Establishing a national SARS-CoV-2 surveillance network across South Africa to support wastewaterbased genomic and epidemiological monitoring of the COVID pandemic, 2020-2021
Journal of Public Health in Africa
; 13:12, 2022.
Article
in English
| EMBASE | ID: covidwho-2006871
ABSTRACT
Introduction/ Background:
Findings from wastewater-based epidemiology (WBE) surveillance of SARS-CoV-2 are increasingly used to monitor the epidemiology of SARS-CoV-2. We report on the findings from the South African Collaboration COVID-19 Environmental Surveillance System (SACCESS) laboratories and compare these with clinically obtained data.Methods:
Wastewater grab or passive samples and underwent concentration, RNA extraction, reverse-transcriptasepolymerase chain reaction (RT-PCR) detection and quantification of SARS-CoV-2. Following whole genome amplicon-based sequencing, nonsynonymous mutations in the spike protein specific to variants of concern (VOCs) were identified. Quantitative RNA concentrations in genome copies/mL and the read-frequencies of lineagespecific single nucleotide polymorphisms (SNPs) in the spike protein of SARS-CoV-2 were plotted alongside official case load and SARS-Cov-2 lineage distribution by epidemiological week (provided by NICD SARS-CoV-2 epidemiology team and the Centre for Respiratory Diseases and Meningitis of the NICD).Results:
Results from 95 wastewater treatment plants (WWTPs) across 9 provinces and all eight metropolitan areas of South Africa were collected weekly, biweekly or monthly from June 2020-October 2021 illustrate that increases and decreases in SARSCoV- 2 concentrations at all sites corresponded to metro-specific timing of the peak and post-peak decline in clinical cases. Increases in SARS-CoV-2 concentrations consistently preceded increases in clinical cases. In 18 WWTPs genomic analysis detected SNPs corresponding to prevalent VOCs and documented the change from beta to delta variant over the third SARS-CoV-2 wave. Impact Without sufficient evidence that WBE findings correspond with clinical epidemiology and genomic results, public health authorities are often reluctant to use these data to guide decision making. Our findings illustrated that WBE monitoring of SARS-CoV-2 and detection of SNPs specific to SARS-CoV-2 variants correspond with clinical epidemiology and genomic findings.Conclusion:
Wastewater based epidemiology including genotyping should be integrated into SARS-CoV-2 surveillance networks to support decision-making regarding public health interventions to contain SARS-CoV-2. Additional analyses to support interpretation of quantitative and genomic results should be done.
endogenous compound; virus spike protein; amplicon; conference abstract; controlled study; coronavirus disease 2019; decision making; environmental surveillance; gene frequency; genetic association; genotyping; human; meningitis; nonhuman; pandemic; public health; quantitative analysis; respiratory tract disease; RNA extraction; SARS-CoV-2 Delta; Severe acute respiratory syndrome coronavirus 2; single nucleotide polymorphism; South Africa; variant of concern; waste water treatment plant; wastewater-based epidemiology
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Collection:
Databases of international organizations
Database:
EMBASE
Type of study:
Observational study
Language:
English
Journal:
Journal of Public Health in Africa
Year:
2022
Document Type:
Article
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