WASTEWATER-BASED EPIDEMIOLOGY FOR SARS-COV-2 IN SOUTH AFRICA INCLUDING WASTEWATER GENOMICS

This report is based on data collected up to 10 May 2024 (week  19 of 2024)

Key highlights:

Wastewater levels, Epidemiological week 48 (2023) – 19(2024)

  • From weeks 48-52 the cumulative SARS-CoV-2 levels measured at wastewater treatment works (WWTW) has 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 Epi weeks 1-6 lower levels were observed nationally, with an increase to above 2 log (100) genome copies/ml seen in week 7 and a subsequent decrease to about one log genome copies/ml of wastewater 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 drop slightly to moderate in Epi week 17 and have decrease further in Epi week 19.
  • 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)-17 (2024)

  • Omicron lineage BA.2.86.X, and JN.1.X sub-lineages were the dominant lineages circulating in wastewater samples between January 2024 – April 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 19  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/  

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 52 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 50 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 48 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 46 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 45 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 44 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 43 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 42 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 41 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 39 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 37 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 36 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 35 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 33 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 32 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 30 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 29 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 27 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 33 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 32 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 30 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 29 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 27 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 25 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 23 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 20 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 18 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 17 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 16 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 15 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 13 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 11 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 10 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 9 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 8 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 7 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 6 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 5 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 4 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 3 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 51 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 49 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 48 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 47 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 46 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 45 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 44 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 43 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 42 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 41 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 40 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 39 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 38 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 37 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 35 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 34 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 33 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 32 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 31 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 30 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 28 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 27 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 26 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 25 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 24 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 23 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 22 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 21 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 20 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 19 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 18 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 17 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 16 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 15 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 14 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa INCLUDING GENOMICS (week 12 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 11 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 10 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 9 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 8 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 7 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 6 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 5 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 3 2022)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 33 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 32 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 30 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 29 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 27 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 25 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 23 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 20 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 18 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 17 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 16 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 15 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 13 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 11 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 10 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 9 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 8 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 7 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 6 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 5 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 4 2023)

Wastewater-based epidemiology for SARS-CoV-2 surveillance in South Africa (week 3 2023)