Computationally optimized broadly reactive antigens for influenza

Abstract

The development of a computationally optimized influenza HA protein that elicits broadly reactive immune response to all H5N1 influenza virus isolates is described. The optimized HA protein was developed through a series of HA protein alignments, and subsequent generation of consensus sequences, for clade 2 H5N1 influenza virus isolates. The final consensus HA amino acid sequence was reverse translated and optimized for expression in mammalian cells. Influenza virus-like particles containing the optimized HA protein are an effective vaccine against H5N1 influenza virus infection in animals.

1 . A method of eliciting a broadly reactive immune response against influenza virus in a subject, comprising
 generating an optimized influenza virus polypeptide sequence comprising the steps of:
 (i) obtaining the amino acid sequences of the polypeptide from a group of influenza virus isolates, wherein the influenza virus isolates are from the same subtype; 
 (ii) organizing the amino acid sequences of the polypeptide from the group of influenza virus isolates by clade or sub-clade and then by geographical region within each clade or sub-clade; 
 (iii) aligning the amino acid sequences within each geographical region to generate primary consensus sequences, wherein each geographic region is represented by a primary consensus sequence; 
 (iv) aligning the primary consensus sequences to generate secondary consensus sequences, wherein each clade or sub-clade is represented by a secondary consensus sequence; and 
 (v) aligning the secondary consensus sequences, thereby generating the optimized influenza virus polypeptide sequence; and 
   administering the optimized influenza virus polypeptide to the subject.   
     
     
         2 . The method of  claim 1 , wherein generating the optimized influenza virus polypeptide sequence further comprises:
 (vi) reverse translating the optimized influenza virus polypeptide sequence to generate a coding sequence; and   (vii) optimizing the coding sequence for expression in mammalian cells.   
     
     
         3 . The method of  claim 1 , comprising administering a virus-like particle (VLP) comprising the optimized influenza virus polypeptide sequence to the subject. 
     
     
         4 . The method of  claim 3 , wherein the influenza virus is an H5N1 virus and the VLP elicits a broadly reactive immune response against H5N1 influenza. 
     
     
         5 . The method of  claim 4 , wherein the VLP elicits a protective immune response against at least 80% of known H5N1 isolates. 
     
     
         6 . The method of  claim 1 , wherein the geographical region is a continent. 
     
     
         7 . The method of  claim 1 , wherein the geographical region is a country.