viruses Article Prevalence and Genetic Characterisation of Human Sapovirus from Children with Diarrhoea in the Rural Areas of Vhembe District, South Africa, 2017–2020 Mpho Magwalivha * , Jean-Pierre Kabue Ngandu , Afsatou Ndama Traore and Natasha Potgieter   Citation: Magwalivha, M.; Ngandu, J.-P.K.; Traore, A.N.; Potgieter, N. Prevalence and Genetic Characterisation of Human Sapovirus from Children with Diarrhoea in the Rural Areas of Vhembe District, South Africa, 2017–2020. Viruses 2021, 13, 393. https://doi.org/10.3390/ v13030393 Academic Editor: Susana Guix Received: 27 January 2021 Accepted: 24 February 2021 Published: 1 March 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). Department of Microbiology, School of Mathematical and Natural Sciences, University of Venda, Thohoyando 0950, South Africa; Kabue.Ngandu@univen.ac.za (J.-P.K.N.); Afsatou.Traore@univen.ac.za (A.N.T.); natasha.potgieter@univen.ac.za (N.P.) * Correspondence: mpho.magwalivha@univen.ac.za Abstract: Diarrhoeal disease is considered an important cause of morbidity and mortality in develop- ing areas, and a large contributor to the burden of disease in children younger than five years of age. This study investigated the prevalence and genogroups of human sapovirus (SV) in children ≤5 years of age in rural communities of Vhembe district, South Africa. Between 2017 and 2020, a total of 284 stool samples were collected from children suffering with diarrhoea (n = 228) and from children without diarrhoea (n = 56). RNA extraction using Boom extraction method, and screening for SV using real-time PCR were done in the lab. Positive samples were subjected to conventional RT-PCR targeting the capsid fragment. Positive sample isolates were genotyped using Sanger sequencing. Overall SV were detected in 14.1% (40/284) of the stool samples (16.7% (38/228) of diarrhoeal and 3.6% (2/56) of non-diarrhoeal samples). Significant correlation between SV positive cases and wa- ter sources was noted. Genogroup-I was identified as the most prevalent strain comprising 81.3% (13/16), followed by SV-GII 12.5% (2/16) and SV-GIV 6.2% (1/16). This study provides valuable data on prevalence of SV amongst outpatients in rural and underdeveloped communities, and highlights the necessity for further monitoring of SV circulating strains as potential emerging strains. Keywords: hospitalized patients; outpatients; rural communities; sapovirus 1. Introduction Diarrhoeal diseases are recognized as the third leading cause of death among children under five years of age in South Africa (SA) [1,2]. The effects of poor sanitation and hygiene practices, quality of supplied water may play an important role in the burden of diarrhoeal disease which is a major concern in developing countries [1,3,4]. Viral infections may present from asymptomatic to relatively mild diarrhoea with a headache and fever, to severe watery diarrhoea accompanied with abdominal cramps [5]. Sapovirus is an enteric virus, and is recognized as a public health problem causing acute gastroenteritis in people of all age groups globally, and it also causes outbreaks in semi-closed settings, like orphanages and elderly care facilities [6]. Sapovirus has been asso- ciated with persistence vomiting suggested to possibly cause gastroenteritis in humans [7]. The increase of acute gastroenteritis associated with sapovirus (SV) has been reported and recognized as a major public health problem particularly in developing countries [8,9]. It is documented that after the successful deployment of the Rotavirus vaccine, SVs have emerged as the second most commonly etiological virus behind Norovirus in children with acute diarrhoea [9]. In addition, a longitudinal study by MAL-ED reported SV as a notable second highest attributable incidence of diarrhoea within the enrolled rural community in South Africa [10]. Sapovirus is a single-stranded, positive-sense RNA virus, with three open reading frames (ORFs) identified as ORF1, ORF2, and ORF3, of which ORF1 region is labelled Viruses 2021, 13, 393. https://doi.org/10.3390/v13030393 https://www.mdpi.com/journal/viruses