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Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1-BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa.
Johnson, Rabia; Mangwana, Noluxabiso; Sharma, Jyoti R; Muller, Christo J F; Malemela, Kholofelo; Mashau, Funanani; Dias, Stephanie; Ramharack, Pritika; Kinnear, Craig; Glanzmann, Brigitte; Viraragavan, Amsha; Louw, Johan; Surujlal-Naicker, Swastika; Nkambule, Sizwe; Webster, Candice; Mdhluli, Mongezi; Gray, Glenda; Mathee, Angela; Preiser, Wolfgang; Vorster, Alvera; Dalvie, Shareefa; Street, Renee.
  • Johnson R; Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
  • Mangwana N; Division of Medical Physiology, Faculty of Medicine and Health Sciences, Centre for Cardio-metabolic Research in Africa, Stellenbosch University, Tygerberg, South Africa.
  • Sharma JR; Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
  • Muller CJF; Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
  • Malemela K; Division of Medical Physiology, Faculty of Medicine and Health Sciences, Centre for Cardio-metabolic Research in Africa, Stellenbosch University, Tygerberg, South Africa.
  • Mashau F; Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
  • Dias S; Division of Medical Physiology, Faculty of Medicine and Health Sciences, Centre for Cardio-metabolic Research in Africa, Stellenbosch University, Tygerberg, South Africa.
  • Ramharack P; Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa.
  • Kinnear C; Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
  • Glanzmann B; Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
  • Viraragavan A; Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
  • Louw J; Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
  • Surujlal-Naicker S; Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
  • Nkambule S; Genomics Centre, South African Medical Research Council, Tygerberg, South Africa.
  • Webster C; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.
  • Mdhluli M; Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
  • Gray G; Genomics Centre, South African Medical Research Council, Tygerberg, South Africa.
  • Mathee A; Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
  • Preiser W; Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa.
  • Vorster A; Scientific Services, Water, and Sanitation Department, City of Cape Town Metropolitan Municipality, Cape Town, South Africa.
  • Dalvie S; Environment and Health Research Unit, South African Medical Research Council, Durban, South Africa.
  • Street R; Environment and Health Research Unit, South African Medical Research Council, Johannesburg, South Africa.
J Infect Dis ; 226(8): 1418-1427, 2022 10 17.
Article in English | MEDLINE | ID: covidwho-2070119
ABSTRACT
This study was one of the first to detect Omicron sublineages BA.4 and BA.5 in wastewater from South Africa. Spearman rank correlation analysis confirmed a strong positive correlation between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA in wastewater samples and clinical cases (r = 0.7749, P < .0001). SARS-CoV-2 viral load detected in wastewater, resulting from the Delta-driven third wave, was significantly higher than during the Omicron-driven fourth wave. Whole-genome sequencing confirmed presence of Omicron lineage defining mutations in wastewater with the first occurrence reported 23 November 2021 (BA.1 predominant). The variant spread rapidly, with prevalence of Omicron-positive wastewater samples rising to >80% by 10 January 2022 with BA.2 as the predominant sublineage by 10 March 2022, whilst on 18 April 2022 BA.4 and BA.5 were detected in selected wastewater sites. These findings demonstrate the value of wastewater-based epidemiology to monitor the spatiotemporal spread and potential origin of new Omicron sublineages.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Variants Limits: Humans Country/Region as subject: Africa Language: English Journal: J Infect Dis Year: 2022 Document Type: Article Affiliation country: Infdis

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Variants Limits: Humans Country/Region as subject: Africa Language: English Journal: J Infect Dis Year: 2022 Document Type: Article Affiliation country: Infdis