Early Detection of the Emerging SARS-CoV-2 BA.2.86 Lineage Through Wastewater Surveillance Using a Mediator Probe PCR Assay — Shenzhen City, Guangdong Province, China, 2023

Du, Chen; ,; Peng, Yuejing; Lyu, Ziquan; Yue, Zhijiao; Fu, Yulin; Yao, Xiangjie; Tang, Jinzhen; Luo, Guixian; Gao, Chenxi; Fang, Shisong; Shi, Xiaolu; Wan, Chengsong; Li, Yinghui; Hu, Qinghua; ,; ,; ,

doi:10.46234/ccdcw2024.063

China CDC Weekly

2024

DOI: 10.46234/ccdcw2024.063

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Early Detection of the Emerging SARS-CoV-2 BA.2.86 Lineage Through Wastewater Surveillance Using a Mediator Probe PCR Assay — Shenzhen City, Guangdong Province, China, 2023

Chen Du,

Yuejing Peng,

Ziquan Lyu

et al.

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Cited by 3 publications

References 16 publications

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Rapid and extensive SARS-CoV-2 Omicron variant infection wave revealed by wastewater surveillance in Shenzhen following the lifting of a strict COVID-19 strategy

Li,

Du,

et al. 2024

Science of The Total Environment

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Rapid and extensive SARS-CoV-2 Omicron variant infection wave revealed by wastewater surveillance in Shenzhen following the lifting of a strict COVID-19 strategy

Li,

Du,

et al. 2024

Science of The Total Environment

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Estimating epidemic trajectories of SARS-CoV-2 and influenza A virus based on wastewater monitoring and a novel machine learning algorithm

Fu,

Zhang,

et al. 2024

Science of The Total Environment

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

Shempela,

Muleya,

Mudenda

et al. 2024

IJMS

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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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Early Detection of the Emerging SARS-CoV-2 BA.2.86 Lineage Through Wastewater Surveillance Using a Mediator Probe PCR Assay — Shenzhen City, Guangdong Province, China, 2023

Cited by 3 publications

References 16 publications

Rapid and extensive SARS-CoV-2 Omicron variant infection wave revealed by wastewater surveillance in Shenzhen following the lifting of a strict COVID-19 strategy

Rapid and extensive SARS-CoV-2 Omicron variant infection wave revealed by wastewater surveillance in Shenzhen following the lifting of a strict COVID-19 strategy

Estimating epidemic trajectories of SARS-CoV-2 and influenza A virus based on wastewater monitoring and a novel machine learning algorithm

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

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