This report is based on data collected up to 7 June 2024 (week  23 of 2024)

Key highlights:

Wastewater levels, Epidemiological week 48 (2023) – 23(2024)

• From weeks 48-13 the cumulative SARS-CoV-2 levels measured at wastewater treatment works (WWTW) have remained around one log genome copies/ml of wastewater. This has followed on from the increases observed in weeks 31-41, when the cumulative SARS-CoV-2 levels in wastewater at sentinel sites in South Africa showed increases to levels above 2 log (100) genome copies/ml of wastewater, up from below one log copy/ml in epidemiological week 22 (first week in June 2023). From week 45, levels measured below 2 log genome copies/ml of wastewater.
• In weeks 1-6, lower levels were observed nationally, with an increase seen in week 7 and a subsequent decrease in week 8. Levels increased to moderate in Epi week 10. Levels increased to high (above 2 log (100) genome copies/ml) in Epi week 14 and remain high in Epi week 16. Levels dropped slightly to moderate in Epi week 17 and have decreased further in Epi week 19. Levels increased to high (above 2 log (100) genome copies/ml) in Epi week 21 and decreased to moderate in Epi week 23.
• Correlation with syndromic surveillance for influenza-like illness (ILI) and severe acute respiratory infection findings (SARI) is required to determine the clinical and public health significance of ongoing transmission. https://www.nicd.ac.za/diseases-a-z-index/disease-index-covid-19/surveillance-reports/weekly-respiratory-pathogens-surveillance-report-week/

Wastewater genomics, Epidemiological weeks 48 (2023)- 23(2024)

• The Omicron lineage BA.2.86.X (this includes KP.1 and BA.2.86.1), and JN.1.X sub-lineages were the dominant lineages circulating in wastewater samples between January 2024 – May 2024 (Epiweek 1-10).
• In clinical samples, BA.2.86 was also the dominant lineage circulating throughout November 2023 and January 2024, followed by XBB.1.5*, XBB.1.19* and JN.1*.
• The Omicron lineage BA.2.86, JN.1* and Recombinant lineages are circulating in KwaZulu-Natal in eThekwini (in the catchments of Northern and Central WWTWs). In Gauteng, in the City of Johannesburg (in catchments of Northern and Goudkoppies WWTWs), in Ekurhuleni (in the catchments of Olifantsfontein, Vlakplaats, and Hartebeesfontein WWTWs), and the City of Tshwane (in the catchment of Daspoort WWTP) BA.2.86.X and JN.1.X are the dominantly circulating. It is also circulating in Eastern Cape in Buffalo City (in the catchment of Mdantsane WWTW ), in Western Cape, in the City of Cape Town (in the catchment of Borches Quarry WWTW), Free State, in Mangaung (catchments Bloemspruit and Sterkwater WWTWs) and North West (Boitekong). In Limpopo (Musina) and Mpumalanga (Kingstonvale) BA.2.86.X lineage was the main lineage detected.

Interpretation: Ongoing transmission of SARS-CoV-2 due to Omicron lineages including the new lineage BA.2.86 and JN.1  lineages.

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 23  2024)

Wastewater surveillance for SARS-CoV-2 RNA is being undertaken by the South African medical research council (SA-MRC) at additional sites. Click here to view the results https://www.samrc.ac.za/wbe/