Tracking the circulating SARS-CoV-2 variant of concern in South Africa using wastewater-based epidemiology
Abstract This study uses wastewater-based epidemiology (WBE) to rapidly and, through targeted surveillance, track the geographical distribution of SARS-CoV-2 variants of concern (Alpha, Beta and Delta) within 24 wastewater treatment plants (WWTPs) in the Western Cape of South Africa. Information obt...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-01-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-05110-4 |
| _version_ | 1818954744759058432 |
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| author | Rabia Johnson Jyoti R. Sharma Pritika Ramharack Noluxabiso Mangwana Craig Kinnear Amsha Viraragavan Brigitte Glanzmann Johan Louw Nada Abdelatif Tarylee Reddy Swastika Surujlal-Naicker Sizwe Nkambule Nomfundo Mahlangeni Candice Webster Mongezi Mdhluli Glenda Gray Angela Mathee Wolfgang Preiser Christo Muller Renee Street |
| author_facet | Rabia Johnson Jyoti R. Sharma Pritika Ramharack Noluxabiso Mangwana Craig Kinnear Amsha Viraragavan Brigitte Glanzmann Johan Louw Nada Abdelatif Tarylee Reddy Swastika Surujlal-Naicker Sizwe Nkambule Nomfundo Mahlangeni Candice Webster Mongezi Mdhluli Glenda Gray Angela Mathee Wolfgang Preiser Christo Muller Renee Street |
| author_sort | Rabia Johnson |
| collection | DOAJ |
| description | Abstract This study uses wastewater-based epidemiology (WBE) to rapidly and, through targeted surveillance, track the geographical distribution of SARS-CoV-2 variants of concern (Alpha, Beta and Delta) within 24 wastewater treatment plants (WWTPs) in the Western Cape of South Africa. Information obtained was used to identify the circulating variant of concern (VOC) within a population and retrospectively trace when the predominant variant was introduced. Genotyping analysis of SARS-CoV-2 showed that 50% of wastewater samples harbored signature mutations linked to the Beta variant before the third wave, with the Delta variant absent within the population. Over time, the prevalence of the beta variant decreased steadily. The onset of the third wave resulted in the Delta variant becoming the predominant variant, with a 100% prevalence supporting the theory that the Delta variant was driving the third wave. In silico molecular docking analysis showed that the signature mutations of the Delta variant increased binding to host proteins, suggesting a possible molecular mechanism that increased viral infectivity of the Delta variant. |
| first_indexed | 2024-12-20T10:26:55Z |
| format | Article |
| id | doaj.art-cd80a41e22774012a8473a994b729523 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-20T10:26:55Z |
| publishDate | 2022-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-cd80a41e22774012a8473a994b7295232022-12-21T19:43:49ZengNature PortfolioScientific Reports2045-23222022-01-0112111210.1038/s41598-022-05110-4Tracking the circulating SARS-CoV-2 variant of concern in South Africa using wastewater-based epidemiologyRabia Johnson0Jyoti R. Sharma1Pritika Ramharack2Noluxabiso Mangwana3Craig Kinnear4Amsha Viraragavan5Brigitte Glanzmann6Johan Louw7Nada Abdelatif8Tarylee Reddy9Swastika Surujlal-Naicker10Sizwe Nkambule11Nomfundo Mahlangeni12Candice Webster13Mongezi Mdhluli14Glenda Gray15Angela Mathee16Wolfgang Preiser17Christo Muller18Renee Street19Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC)Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC)Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC)Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC)Genomics Centre, South African Medical Research Council (SAMRC)Genomics Centre, South African Medical Research Council (SAMRC)Genomics Centre, South African Medical Research Council (SAMRC)Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC)Biostatistics Research Unit, South African Medical Research Council (SAMRC)Biostatistics Research Unit, South African Medical Research Council (SAMRC)Scientific Services, Water and Sanitation Department, City of Cape Town Metropolitan MunicipalityEnvironment and Health Research Unit, South African Medical Research Council (SAMRC)Environment and Health Research Unit, South African Medical Research Council (SAMRC)Environment and Health Research Unit, South African Medical Research Council (SAMRC)Office of the President, South African Medical Research CouncilOffice of the President, South African Medical Research CouncilEnvironment and Health Research Unit, South African Medical Research Council (SAMRC)Division of Medical Virology at NHLS Tygerberg Hospital and Faculty of Medicine and Health Sciences, Stellenbosch UniversityBiomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC)Environment and Health Research Unit, South African Medical Research Council (SAMRC)Abstract This study uses wastewater-based epidemiology (WBE) to rapidly and, through targeted surveillance, track the geographical distribution of SARS-CoV-2 variants of concern (Alpha, Beta and Delta) within 24 wastewater treatment plants (WWTPs) in the Western Cape of South Africa. Information obtained was used to identify the circulating variant of concern (VOC) within a population and retrospectively trace when the predominant variant was introduced. Genotyping analysis of SARS-CoV-2 showed that 50% of wastewater samples harbored signature mutations linked to the Beta variant before the third wave, with the Delta variant absent within the population. Over time, the prevalence of the beta variant decreased steadily. The onset of the third wave resulted in the Delta variant becoming the predominant variant, with a 100% prevalence supporting the theory that the Delta variant was driving the third wave. In silico molecular docking analysis showed that the signature mutations of the Delta variant increased binding to host proteins, suggesting a possible molecular mechanism that increased viral infectivity of the Delta variant.https://doi.org/10.1038/s41598-022-05110-4 |
| spellingShingle | Rabia Johnson Jyoti R. Sharma Pritika Ramharack Noluxabiso Mangwana Craig Kinnear Amsha Viraragavan Brigitte Glanzmann Johan Louw Nada Abdelatif Tarylee Reddy Swastika Surujlal-Naicker Sizwe Nkambule Nomfundo Mahlangeni Candice Webster Mongezi Mdhluli Glenda Gray Angela Mathee Wolfgang Preiser Christo Muller Renee Street Tracking the circulating SARS-CoV-2 variant of concern in South Africa using wastewater-based epidemiology Scientific Reports |
| title | Tracking the circulating SARS-CoV-2 variant of concern in South Africa using wastewater-based epidemiology |
| title_full | Tracking the circulating SARS-CoV-2 variant of concern in South Africa using wastewater-based epidemiology |
| title_fullStr | Tracking the circulating SARS-CoV-2 variant of concern in South Africa using wastewater-based epidemiology |
| title_full_unstemmed | Tracking the circulating SARS-CoV-2 variant of concern in South Africa using wastewater-based epidemiology |
| title_short | Tracking the circulating SARS-CoV-2 variant of concern in South Africa using wastewater-based epidemiology |
| title_sort | tracking the circulating sars cov 2 variant of concern in south africa using wastewater based epidemiology |
| url | https://doi.org/10.1038/s41598-022-05110-4 |
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