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

This report is based on data collected up to 15 September 2023 (week 37 of 2023)

Key highlights:

Wastewater levels, Epidemiological weeks 33-37

  • From weeks 33-37, the cumulative SARS-CoV-2 levels measured at wastewater treatment works (WWTW) has remained around 2 log (100) genome copies/ml of wastewater. This has followed on from the increases observed in weeks 31-33, 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).
  •  In weeks 33-37 increases and/or higher levels have been seen in Gauteng (Daspoort WWTW) and Cape Town (in Borcheds Quarry WWTW and Zandevleit WWTW).
  • 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 31-35 (No new data since the last report)

  • No new genomics results were obtained for week 35.
  • From weeks 31-33, samples from 9 of 16 WWTP have genomic sequencing results, as SARS-CoV-2 sequencing coverage in the remaining samples are too low for meaningful interpretation.
  • Omicron lineages XBB.1.5 followed by XBB.1.16 and XBB sub-lineages remain the dominant lineages circulating in clinical samples in June, July and August 2023
  • • The Omicron lineage BA.2.86 is evidently circulating in KwaZulu-Natal in eThekwini (in the catchments of Northern and Central WWTPs), and in Gauteng, in the City of Johannesburg (catchment of Northern WWTP) and the City of Tshwane (in Rooiwal WWTP catchment).
  • • The Omicron lineages EG.5 and EG.5.1 are evidently present in City of Johannesburg (Northern WWTP) as the mutation F456L, which is signature to this lineage has been found in Northern Gauteng in epi week 31 (03 August, 2023).

Interpretation: Ongoing transmission of SARS-CoV-2 due to Omicron lineages including the new lineages BA.2.86 and EG.5, and EG.5.1 at higher levels than June 2023.

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

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 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)