Evidence of discordant genetic linkage in the VP4, VP6, VP7 and NSP4 encoding genes of rotavirus strains from adolescent and adult patients with acute gastroenteritis

The vast diversity within rotavirus strains circulating in the developing countries continues to be a major challenge for the efficacy of currently used preset rotavirus vaccines. The sequence analysis and phylogeny of multiple genes of rotavirus strains enable identification of reassortant strains and their human or animal origin. The objective of this study was to monitor the genetic linkage between the rotavirus VP4(P), VP6(I), VP7(G) and NSP4(E) encoding genes. The G, P, I and E genotypes of a total of 80 rotavirus strains isolated from adolescent and adult cases of acute gastroenteritis at the two time points 1993–1996 (n = 67) and 2004–2007 (n = 13)] were determined by nucleotide sequencing and phylogenetic analysis. The rotavirus strains from the 1990s and 2000s revealed common combinations of genotypes (G1–P8]–I1–E1, G2–P4]–I2–E2, G3–P8]–I1–E1 and G4–P8]–I1–E1) in 47.8% and 30.8%, unusual combinations of the same genotypes (G2–P8]–I2–E2, G9–P6]–I1–E1, G9–P6]–I1–E2, G9–P6]–I2–E1 and G4–P4]–I1–E2, G1–P4]–I2–E1, G9–P4]–I1–E1) in 7.5% and 23% and mixed infections of different G and P genotypes in 31.3% and 46.2%, respectively. Discordance in the association of I with E, G with I and E and P with I and E genotypes was found to be contributed respectively by 23.8–38.5%, 40.3–69.8% and 49.3–61.5% of the rotavirus strains at the two time points.The data suggest relatively high occurrence of intergenogroup reassortment in circulating rotavirus strains emphasizing the need for continuous surveillance and whole genome sequence based characterization of rotavirus strains for better understanding of their evolution and ecology.