Assessment of norovirus diversity and viability in wastewater from Pretoria, South Africa (SA), using next-generation sequencing (NGS) and advanced molecular assays

The study investigated norovirus diversity in wastewater. This study aimed to assess norovirus diversity and viability in wastewater from Pretoria, South Africa (SA), using next-generation sequencing (NGS) and advanced molecular assays. Between June 2018 and August 2020, 200 samples comprising raw sewage and final effluent were collected biweekly from two wastewater treatment works (WWTWs). Viruses were concentrated using skimmed milk flocculation and glass wool adsorption-elution methods. Noroviruses were detected in 81% of samples, with a higher positivity rate in raw sewage (89%) compared to final effluent (73%). Amplicon-based NGS targeting the norovirus BC genotyping region revealed 89 distinct genogroup (G) I and GII RNA-dependent RNA polymerase-capsid combinations, including 51 putative novel recombinants and one emerging novel strain, emphasizing the significant genetic variability present in wastewater.