title: West Nile virus isolates from India: evidence for a distinct genetic lineage.
abstract: The complete genomic sequence of one human isolate of West Nile virus (WNV) and the partial genomic sequences of 14 other strains from India isolated in the period 1955-1982 from different hosts and geographical areas were determined. Phylogenetic analyses based on complete and partial genomic sequences (921 nt of the C-prM-E region) revealed that WNV could be classified into five distinct groups that differed from each other by 20-25% at the complete genome level and by 20-26% using partial sequences. Of the Indian isolates, 13 formed a distinct genetic lineage, lineage 5, whereas two isolates, one from a human patient (1967) and another from a bat (1968), were related closely to lineage 1 strains. The complete genomic sequence of the Indian isolate, 804994, showed 20-22% genetic divergence from the previously proposed lineage 1 and 2 strains and 24-25% divergence from isolates of the newly proposed lineages 3 (Rabensburg isolate 97-103 of 1997) and 4 (Russian isolate LEIV-Krnd88-190 of 1998). Similarly, the partial genomic sequences of the Indian isolates showed 21-26% divergence from lineage 1 and 2 strains and from the Rabensburg (97-103) and Russian (LEIV-Krnd88-190) isolates. Cross-neutralization using strain-specific polyclonal antibodies against lineage 1 strain Eg-101 and representative Indian strains suggests substantial antigenic variation. This study documents circulation of WNV strains typical to India for 27 years and the introduction of lineage 1 strains during 1967-1968. These results indicate strongly that WNV should be classified into five genetic lineages, with Indian viruses constituting the distinct genetic lineage 5.
authors.affiliation: Microbial Containment Complex Unit, National Institute of Virology (ICMR), Sus Road, Pashan, Pune 411 021, India.
authors.forename: Vijay P
authors.initials: VP
authors.lastname: Bondre
authors.affiliation: Microbial Containment Complex Unit, National Institute of Virology (ICMR), Sus Road, Pashan, Pune 411 021, India.
authors.forename: R S
authors.initials: RS
authors.lastname: Jadi
authors.affiliation: Microbial Containment Complex Unit, National Institute of Virology (ICMR), Sus Road, Pashan, Pune 411 021, India.
authors.forename: A C
authors.initials: AC
authors.lastname: Mishra
authors.affiliation: Microbial Containment Complex Unit, National Institute of Virology (ICMR), Sus Road, Pashan, Pune 411 021, India.
authors.forename: P N
authors.initials: PN
authors.lastname: Yergolkar
authors.affiliation: Microbial Containment Complex Unit, National Institute of Virology (ICMR), Sus Road, Pashan, Pune 411 021, India.
authors.forename: V A
authors.initials: VA
authors.lastname: Arankalle
mesh_terms: D000818:Animals; D000914:Antibodies, Viral / Q000276:immunology; D000940:Antigenic Variation; D003429:Cross Reactions; D016679:Genome, Viral; D006801:Humans; D007194:India; D051379:Mice; D009500:Neutralization Tests; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D014901:West Nile Fever / Q000821:virology; D014902:West Nile virus / Q000145:classification / Q000235:genetics* / Q000276:immunology / Q000302:isolation & purification*
chemical_list: D000914:Antibodies, Viral; D012367:RNA, Viral