Attenuated viruses useful for vaccines

Abstract

This invention provides an attenuated virus which comprises a modified viral genome containing nucleotide substitutions engineered in multiple locations in the genome, wherein the substitutions introduce synonymous deoptimized codons into the genome. The instant attenuated virus may be used in a vaccine composition for inducing a protective immune response in a subject. The invention also provides a method of synthesizing the instant attenuated virus. Further, this invention further provides a method for preventing a subject from becoming afflicted with a virus-associated disease comprising administering to the subject a prophylactically effective dose of a vaccine composition comprising the instant attenuated virus.

1 .- 81 . (canceled) 
     
     
         82 . A method for eliciting an immune response in a subject comprising administering to the subject an effective dose of an immunogenic composition, wherein the immunogenic composition comprises a modified virus and a pharmaceutically acceptable carrier and wherein the modified virus comprises a viral genome comprising a modified virus protein-encoding sequence having synonymous codons from the coding sequence of a parent virus in a rearranged order, wherein said rearrangement provides a reduced codon pair bias relative to a mammalian host over the coding sequence, in comparison to the coding region of the parent virus, without changing codon usage of the parent virus, wherein the codon pair bias is calculated by the following formula: 
       
         
           
             
               CPB 
               = 
               
                 
                   ∑ 
                   
                     i 
                     = 
                     1 
                   
                   k 
                 
                 
                   CPSi 
                   
                     k 
                     - 
                     1 
                   
                 
               
             
           
         
         wherein, the codon pair bias (CPB) of a protein encoding sequence is the arithmetic mean of the codon pair scores (CPS) of the individual codon pairs (i) contained within said protein encoding sequence of k codons in length; and 
         wherein the modified protein encoding sequence has a codon pair bias at least 0.05 less than the codon pair bias of the parent protein encoding sequence. 
       
     
     
         83 . A method for delaying the onset of, or slowing the rate of progression of, a virus-associated disease in a virus-infected subject comprising administering to the subject an effective dose of an immunogenic composition, wherein the immunogenic composition comprises a modified virus and a pharmaceutically acceptable carrier and wherein the modified virus comprises a viral genome comprising a modified virus protein-encoding sequence having synonymous codons from the coding sequence of a parent virus in a rearranged order, wherein said rearrangement provides a reduced codon pair bias relative to a mammalian host over the coding sequence, in comparison to the coding region of the parent virus, without changing codon usage of the parent virus, wherein the codon pair bias is calculated by the following formula: 
       
         
           
             
               CPB 
               = 
               
                 
                   ∑ 
                   
                     i 
                     = 
                     1 
                   
                   k 
                 
                 
                   CPSi 
                   
                     k 
                     - 
                     1 
                   
                 
               
             
           
         
         wherein, the codon pair bias (CPB) of a protein encoding sequence is the arithmetic mean of the codon pair scores (CPS) of the individual codon pairs (i) contained within said protein encoding sequence of k codons in length; and 
         wherein the modified protein encoding sequence has a codon pair bias at least 0.05 less than the codon pair bias of the parent protein encoding sequence. 
       
     
     
         84 . A method for preventing a subject from becoming afflicted with a virus-associated disease comprising administering to the subject an effective dose of an immunogenic composition, wherein the immunogenic composition comprises a modified virus and a pharmaceutically acceptable carrier and wherein the modified virus comprises a viral genome comprising a modified virus protein-encoding sequence having synonymous codons from the coding sequence of a parent virus in a rearranged order, wherein said rearrangement provides a reduced codon pair bias relative to a mammalian host over the coding sequence, in comparison to the coding region of the parent virus, without changing codon usage of the parent virus, wherein the codon pair bias is calculated by the following formula: 
       
         
           
             
               CPB 
               = 
               
                 
                   ∑ 
                   
                     i 
                     = 
                     1 
                   
                   k 
                 
                 
                   CPSi 
                   
                     k 
                     - 
                     1 
                   
                 
               
             
           
         
         wherein, the codon pair bias (CPB) of a protein encoding sequence is the arithmetic mean of the codon pair scores (CPS) of the individual codon pairs (i) contained within said protein encoding sequence of k codons in length; and 
         wherein the modified protein encoding sequence has a codon pair bias at least 0.05 less than the codon pair bias of the parent protein encoding sequence. 
       
     
     
         85 . A modified virus, wherein the modified virus comprises a viral genome comprising a modified virus protein-encoding sequence having a plurality of codons replaced with synonymous codons that are less frequently used in the host.