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 isolates. Crossneutralization 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.

Recent progress in West Nile virus diagnosis and vaccination

“…The lineage 3 is represented by a virus strain that was isolated from mosquitoes in the Czech Republic, designated the Rabensburg virus [50] and lineage 4 was isolated from a thick from the Caucasus [51]. WNV strains from India belonging to a subcluster of lineage 1 are sometimes classified as lineage 5 [52]. The Sarawak Kunjin virus strain is significantly different to the other Kunjin viruses, and therefore re-classification of this virus as lineage 6 has been proposed.…”

The contribution of rodent models to the pathological assessment of flaviviral infections of the central nervous system

“…Lineages 3 and 4 comprise isolates obtained from Central and Eastern Europe [9], but these viruses have not been associated with human illnesses. Lineage 5 is comprised of contemporary WNVs isolated in India [15].…”

Assessing the Risks of West Nile Virus–Infected Mosquitoes from Transatlantic Aircraft: Implications for Disease Emergence in the United Kingdom

“…There are two principal lineages: lineage 1 is detected throughout the world, whereas lineage 2 is detected in sub-Saharan Africa ) and more recently in Hungary (Bakonyi et al 2006). Recent data suggest that WNV should be classified into five genetic lineages, with Indian viruses constituting the distinct genetic lineage 5 (Bondre et al 2007). Other Flaviviruses include St. Louis Encephalitis, Japanese Encephalitis, Dengue, Yellow Fever, Usutu, and Tick-borne Encephalitis.…”