Wastewater Surveillance of SARS-CoV-2 in Zambia: An Early Warning Tool

Wastewater Surveillance of SARS-CoV-2 in Zambia: An Early Warning Tool

Wastewater-based surveillance has emerged as an important method for monitoring the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This study investigated the presence of SARS-CoV-2 in wastewater in Zambia. We conducted a longitudinal study in the Copperbelt and Eastern provinces of Z...

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Bibliographic Details
Published in:International journal of molecular sciences Vol. 25; no. 16; p. 8839
Main Authors: Shempela, Doreen Mainza, Muleya, Walter, Mudenda, Steward, Daka, Victor, Sikalima, Jay, Kamayani, Mapeesho, Sandala, Dickson, Chipango, Chilufya, Muzala, Kapina, Musonda, Kunda, Chizimu, Joseph Yamweka, Mulenga, Chilufya, Kapona, Otridah, Kwenda, Geoffrey, Kasanga, Maisa, Njuguna, Michael, Cham, Fatim, Simwaka, Bertha, Morrison, Linden, Muma, John Bwalya, Saasa, Ngonda, Sichinga, Karen, Simulundu, Edgar, Chilengi, Roma
Format: Journal Article
Language:English
Published: Switzerland MDPI AG 14-08-2024
MDPI
Subjects:
Asymptomatic
COVID-19
COVID-19 - epidemiology
COVID-19 - virology
Disease transmission
early warning
Epidemiology
Genomes
Health surveillance
Humans
Longitudinal Studies
Mutation
Pandemics
Phylogenetics
Phylogeny
Ribonucleic acid
RNA
SARS-CoV-2
SARS-CoV-2 - genetics
SARS-CoV-2 - isolation & purification
Severe acute respiratory syndrome coronavirus 2
surveillance
Trends
wastewater
Wastewater - virology
Whole Genome Sequencing - methods
Zambia
Zambia - epidemiology
Zambia
COVID-19
SARS-CoV-2
wastewater
Zambia
surveillance
early warning
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Summary:Wastewater-based surveillance has emerged as an important method for monitoring the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This study investigated the presence of SARS-CoV-2 in wastewater in Zambia. We conducted a longitudinal study in the Copperbelt and Eastern provinces of Zambia from October 2023 to December 2023 during which 155 wastewater samples were collected. The samples were subjected to three different concentration methods, namely bag-mediated filtration, skimmed milk flocculation, and polythene glycol-based concentration assays. Molecular detection of SARS-CoV-2 nucleic acid was conducted using real-time Polymerase Chain Reaction (PCR). Whole genome sequencing was conducted using Illumina COVIDSEQ assay. Of the 155 wastewater samples, 62 (40%) tested positive for SARS-CoV-2. Of these, 13 sequences of sufficient length to determine SARS-CoV-2 lineages were obtained and 2 sequences were phylogenetically analyzed. Various Omicron subvariants were detected in wastewater including BA.5, XBB.1.45, BA.2.86, and JN.1. Some of these subvariants have been detected in clinical cases in Zambia. Interestingly, phylogenetic analysis positioned a sequence from the Copperbelt Province in the B.1.1.529 clade, suggesting that earlier Omicron variants detected in late 2021 could still be circulating and may not have been wholly replaced by newer subvariants. This study stresses the need for integrating wastewater surveillance of SARS-CoV-2 into mainstream strategies for monitoring SARS-CoV-2 circulation in Zambia.
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ISSN:1661-6596
1422-0067
1422-0067
DOI:10.3390/ijms25168839