Abstract:
The genogroup II genotype 4 (GII.4) noroviruses are a major cause of viral gastroenteritis.
Since the emergence of the Sydney_2012 variant, no novel norovirus GII.4 variants have been
reported. The high diversity of noroviruses and periodic emergence of novel strains necessitates
continuous global surveillance. The aim of this study was to assess the diversity of noroviruses in
selected wastewater samples from Pretoria, South Africa (SA) using amplicon-based next-generation
sequencing (NGS). Between June 2018 and August 2020, 200 raw sewage and final effluent samples
were collected fortnightly from two wastewater treatment plants in Pretoria. Viruses were recovered
using skimmed milk flocculation and glass wool adsorption-elution virus recovery methods
and screened for noroviruses using a one-step real-time reverse-transcription PCR (RT-PCR). The
norovirus BC genotyping region (570–579 bp) was amplified from detected norovirus strains and
subjected to Illumina MiSeq NGS. Noroviruses were detected in 81% (162/200) of samples. The
majority (89%, 89/100) of raw sewage samples were positive for at least one norovirus, compared
with 73% (73/100) of final effluent samples. Overall, a total of 89 different GI and GII RdRp-capsid
combinations were identified, including 51 putative novel recombinants, 34 previously reported
RdRp-capsid combinations, one emerging novel recombinant and three Sanger-sequencing confirmed
novel recombinants.
