Sequence data for enteroviruses detected in both stool specimens and wastewater samples

The purpose of this study was to survey enteroviruses circulating within the Gauteng province of South Africa from January to September 2021. To assess whether EVs were still present during a similar period (2019-2022), the following study was conducted in two parts. In the first part of the study, stool specimens submitted to the National Health Laboratory Service Tshwane Academic Division (NHLS-TAD) laboratory from public hospitals were collected. These specimens were obtained from hospitalised patients with AGE and were collected between 2019 and 2021. The specimens were screened for the presence of EVs using a real-time polymerase chain reaction assay (RT-PCR), after which all EV positive specimens were genotyped using Sanger sequencing and basic local alignment search tool (BLAST) analysis. The second part of the study involved the screening of wastewater samples, taken from four sites in the Gauteng province of South Africa between March 2021 and April 2022, for the presence of EVs. These samples’ nucleic acids were extracted using an automated extraction method and were screened using the same RT-PCR as in the first part of the study. All EV positive samples then underwent next-generation sequencing (NGS) to determine the identity of all EVs in each sample, after which phylogenetic analysis was again performed as in part one. In total 138 stool specimens were screened: 26 specimens from 2019, 64 specimens from 2020, and 48 specimens from 2021.