Genetic variability of human rotavirus strains isolated from Eastern and Northern India

Abstract

An epidemiological study was conducted in Eastern and Northern India to determine the genomic diversity of rotaviruses in these parts of the country. In 2001, a total of 126 Group A rotavirus positive samples were detected from children below 4 years of age with diarrhoea from Kolkata, Dibrugarh and Bhubaneswar in Eastern India, and Chandigarh, a city in Northern India. All the samples were genotyped for VP7 (G-type) and VP4 (P-type) gene by reverse transcription (RT) and multiplex PCR using different type specific primers. The strains with G1P[8] (32.5%) was predominant as reported earlier [Das et al. (2002) J Clin Microbiol 40:146-149] followed by G2P[4](4.7%) and only one sample was of G4P[8] specificity. Along with these common types some rare strains like G1P[6], G2P[8], G2P[6], G4P[4], and G4P[6] were also detected in 14.3% of cases. Thirty percent of samples in this study were mixed infections and 21 (16.7%) specimens remained untypeable either for the VP7 or for the VP4 gene. After sequencing of the VP7 gene, two G9 strains (RMC321 and ISO-3) were identified with P[8] and P[19] specificities. Sequence analysis revealed that they have much lower homology to the G9 strains (116E, INL1, and G16) isolated earlier from Indian subcontinent, but have much higher homology to isolates from Argentina, Brazil, Malawi, Taiwan, and USA suggesting a separate progenitor for these strains.

Emergence of G12 Rotavirus Strains in Delhi, India, in 2000 to 2007

“…The low detection rates of G/P-nontypeable strains compared to those reported by some other studies, particularly compared to those in our previous report, may be attributed to differences in the RT-PCR assay that we employed, such as the use of more sensitive enzymes and the addition of both G12-specific primers and an alternate set of consensus primers (1,15). Our observation of a high percentage of unusual rotavirus strains was in agreement with data from several other studies from the Indian subcontinent (3,13,18,26,27). Additionally, genomic diversity among the regionally common rotavirus strains (G9P [6] and G2P [6]), particularly in regard to the migration pattern of various gene segments, could be attributed to a close association of humans with domesticated animals and/or a frequent occurrence of mixed infections (5, 14, 17, 21-24, 27, 32, 54).…”

Spike Protein VP8* of Human Rotavirus Recognizes Histo-Blood Group Antigens in a Type-Specific Manner

“…Since the P [6] RVs bind H type 1 only, the higher prevalence of P [6] RVs in the African countries could be due to a higher rate of the Le aϪbϪ phenotypes in these regions. However, high prevalence or endemicity of P [6] RVs has also been reported for India and for non-African newborn infants (3,12,30,35). One report did not show association of secretor status with RV infection in children (1).…”

Evidence for Bovine Origin of VP4 and VP7 Genes of Human Group A Rotavirus G6P[14] and G10P[14] Strains

“…Multiplex seminested PCR using type-specific primers described earlier (2,(5)(6)(7)(8)10) and/or sequencing-based genotyping of 130 (22.7%) group A rotavirus strains (designated RUBV strains for ruminant [RU] and bovine [BV]) detected by RNA electrophoresis in polyacrylamide gels from diarrheic calves (n ϭ 573) from November 2001 to March 2005 in and around Kolkata in eastern India revealed an increased prevalence of G6P [11] strains (89.2%) ( Table 1). All 116 RUBV G6P [11] strains exhibited identical electropherotypes in polyacrylamide gels, and 23 of these strains, detected during different time periods of the year and scattered over the entire surveillance period, were sequenced for the VP7 and VP8* genes.…”