Rotavirus strains in children less than 5 years of age: A case control study

Background: Globally, rotavirus A (RV) is a leading cause of acute gastroenteritis (AGE) in young children under 5 years. The main aim of this study was to describe the prevalence of RV in children with and without diarrhea whose age ranged from 3 months to 5 years from two different hospitals of Nepal. We also described the diversity of rotavirus circulating during the pre-vaccination period in Nepal between 2006-2009. Materials and methods: A total of 2400 stool samples collected from children's years with diarrhea (cases, N = 1200) and without diarrhea (controls, N = 1200) were tested for the presence of RV by both enzyme-linked immunosorbent assay and real-time reverse transcription polymerase chain reaction (RT-PCR). All samples positive for RT PCR and/or ELISA were further characterized for G and P genotypes by conventional RT-PCR. Results: In total, 500 of the 2398 (20.8 %) samples (424 cases and 76 controls), were positive for RV. The most frequently detected G-types were G12, G1, and G9 and P-types were P[8] and P[6]. The predominant genotypes G12P[6], G12P[8], G1P[8] and G9P[8] were identified in 27.8 %, 24.2 %, 11.8 % and 10.8 % of the samples, respectively. Conclusion: This study observed high prevalence of G12P[6] rotavirus circulating in Nepal before vaccine introduction and they may pose an emerging challenge to current and future vaccine. Therefore, continuous molecular surveillance of circulating genotypes and emerging rotavirus strain should be carried out to better understand the effectiveness of vaccination program.