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. 2024 Aug 14;25(16):8839.
doi: 10.3390/ijms25168839.

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

Doreen Mainza Shempela  1 , Walter Muleya  2 , Steward Mudenda  3 , Victor Daka  4 , Jay Sikalima  1 , Mapeesho Kamayani  1 , Dickson Sandala  1 , Chilufya Chipango  1 , Kapina Muzala  5 , Kunda Musonda  5 , Joseph Yamweka Chizimu  5 , Chilufya Mulenga  5 , Otridah Kapona  5 , Geoffrey Kwenda  6 , Maisa Kasanga  7 , Michael Njuguna  8 , Fatim Cham  8 , Bertha Simwaka  8 , Linden Morrison  8 , John Bwalya Muma  9 , Ngonda Saasa  9 , Karen Sichinga  1 , Edgar Simulundu  10 , Roma Chilengi  5
Affiliations

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

Doreen Mainza Shempela et al. Int J Mol Sci. .

Abstract

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.

Keywords: COVID-19; SARS-CoV-2; Zambia; early warning; surveillance; wastewater.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Positivity trends of SARS-CoV-2 in wastewater over the data collection period (October 2023 to December 2023).
Figure 2
Figure 2
SARS-CoV-2 positivity trends in wastewater and clinical cases.
Figure 3
Figure 3
SARS-CoV-2 variants detected from wastewater samples per study sites. The key for sampling sites abbreviations is as follows: CHP5—Chipata Pump Station; CMPP7—Chipata Motel Ponds; KA—Kalulushi; LTP8—Lubuto; MDP10—Mindolo; NEB3,4,6,9—Nkana East; NES5—Nkana East treatment plant; OKP3—Old Kanini.
Figure 4
Figure 4
SARS-CoV-2 variants isolated per sampling period. The key for sampling sites abbreviations is as follows: CHP5—Chipata Pump Station; CMPP7—Chipata Motel Ponds; KA—Kalulushi treatment plant; LTP8—Lubuto treatment plant; MDP10—Mindolo Ponds; NEB3,4,6—Nkana East treatment plant; NEP9—Nkana East treatment plant; NES5—Nkana East treatment plant; OKP3—Old Kanini treatment plant.
Figure 5
Figure 5
Sequencing of SARS-CoV-2 results comparing wastewater-based surveillance (WWBS) variants (blue shade) versus reported Omicron subvariants in clinical cases.
Figure 6
Figure 6
Maximum likelihood phylogenetic analysis of SARS-CoV-2. Sequences generated in this study are highlighted in black. The tree scale indicates the number of nucleotide substitutions per site.
Figure 7
Figure 7
Geographical map showing sampling sites for (A) Copperbelt and (B) Eastern provinces of Zambia. The red pins with black circles represent eight sampling sites with nine and seven collections while the black pin with a light-yellow circle represent one site with one collection.
See this image and copyright information in PMC

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Grants and funding

This research received no external funding.

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