Sewage surveillance of SARS-CoV-2 at student campus residences in the Western Cape, South Africa

Abstract

The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic capacity is limited in defined communities, posing a challenge in tracking and tracing new infections. Monitoring student residences, which are considered infection hotspots, with targeted wastewater surveillance is crucial. This study evaluated the efficacy of SARS-CoV-2 targeted wastewater surveillance for outbreak mitigation at Stellenbosch University's student residences in South Africa. Using torpedo-style passive sampling devices, wastewater samples were collected biweekly from manholes at twelve Stellenbosch University Tygerberg (SUT) campus and Stellenbosch University-Main (SUM) campus student residences. The surveillance led to an early warning detection of SARS-CoV-2 presence on campus, followed by an informed management strategy leading to restriction of student activities on campus and a delay in the onset of the third wave that was experienced throughout the country. Moreover, the study highlighted the extent of possible infections at defined locations even when a low number of confirmed coronavirus disease 2019 (COVID-19) cases were reported. The study also tracked the surge of the Delta and Omicron variants in the student residences using the Thermo Fisher TaqMan® RT-qPCR genotyping assay.

Keywords: COVID-19; Institution; Near-source WBE; Passive sampling; SARS-CoV-2; Student campus residences; Wastewater; Wastewater-based epidemiology.

Graphical abstract

Fig. 1

Map representing Stellenbosch University's two major campuses. Stellenbosch University's main campus and Stellenbosch University Tygerberg medical campus. Suburb shapefiles were obtained from the City of Cape Town open data portal. Coordinates for each WWTP were verified using Google Earth. All maps were produced using ArcGIS 10.6.1.

Fig. 2

Temporal change in viral RNA genome copies per millilitre of the N-gene SARS-CoV-2 targets at the Stellenbosch University campuses superimposed with 7-day moving average clinical cases for the respective districts during the period of the current study. The 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). A) Stellenbosch University Tygerberg campus wastewater data (line graph) with 7-day moving average of Tygerberg subdistrict moving average clinical cases of SARS-CoV-2. B) Stellenbosch University Main campus wastewater data (line graph) with a 7-day moving average of Cape Winelands district moving average clinical cases of SARS-CoV-2. I) Yellow shade represents the beginning of the surveillance and the introduction of the Delta variant (reduction of student campus activity) II) Red shade represents the period after recess when students had moved back to their residences III) Green shade represents a period where wastewater viral load and reported cases were low.

Fig. 3

Correlation of Stellenbosch University's residence wastewater viral load to 7-day moving average clinical case data in the respective districts. A) Correlation of SUT campus wastewater data to Tygerberg sub-district B) Correlation of SUM campus wastewater data to Cape Winelands district.

Fig. 4

Mutation frequency linked to two VOCs at the Stellenbosch University Tygerberg campus. (A) Mutations characterizing Beta variants, they include N501Y, K414N and E484K. (B) Mutations characterizing the Delta variant which includes L425R and P681R.

Fig. 5

Mutation frequency linked to two VOCs at the Stellenbosch University Main campus. (A) Mutations characterizing Beta variants, they include N501Y, K414N and E484K. (B) Mutations characterizing the Delta variant which includes L425R and P681.

Fig. 6

Stellenbosch University wastewater temporal analysis of SARS-CoV-2 VOCs overlayed with Western Cape's genomic sequencing data sourced from the publicly available GISAID presented by National Institute for communicable diseases (https://www.nicd.ac.za/diseases-a-z-index/disease-index-covid-19/sars-cov-2-genomic-surveillance-update/). A) Stellenbosch University Tygerberg campus B) Stellenbosch University Main campus.