISPAAIAS NCYSSLILDY FSYPLSMKSD LSVSSAGPIS QFNYKQSFSN

481

PTCLILATVP HNLTTITKPL KYSYINKCSR LLSDDRTEVP QLVNANQYSP CVSIVPSTVW

541

EDGDYYRKQL SPLEGGGWLV ASGSTVAMTE QLQMGFGITV QYGTDTNSVC PKL DLGDSLT

601

ITNRLGKCVD YSLYGVTGRG VFQNCTAVGV KQQRFVYDSF DNLVGYYSDD GNYYCVRPCV

661

SVPVSVIyDK STNLHATLFG SVACEHVTTM MSQFSRLTQS NLRRRDSNIP LQTAVGCVIG

721

LSNNSLVVSD CKLPLGQSLC AVPPVSTFRS YSASQFQLAV LNYTSPIVVT PINSSGFTAA

781

IPTNFSFSVT QEYIETSIQK VTVDCKQYVC NGFTRCEKLL VEYGQFCSKI NQALHGANLR

841

QDESVYSLYS NIKTTSTQTL EYGLNGDFNL TLLQVPQIGG SSSSYRSAIE DLLFDKVTIA

901

DPGYMQGYDD CMKQGPQSAR DLICAQYVSG YKVLPPLYDP NMEAAYTSSL LGSIAGAGWT

961

AGLSSFAAIP FAQSMFYRLN GVG ITQQVLS ENQKIIANKF NQALGAMQTG FTTTNLAFNK

1021

VQDAVNANAM ALSKLAAELS NTFGAISSSI SDILARLDTV EQEAQIDRLI NGRLTSLNAF

1081

VAQQLVRTEA AARSAQLAQD KVNECVKSQS KRNGFCGTGT HIVSFAINAP NGLYFFHVGY

1141

QPTSHVNATA AYGLCNTENP PKCIAPIDGY FVLNQTTSTA RSSGDQHWYY TGSSFFHPEP

1201

ITEANSKYVS MDVKFENLTN KLPPPLLSNS TDLDFKDELE EFFKNVSSQG PNFQEISKIN

1261

TTLLNLNTEL MVLSEVVKQL NESYIDLKEL GNYTFYQKWP WYIWLGFIAG LVALALCVFF

1321

ILCCTGCGTS CLGKLKCNRC CDSYDEYEVE KIHVH .

9. An isolated nucleic acid molecule encoding the chimeric coronavirus spike protein of claim 1 .

10. A vector comprising the isolated nucleic acid molecule encoding the chimeric coronavirus spike protein of claim 1 .

11. A Venezuelan equine encephalitis replicon particle (VRP) comprising the isolated nucleic acid molecule encoding the chimeric coronavirus spike protein of claim 1 .

12. A virus like particle (VLP) comprising the chimeric coronavirus spike protein of claim 1 and a matrix protein of any virus that can form a VLP.

13. A coronavirus particle comprising the chimeric coronavirus spike protein of claim 1 .

14. A population of VLPs of claim 12 .

15. A composition comprising the chimeric spike protein of claim 1 in a pharmaceutically acceptable carrier.

16. A composition comprising the nucleic acid molecule of claim 9 in a pharmaceutically acceptable carrier.

17. A composition comprising the vector of claim 10 in a pharmaceutically acceptable carrier.

18. A composition comprising the VRP of claim 11 in a pharmaceutically acceptable carrier.

19. A composition comprising the population of claim 14 in a pharmaceutically acceptable carrier.

20. A method of producing an immune response to a coronavirus in a subject, comprising administering to the subject an effective amount of the chimeric coronavirus spike protein of claim 1 , thereby producing an immune response to a coronavirus in the subject.

21. A method of treating a coronavirus infection in a subject in need thereof, comprising administering to the subject an effective amount of the chimeric coronavirus spike protein of claim 1 , thereby treating a coronavirus infection in the subject.

22. A method of preventing a disease or disorder caused by a coronavirus infection in a subject, comprising administering to the subject an effective amount of the chimeric coronavirus spike protein of claim 1 , thereby preventing a disease or disorder caused by a coronavirus infection in the subject.

23. A method of protecting a subject from the effects of coronavirus infection, comprising administering to the subject an effective amount of the chimeric coronavirus spike protein of claim 1 , thereby protection the subject from the effects of coronavirus infection.