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.

COVID-19 / epidemiology Humans Prevalence RNA, Viral / genetics SARS-CoV-2 / genetics South Africa / epidemiology Wastewater
B.1.5.9 (Omicron) B.1.617.2 (Delta) lineages BA.1 BA.2 BA.3 SARS-CoV-2 and BA.5 genotyping wastewater-based epidemiology

Journal

The Journal of infectious diseases
ISSN: 1537-6613
Titre abrégé: J Infect Dis
Pays: United States
ID NLM: 0413675

Informations de publication

Date de publication:
17 10 2022
Historique:
received: 24 05 2022
accepted: 24 08 2022
pubmed: 27 8 2022
medline: 19 10 2022
entrez: 26 8 2022
Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1093/infdis/jiac356 PMID: 36017801 PMC: PMC9574669
pubmed: 36017801
pii: 6677087
doi: 10.1093/infdis/jiac356
pmc: PMC9574669
doi:

Substances chimiques

RNA, Viral 0
Waste Water 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1418-1427

Informations de copyright

© The Author(s) 2022. Published by Oxford University Press on behalf of Infectious Diseases Society of America.

Déclaration de conflit d'intérêts

Potential conflicts of interest. All authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed. The authors have no conflicts of interest to declare.

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Auteurs

Rabia Johnson (R)

Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
Division of Medical Physiology, Faculty of Medicine and Health Sciences, Centre for Cardio-metabolic Research in Africa, Stellenbosch University, Tygerberg, South Africa.

Noluxabiso Mangwana (N)

Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.

Jyoti R Sharma (JR)

Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
Division of Medical Physiology, Faculty of Medicine and Health Sciences, Centre for Cardio-metabolic Research in Africa, Stellenbosch University, Tygerberg, South Africa.

Christo J F Muller (CJF)

Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
Division of Medical Physiology, Faculty of Medicine and Health Sciences, Centre for Cardio-metabolic Research in Africa, Stellenbosch University, Tygerberg, South Africa.
Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa.

Kholofelo Malemela (K)

Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.

Funanani Mashau (F)

Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.

Stephanie Dias (S)

Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.

Pritika Ramharack (P)

Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.

Craig Kinnear (C)

Genomics Centre, South African Medical Research Council, Tygerberg, South Africa.
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.

Brigitte Glanzmann (B)

Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.

Amsha Viraragavan (A)

Genomics Centre, South African Medical Research Council, Tygerberg, South Africa.

Johan Louw (J)

Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa.

Swastika Surujlal-Naicker (S)

Scientific Services, Water, and Sanitation Department, City of Cape Town Metropolitan Municipality, Cape Town, South Africa.

Sizwe Nkambule (S)

Environment and Health Research Unit, South African Medical Research Council, Durban, South Africa.

Candice Webster (C)

Environment and Health Research Unit, South African Medical Research Council, Johannesburg, South Africa.

Mongezi Mdhluli (M)

Chief Research Operations Office, South African Medical Research Council, Tygerberg, South Africa.

Glenda Gray (G)

Office of the President, South African Medical Research Council, Tygerberg, South Africa.

Angela Mathee (A)

Environment and Health Research Unit, South African Medical Research Council, Johannesburg, South Africa.

Wolfgang Preiser (W)

Division of Medical Virology, National Health Laboratory Services Tygerberg Hospital, and Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.

Alvera Vorster (A)

Central Analytical Facilities, Stellenbosch University, Cape Town, South Africa.

Shareefa Dalvie (S)

Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa.
Department of Psychiatry and Neuroscience Institute, South African Medical Research Council, Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa.

Renee Street (R)

Environment and Health Research Unit, South African Medical Research Council, Durban, South Africa.

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