Multiple novel human norovirus recombinants identified in wastewater in Pretoria, South Africa by next-generation sequencing

Show simple item record Mabasa, V.V. Van Zyl, W.B. Ismail, Arshad Allam, Mushal Taylor, Maureen B. Mans, Janet 2023-03-17T05:38:28Z 2023-03-17T05:38:28Z 2022-12-07
dc.description SUPPLEMENTARY MATERIAL : TABLE S1: Norovirus GI and GII viruses and their respective merged reads from sequencing pools; TABLE S2: Summary of putative novel GI and GII recombination breakpoints from strains identified in this study. en_US
dc.description.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. en_US
dc.description.department Medical Virology en_US
dc.description.librarian am2023 en_US
dc.description.sponsorship The National Health Laboratory Service Research Trust Grant. en_US
dc.description.uri en_US
dc.identifier.citation Mabasa, V.V.; Van Zyl, W.B.; Ismail, A.; Allam, M.; Taylor, M.B.; Mans, J. Multiple Novel Human Norovirus Recombinants Identified in Wastewater in Pretoria, South Africa by Next-Generation Sequencing. Viruses 2022, 14, 2732. en_US
dc.identifier.issn 1999-4915 (online)
dc.identifier.other 10.3390/v14122732
dc.language.iso en en_US
dc.publisher MDPI en_US
dc.rights © 2022 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. en_US
dc.subject Norovirus en_US
dc.subject Recombinants en_US
dc.subject Wastewater en_US
dc.subject Next-generation sequencing (NGS) en_US
dc.subject Pretoria, South Africa en_US
dc.subject Genogroup II genotype 4 (GII.4) en_US
dc.title Multiple novel human norovirus recombinants identified in wastewater in Pretoria, South Africa by next-generation sequencing en_US
dc.type Article en_US

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