Patent ID: 6337181
Filing Date: 2002-01-08
Classification: G01N

Abstract:
A method of determining which naturally occurring amino acid variants of a protein, protein subregion, or antigenic site of a virus are selectively advantageous to said virus, said method comprising the following steps:aligning multiple nucleotide sequences of said protein subregion, or antigenic site to each other (multiple sequence alignment); for each aligned amino acid position (nucleotide codon), identifying as selectively advantageous to said virus the consensus (most common, mode) amino acid; for each aligned amino acid position (nucleotide codon), determining the replacement to silent ratio of each amino acid replacement mutation (observed R:S); for each aligned amino acid position (nucleotide codon), determining the replacement to silent ratio that would be expected if nucleotide mutation were neutral (expected R:S); for each aligned amino acid position (nucleotide codon), comparing said observed R:S to said expected R:S by means of a statistical test; for each aligned amino acid position (nucleotide codon), identifying as selectively advantageous to said virus non-consensus amino acid replacement variants that are determined by said statistical test to have a said observed R:S significantly higher than said expected R:S; whereby identifying which naturally occurring amino acid variants of said viral protein, protein subregion, or antigenic site are selectively advantageous to said virus.