Alphavirus vectors and virosomes with modified HIV genes for use as vaccines

Abstract

The present invention provides methods and compositions comprising a population of alphavirus replicon particles comprising two or more isolated nucleic acids selected from 1) an isolated nucleic acid encoding an env gene product or an immunogenic fragment thereof of a human immunodeficiency virus, 2) an isolated nucleic acid encoding a gag gene product or an immunogenic fragment thereof of a human immunodeficiency virus, wherein the gag gene product or immunogenic fragment thereof is modified to inhibit formation of virus-like particles containing the gag gene product or the immunogenic fragment thereof and their release from a cell, and 3) an isolated nucleic acid encoding a pol gene product or an immunogenic fragment thereof of a human immunodeficiency virus, wherein the pol gene product or immunogenic fragment thereof is modified to inhibit protease, integrase, RNase H and/or reverse transcriptase activity, and wherein the nucleic acids are each contained within a separate alphavirus replicon particle.

1 - 75 . (canceled)  
     
     
         76  ( 1 ). A composition comprising two or more isolated nucleic acids selected from the group consisting of an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C env gene product or a fragment containing an epitope thereof, an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C gag gene product or a fragment containing an epitope thereof, wherein the gag gene product or said fragment thereof is modified to inhibit formation of virus-like particles containing the gag gene product or-said fragment thereof and their release from a cell, and an isolated nucleic acid encoding a human immunodeficiency virus Clade C pol gene product or a fragment containing an epitope thereof, wherein the pol gene product or said fragment thereof is modified to inhibit reverse transcriptase activity.  
     
     
         77  ( 2 ). A composition comprising a population of alphavirus replicon particles comprising two or more isolated nucleic acids selected from the group consisting of 1) an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C env gene product, or a fragment containing an epitope thereof, 2) an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C gag gene product, or a fragment containing an epitope thereof, wherein the gag gene product or said fragment thereof is modified to inhibit formation of virus-like particles containing the gag gene product or said fragment thereof and their release from a cell, and 3) an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C pol gene product, or a fragment containing an epitope thereof, wherein the pol gene product or said fragment thereof is modified to inhibit reverse transcriptase activity.  
     
     
         78  ( 3 ). A composition comprising a population of alphavirus replicon particles comprising two or more isolated nucleic acids selected from the group consisting of 1) an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C env gene product, or a fragment containing an epitope thereof, 2) an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C gag gene product, or a fragment containing an epitope thereof, wherein the gag gene product or said fragment thereof is modified to inhibit formation of virus-like particles containing the gag gene product or said fragment thereof and their release from a cell, and 3) an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C pol gene product, or a fragment containing an epitope thereof, wherein the pol gene product or said fragment thereof is modified to inhibit reverse transcriptase activity, and wherein the alphavirus replicon particles comprise a replicon RNA or at least one structural protein which comprises one or more attenuating mutations.  
     
     
         79  ( 4 ). The composition of claim  2 , wherein the alphavirus replicon particles are Venezuelan equine encephalitis virus (VEE) replicon particles.  
     
     
         80  ( 5 ). The composition of claim  4 , wherein a structural protein of the VEE replicon particle comprises an attenuating mutation selected from the group consisting of: a mutation in codons at E2 amino acid position 76 which specifies an attenuating amino acid; a mutation in codons at E2 amino acid position 120 which specifies an attenuating amino acid; a mutation in codons at E2 amino acid position 209 which specifies an attenuating amino acid; a mutation in codons at E1 amino acid 272 which specifies an attenuating amino acid; a mutation in codons at E1 amino acid 81 which specifies an attenuating amino acid; a mutation in codons at E1 amino acid 253 which specifies an attenuating mutation, a combination mutation of the deletion of E3 codons 56-59 together with a mutation in codons at E1 amino acid 253 which specifies an attenuating mutation, and any combination thereof.  
     
     
         81  ( 6 ). A composition comprising a population of Venezuelan equine encephalitis virus (VEE) replicon particles comprising two or more isolated nucleic acids selected from the group consisting of 1) an isolated nucleic acid encoding an env gene product, or a fragment containing an epitope thereof, of a human immunodeficiency virus, 2) an isolated nucleic acid encoding a gag gene product, or a fragment containing an epitope thereof, of a human immunodeficiency virus, wherein the gag gene product or said fragment thereof is modified to inhibit formation of virus-like particles containing the gag gene product or said fragment thereof and their release from a cell, and 3) an isolated nucleic acid encoding a pol gene product, or a fragment containing an epitope thereof, of a human immunodeficiency virus, wherein the pol gene product or said fragment thereof is modified to inhibit reverse transcriptase activity.  
     
     
         82  ( 7 ). The composition of claim  6 , wherein a structural protein of the VEE replicon particle comprises an attenuating mutation selected from the group consisting of: a mutation in codons at E2 amino acid position 76 which specifies an attenuating amino acid; a mutation in codons at E2 amino acid position 120 which specifies an attenuating amino acid; a mutation in codons at E2 amino acid position 209 which specifies an attenuating amino acid; a mutation in codons at E1 amino acid 272 which specifies an attenuating amino acid; a mutation in codons at E1 amino acid 81 which specifies an attenuating amino acid; a mutation in codons at E1 amino acid 253 which specifies an attenuating mutation, a combination mutation of the deletion of E3 codons 56-59 together with a mutation in codons at E1 amino acid 253 which specifies an attenuating mutation, and any combination thereof.  
     
     
         83  ( 8 ). A composition comprising a population of South African Arbovirus No. 86 (S.A.A.R.86) replicon particles comprising two or more isolated nucleic acids selected from the group consisting of 1) an isolated nucleic acid encoding an env gene product, or a fragment containing an epitope thereof, of a human immunodeficiency virus, 2) an isolated nucleic acid encoding a gag gene product, or a fragment containing an epitope thereof, of a human immunodeficiency virus, wherein the gag gene product or said fragment thereof is modified to inhibit formation of virus-like particles containing the gag gene product or said fragment thereof and their release from a cell, and 3) an isolated nucleic acid encoding a pol gene product, or a fragment containing an epitope thereof, of a human immunodeficiency virus, wherein the pol gene product or said fragment thereof is modified to inhibit reverse transcriptase activity.  
     
     
         84  ( 9 ). The composition of claim  8 , wherein a nonstructural protein gene product and/or structural protein of the S.A.A.R.86 replicon particle comprises an attenuating mutation selected from the group consisting of: a mutation in codons at nsP1 amino acid position 538 which specifies an attenuating amino acid; a mutation in codons at E2 amino acid position 304 which specifies an attenuating amino acid; a mutation in codons at E2 amino acid position 314 which specifies an attenuating amino acid; a mutation in codons at E2 amino acid 376 which specifies an attenuating amino acid; a mutation in codons at E2 amino acid 372 which specifies an attenuating amino acid; a mutation in codons at nsP2 amino acid 96 which specifies an attenuating mutation, a mutation in codons at nsP2 amino acid 372 which specifies an attenuating mutation; in combination a mutation in codons at E2 amino acids 304, 314, 372 and 376; a mutation in codons at E2 amino acid 378 which specifies an attenuating mutation; a mutation in codons at nsP2 amino acid 372 which specifies an attenuating mutation; in combination, mutations in codons at nsP2 amino acids 96 and 372 which specify an attenuating mutation; a mutation at nsP2 amino acid 529 which specifies an attenuating mutation; a mutation in codons at nsP2 amino acid 571 which specifies an attenuating mutation; a mutation in codons at nsP2 amino acid 682 which specifies an attenuating mutation; a mutation in codons at nsP2 amino acid 804 which specifies an attenuating mutation; a mutation in codons at nsP3 amino acid 22 which specifies an attenuating mutation; in combination, mutations in codons at nsP2 amino acids 529, 871, 682 and 804 and in codons at nsP3 amino acid 22 which specify attenuating mutations, and any combination thereof.  
     
     
         85  ( 10 ). A method of inducing an immune response to human immunodeficiency virus in a subject, comprising administering to the subject an immunogenic amount of the composition of claim  6 .  
     
     
         86  ( 11 ). A method of inducing an immune response to human immunodeficiency virus in a subject, comprising administering to the subject an immunogenic amount of the composition of claim  7 .  
     
     
         87  ( 12 ). A method of inducing an immune response to human immunodeficiency virus in a subject, comprising administering to the subject an immunogenic amount of the composition of claim  8 .  
     
     
         88  ( 13 ). A method of inducing an immune response to human immunodeficiency virus in a subject, comprising administering to the subject an immunogenic amount of the composition of claim  9 .  
     
     
         89  ( 14 ). The method of claim  10 , wherein the amount of the composition administered to the subject is about 10 3  to about 10 7  particles.  
     
     
         90  ( 15 ). The method of claim  11 , wherein the amount of the composition administered to the subject is about 10 3  to about 10 7  particles.  
     
     
         91  ( 16 ). A composition comprising two or more isolated nucleic acids selected from the group consisting of an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C env gene product or a fragment containing an epitope thereof, an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C gag gene product or a fragment containing an epitope thereof, wherein the gag gene product or said fragment thereof is modified to inhibit formation of virus-like particles containing the gag gene product or-said fragment thereof and their release from a cell, and an isolated nucleic acid encoding a human immunodeficiency virus Clade C pol gene product or a fragment containing an epitope thereof, wherein the pol gene product or said fragment thereof comprises a modification resulting in deletion or inactivation of protease, integrase, RNase H and reverse transcriptase functions in the pol gene product or said fragment thereof.  
     
     
         92  ( 17 ). A composition comprising a population of alphavirus replicon particles comprising two or more isolated nucleic acids selected from the group consisting of 1) an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C env gene product, or a fragment containing an epitope thereof, 2) an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C gag gene product, or a fragment containing an epitope thereof, wherein the gag gene product or said fragment thereof is modified to inhibit formation of virus-like particles containing the gag gene product or said fragment thereof and their release from a cell, and 3) an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C pol gene products or a fragment containing an epitope thereof, wherein the pol gene product or said fragment thereof comprises a modification resulting in deletion or inactivation of protease, integrase, RNase H and reverse transcriptase functions in the pol gene product or said fragment thereof.  
     
     
         93  ( 18 ). A composition comprising a population of alphavirus replicon particles comprising two or more isolated nucleic acids selected from the group consisting of 1) an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C env gene product, or a fragment containing an epitope thereof, 2) an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C gag gene product, or a fragment containing an epitope thereof, wherein the gag gene product or said fragment thereof is modified to inhibit formation of virus-like particles containing the gag gene product or said fragment thereof and their release from a cell, and 3) an isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C pol gene product, or a fragment containing an epitope thereof, wherein the pol gene product or said fragment thereof comprises a modification resulting in deletion or inactivation of protease, integrase, RNase H and reverse transcriptase functions in the pol gene product or said fragment thereof, and wherein the alphavirus replicon particles comprise a replicon RNA or at least one structural protein which comprises one or more attenuating mutations.  
     
     
         94  ( 19 ). An isolated nucleic acid encoding a human immunodeficiency virus 1 Clade C pol gene product or a fragment containing an epitope thereof of a human immunodeficiency virus, wherein the pol gene product or said fragment thereof comprises a modification resulting in deletion or inactivation of integrase, RNase H and reverse transcriptase functions in the pol gene product or said fragment thereof.  
     
     
         95  ( 20 ). A composition comprising the nucleic acid of claim  19 .  
     
     
         96  ( 21 ). A vector comprising the nucleic acid of claim  19 .  
     
     
         97  ( 22 ). A cell comprising the vector of claim  21 .  
     
     
         98  ( 23 ). An alphavirus replicon particle comprising the nucleic acid of claim  19 .  
     
     
         99  ( 24 ). The alphavirus replicon particle of claim  23 , wherein the alphavirus replicon particle is a Venezuelan equine encephalitis virus (VEE) replicon particle.  
     
     
         100  ( 25 ). The VEE replicon particle of claim  24 , wherein a structural protein of the VEE replicon particle comprises an attenuating mutation selected from the group consisting of: a mutation in codons at E2 amino acid position 76 which specifies an attenuating amino acid; a mutation in codons at E2 amino acid position 120 which specifies an attenuating amino acid; a mutation in codons at E2 amino acid position 209 which specifies an attenuating amino acid; a mutation in codons at E1 amino acid 272 which specifies an attenuating amino acid; a mutation in codons at E1 amino acid 81 which specifies an attenuating amino acid; a mutation in codons at E1 amino acid 253 which specifies an attenuating mutation, a combination mutation of the deletion of E3 codons 56-59 together with a mutation in codons at E1 amino acid 253 which specifies an attenuating mutation, and any combination thereof.  
     
     
         101  ( 26 ). The alphavirus replicon particle of claim  23 , wherein the alphavirus replicon particle is a South African Arbovirus 86 virus (S.A.A.R.86) replicon particle.  
     
     
         102  ( 27 ). A method of inducing an immune response to human immunodeficiency virus in a subject, comprising administering to the subject an immunogenic amount of the alphavirus replicon particle of claim  23 .  
     
     
         103  ( 28 ). The method of claim  27 , wherein the amount administered to the subject is about 10 3  to about 10 7  alphavirus replicon particles.  
     
     
         104  ( 29 ). A method of inducing an immune response in a subject, comprising administering to the subject an immunogenic amount of the alphavirus replicon particle of claim  24 .  
     
     
         105  ( 30 ). The method of claim  29 , wherein the amount administered to the subject is about 10 3  to about 10 7  alphavirus replicon particles.  
     
     
         106  ( 31 ). A method of inducing an immune response in a subject, comprising administering to the subject an immunogenic amount of the alphavirus replicon particle of claim  25 .  
     
     
         107  ( 32 ). The method of claim  31 , wherein the amount administered to the subject is about 10 3  to about 10 7  alphavirus replicon particles.