Correlating SARS-CoV-2 Variants from Wastewater with Clinical Cases in South Africa

Mukhlid Yousif of Wits Health Consortium (Pty) Limited in South Africa will sequence SARS-CoV-2 in sewage samples collected periodically from 40 wastewater treatment facilities across South Africa for the early detection of potentially dangerous variants to inform public health policies. Genome sequencing using sewage samples can monitor the molecular epidemiology and diversity of circulating SARS-CoV-2 variants, and also identify new variants even before they can be detected in the clinic. They will collect a total of 528 wastewater samples over a twelve-month period and process them for sequencing to identify novel mutations or mutations that are unique to variants-of-concern, especially those not yet reported in Africa. They will also compare these data with sequences of SARS-CoV-2 variants from local COVID-19 patients to support interpretation of wastewater sequencing results. Results will be immediately published online and communicated to provincial and national COVID incident management teams.