Molecular characterization of the VP7 gene of Rotavirus isolated from a clinical sample of Calcutta, India

The gene coding for outer capsid protein, VP7 of rotaviruses detected among the children suffering from watery diarrhea in the eastern part of India w as studied. The full length gene, coding for VP7 was synthesized from a loc al strain, WD33, by combined reverse transcriptase-polymerase chain reactio n. A total of 42 fecal RNA out of 93 rotavirus-positive samples hybridized with this DNA, indicating the prevalence of this strain in the community. C omparison of the nucleotide and deduced amino acid sequence with the VP7 ge ne of other serotypes revealed that the local strain,WD33, resembled closel y with GI serotype, the homology being 94 and 97%, respectively. Multiplex PCR using the specific oligonucleotide primers also amplified the G1 specif ic DNA fragment. The overall change of 16 amino acids was noticed when comp ared with G1 specific prototype Wa strain of which nine amino acids are wit hin the neutralization domain. However, the phylogenetic tree constructed b y comparing the G1 strains from different countries demonstrated that this strain WD33 clustered as a distinct sub-lineage of lineage IV and not with Wa strain, that clustered with lineage III. (C) 2001 Elsevier Science B.V. All rights reserved.