Phylogenetic Analysis of Rotaviruses Detected in Hospitalized Children from Karachi Pakistan Reveals only 72% Similarity with Vaccine Strains - Abstract
Introduction: Rotavirus is a well-known universal cause of pediatric gastroenteritis. It carries the highest gastroenteritis global disease burden in pediatric age group.
Objective: Present study was conducted to examine the molecular analysis of circulating strains of rotavirus in southern Karachi and other regions of Pakistan with the global
strains; and to determine their relationship with the vaccine strains to define and predict the efficacy of available vaccines.
Place and Duration of Study: Pediatrics department of PNS Shifa Hospital and Abbasi Shaheed Hospital Karachi during November 2014 to August 2016.
Study Design: It was a perspective observational study.
Methodology: Stool samples collected from hospitalized children under five years of age. Rotavirus detection was performed through ELISA. Samples were genotyped by
Polymerase chain reaction. The strains of G3 and G12 were sequenced and submitted to Genbank NCBI. MK355446 and MK904566 were assigned to G12 rotavirus sequences
while MK355445 and MK185023 to G3 rotavirus sequences. These sequences were aligned and matched against regional and global strains as well as with the available vaccine strains.
Results: Our G3 strain sequences were found 99-100% similar with the reference strains, and 95% similar with the G1[P8] wild type, rotarix and pentavalent reassortant Rotateq strains, while our G12 sequence was found to have 97-100% similarity with the reference sequences from the world. However, these strains are at far distance from available vaccine strains (72% similarity).
Conclusion: The G12 sequence with 72% similarity with vaccine strains raises the question for use of these vaccines in our community and becoming a cause of prolonged surveillance of this virus burden and circulating viral strain type.