Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Oct 17;226(8):1418-1427.
doi: 10.1093/infdis/jiac356.

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

Rabia Johnson  1   2 , Noluxabiso Mangwana  1 , Jyoti R Sharma  1   2 , Christo J F Muller  1   2   3 , Kholofelo Malemela  1 , Funanani Mashau  1 , Stephanie Dias  1 , Pritika Ramharack  1   4 , Craig Kinnear  5   6 , Brigitte Glanzmann  4 , Amsha Viraragavan  5 , Johan Louw  1   3 , Swastika Surujlal-Naicker  7 , Sizwe Nkambule  8 , Candice Webster  9 , Mongezi Mdhluli  10 , Glenda Gray  11 , Angela Mathee  9 , Wolfgang Preiser  12 , Alvera Vorster  13 , Shareefa Dalvie  1   14 , Renee Street  8
Affiliations

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

Rabia Johnson et al. J Infect Dis. .

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.

Keywords: 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.

PubMed Disclaimer

Conflict of interest statement

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.

Figures

Figure 1.
Figure 1.
Correlation analysis and quantification of SARS-CoV-2 viral RNA in wastewater. A and B, Positive correlation between SARS-CoV-2 viral RNA per mL of wastewater at 27 Western Cape wastewater treatment plants and positive clinical case data. Results were expressed as standard deviation (SD). Clinical data was sourced from the publicly available South African Western Cape Government's Department of Health COVID-19 Response dashboard (https://coronavirus.westerncape.gov.za/COVID-19-dashboard). Abbreviations: gc, genome copies; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.
Figure 2.
Figure 2.
Temporal dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in municipal wastewater superimposed on the epidemiological clinical data. Trends in SARS-CoV-2 viral RNA from (A) City of Cape Town and (B) Breede Valley superimposed on clinical case data that tested positive for SARS-CoV-2 (area graphs). Results were expressed as standard deviation (SD). Line graphs represent SARS-CoV-2 gc/mL of RNA concentration in municipal wastewater measured with qRT-PCR using the N1 and N2 primer pairs. Clinical data was sourced from the publicly available South African Western Cape Government's Department of Health COVID-19 Response dashboard (https://coronavirus.westerncape.gov.za/COVID-19-dashboard). Abbreviations: gc, genome copies; qRT-PCR, quantitative reverse transcription polymerase chain reaction; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.
Figure 3.
Figure 3.
Temporal analysis of SARS-CoV-2 VOCs in wastewater treatment plants in the Western Cape. A, Viral load in Delta-driven third wave versus Omicron-driven fourth wave. B, Data obtained from SNP genotyping and genomic sequencing data as classified by Pangolin (version 3.1.20, lineage version 28 February 2022; https://pangolin.cog-uk.io/) and mutation detection as classified by most likely lineage to a given SARS-CoV-2 genome sequence ** P = .006. Results were expressed as standard deviation (SD). Abbreviations: gc, genome copies; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; SNP, single-nucleotide polymorphism; VOC, variant of concern.
Figure 4.
Figure 4.
Spatiotemporal analysis of variants of concern in Breede Valley area Omicron and its sublineages. Pangolin classified sublineages as classified by key amino acid mutations of the Omicron variant in (A) Rawsonville, (B) Touws River, and (C) Worcester wastewater treatment plants, classified by Pangolin https://pangolin.cog-uk.io/ version 4.0.5, lineages version 9 March 2022. Abbreviations: gc, genome copies; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.
Figure 5.
Figure 5.
City of Cape Town wastewater temporal trends: (A) Athlone, (B) Mitchells Plein, (C) Macassar, and (D) Wesfleur WWTPs. Pangolin classified sublineages by key amino acid mutations of the Omicron variant in WWTP in the City of Cape Town, classified as per Pangolin https://pangolin.cog-uk.io/ version 4.0.5, lineages version 9 March 2022. Abbreviations: gc, genome copy; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; WWTP, wastewater treatment plant.
Figure 6.
Figure 6.
City of Cape Town wastewater temporal trends: (A) Gordons Bay, (B) Wildvoelvlei, (C) Camps Bay, and (D) Melkbosstrand WWTPs. Pangolin classified sublineages by key amino acid mutations of the Omicron variant in WWTP in the City of Cape Town, classified as per Pangolin https://pangolin.cog-uk.io/ version 4.0.5, lineages version 9 March 2022. Abbreviations: gc, genome copy; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; WWTP, wastewater treatment plant.
See this image and copyright information in PMC

References

    1. Tong C, Shi W, Zhang A, Shi Z. Tracking and controlling the spatiotemporal spread of SARS-CoV-2 Omicron variant in South Africa. Travel Med Infect Dis 2022; 46:102252. - PMC - PubMed
    1. World Health Organization . Update on Omicron, 2021. https://www.who.int/news/item/28-11-2021-update-on-omicron. [Accessed: 16 March 2022].
    1. Khandia R, Singhal S, Alqahtani T, et al. . Emergence of SARS-CoV-2 Omicron (B. 1.1. 529) variant, salient features, high global health concerns and strategies to counter it amid ongoing COVID-19 pandemic. Environ Res 2022; 209:112816. - PMC - PubMed
    1. Gagne M, Moliva JI, Foulds KE, et al. . mRNA-1273 or mRNA-Omicron boost in vaccinated macaques elicits comparable B cell expansion, neutralizing antibodies and protection against Omicron. Cell 185(9):1556–15712022. - PMC - PubMed
    1. Iuliano AD, Brunkard JM, Boehmer TK, et al. . Trends in disease severity and health care utilization during the early Omicron variant period compared with previous SARS-CoV-2 high transmission periods—United States, December 2020–January 2022. MMWR Morb Mortal Wkly Rep 2022; 71:146–52. - PMC - PubMed

Publication types