Molecular characterization of human sapoviruses circulation in the rural communities of Limpopo Province, South Africa

Abstract

Background: Viral diarrhoea is a common cause of mortality among children less than five years of age in developing countries. Sapovirus (SV), one of the enteric viruses has been reported to be associated with viral diarrhoea worldwide. Reported studies on SVs in selected provinces of South Africa (SA) have been published based on the patients admitted in the hospitals located in the urban areas. There is a need for continuous epidemiological studies of SVs from the rural based regions within SA, especially from outpatients reporting in rural health care centers. Objective: To determine the genotypes, characterize, and analyze a capsid protein of the detected human Sapovirus strains associated with diarrhoea in children less than 5 years of age from rural communities in SA, and also compare the detected SV strains in this study with other strains reported elsewhere around the world. Method: A review article on the prevalence of human SV in developing countries was compiled to support the rationale of this study. To find the SV genotypes, characterizing, and comparing them with previously reported SV strains, an investigation on the “Prevalence and genetic characterisation of human sapovirus from children in the rural areas of Vhembe district” was conducted. A total of 284 stool samples were collected from children under 5 years of age suffering with diarrhoea (n=228) and without diarrhoea (n=56). Samples were screened for SV using real-time PCR. Sapovirus positive samples were further analysed for genogrouping by a One-Step Ahead RT- ix PCR, and SV Strains were genotyped using Sanger sequencing. A polyprotein (partial capsid protein) was successfully amplified using One-Step RT-PCR from 25% (10/40) positive samples, and further sequenced using Sanger method. Results: From a review report, 6.5% prevalence rate for SV in the low and middle income countries was determined, with significance difference of SV prevalent rate seen between low income and middle income countries. This study reports 14.1% (40/284) SV detection from stool samples [16.7% (38/228) of diarrhoeal and 3.6% (2/56) of non-diarrhoeal samples]. Genogroup-I was found as the most prevalent strain comprising 68.75% (11/16), followed by SV-GII 18.75% (3/16), and SV-GIV 6.25% (1/16), with GI and GII detected in 6.25% (1/16) of the sample. Significant correlation between SV positive cases and water sources was noted (Chapter 4). A partial VP1 was successfully sequenced from 10/16 amplicons, and results showed genotype GI.1 to be the most prevalent (60%; 6/10), followed by 20% of SV-GII.1, and 10% of each SV-GI.3 and SV-GII.3 (Chapter 5). The relatedness of strains detected from non-human host with the detected strains from this study was noted with a concern (Chapters 4 and 5). Conclusion: The presence of SV, and substantial evidence of SV associated with diarrhoeal disease in low income regions was determined. This study defined human SV strains in rural communities from Vhembe district, and therefore outpatients in rural settings are possibly at a risk of the burden of diarrhoeal disease triggered by enteric-viruses among other pathogens. However, reports on SV as an emerging diarrhoeal causative agents in the developing regions are limited. Investigations on the analysis and surveillance of human SV strains in rural settings (at a community or household level) is essential to assess burden of diseases.