Molecular epidemiology of sapoviruses and novel noroviruses in South Africa

Abstract

Sapoviruses (SaVs) and noroviruses (NoVs) are genera of the Caliciviridae (CV) family and cause gastroenteritis in humans worldwide. They are small, single-stranded RNA viruses and each genus is further divided into 5 genogroups (GI-GV), of which four (GI, GII, GIV, and GV) infect humans in SaVs and three (GI, GII and GIV) in NoVs. Caliciviruses are non-enveloped which makes them stable in the environment and consequently well-suited to water contamination. Selected members of the CV family, namely NoV GI and GII, are responsible for a large proportion of CV-associated gastroenteritis and are therefore frequently detected and characterised. As a result, the detection of other family members such as SaVs and NoV GIV has been overshadowed. In addition, NoV genotypes are most often characterised based either on the capsid gene or RNA dependent RNA polymerase gene, but seldom both. Consequently, NoV recombinants frequently remain unidentified. There is currently very little data on SaVs circulating in the environment and in a clinical setting in South Africa (SA) and there is no data on NoV GIV or NoV recombinants in SA. The aim of this study was to investigate the molecular epidemiology of SaVs and novel NoVs, including NoV GIV and recombinants, in clinical specimens and environmental samples in SA. Initially, the detection methodology for SaV and NoV GIV was optimised through the construction of RNA standards for SaV and NoV GIV and the development and application of a competitive IAC for the detection of SaVs. The prevalence and genetic diversity of SaVs in the environment in SA was determined for the first time through detection and genotyping of the virus in river water, wastewater and irrigation water from several provinces in SA. Sapoviruses were detected in 75% of water samples, with concentrations ranging from 1.15 x 104 copies/ml to 1.62 x 107 copies/ml. Twelve different SaV genotypes were identified, with GI.2 being detected most often. Sapoviruses were also detected and characterised from stool specimens from hospitalised patients with gastroenteritis in several provinces of SA, providing new data on the genetic diversity of SaVs circulating in patients with gastroenteritis. Sapoviruses were detected in 9% of clinical specimens and twelve different genotypes were identified. Sapovirus genogroup IV was detected most often, followed closely by GI.2. Sapovirus concentrations in stool ranged from 1.43 x 105 copies/g stool to 1.21 x 1011 copies/g stool. Norovirus GIV was not detected in any of the environmental samples or clinical specimens from several provinces in SA, providing important baseline data for future molecular epidemiological studies on NoV GIV in SA. Lastly, this study documents the first report of one SaV and six NoV recombinants identified in hospitalised paediatric patients with gastroenteritis in SA, including novel NoV recombinants which to date, have not been reported in other countries. The information from this study provides valuable new data from SA and contributes to the knowledge of HuCVs on an international level.