Molecular Characterization of Group Rotaviruses Detected From Ashaiman in the Greater Accra Region of Ghana (2014-2016)

Abstract

Group A Rotaviruses (RVAs) are the most important etiological agents of acute gastroenteritis (AGE) in children less than 5 years of age. Mortality resulting from RVA gastroenteritis is higher in developing countries than in developed ones, causing a huge public health burden in global regions like Africa and South East Asia. The aim of this study was to investigate the strains of RVAs causing AGE in children less than 5 years of age in Ashaiman after the introduction of the Rotarix™ vaccine into the Expanded Programme on Immunization. Stools samples were collected from children less than 5 years of age who visited Ashaiman Polyclinic with AGE. The samples were tested by enzyme immunoassay (EIA) and the EIA negative samples were subjected to non-structural protein 3 (NSP3) qRT-PCR. One-Step multiplex RT-PCR was performed on EIA and NSP3 positive samples for gel based binomial genotyping. Sanger sequencing was performed to confirm the gel based genotyping results. RVA strains were selected from the gel based genotyping for full genome characterization (FGC) using Illumina MiSeq. Maximum likelihood trees were drawn for VP7 and VP4 genes using Tamura 3 parameter evolutionary model for 1000 bootstraps using MEGA 6.0 software. RVA prevalence was found to be 39% (145/369). Five VP7 (G1,G3,G9, G10 and G12) and three VP4 (P[4], P[6] and P[8]) genotypes which were phylogenetically identical within genotypes and more related to African strains were detected. There were 8 G/P combinations and 7 mixed infections. FGC result gave Wa-like, Ds-1 like and Wa-/ Ds-1 like constellations which suggests zoonotic transmission. For the first time, a unique strain; RVA/Human-wt/GHA/020/2015/G10P[8]-I1-R5-C2-M2-A3-N2-T1-E1-H2 has been characterized from this study and justify the need for full genome sequencing of rotaviruses in surveillance studies. The findings thus confirmed that, insanitary setting could create a conducive environment for RV co-infections and the upsurge of RV diversity