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  • C07K2317/00—Immunoglobulins specific features
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  • C07K2317/34—Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
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  • C12N2770/20034—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
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  • C12N2770/00011—Details
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  • C12N2770/36111—Alphavirus, e.g. Sindbis virus, VEE, EEE, WEE, Semliki
  • C12N2770/36141—Use of virus, viral particle or viral elements as a vector
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  • C12N2770/00011—Details
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  • C12N2770/36111—Alphavirus, e.g. Sindbis virus, VEE, EEE, WEE, Semliki
  • C12N2770/36141—Use of virus, viral particle or viral elements as a vector
  • C12N2770/36144—Chimeric viral vector comprising heterologous viral elements for production of another viral vector

Definitions

• the present invention relates to methods and compositions comprising a chimeric coronavirus spike protein for treating and/or preventing a disease or disorder caused by a coronavirus infection.
• Coronaviruses constitute a group of phylogenetically diverse enveloped viruses that encode the largest plus strand RNA genomes and replicate efficiently in most mammals.
• Severe Acute Respiratory Syndrome Coronavirus (SARS- CoV) emerged in 2002-2003 causing acute respiratory distress syndrome (ARDS) with 10% mortality overall and up to 50% mortality in aged individuals.
• Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV) emerged in the Middle East in April of 2012, manifesting as severe pneumonia, acute respiratory distress syndrome (ARDS) and acute renal failure. The virus is still circulating and has been shown to have a mortality rate of -49%. Platforms for generating reagents and therapeutics are needed to detect and control the emergence of new strains, especially early in an outbreak prior to the development of type specific serologic reagents and therapeutics.
• the present invention overcomes previous shortcomings in the art by providing methods and compositions comprising a chimeric coronavirus spike protein for treating/and or preventing diseases and disorders caused by infection by a coronavirus.
• the present invention provides 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 the 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 SI domain as located in a nonchimeric coronavirus spike protein immediately downstream of the RBD, contiguous with a portion comprising 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 corona
• the present invention further provides an isolated nucleic acid molecule encoding the chimeric coronavirus spike protein of this invention, as well as a vector comprising the isolated nucleic acid molecule. Also provided are compositions comprising the chimeric coronavirus spike proteins, isolated nucleic acid molecules and/or vectors of this invention in a pharmaceutically acceptable carrier.
• the present invention provides a method of producing an immune response to a coronavirus in a subject, treating a coronavirus infection in a subject, preventing a disease or disorder caused by coronavirus infection in a subject and/or protecting a subject from the effects of coronavirus infection, comprising administering to the subject an effective amount of the chimeric coronavirus spike protein, the isolated nucleic acid molecule the vector and/or the composition of this invention, or any combination thereof, thereby producing an immune response to a coronavirus in the subject, treating a coronavirus infection in the subject, preventing a disease or disorder caused by coronavirus infection in the subject and/or protecting the subject from the effects of coronavirus infection.
• the present invention provides a method of identifying a coronavirus spike protein for administration to elicit an immune response to coronavirus in a subject infected by a coronavirus and/or a subject at risk of coronavirus infection and/or to a subject for whom eliciting an immune response to a coronavirus is needed or desired, comprising: a) contacting a sample obtained from a subject infected with a coronavirus with a panel of proteins comprising: 1) one or more chimeric coronavirus spike proteins from a subgroup 2c coronavirus, 2) one or more chimeric coronavirus spike proteins from a subgroup 2b coronavirus, 3) one or more spike proteins from a subgroup 2a coronavirus, 4) one or more chimeric coronavirus spike proteins from a subgroup 2d coronavirus, 5) one or more chimeric coronavirus spike proteins from a subgroup la coronavirus, 6) one or more chimeric
• Also provided herein is a method of identifying an antibody that neutralizes a coronavirus infecting a subject, comprising: a) isolating a coronavirus from a sample of a subject infected with a coronavirus and/or suspected of being infected with a coronavirus; b) contacting the coronavirus of (a) with a panel of antibodies comprising: 1) an antibody reactive with a chimeric coronavirus spike protein from a subgroup 2c coronavirus, 2) an antibody reactive with a chimeric coronavirus spike protein from a subgroup 2b coronavirus, 3) an antibody reactive with a chimeric coronavirus spike protein from a subgroup 2a coronavirus, 4) an antibody reactive with a chimeric coronavirus spike protein from a subgroup 2d coronavirus, 5) an antibody reactive with a chimeric coronavirus spike protein from a subgroup la coronavirus, 6) an antibody reactive with a
• compositions of (b) identifies the antibody of that coronavirus/antibody composition as an antibody that neutralizes the coronavirus infecting the subject.
• Fig. 1 Phylogenetic tree of the eoronaviruses.
• the chimeric spike antigen HKU3- Smix belongs to subgroup 2b, and the antigenic components of the chimeric antigen are derived from BtCoV HKU 3S, SARS CoV S, and BtCoV 279 S, all of which are circled.
• the other S antigens representing other subgroups of CoVs are indicated in dashed circles as controls.
• Fig. 2 Design of the chimeric spike antigen.
• the chimeric spike antigen HKU3- Smix has components from HKU3 S, SARS CoV S RBD, and BtCoV 279S.
• the specific amino acid residues adopted from each of the spike proteins are indicated in the figure.
• the S1/S2 boundary is indicated (761aa).
• S2/Tm domain is indicated (1 194aa).
• the top panel represents the spike protein organization in the SARS-CoV Spike, showing the spread of the neutralizing epitope across various domains of the SARS-CoV spike protein.
• Fig. 3 Cross reactivity of antisera to chimeric spike antigen, with spike proteins from different CoVs.
• Mouse antisera to chimeric spike antigen (HKU 3 S MIX), SARS S, BAT 1 A S, HKU2.298 S, HKU 4.2 S, and HKU9.4S were analyzed for their cross reactivity with these antigens.
• Antisera to chimeric spike antigen recognizes SARS S (Panel B) and vice versa (Panel A). Note that there is no cross reactivity between S proteins of other subgroups.
• Chimeric antigen HKU 3 S MIX protects against lethal SARS CoV
• Panel A Percent weight loss of young Balb/C mice immunized with chimeric Antigen HKU 3 S MIX , SARS S and HKU9.4S (negative control) and challenged with lethal dose of mouse adapted SARS CoV (MA 15 virus). Mice immunized with chimeric antigen, SARS S show no weight loss.
• Panel B Lung titers on Day 2 post infection of the same groups of mice shown above. Note that there is no virus detected in groups of mice vaccinated with HKU 3 S MIX and SARS S.
• Panel A Percent weight loss of young Balb/C mice immunized with chimeric spike antigen HKU 3 S MIX , SARS S and HKU9.4S (negative control) and challenged with lethal dose of heterologous mouse adapted SARS CoV (GD03 MA virus). Mice immunized with chimeric spike antigen, SARS S show no weight loss.
• Panel B Lung titers on Day 2 post infection of the same groups of mice shown above. Viral replication is reduced on D2 and no virus is detected in groups of mice vaccinated with HKU 3 S MIX and SARS S.
• Fig. 6 Schematic of the HKU2 virus with the chimeric antigen HKU 3 S Mix- Panel A. The HKU3 virus which has the chimeric antigen HKU 3 S MIX is shown. The open reading frames are indicated. Panel B. Growth curve of HKU 3 virus with the chimeric spike antigen HKU 3 S MIX. The HKU3 virus which has the chimeric spike antigen HKU 3 S MIX grows similar to SARS CoV in Vero cells.
• Fig. 7 Schematic of the BAT-SRBDMAv.
• This virus has the I 1KU3 backbone, with the spike protein containing a chimera of HKU3 spike and receptor binding domain from SARS-CoV spike 21 Oaa.
• This virus was created by serial passage of the parent virus in 20 week old Balb/C mice, resulting in virulent phenotype.
• the amino acid mutations essential for mouse adaptation are indicated and for comparison, the mouse adapted SARS-CoV is shown with the mouse adapted mutations.
• Chimeric spike antigen HKU 3 S MIX protects against lethal challenge with BAT-SRBD-Mav when compared.
• Panels A and B Percent weight loss of young Balb/C mice immunized with chimeric antigen HKU 3 S MIX , SARS S, BtCoV 279 S, and BtCoV HKU S and challenged with lethal dose of heterologous mouse adapted BAT-SRBD-MAv. Mice immunized with chimeric antigen, SARS S show no weight loss, whereas there is about 3-5% weight loss with HKU 3 S and BtCoV 279 S.
• Panel C Lung titers on Day 2 post infection of the same groups of mice shown above. Viral replication is reduced on D2 in BtCoV 279 S and HKU3 S group, but no virus is detected in groups of mice vaccinated with
• Fig. 9 Design of the chimeric spike antigen for subgroup 2c.
• the chimeric spike antigen 2c has components from H U4.2 S, MERS-CoV S RBD, and BtCoV 5.5S.
• the specific amino acid residues adopted from each of the spike proteins are indicated.
• S1/S2 boundary is indicated (730aa).
• S2/Tm domain is indicated ( ⁇ 1 190aa).
• FIG. 10 Characterization of VRP 3526 Platform.
• Panel A VEE 3526 replicon CoV S protein expression construct. The capsid and E glycoprotein genes from Venezuelan equine encephalitis virus are replaced with the Coronavirus Spike Protein gene S. The VEE capsid and E glycoproteins are supplied in separate constructs. When cells are transfected with all three constructs, VEE replicons encoding CoV S are formed.
• Panel B Titers of S protein vaccines from all three different coats determined on BHK cells by an IFA assay.
• Panel C Western blot from independent experiments showing expression of SARS-CoV S protein from VRP 3526 S and VRP 3000 S vaccines in Vero cells. Lower panel indicates actin.
• Fig. 11 Young adult mice are protected from homologous (MA15) and heterologous (MA 15 GD03S) SARS-CoV challenge by VRP 3526 S vaccine.
• Panels A & B Percent weight loss of young adult mice immunized with indicated vaccines, and challenged with 105 pfu of rM A 15 (homologous) and rMA15-GD03S (heterologous) respectively.
• Panels C&D Lung titers on 2DPI infection determined by plaque assay Vero cells from experiments in Panel A and B respectively. Error bars indicate SEM. * indicates (p ⁇ 0.()5 in Mann- Whitney Test).
• Fig.12. Aged mice are protected from homologous (MA15) SARS-CoV challenge by VRP 3526 S vaccine.
• Panel A Percent weight loss of one year old mice immunized with S protein based vaccines from three different coats, and challenged withl 05 pfu of rMAl 5.
• Panel B and C Lung titers on 2DPI (Panel B), and 4DPI (Panel C) determined by plaque assay Vero cells. Error bars indicate SEM. Significance as determined by Mann- Whitney test (p ⁇ 0.05, indicated by asterisk).
• VRP 3526 elicits high Antibody response in young and aged animals.
• Panels A and B ELISA results showing IgG titers to S protein, elicited in young mice (Panel A) and aged mice (Panel B) by indicated vaccine groups.
• Panels C and D Neutralization potential (to SARS-CoV) of antibodies elicited by indicated vaccine groups in young mice (Panel C), and aged mice (Panel D), as measured by PRNT assay. Error bars indicate SD.
• Fig. 1 Design of a Chimeric Spike based CoV Vaccine.
• Panel A Phylogenetic tree showing Coronaviruses in subgroup 2b. The circles represent three viruses from which specific regions of S proteins are combined to form the chimeric spike.
• Panel B Western blots showing that serum raised to the Chimera S or SARS-CoV Urbani S recognize the Chimeric Spike due to overlapping epitopes.
• Panel C Design of the Chimeric Spike antigen utilizing portions of SARS-COV, BtCoV HKU3 and BtCoV 279 Spike.
• the Chimera S contains the following epitopes from N terminus: a portion of ectodomain from BtCoV HKU3; a portion of Receptor Binding Domain (RBD) from SARS-CoV; a region from S 1/S2 from BtCoV HKU3 ; followed by a region containing S2/Tm from the BtCoV 279 Spike.
• RBD Receptor Binding Domain
• HKU3-SRBD-MA chimeric HKU3 virus containing the Receptor binding domain (green color) from SARS-CoV S protein.
• the Open Reading Frames are Indicated.
• the asterisk indicates Y436H mutation which enhances replication in mice.
• HKU3-SRBD-MA was serially passaged in 20 week old
• Fig.17 HKU-3-SRBD-MAv causes severe respiratory disease in 20wk old Balb/c mice culminating in lethality.
• Panel A Percent weight loss of 20 wk old Balb/c mice
• Panel A Percent weight loss of 20 wk old Balb/C mice immunized with SARS CoV S,
• the present invention is based on the production and development of a chimeric coronavirus spike protein which induces a neutralizing immune response to coronavirus, for use for example, in the treatment and/or prevention of a disease or disorder caused by infection by a variety of different coronavirus strains.
• the present invention provides 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 the 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 SI domain as located in a nonchimeric coronavirus spike protein immediately downstream of the RBD, contiguous with a portion comprising 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
• orientation from amino to carboxy terminus it is meant that the regions of the chimeric coronavirus spike protein are present from left to right in the same orientation as the amino terminus and carboxy terminus of a protein.
• This term is intended to describe orientation only and does not mean that the first region as described in the chimeric coronavirus structural protein is present at the exact amino terminus in all embodiments although that could be the case in some embodiments..
• this term does not mean that the fourth region as described in the chimeric coronavirus structural protein is present at the exact carboxy terminus in all embodiments although that could be the case in some embodiments.
• FIGS 2 and 9 Representative nonlimiting examples of a chimeric coronavirus spike protein of this invention are shown in Figures 2 and 9, each of which show a schematic of a subgroup b coronavirus spike protein and a subgroup c coronavirus spike protein, respectively with the regions described above shown in their locations in a nonchimeric (e.g., wild type) coronavirus spike protein.
• the chimeric coronavirus spike protein of this invention can be produced by combining domains or portions of coronavirus spike proteins as described above from subgroup la coronaviruses, subgroup lb coronaviruses, subgroup 2a coronaviruses, subgroup 2b coronaviruses, subgroup 2c coronaviruses, or subgroup 2d coronaviruses.
• the present invention provides a chimeric subgroup 2b coronavirus spike protein comprising, in orientation from amino to carboxy terminus: a) a first region comprising amino acids 1-325 of a spike protein of a first subgroup 2b coronavirus; b) a second region comprising amino acids 322-500 of a spike protein of a second subgroup 2b coronavirus; c) a third region comprising amino acids 488-842 of a spike protein of said first subgroup 2b coronavirus; and) a fourth region comprising amino acids 842-1241 of a spike protein of a third subgroup 2b coronavirus.
• the amino acid sequence of the chimeric coronavirus spike protein of this example is shown below, with these four regions identified (first and third regions from said first subgroup 2b coronavirus shown in bold; second region from said second subgroup 2b coronavirus shown with underline; and fourth region from said third subgroup 2b coronavirus shown in italics).
• the exemplary chimeric coronavirus spike protein shown above was produced from the following three subgroup 2b coronaviruses:
• SARS CoV Urbani spike protein (Accession No. ⁇ 13441.1) (second coronavirus)
• the length in amino acid residues of the respective regions of the chimeric subgroup 2b coronavirus spike protein can vary.
• the first region can comprise amino acid 1 through amino acid 320, amino acid 1 through amino acid 321, amino acid 1 through amino acid 322, amino acid 1 through amino acid 323, amino acid 1 through amino acid 324, amino acid 1 through amino acid 325, amino acid 1 through amino acid 326, amino acid 1 through amino acid 327, amino acid 1 through amino acid 328, amino acid 1 through amino acid 329 or amino acid 1 through amino acid 330 of a subgroup 2b
• coronavirus spike protein which is a first coronavirus.
• Amino acid numbering is based on the numbering of amino acid residues in a subgroup 2b coronavirus spike protein, representative examples of which are provided herein.
• the amino end of the second region can begin at amino acid 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329 or 330 of a subgroup 2b coronavirus spike protein and be contiguous through amino acid 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524 or 5
• the amino end of the third region can begin at amino acid 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509 or 510 of a subgroup 2b coronavirus spike protein and be contiguous through amino acid 825, 826, 827, 828, 829, 830, 831 , 832, 833, 834, 835, 836, 837, 838, 839, 840, 841, 842, 843, 844, 845, 846, 847, 848, 849 or 850 of a subgroup 2b coronavirus spike protein.
• the amino end of the fourth region can begin at amino acid 825, 826, 827, 828, 829, 830, 831 , 832, 833, 834, 835, 836, 837, 838, 839, 840, 841, 843, 844, 845, 846, 847, 848, 849 or 850 of a subgroup 2b coronavirus spike protein and be contiguous through amino acid 1225, 1226, 1227, 1228, 1229, 1230, 1231, 1232, 1233, 1234, 1235, 1236, 1237, 1238, 1240, 1241, 1242 or the final amino acid at the carboxy terminus of a subgroup 2b coronavirus spike protein.
• the fourth region of the chimeric coronavirus spike protein is from a third coronavirus that is different from the first coronavirus and the second coronavirus used to produce the chi
• the present invention provides a chimeric subgroup
• 2c coronavirus spike protein comprising, in orientation from amino to carboxy terminus: a) a first region comprising amino acids 1-371 of a spike protein of a first subgroup 2c coronavirus; b) a second region comprising amino acids 367-588 of a spike protein of a second subgroup 2c coronavirus; c) a third region comprising amino acids 594-983 of the spike protein of said first subgroup 2c coronavirus; and) a fourth region comprising amino acids 986-1357 of a spike protein of a third subgroup 2c coronavirus.
• the amino acid sequence of the chimeric coronavirus spike protein of this example is shown below, with these four regions identified (first and third regions from said first subgroup 2c coronavirus shown in bold; second region from said second subgroup 2c coronavirus shown with underline; and fourth region from said third subgroup 2c coronavirus shown in italics).
• 1 MTLLMCIiLMS LLIFVRGCDS QFVDMSPASN TSECLESQVD AAAFSKLMWP YPIDPS VDG
• the exemplary chimeric coronavirus spike protein shown above was produced from the following three subgroup 2c coronaviruses:
• MERS-CoV spike protein GenBank Accession No. AFS88936.1
• GYQPTSHVNA TAAYGLCNTE NPPKCIAPID
• GYFVLNQTTS TARSSGDQHW YYTGSSFFHP
• EPITEANSKY VSMDVKFENL TNKLPPPLLS NSTDLDFKDE LEEFFKNVSS QGPNFQEISK
• the length in amino acid residues of the respective regions of the chimeric subgroup 2c coronavirus spike protein can vary.
• the first region can comprise amino acid 1 through amino acid 365, amino acid 1 through amino acid 366, amino acid 1 through amino acid 367, amino acid 1 through amino acid 368, amino acid 1 through amino acid 369, amino acid 1 through amino acid 370, amino acid 1 through amino acid 371, amino acid 1 through amino acid 372, amino acid 1 through amino acid 373, amino acid 1 through amino acid 374 or amino acid 1 through amino acid 375 of a subgroup 2c
• coronavirus spike protein which is a first coronavirus.
• Amino acid numbering is based on the numbering of amino acid residues in a subgroup 2c coronavirus spike protein, representative examples of which are provided herein.
• the amino end of the second region can begin at amino acid 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374or 375 of a subgroup 2c coronavirus spike protein and be contiguous through amino acid 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591 , 592, 593, 594, 595, 596, 597, 598, 599 or 600 of a subgroup 2c coronavirus spike protein of a second coronavirus that is different from the first coronavirus.
• the amino end of the third region can begin at amino acid 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591, 592, 593, 594, 595, 596, 597, 598, 599 or 600 of a subgroup 2c coronavirus spike protein and be contiguous through amino acid 975, 976, 977, 978, 979, 980, 981, 982, 983, 984, 985, 986, 987, 988, 989, 990, 991, 992, 993, 994, 995, 996, 997, 998, 999 or 1000 of a subgroup 2c coronavirus spike protein.
• the third region of the chimeric coronavirus spike protein is from the subgroup 2c coronavirus that is the first coronavirus.
• the amino end of the fourth region can begin at amino acid 975, 976, 977, 978, 979, 980, 981, 982, 983, 984, 985, 986, 987, 988, 989, 990, 991, 992, 993, 994, 995, 996, 997, 998, 999 or 1000 of a subgroup 2c coronavirus spike protein and be contiguous through amino acid 1345, 1346, 1347, 1348, 1349, 1350, 1351, 1352, 1353, 1354, 1355, 1356, 1357, 1358, 1359, 1360, 1361, 1362, 1363, 1364, 1365, 1366, 1367, 1368, 1369, 1370 or the final amino acid at the carboxy terminus of
• the fourth region of the chimeric coronavirus spike protein is from a third subgroup 2c coronavirus that is different from the first subgroup 2c coronavirus and the second subgroup 2c coronavirus used to produce this chimeric coronavirus spike protein.
• a chimeric coronavirus spike protein of this invention can be made from any combination of three different coronaviruses from any subgroup, including subgroup la, subgroup lb, subgroup 2a, subgroup 2d and subgroup 3 in addition to subgroup 2b and subgroup 2c.
• first, second, third and fourth regions as described above would be applicable to a chimeric coronavirus spike protein of any subgroup and the same variability with regard to the amino acids that define the beginning and end of each of these four regions would be applicable to a chimeric coronavirus spike protein of any subgroup.
• chimeric coronavirus spike proteins produced from the respective coronavirus subgroups la, lb, 2a, 2b, 2c, 2d and 3 can be included in the methods and compositions of this invention in any combination and/or in any ratio relative to one another, as would be well understood to one of ordinary skill in the art.
• Nonlimiting examples of subgroup 2b coronaviruses that can be used to produce the chimeric coronavirus spike protein of this invention include Bat SARS CoV (GenBank Accession No. FJ21 1859), SARS CoV (GenBank Accession No. FJ21 1860),
• BtSARS.HKl . l GenBank Accession No. DQ022305), BtSARS.HKU3.2 (GenBank Accession No. DQ084199), BtSARS.HKU3.3 (GenBank Accession No. DQ084200), BtSARS.Rml (GenBank Accession No. DQ412043), BtCoV.279.2005 (GenBank Accession No. DQ648857), BtSARS.Rfl (GenBank Accession No. DQ412042), BtCoV.273.2005 (GenBank Accession No. DQ648856), BtSARS.Rp3 (GenBank Accession No. DQ071615), SARS CoV.A022 (GenBank Accession No.
• GenBank ® Database or later identified, and any combination thereof.
• Nonlimiting examples of subgroup 2c coronaviruses that can be used to produce the chimeric coronavirus capsid protein of this invention include: 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. KF600652.1 ), Middle East respiratory syndrome coronavirus isolate Al-Hasa_18_2013 (GenBank Accession No. KF600652.1 ), Middle East respiratory syndrome coronavirus isolate Al-Hasa_18_2013 (GenBank Accession No. KF600652.1 ), Middle East respiratory syndrome coronavirus isolate Al-Hasa_18_2013 (GenBank Accession No. KF600652.1 ), Middle East respiratory syndrome coronavirus isolate Al-Hasa_18_2013 (GenBank Accession No. KF600652.1 ), Middle East respiratory syndrome coronavirus isolate Al-Hasa_18_2013 (
• KF600644.1 Middle East respiratory syndrome coronavirus isolate Al-Hasa_21_2013 (GenBank Accession No. KF600634), Middle East respiratory syndrome coronavirus isolate Al-l lasa l 9 2013 (GenBank Accession No. KF600632.), Middle East respiratory syndrome coronavirus isolate Buraidah_l_2013 (GenBank Accession No. KF600630. 1 ), Middle East respiratory syndrome coronavirus isolate I Iafr-Al-Batin_ 1 2013 (GenBank Accession No. KF600628.1), Middle East respiratory syndrome coronavirus isolate Al-llasa l 2 2013 (GenBank Accession No. KF600627.1), Middle East respiratory syndrome coronavirus isolate Bisha_l_2012 (GenBank Accession No.
• KF 186566.1 Middle East respiratory syndrome coronavirus isolate Al-Hasa_4_2013 (GenBank Accession No. KF 186564.1), Middle East respiratory syndrome coronavirus (GenBank Accession No. ⁇ 92507.1 ), Betacoronavirus England 1-Nl (GenBank Accession No. NC_019843), MERS-CoV SA-N l (GenBank Accession No.
• BtCoV.HKU5.2 GenBank Accession No. EF065510
• BtCoV.HKU5.3 GenBank Accession No. EF065511
• human betacoronavirus 2c Jordan-N3/2012 GenBank Accession No.
• KC776174.1 human betacoronavirus 2c EMC/2012 (GenBank Accession No. JX869059.2), Pipistrellus bat coronavirus HKU5 isolates (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:
• 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
• 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: KC5221 19.1 GenBank Accession No: KC5221 18.1 GenBank Accession No: KC5221 17.1 GenBank Accession No: KC5221 16.1 GenBank Accession No: KC5221 15.1 GenBank Accession No: KC5221 14.1 GenBank Accession No: KC5221 13.1 GenBank Accession No: KC5221 12.1 GenBank Accession No: KC5221 1 1 .1 GenBank Accession No: KC522110.1 GenBank Accession No: KC522109.1 GenBank Accession No: KC522108.1 , GenBank Accession No: KC522107.1 , GenBank Acces
• 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
• Nonlimiting examples of a subgroup la coronavirus of this invention include
• FCov.FIPV.79.1 146.VR.2202 GenBank Accession No. NV_007025), transmissible gastroenteritis virus (TGEV) (GenBank Accession No. NCJ302306; GenBank Accession No. Q81 1789.2; GenBank Accession No. DQ81 1786.2; GenBank Accession No. DQ81 1788.1 ; GenBank Accession No. DQ81 1785.1 ; GenBank Accession No. X52157.1 ; GenBank Accession No. AJ01 1482.1 ; GenBank Accession No. KC962433.1; GenBank Accession No. AJ271965.2; GenBank Accession No. JQ693060.1; GenBank Accession No.
• GenBank Accession No. JQ693060.1 GenBank Accession No. JQ693059.1 ; GenBank Accession No. JQ693058.1 ; GenBank Accession No. JQ693057.1 ; GenBank Accession No. JQ693052.1 ; GenBank Accession No. JQ693051.1 ; GenBank Accession No. JQ693050.1), porcine reproductive and respiratory syndrome virus (PRRSV) (GenBank Accession No. NC 001961.1 ; GenBank Accession No. DQ811787), as well as any other subgroup la coronavirus now known (e.g., as can be found in the GenBank ® Database) or later identified, and any combination thereof.
• PRRSV porcine reproductive and respiratory syndrome virus
• Nonlimiting examples of a subgroup lb coronavirus of this invention include
• BtCoV.lA.AFCD62 GenBank Accession No. NC_010437
• GenBank Accession No. NC_010436 BtCov.HKU8.AFCD77 (GenBank Accession No. NC_010438), BtCoV.512.2005 (GenBank Accession No. DQ648858), porcine epidemic diarrhea virus PEDV.CV777 (GenBank Accession No. NC 003436, GenBank Accession No. DQ355224.1, GenBank Accession No. DQ355223.1, GenBank Accession No. DQ355221.1, GenBank Accession No. JN601062.1. GenBank Accession No. JN601061 .1 , GenBank Accession No. JN601060.1 , GenBank Accession N0.JN601059.1. GenBank Accession No. JN601058.1, GenBank Accession N0.JN601057.1 , GenBank Accession N0.JN601056.1 , GenBank Accession No. JN601055.1 , GenBank Accession No. JN601054.1 , GenBank Accession No. JN601054.1 , GenBank
• GenBank Accession No. JN601053.1 GenBank Accession No. JN601052.1 , GenBank Accession No. JN400902.1 , GenBank Accession No.JN547395.1 , GenBank Accession No. FJ687473.1 , GenBank Accession No.FJ687472.1 , GenBank Accession No. FJ687471.1. GenBank Accession No. FJ687470.1. GenBank Accession No. FJ687469.1 , GenBank Accession No.FJ687468.1, GenBank Accession No. FJ687467.1, GenBank Accession No. FJ687466.1, GenBank Accession No. FJ687465.1, GenBank Accession No. FJ687464.1, GenBank Accession No.
• GenBank Accession No.FJ687462.1 GenBank Accession No. FJ687461.1, GenBank Accession No. FJ687460.1, GenBank Accession No. FJ687459.1, GenBank Accession No. FJ687458.1, GenBank Accession No. FJ687457.1, GenBank Accession No. FJ687456.1, GenBank Accession No. FJ687455.1, GenBank Accession No. FJ687454.1, GenBank Accession No. FJ687453 GenBank Accession No. FJ687452.1, GenBank Accession No. FJ687451.1 , GenBank Accession No.
• GenBank Accession No.FJ687449.1 GenBank Accession No. AF500215.1, GenBank Accession No. KF476061.1 , GenBank Accession No. KF476060.1 , GenBank Accession No. KF476059.1 , GenBank Accession No. KF476058.1, GenBank Accession No. KF476057.1, GenBank
• BtCoV.HKU2.HK.33.2006 GenBank Accession No. EF203067
• BtCoV.HKU2.HK.46.2006 GenBank Accession No. EF203065
• BtCo V .11KU2.GD .430.2006 GenBank Accession No. EF203064
• any other subgroup lb coronavirus now known e.g., as can be found in the GenBank ® Database
• Nonlimiting examples of a subgroup 2a coronavirus of this invention include HCoV.I lKU l .CN5 (GenBank Accession No. DQ339101 ), MHV.A59 (GenBank Accession No. NC_001846), PHEV.VW572 (GenBank Accession No. NC _007732),
• HCoV.OC43.ATCC.VR.759 GenBank Accession No. NC 005147
• bovine enteric coronavirus BCoV.ENT
• GenBank Accession No. NC 003045 bovine enteric coronavirus
• any other subgroup 2a coronavirus now known (e.g., as can be found in the GenBank® Database) or later identified, and any combination thereof.
• Nonlimiting examples of a subgroup 2d coronavirus of this invention include BtCoV.HKU9.2 (GenBank Accession No. EF065514), BtCoV.HKU9.1 (GenBank Accession No. NC_009021), BtCoV.HkU9.3 (GenBank Accession No. EF065515), BtCoV.HKU9.4 (GenBank Accession No. EF065516), as well as any other subgroup 2d coronavirus now known (e.g., as can be found in the GenBank® Database) or later identified, and any combination thereof.
• Nonlimiting examples of a subgroup 3 coronavirus of this invention include
• Nonlimiting examples of a subgroup 3 coronavirus of this invention include
• IBV.Beaudette.IBV.p65 GenBank Accession No. DQ001339
• any other subgroup 3 coronavirus now known e.g., as can be found in the GenBank Database
• any other subgroup 3 coronavirus now known (e.g., as can be found in the GenBank Database) or later identified, and any combination thereof.
• the present invention further provides an isolated nucleic acid molecule encoding the chimeric coronavirus spike protein of this invention.
• a nucleic acid molecule of this invention can be a cDNA.
• a vector e.g., a viral or bacterial vector
• plasmid or other nucleic acid construct comprising the isolated nucleic acid molecule of this invention.
• VRP Venezuelan equine encephalitis replicon particle
• the present invention provides a virus like particle (VLP) comprising the chimeric coronavirus spike protein of any of this invention and a matrix protein of any virus that can form a VLP.
• VLP virus like particle
• the present invention also provides a coronavirus particle comprising the chimeric coronavirus spike protein of this invention.
• cells e.g., isolated cells
• the vectors, nucleic acid molecules, VLPs, VRPs, and/or coronavirus particles of the invention are also provided.
• VLPs any of the VLPs, VRPs and /or coronavirus particles of this invention, as well as a population of virus particles that are used as viral vectors encoding the chimeric coronavirus spike protein of this invention.
• the chimeric coronavirus spike proteins of this invention can be produced as recombinant proteins, e.g., in a eukaryotic cell system for recombination protein production.
• the invention also provides immunogenic compositions comprising the cells, vectors, nucleic acid molecules, VLPs, VRPs, coronavirus particles and/or populations of the invention.
• the composition can further comprise a pharmaceutically acceptable carrier.
• the present invention further provides a method of producing an immune response to a coronavirus in a subject, comprising administering to the subject an effective amount of a chimeric coronavirus spike protein, a nucleic acid molecule, a vector, a VRP, a VLP, a coronavirus particle, population and/or a composition of this invention, including any combination thereof, thereby producing an immune response to a coronavirus in the subject.
• the present invention provides a method of treating a coronavirus infection in a subject in need thereof, comprising administering to the subject an effective amount of a chimeric coronavirus spike protein, a nucleic acid molecule, a vector, a VRP, a VLP, a coronavirus particle, population and/or a composition of this invention, including any combination thereof, thereby treating a coronavirus infection in the subject.
• 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 a chimeric coronavirus spike protein, a nucleic acid molecule, a vector, a VRP, a VLP, a coronavirus particle, population and/or a composition of this invention, including any combination thereof, thereby preventing a disease or disorder caused by a coronavirus infection in the subject.
• the present invention provides a method of protecting a subject from the effects of coronavirus infection, comprising administering to the subject an effective amount of a chimeric coronavirus spike protein, a nucleic acid molecule, a vector, a VRP, a VLP, a coronavirus particle, population and/or a composition of this invention, including any combination thereof, thereby protecting the subject from the effects of coronavirus infection.
• the chimeric coronavirus spike proteins of this invention can be used to immunize a subject against infection by a newly emerging coronavirus, as well as treat a subject infected with a newly emerging coronavirus.
• the chimeric subgroup 2b coronavirus spike proteins of this invention can be used to immunize against and/or treat infection by bat SARS CoV like virus strains such as Rs SHC014 (GenBank ® Accession No. KC881005), Rs3367 (GenBank ® Accession No. KC881006) and/or WiVl S (GenBank ® Accession No. KC881007).
• bat SARS CoV like virus strains such as Rs SHC014 (GenBank ® Accession No. KC881005), Rs3367 (GenBank ® Accession No. KC881006) and/or WiVl S (GenBank ® Accession No. KC881007).
• the present invention provides a method of identifying a coronavirus spike protein for administration to elicit an immune response to coronavirus in a subject infected by a coronavirus and/or a subject at risk of coronavirus infection and/or to a subject for whom eliciting an immune response to a coronavirus is needed or desired, comprising: a) contacting a sample obtained from a subject infected with a coronavirus with a panel of proteins comprising: 1) one or more chimeric coronavirus spike proteins from a subgroup 2c coronavirus, 2) one or more chimeric coronavirus spike proteins from a subgroup 2b coronavirus, 3) one or more spike proteins from a subgroup 2a coronavirus, 4) one or more chimeric coronavirus spike proteins from a subgroup 2d coronavirus, 5) one or more chimeric coronavirus spike proteins from a subgroup 1 a coronavirus, 6) one or
• the method set forth above can further comprise the step of administering the coronavirus spike protein identified according to the method to the subject of (a) and/or to a subject at risk of coronavirus infection and/or to a subject infected with a coronavirus and/or to a subject for whom eliciting an immune response to a coronavirus is needed or desired.
• a method is also provided herein of identifying an antibody that neutralizes a coronavirus infecting a subject, comprising: a) isolating a coronavirus from a sample of a subject infected with a coronavirus and/or suspected of being infected with a coronavirus; b) contacting the coronavirus of (a) with a panel of antibodies comprising: 1) an antibody reactive with a chimeric coronavirus spike protein from a subgroup 2c coronavirus, 2) an antibody reactive with a chimeric coronavirus spike protein from a subgroup 2b coronavirus, 3) an antibody reactive with a chimeric coronavirus spike protein from a subgroup 2a coronavirus, 4) an antibody reactive with a chimeric coronavirus spike protein from a subgroup 2d coronavirus, 5) an antibody reactive with a chimeric coronavirus spike protein from a subgroup la coronavirus, 6) an antibody reactive with a
• coronavirus/antibody compositions of (b) identifies the antibody of that coronavirus/antibody composition as an antibody that neutralizes the coronavirus infecting the subject.
• the method set fort above can further comprise the step of administering the antibody identified according to the method to the subject of (a) and/or to a subject infected with a coronavirus and/or to a subject at risk of coronavirus infection and/or to a subject for whom eliciting an immune response to a coronavirus is needed or desired.
• a or “an” or “the” can mean one or more than one.
• a cell can mean one cell or a plurality of cells.
• the term "about,” as used herein when referring to a measurable value such as an amount of a compound or agent of this invention, dose, time, temperature, and the like, is meant to encompass variations of ⁇ 20%, ⁇ 10%, ⁇ 5%, ⁇ 1%, ⁇ 0.5%, or even + 0.1% of the specified amount.
• the transitional phrase "consisting essentially of means that the scope of a claim is to be interpreted to encompass the specified materials or steps recited in the claim, "and those that do not materially affect the basic and novel characteristic(s)" of the claimed invention. See, In re Herz, 537 F.2d 549, 551-52, 190 USPQ 461 , 463 (CCPA 1976) (emphasis in the original); see also MPEP ⁇ 21 1 1.03.
• sample or biological sample of this invention can be any biological material, such as a biological fluid, an extract from a cell, an extracellular matrix isolated from a cell, a cell (in solution or bound to a solid support), a tissue, a tissue homogenate, and the like as are well known in the art.
• an antigen/antibody complex In the methods of this invention in which formation of an antigen/antibody complex is detected, a variety of assays can be employed for such detection. For example, various immunoassays can be used to detect antibodies or proteins (antigens) of this invention. Such immunoassays typically involve the measurement of antigen/antibody complex formation between a protein or peptide (i.e., an antigen) and its specific antibody.
• a protein or peptide i.e., an antigen
• the immunoassays of the invention can be either competitive or noncompetitive and both types of assays are well-known and well-developed in the art.
• competitive binding assays antigen or antibody competes with a detectably labeled antigen or antibody for specific binding to a capture site bound to a solid surface.
• concentration of labeled antigen or antibody bound to the capture agent is inversely proportional to the amount of free antigen or antibody present in the sample.
• Noncompetitive assays of this invention can be, for example, sandwich assays, in which, for example, the antigen is bound between two antibodies.
• One of the antibodies is used as a capture agent and is bound to a solid surface.
• the other antibody is labeled and is used to measure or detect the resultant antigen/antibody complex by e.g., visual or instrument means.
• a number of combinations of antibody and labeled antibody can be used, as are well known in the art.
• the antigen/antibody complex can be detected by other proteins capable of specifically binding human immunoglobulin constant regions, such as protein A, protein L or protein G. These proteins are normal constituents of the cell walls of streptococcal bacteria. They exhibit a strong nonimmunogenic reactivity with
• immunoglobulin constant regions from a variety of species. (See, e.g., Kronval et al. J.
• the non-competitive assays need not be sandwich assays.
• the antibodies or antigens in the sample can be bound directly to the solid surface. The presence of antibodies or antigens in the sample can then be detected using labeled antigen or antibody, respectively.
• antibodies and/or proteins can be conjugated or otherwise linked or connected (e.g., covalently or noncovalently) to a solid support (e.g., bead, plate, slide, dish, membrane or well) in accordance with known techniques.
• Antibodies can also be conjugated or otherwise linked or connected to detectable groups such as radiolabels (e.g., 35 S, 125 1, 32 P, 13 H, 14 C, 131 I), enzyme labels (e.g., horseradish peroxidase, alkaline
• phosphatase phosphatase
• gold beads chemiluminescence labels
• ligands e.g., biotin
• fluorescence labels e.g., fluorescein
• a variety of organic and inorganic polymers can be used as the material for the solid surface.
• Nonlimiting examples of polymers include polyethylene, polypropylene, poly(4-methylbutene), polystyrene, polymethacrylate, poly(ethylene terephthalate), rayon, nylon, poly(vinyl butyrate), polyvinylidene difluoride (PVDF), silicones, polyformaldehyde, cellulose, cellulose acetate, nitrocellulose, and the like.
• Other materials that can be used include, but are not limited to, paper, glass, ceramic, metal, metalloids, semiconductive materials, cements and the like.
• substances that form gels such as proteins (e.g., gelatins), lipopolysaccharides, silicates, agarose and
• polyacrylamides can be used.
• Polymers that form several aqueous phases such as dextrans, polyalkylene glycols or surfactants, such as phospholipids, long chain (12-24 carbon atoms) alkyl ammonium salts and the like are also suitable.
• surfactants such as phospholipids, long chain (12-24 carbon atoms) alkyl ammonium salts and the like are also suitable.
• the solid surface is porous, various pore sizes can be employed depending upon the nature of the system.
• immunoassay systems including but not limited to, radio- immunoassays (R1A), enzyme-linked immunosorbent assays (ELISA) assays, enzyme immunoassays (EIA), "sandwich” assays, gel diffusion precipitation reactions,
• R1A radio- immunoassays
• ELISA enzyme-linked immunosorbent assays
• EIA enzyme immunoassays
• immunodiffusion assays agglutination assays, immunofluorescence assays, fluorescence activated cell sorting (FACS) assays, immunohistochemical assays, protein A immunoassays, protein G immunoassays, protein L immunoassays, biotin/avidin assays, biotin/streptavidin assays, Immunoelectrophoresis assays, precipitation/flocculation reactions, immunoblots (Western blot; dot/slot blot); immunodiffusion assays; liposome immunoassay,
• the methods of this invention can also be carried out using a variety of solid phase systems, such as described in U.S. Patent No. 5,879,881, as well as in a dry strip lateral flow system (e.g., a "dipstick” system), such as described, for example, in U.S. Patent Publication No. 20030073147, the entire contents of each of which are incorporated by reference herein.
• solid phase systems such as described in U.S. Patent No. 5,879,881
• a dry strip lateral flow system e.g., a "dipstick” system
• Embodiments of the present invention include monoclonal antibodies produced from B cells isolated from a subject of this invention that has produced an immune response against the chimeric coronavirus spike protein of this invention, wherein said monoclonal antibodies are specific to epitopes present on the chimeric coronavirus spike protein.
• Such monoclonal antibodies can be specific for an epitope in any of the first, second, third or fourth regions of the chimeric coronavirus spike protein of this invention as described herein.
• antibody or “antibodies” as used herein refers to all types of
• the antibody can be monoclonal or polyclonal and can be of any species of origin, including, for example, mouse, rat, rabbit, horse, goat, sheep or human, or can be a chimeric or humanized antibody. See, e.g. , Walker et al., Molec. Immunol. 26:403-11 (1989).
• the antibodies can be recombinant monoclonal antibodies produced according to the methods disclosed in U.S. Patent No. 4,474,893 or U.S. Patent No. 4,816,567.
• the antibodies can also be chemically constructed according to the method disclosed in U.S. Patent No. 4,676,980.
• the antibody can further be a single chain antibody or bispecific antibody.
• the antibody can also be humanized for administration to a human subject.
• Antibody fragments included within the scope of the present invention include, for example, Fab, F(ab')2, and Fc fragments, and the corresponding fragments obtained from antibodies other than IgG.
• Such fragments can be produced by known techniques.
• F(ab')2 fragments can be produced by pepsin digestion of the antibody molecule, and Fab fragments can be generated by reducing the disulfide bridges of the F(ab')2 fragments.
• Fab expression libraries can be constructed to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity (Huse et ah, (1989) Science 254: 1275-1281).
• Monoclonal antibodies can be produced in a hybridoma cell line according to the technique of Kohler and Milstein, (1975) Nature 265:495-97.
• a solution containing the appropriate antigen can be injected into a mouse and, after a sufficient time, the mouse sacrificed and spleen cells obtained.
• the spleen cells are then immortalized by fusing them with myeloma cells or with lymphoma cells, typically in the presence of polyethylene glycol, to produce hybridoma cells.
• the hybridoma cells are then grown in a suitable medium and the supernatant screened for monoclonal antibodies having the desired specificity.
• Monoclonal Fab fragments can be produced in bacterial cell such as E. coli by recombinant techniques known to those skilled in the art. See, e.g. , W. Huse, (1989) Science 246: 1275-81.
• Antibodies can also be obtained by phage display techniques known in the art or by immunizing a heterologous host with a cell containing an epitope of interest.
• Nedo virus refers to viruses within the order Nidovirales, including the families Coronaviridae and Arteriviridae. All viruses within the order Nidovirales share the unique feature of synthesizing a nested set of multiple subgenomic mRNAs. See M. Lai and K. Holmes, Coronaviridae: The Viruses and Their Replication, in Fields Virology, pg 1 163, (4 th Ed. 2001). Particular examples of Coronaviridae include, but are not limited to, toroviruses and coronaviruses.
• Coronavirus refers to a genus in the family Coronaviridae, which family is in turn classified within the order Nidovirales.
• the coronaviruses are large, enveloped, positive-stranded RNA viruses. They have the largest genomes of all RNA viruses and replicate by a unique mechanism that results in a high frequency of recombination.
• the coronaviruses include antigenic groups I, II, and III.
• coronaviruses include SARS coronavirus, MERS coronavirus, transmissible gastroenteritis virus (TGEV), human respiratory coronavirus, porcine respiratory coronavirus, canine coronavirus, feline enteric coronavirus, feline infectious peritonitis virus, rabbit coronavirus, murine hepatitis virus, sialodacryoadenitis virus, porcine hemagglutinating encephalomyelitis virus, bovine coronavirus, avian infectious bronchitis virus, and turkey coronavirus, as well as chimeras of any of the foregoing. See Lai and Holmes "Coronaviridae: The Viruses and Their
• a "nidovirus permissive cell” or “coronavirus permissive cell” as used herein can be any cell in which a coronavirus can at least replicate, including both naturally occurring and recombinant cells. In some embodiments the permissive cell is also one that the nidovirus or coronavirus can infect. The permissive cell can be one that has been modified by recombinant means to produce a cell surface receptor for the nidovirus or coronavirus.
• an “isolated” nucleic acid molecule is one that is chemically synthesized (e.g., derived from reverse transcription) or is separated from other nucleic acid molecules that are present in the natural source of the nucleic acid molecule.
• an “isolated” nucleic acid molecule is free of sequences (preferably protein encoding sequences) that naturally flank the nucleic acid (i.e., sequences located at the 5' and 3' ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived.
• the isolated nucleic acid molecule can contain less than about 5 kB.
• nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived.
• an "isolated" nucleic acid molecule such as a cDNA molecule
• a nucleic acid of this invention has at least about 50%
• nucleic acid sequence homology with the sequences specifically disclosed herein.
• the term "homology” as used herein refers to a degree of similarity between two or more sequences. There can be partial homology or complete homology (i.e., identity).
• a partially homologous sequence that at least partially inhibits an identical sequence from hybridizing to a target nucleic acid is referred to using the functional term "substantially homologous.”
• the inhibition of hybridization to the target sequence can be examined using a hybridization assay (Southern or northern blot, solution hybridization and the like) under conditions of low stringency.
• a substantially homologous sequence or hybridization probe will compete for and inhibit the binding of a completely homologous sequence to the target sequence under conditions of low stringency. This is not to say that conditions of low stringency are such that non-specific binding is permitted; low stringency conditions require that the binding of two sequences to one another be a specific (i.e., selective) interaction.
• the absence of non-specific binding can be tested by the use of a second target sequence, which lacks even a partial degree of complementarity (e.g., less than about 30% identity). In the absence of non-specific binding, the probe will not hybridize to the second non-complementary target sequence.
• nucleic acids encoding a cDNA of a coronavirus that hybridize under the conditions described herein to the complement of the sequences specifically disclosed herein can also be used according to the present invention.
• hybridization refers to any process by which a first strand of nucleic acid binds with a second strand of nucleic acid through base pairing.
• stringent refers to hybridization conditions that are commonly understood in the art to define the commodities of the hybridization procedure.
• High stringency hybridization conditions that will permit homologous nucleotide sequences to hybridize to a nucleotide sequence as given herein are well known in the art.
• hybridization of such sequences to the nucleic acid molecules disclosed herein can be carried out in 25% formamide, 5X SSC, 5X Denhardt's solution and 5% dextran sulfate at 42°C, with wash conditions of 25% formamide, 5X SSC and 0.1% SDS at 42°C, to allow hybridization of sequences of about 60%> homology.
• Another example includes hybridization conditions of 6X SSC, 0.1% SDS at about 45°C, followed by wash conditions of 0.2X SSC, 0.1% SDS at 50-65°C.
• Another example of stringent conditions is represented by a wash stringency of 0.3 M NaCl, 0.03M sodium citrate, 0.1%> SDS at 6 ( ) " 70"C using a standard hybridization assay (see SAMBROO et al, EDS., MOLECULAR CLONING: A
• nucleic acids, proteins, peptides, viruses, vectors, particles, antibodies and populations of this invention are intended for use as therapeutic agents and immunological reagents, for example, as antigens, immunogens, vaccines, and/or nucleic acid delivery vehicles.
• the present invention provides a composition comprising the nucleic acid, virus, vector, particle, antibody and/or population of this invention in a pharmaceutically acceptable carrier.
• the compositions described herein can be formulated for use as reagents (e.g., to produce antibodies) and/or for administration in a pharmaceutical carrier in accordance with known techniques. See, e.g., Remington, The Science And Practice of Pharmacy (latest edition).
• a chimeric coronavirus spike protein is being administered, delivered and/or introduced into a subject, e.g., to elicit or induce an immune response
• the protein can be administered, delivered and/or introduced into the subject as a protein present in an inactivated (e.g., inactivated through UV irradiation or formalin treatment) coronavirus.
• the protein or active fragment thereof of this invention can be administered, delivered and/or introduced into the subject according to any method now known or later identified for administration, introduction and/or delivery of protein or active fragment thereof, as would be well known to one of ordinary skill in the art.
• Nonlimiting examples include administration of the protein or fragment with a protease inhibitor or other agent to protect it from degradation and/or with a polyalkylene glycol moiety (e.g., polyethylene glycol).
• the coronavirus protein or active fragment thereof can be administered to a subject as a nucleic acid molecule, which can be a naked nucleic acid molecule or a nucleic acid molecule present in a vector (e.g., a delivery vector, which in some embodiments can be a VRP).
• a nucleic acid molecule which can be a naked nucleic acid molecule or a nucleic acid molecule present in a vector (e.g., a delivery vector, which in some embodiments can be a VRP).
• the nucleic acids and vectors of this invention can be administered orally, intranasally, parenterally (e.g., intravenously), by intramuscular injection, by intraperitoneal injection, transdermally, extracorporeally, topically or the like.
• the nucleic acids of the present invention can be in the form of naked DNA or the nucleic acids can be in a vector for delivering the nucleic acids to the cells for expression of the polypeptides and/or fragments of this invention.
• the vector can be a commercially available preparation or can be constructed in the laboratory according to methods well known in the art.
• Delivery of the nucleic acid or vector to cells can be via a variety of mechanisms, including but not limited to recombinant vectors including bacterial, viral and fungal vectors, liposomal delivery agents, nanoparticles, and gene gun related-mechanisms.
• delivery can be via a liposome, using commercially available liposome preparations such as LIPOFECTIN, LIPOFECTAMINE (GIBCO-BRL, Inc., Gaithersburg, MD). SUPERFECT (Qiagen, Inc. Hilden, Germany) and TRANSFECTAM (Promega Biotec, Inc., Madison, WI), as well as other liposomes developed according to procedures standard in the art.
• the nucleic acid or vector of this invention can be delivered in vivo by electroporation, the technology for which is available from Genetronics, Inc. (San Diego, CA) as well as by means of a SONOPORATIQN machine (ImaRx
• vector delivery can be via a viral system, such as a retroviral vector system, which can package a recombinant retroviral genome.
• the recombinant retrovirus can then be used to infect and thereby deliver to the infected cells nucleic acid encoding the polypeptide and/or fragment of this invention.
• the exact method of introducing the exogenous nucleic acid into mammalian cells is, of course, not limited to the use of retroviral vectors.
• adenoviral vectors alphaviral vectors (e.g., VRPs), adeno-associated viral (AAV) vectors, lentiviral vectors, pseudotyped retroviral vectors and vaccinia viral vectors, as well as any other viral vectors now known or developed in the future.
• Physical transduction techniques can also be used, such as liposome delivery and receptor-mediated and other endocytosis mechanisms. This invention can be used in conjunction with any of these or other commonly used gene transfer methods.
• cells or tissues can be removed and maintained outside the body according to standard protocols well known in the art.
• the nucleic acids and vectors of this invention can be introduced into the cells via any gene transfer mechanism, such as, for example, virus-mediated gene delivery, calcium phosphate mediated gene delivery, electroporation, microinjection or proteoliposomes.
• the transduced cells can then be infused (e.g., in a pharmaceutically acceptable carrier) or transplanted back into the subject per standard methods for the cell or tissue type. Standard methods are known for transplantation or infusion of various cells into a subject.
• Parenteral administration of the peptides, polypeptides, nucleic acids and/or vectors of the present invention, if used, is generally characterized by injection.
• Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions.
• parenteral administration includes intradermal, intranasal, subcutaneous, intramuscular, intraperitoneal, intravenous and intratracheal routes, as well as a slow release or sustained release system such that a constant dosage is maintained. See, e.g., U.S. Patent No.
• composition of this invention is typically admixed with, inter alia, a pharmaceutically acceptable carrier.
• pharmaceutically acceptable carrier is meant a carrier that is compatible with other ingredients in the pharmaceutical composition and that is not harmful or deleterious to the subject.
• pharmaceutically acceptable component such as a salt, carrier, excipient or diluent of a composition according to the present invention is a component that (i) is compatible with the other ingredients of the composition in that it can be combined with the compositions of the present invention without rendering the
• composition unsuitable for its intended purpose, and (ii) is suitable for use with subjects as provided herein without undue adverse side effects (such as toxicity, irritation, and allergic response). Side effects are "undue” when their risk outweighs the benefit provided by the composition.
• pharmaceutically acceptable components include, without limitation, any of the standard pharmaceutical carriers such as phosphate buffered saline solutions, water, emulsions such as oil/water emulsion, microemulsions and various types of wetting agents.
• a pharmaceutically acceptable carrier can comprise, consist essentially of or consist of one or more synthetic components (e.g., components that do not naturally occur in nature), as are known in the art.
• the carrier may be a solid or a liquid, or both, and is preferably formulated with the composition of this invention as a unit-dose formulation.
• the pharmaceutical compositions are prepared by any of the well-known techniques of pharmacy including, but not limited to, admixing the components, optionally including one or more accessory ingredients.
• Exemplary pharmaceutically acceptable carriers include, but are not limited to, sterile pyrogen-free water and sterile pyrogen- free physiological saline solution. Such carriers can further include protein (e.g., serum albumin) and sugar (sucrose, sorbitol, glucose, etc.)
• protein e.g., serum albumin
• sugar sucrose, sorbitol, glucose, etc.
• compositions of this invention include those suitable for oral, rectal, topical, inhalation (e.g., via an aerosol) buccal (e.g., sub-lingual), vaginal, parenteral (e.g., subcutaneous, intramuscular, intradermal, intraarticular, intrapleural, intraperitoneal, intracerebral, intraarterial, or intravenous), topical (i.e., both skin and mucosal surfaces, including airway surfaces) and transdermal administration.
• the compositions herein may also be administered via a skin scarification method, or transdermally via a patch or liquid.
• the compositions may be delivered subdermally in the form of a biodegradable material that releases the compositions over a period of time.
• a subject of this invention is any animal that is capable of producing an immune response against a coronavirus.
• a subject of this invention can also be any animal that is susceptible to infection by coronavirus and/or susceptible to diseases or disorders caused by coronavirus infection.
• a subject of this invention can be a mammal and in particular embodiments is a human, which can be an infant, a child, an adult or an elderly adult.
• a "subject at risk of infection by a coronavirus"' or a "subject at risk of coronavirus infection” is any subject who may be or has been exposed to a coronavirus.
• an "effective amount” refers to an amount of a compound or composition that is sufficient to produce a desired effect, which can be a therapeutic, prophylactic and/or beneficial effect.
• the present invention provides a method of inducing or eliciting an immune response in a subject, comprising administering to the subject an effective amount of a virus, vector, particle, population and/or composition of this invention.
• the present invention also provides a method of treating and/or preventing a coronavirus infection in a subject, comprising administering to the subject an effective amount of a virus, vector, particle, population and/or composition of this invention.
• the terms “treat,” “treating” and “treatment” include any type of mechanism, action or activity that results in a change in the medical status of a subject, including an improvement in the condition of the subject (e.g., change or improvement in one or more symptoms and/or clinical parameters), delay in the progression of the condition, delay of the onset of a disease or illness, etc.
• an effective amount of a virus or virus particle (e.g., VRP) of this invention is from about 10 4 to about 10 10 , preferably from about 10 5 to about 10 9 , and in particular from about 10 6 to about 10 8 infectious units (IU, as measured by indirect immunofluorescence assay), or virus particles, per dose, which can be administered to a subject, depending upon the age, species and/or condition of the subject being treated.
• a dose range of from about 1 to about 100 micrograms can be used.
• the optimal dosage would need to be determined for any given antigen or vaccine, e.g., according to the method of production and resulting immune response.
• the dosage for administration of adenovirus to humans can range from about 10 7 to 109 plaque forming units (pfu) per injecti *on, but can be as high as 10 12 , 10 15 and/or 10 20 pfu per injection.
• a subject will receive a single injection. If additional injections are necessary, they can be repeated at daily/weekly/monthly intervals for an indefinite period and/or until the efficacy of the treatment has been established.
• the efficacy of treatment can be determined by evaluating the symptoms and clinical parameters described herein and/or by detecting a desired immunological response.
• nucleic acid or vector required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the particular nucleic acid or vector used, its mode of administration and the like. Thus, it is not possible to specify an exact amount for every nucleic acid or vector. However, an appropriate amount can be determined by one of ordinary skill in the art using only routine
• a dosage range of from about 20 to about 40 international Units /Kilogram can be used, although it would be well understood that optimal dosage for administration to a subject of this invention needs to be determined, e.g., according to the method of production and resulting immune response.
• compositions can be administered with an adjuvant.
• adjuvant describes a substance, which can be any immunomodulating substance capable of being combined with the polypeptide or nucleic acid vaccine to enhance, improve or otherwise modulate an immune response in a subject without deleterious effect on the subject.
• Non-limiting examples of adjuvants that can be used in the vaccine of the present invention include the RIBI adjuvant system (Ribi Inc., Hamilton, Mont.), alum, mineral gels such as aluminum hydroxide gel, oil-in-water emulsions, water-in-oil emulsions such as, e.g., Freund's complete and incomplete adjuvants, Block copolymer (CytRx, Atlanta Ga.), QS-21 (Cambridge Biotech Inc., Cambridge Mass.), SAF-M (Chiron, Emeryville Calif.),
• AMPHIGENTM adjuvant, saponin, Quil A or other saponin fraction, monophosphoryl lipid A, and Avridine lipid-amine adjuvant.
• Non-limiting examples of oil-in-water emulsions useful in the vaccine of the invention include modified SEAM62 and SEAM 1/2 formulations.
• Modified SEAM 62 is an oil-in-water emulsion containing 5% (v/v) squalene (Sigma), 1 % (v/v) SPANTM 85 detergent (ICI Surfactants), 0.7% (v/v) TWEENTM 80 detergent (ICI Surfactants), 2.5% (v/v) ethanol, 200 pg/ml Quil A, 100 ug/ml cholesterol, and 0.5% (v/v) lecithin.
• Modified SEAM 1/2 is an oil-in-water emulsion comprising 5% (v/v) squalene, 1% (v/v) SPANTM 85 detergent, 0.7% (v/v) Tween 80 detergent, 2.5% (v/v) ethanol, 100 ug/ml Quil A, and 50 ug/ml cholesterol.
• Other immunomodulatory agents that can be included in the vaccine include, e.g., one or more interleukins, interferons, or other known cytokines.
• VEE replicon vectors can be used to express coronavirus structural genes in producing combination vaccines.
• Dendritic cells which are professional antigen-presenting cells and potent inducers of T-cell responses to viral antigens, are preferred targets of VEE and VEE replicon particle infection, while SARS coronavirus targets the mucosal surfaces of the respiratory and gastrointestinal tract.
• SARS coronavirus targets the mucosal surfaces of the respiratory and gastrointestinal tract.
• Combination prime-boost vaccines e.g., DNA immunization and vaccinia virus vectors
• have dramatically enhanced the immune response (notably cellular responses) against target papillomavirus and lentivirus antigens compared to single-immunization regimens Choen et al. (2000) Vaccine 18:2015-2022; Gonzalo et al. (1999) Vaccine 17:887-892; Hanke et al. (1998) Vaccine 16:439-445; Pancholi et al. (2000) J Infect. Dis. 182: 18-27).
• Using different recombinant viral vectors influenza and vaccinia
• the present invention also provides methods of combining different recombinant viral vectors (e.g., VEE and coronavirus) in prime boost protocols.
• VRPs Venezuelan Equine Encephalitis Virus
• VEEV Venezuelan Equine Encephalitis Virus
• BSL3 biological safety laboratory level 3
• BSL2 biological safety laboratory level 2
• VRP 3526 S Respiratory Syndrome Coronavirus
• SARS-CoV originated from a pool of heterologous viruses circulating in bats, confounding vaccine and therapeutic design should future outbreaks emerge.
• the VRP 3526 platform was used and a synthetically designed chimeric S protein containing different regions of S proteins from of BtCoV HKU3, SARS CoV S and BtCoV 279 S was constructed in V3526 backbone (Chimera S). Chimera S was efficiently expressed and was recognized by polyclonal serum to SARS-CoV. Chimera S was also effective in protecting mice from SARS disease induced by several divergent strains of SARS CoV belonging to subgroup 2b.
• HKU3 -S RB D-M Av receptor binding domain from H U3 Spike was replaced by SARS-CoV RBD.
• RBD receptor binding domain from H U3 Spike was replaced by SARS-CoV RBD.
• SARS-CoV RBD receptor binding domain from H U3 Spike was replaced by SARS-CoV RBD.
• the Chimera S vaccine and SARS-CoV S vaccine was successful in eliciting complete protection from weight loss and viral replication caused by HKU3-SRBD-MAV, where as BtCoV 279 S and BtCoV H U 3 S elicited partial protection.
• the results as shown in Figs. 10-18 demonstrate: 1) the generation of a VRP 3526 platform that can be prepared under BSI.2; 2) that the VRP 3526 platform has efficacy in young and aged models of SARS disease; 3) the generation of a subgroup specific Chimeric S protein vaccine for coronaviruses; 4) the creation of a subgroup specific lethal zoonotic challenge virus (HKU3-SRBD-MAv) that is representative of a virus that may emerge into the human population in the future; 5) the generation of a Chimera S vaccine that is effective in protection from divergent strains of lethal SARS CoV and HKU3-SRBD-MAv; 6) that a Chimeric Spike vaccine design can be effectively applied to coronaviruses from other subgroups; and 7) that the VRP 3526 platform and chimeric spike vaccine design can be broadly applicable to other zoonotic viruses that may emerge into humans.
• HKU3-SRBD-MAv subgroup specific lethal zoonotic challenge virus

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