Neutralization of flaviviruses by antibody is primarily mediated via epitopes in the viral envelope (E) protein. Comparative studies using neutralizing monoclonal antibodies revealed differential expression of epitopes within the E protein domain III of ten naturally occurring West Nile virus strains representing major subtypes of genetic lineages 1 and 2. Residues that defined these subtype-specific determinants were identified by mutational studies and found to be surface exposed in the domain III structure. Mutations of residue 332 had the most significant effects on variation of domain III neutralizing epitopes among strains.
