Genetic characterisation of Norovirus strains in outpatient children from rural communities of Vhembe district/South Africa, 2014–2015

Background Norovirus (NoV) is now the most common cause of both outbreaks and sporadic non-bacterial gastroenteritis worldwide. However, data supporting the role of NoV in diarrheal disease are limited in the African continent. Objectives This study investigates the distribution of NoV genotypes circulating in outpatient children from rural communities of Vhembe district/South Africa. Study design Stool specimens were collected from children under five years of age with diarrhea, and controls without diarrhea, between July 2014 and April 2015. NoV-positive samples, detected previously by Realtime PCR, were analysed using conventional RT-PCR targeting the partial capsid and polymerase genes. Nucleotide sequencing methods were performed to genotype the strains. Results The sequence analyses demonstrated multiple NoV genotypes including GI.4 (13.8%), GI.5 (6.9%), GII.14 (6.9%), GII.4 (31%), GII.6 (3.4%), GII.P15 (3.4%), GII.P21 (3.4%) and GII.Pe (31%). The most prevalent NoV genotypes were GII.4 Sydney 2012 variants (n = 7) among the capsid genotypes, GII.Pe (n = 9) among the polymerase genotypes and GII.Pe/GII.4 Sydney 2012 (n = 8) putative recombinants among the RdRp/Capsid genotypes. Two unassigned GII.4 variants were found. Conclusions The findings highlighted NoV genetic diversity and revealed continuous pandemic spread and predominance of GII.Pe/GII.4 Sydney 2012, indicative of increased NoV activity. An unusual RdRp genotype GII.P15 and two unassigned GII.4 variants were also identified from rural settings of the Vhembe district/South Africa. NoV surveillance is warranted to help to inform investigations into NoV evolution and disease burden, and to support on-going vaccine development programmes.