Sequence and phylogenetic analysis of the VP6 and NSP4 genes of human rotavirus strains: Evidence of discordance in their genetic linkage

NSP4 and VP6 genes of a total of 118 rotavirus strains detected in adolescent and adult cases of acute gastroenteritis (AGE) in 1993-1996 and 2004-2007 were characterized to determine their diversity and genetic linkage. Eighty-two percent and 89% of the strains showed amplification of NSP4 and VP6 genes respectively in RT-PCR. Sequencing and phylogenetic analysis of the VP6 genes showed distribution of genogroups in the lineages I-1 (1.4%), I-2 (50.7%) and II-4 (47.9%) in the 1990s and I-2 (73.5%) and II-4 (26.5%) in 2000s, indicating diversity in genogroups at both time points. Amino acid divergence within the genogroup II strains from 1990s and genogroup I strains from the 2000s was noteworthy (4.7-6.7%). Sequencing and phylogenetic analysis of the NSP4 genes showed almost equal distribution (45.0-55.0%) of genotypes A and B however, higher amino acid divergence within the genotype B strains (up to 9.3%) than in genotype A strains (up to 2.9%) at the two-time points. Nearly 70% of the strains showed NSP4-A-VP6-I or NSP4-B-VP6-II genetic linkage. The discordance in the linkage noted in 29.7% of the strains was predominated by NSP4-B and VP6-I combination and appeared strikingly high in the infections caused by unusual and mixed rotavirus strains. This is the first report to describe the phylogenetic analysis of rotavirus NSP4 and VP6 genes and their discordance in adolescent and adult cases with AGE from India. The extensive diversity within the rotavirus genes and their relationship revealed by this study emphasizes the need for evaluation of the rotavirus vaccines being used currently.