Direct detection and characterization of rotavirus into subgroups by dot blot hybridization and correlation with ‘long’ and ‘short’ electropherotypes

Abstract

Backgroud: Enzyme-linked immunosorbent assay (ELISA) and polyacrylamide gel electrophoresis (PAGE) of viral RNA are well-established methods for detection of rotavirus in stool samples. Dot-blot hybridization has also been found to be a sensitive and specific technique for detection and characterization of rotaviruses. Objectives: To compare the performance of dot blot hybridization with ELISA and PAGE for detection of rotavirus in stool samples. To assess the use of dot blot hybridization for characterization of rotaviruses into subgroups. Study design: Stool samples were collected from 214 children presenting to the hospital with acute diarrhoea. These were assayed for rotavirus by ELISA and PAGE. Dot-blot hybridization was done with full length cloned radiolabelled c-DNA probes of gene segment 6 of SA-11 (subgroup I) and Wa (subgroup II) rotaviruses. Results: Out of 214 stool samples 134 were found to be positive for rotavirus by one of the three methods. Among these 134 positive speciments 114 were positive by dot blot hybridization, this included 18 specimens which were positive only by dot blot assay. One-hundred-and-twelve of these 114 specimens could be subgrouped. Fifteen of these were classified as subgroup I, 97 as subgroup II and two had a dual subgroup specificity. Three subgroup 1 strains had a ‘long’ RNA pattern, whereas one subgroup II strain had a ‘short’ RNA pattern which has not been reported earlier for human rotaviruses. Conclusion: Dot blot hybridization as described here is a sensitive and specific assay for detection and subgrouping of rotaviruses. However, as there is a considerable genomic diversity among rotaviruses, the panel should include probes from all the genotypes of gene segment 6.