Coronavirus immunogenic compositions and uses thereof

Abstract

Provided in the present disclosure are immunogenic compounds, pharmaceutical formulations thereof and their use for inducing a protective immune response against 2019 novel coronavirus (SARS-CoV-2) infection and variants in a mammal.

1 . An immunogenic composition comprising a replication defective adenoviral (rdAd) vector, wherein the rdAd vector is selected from:
 a) an rdAd vector comprising an expression cassette comprising a SARS-CoV-2 antigen coding sequence encoding at least one SARS-CoV-2 antigen, optionally wherein said antigen comprises a SARS-CoV-2 spike (S) protein receptor binding domain (RBD);   said immunogenic composition being configured to induce neutralizing antibody and/or cellular immune response against SARS-CoV-2 in a mammalian subject to which said immunogenic composition is administered.   
     
     
         2 . The immunogenic composition of  claim 1 , wherein the expression cassette comprises a SARS-CoV-2 antigen coding sequence for spike (S) protein or the S1 domain of the spike protein. 
     
     
         3 . The immunogenic composition of  claim 1 , wherein the expression cassette comprises a SARS-CoV-2 antigen coding sequence selected from the group consisting of SEQ ID NO: 3; a sequence having at least 80% homology and/or identity to SEQ ID NO: 3; a sequence present in SEQ ID NO: 12; a sequence having at least 80% homology and/or identity to SEQ ID NO: 12; SEQ ID NO: 15; a sequence having at least 80% homology and/or identity to SEQ ID NO: 15; SEQ ID NO: 446; a sequence having at least 80% homology and/or identity to SEQ ID NO: 446; any of SEQ ID NOS: 412-417; any of SEQ ID NOS: 438-445, and any of SEQ ID NOS: 475-476 or 460; a sequence having at least 80% homology and/or identity to any of SEQ ID NOS: 412-417, SEQ ID NOS: 438-445, and SEQ ID NOS: 475-476 and 460. 
     
     
         4 . The immunogenic composition of  claim 1 , wherein the SARS-CoV-2 antigen coding sequence encodes a spike protein sequence comprising a sequence where the S1/S2 cleavable site and/or S2′ are resistant to proteomic degradation, and/or a sequence where the fusion peptide has been deleted or modified to prevent its fusogenic activity, and/or a sequence where the intracellular domain has been modified or partially to alter the endoplasmic reticulum retention motif, optionally comprising a coding sequence encoding a sequence including at least one of NSPQQAQSVAS (SEQ ID NO: 451), NSPSGAGSVAS (SEQ ID NO: 456) or NSP-VAS (SEQ ID NO: 461) at the S1/S2 cleavage site, KRSFIADA (SEQ ID NO: 453), PSKPSKQSF (SEQ ID NO: 457), PSKPSKNSF (SEQ ID NO: 458), PSKPSNASF (SEQ ID NO: 459) at the S2′ cleavage site, or SRLDPPEAEV (SEQ ID NO: 455), and/or any sequence modification presented in Table 1 and/or Table 2. 
     
     
         5 . The immunogenic composition of  claim 1 , wherein the SARS-CoV-2 antigen coding sequence is a sequence presented in SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, or an immunogenic fragment thereof. 
     
     
         6 . The immunogenic composition of  claim 1 , wherein the SARS-CoV-2 antigen coding sequence encodes at least amino acids 331 to 527 of SEQ ID NO: 3. 
     
     
         7 . The immunogenic composition of  claim 6 , wherein the SARS-CoV-2 antigen coding sequence encodes a spike protein receptor binding domain (RBD) sequence comprises one or more of the following substitutions: K417N, K417T, R403K, N439K, G446V, G446S, L452R, G476A, S477N, T478K, E484D, T4781, E484K, F490S, Q493R, S494P, P499H and/or N501Y. 
     
     
         8 . The immunogenic composition of  claim 1 , wherein the SARS-CoV-2 antigen coding sequence encodes a spike protein receptor binding domain (RBD) sequence, or immunogenic fragment thereof, and/or comprises an amino acid sequence of SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NOS: 412-417, SEQ ID NOS: 438-445, SEQ ID NOs 475-476, SEQ ID NO: 446 and SEQ ID NO: 460; or an immunogenic fragment thereof. 
     
     
         9 . (canceled) 
     
     
         10 . (canceled) 
     
     
         11 . The immunogenic composition of  claim 1 , wherein the expression cassette of the replication defective adenoviral vector comprises a coding sequence for a modified version of SEQ ID NO: 411 comprising:
 one or more substitutions of any one or more of amino acids 333-388, 390-395, 397-399, 401-411, 413-415, 417-419, 424, 426-435, 437, 439-442, 444-446, 449, 450, 452, 453, 455-463, 465, 467-473, 475-479, 481-486, 490, 491, 493-495, 499-510, and/or 513-526; one or more substitutions of any one or more of amino acids 367, 403, 417, 439, 446, 449, 452, 453, 455, 456, 470, 473, 475, 476, 477, 478, 484, 486, 490, 493, 494, 495, 496, 499, 500, 501, 502, 503, 504, and/or 505; one or more substitutions selected from the group consisting of amino acid 367 (V) by F, I, L S or A, amino acid 403 (R) by K or S, 417 (K) by N or T; amino acid 439 (N) by K, amino acid 446 (G) by V, S or A; amino acid 449 (Y) by N; amino acid 452 (L) by L, M or Q, amino acid 453 (Y) by F; amino acid 455 (L) by F; amino acid 456 (F) by L; amino acid 470 (T) by I, A or N, amino acid 473 (Y) by V; amino acid 475 (A) by V; amino acid 476 (G) by S or A; amino acid 477 (S) by N, R, T, G, A or I; amino acid 476 (G) by S or A, amino acid 477 (S) by N, R, T, G, A or I, amino acid 478 (T) by I, K, R or A, amino acid 484 (E) by Q, K, D, A or R; amino acid 486 (F) by L or S; amino acid 490 (F) by L or S, amino acid 493 (Q) by L or R; amino acid 494 (S) by P or L, amino acid 495 (Y) by N or F; amino-acid 496 (G) by V or S, amino acid 499 (P) by H, S or R, amino acid 500 (T) by I; amino acid 501 (N) by Y, T or S; amino acid 502 (G) by R, D or C; amino acid 503 (V) by L, I or F; and, amino acid 504 (G) by V, D or S amino acid 505 (Y) by H, E, W or C.   
     
     
         12 - 15 . (canceled) 
     
     
         16 . The immunogenic composition of  claim 1 , wherein the coding sequence encodes at least one or more B cell epitopes, one or more CD8+ T cell epitopes, and/or one or more CD4+ T cell epitopes. 
     
     
         17 . (canceled) 
     
     
         18 . (canceled) 
     
     
         19 . The immunogenic composition of  claim 1 , wherein the replication defective adenoviral vector is a human adenovirus, optionally Ad5 or Ad26. 
     
     
         20 . The immunogenic composition of  claim 1 , wherein the replication defective adenoviral vector is a bovine adenovirus, a canine adenovirus, a non-human primate adenovirus, a chicken adenovirus, or a porcine or swine adenovirus. 
     
     
         21 - 23 . (canceled) 
     
     
         24 . The immunogenic composition of  claim 1 , wherein the rdAd vector comprises at least one polynucleotide sequence encoding at least one SARS-CoV-2 blocking protein; wherein the at least one polynucleotide sequence encodes at least one peptide or polypeptide: that induces an immune response that interferes with the binding of the SARS-CoV-2 S protein to its cellular receptor, directly interferes with the binding of the SARS-CoV-2 S protein to its cellular receptor, is an RBD binding agent, is an ACE2 binding agent, and/or is both an RBD binding agent and an ACE2 binding agent. 
     
     
         25 - 27 . (canceled) 
     
     
         28 . A pharmaceutical formulation, comprising an effective amount of the immunogenic composition of  claim 1 ; and, a pharmaceutically acceptable diluent or carrier. 
     
     
         29 - 35 . (canceled) 
     
     
         36 . A pharmaceutical formulation suitable for intranasal administration to a human subject, comprising:
 an effective amount of at least 10 7  viral particles (vp) of the immunogenic composition of  claim 1  comprising at least one replication defective adenoviral vector comprising an expression cassette comprising a coding sequence encoding at least SARS-CoV-2 spike (S) protein receptor binding domain (RBD), or at least one immunogenic fragment thereof, wherein the effective amount induces a combined mucosal, humoral and T cell protective immune response; and,   a pharmaceutically acceptable diluent or carrier.   
     
     
         37 . (canceled) 
     
     
         38 . (canceled) 
     
     
         39 . A pharmaceutical dosage for intranasal administration, comprising:
 a pharmaceutical acceptable carrier in a spray or aerosol form admixed with an immunogenic composition of  claim 1 , wherein the dosage is configured for intranasal administration to non-invasively induce a protective immune response against SARS-CoV-2.   
     
     
         40 - 43 . (canceled) 
     
     
         44 . A method for inducing an immune response against coronavirus, the method comprising administering an effective amount of the immunogenic composition of  claim 1  to a mammalian subject. 
     
     
         45 . The method of  claim 44 , wherein the immune response is protective against SARS-CoV-2. 
     
     
         46 . A method for inducing an immune response against SARS-CoV-2, the method comprising administering a pharmaceutical formulation of  claim 28  or a pharmaceutical dosage of  claim 39  to a mammalian subject. 
     
     
         47 - 53 . (canceled) 
     
     
         54 . A method of treating or inhibiting the symptoms of a respiratory viral infection in a mammal, said respiratory viral infection causing elevated expression of interleukin-6 (IL-6), interleukin-1-alpha (IL-1α) and/or interleukin-12 (IL-12) in the lung of said mammal, the method comprising: intranasally administering an effective amount of an E1 and E3 deleted adenoviral vector, with or without expressing a SARS-CoV-2 antigen, to the subject, whereby expression of IL-6, IL-1α, and/or IL-12 in the lung is reduced thereby alleviating said symptoms for up to about 28 days following administration of the vector. 
     
     
         55 - 92 . (canceled)