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A Retrospective Analysis of Wastewater Confirms Dominant Circulation of SARS-CoV-2 Delta Variant in Nairobi, Kenya, between April 2021 and August 2021

引用

American Journal of Molecular Biology 2022年第3期12卷 109-121页

作者： Patson Sichamba Fred Wamunyokoli Peter Borus Rosemary Nzunza Opanda Silvanos Samwel Symekher Samoel Ashimosi Khamadi Janet Majanja Meshack Wadegu Esther Chitechi Benlick Mwangi Evans Komen Stephen Ombija wallace dimbuson bulimo Pan African University Institute for Basic Sciences Technology and Innovation (PAUSTI) Nairobi Kenya Jomo Kenyatta University of Agriculture and Technology (JKUAT) Nairobi Kenya Kenya Medical Research Institute Centre for Virus Research Nairobi Kenya

Wastewater surveillance has been applied in various parts of the world to monitor the introduction and transmissions of SARS-CoV-2 variants in a population. The knowledge of SARS-CoV-2 variants circulating in a population is critical to COVID-19 management and timing of the application of public health countermeasures. Contrary to the routine clinical surveillance of SARS-CoV-2 where cases from asymptomatic patients are often underreported, wastewater surveillance offers an unbiased tool for monitoring the extent of SARS-CoV-2 transmissions in a community. The present study aimed to characterize SARS-CoV-2 variants that circulated in Nairobi County, Kenya, between April 2021 and August 2021 utilizing wastewater samples. Viral RNA was extracted from wastewater samples, followed by SARS-CoV-2 screening by real-time RT-qPCR before targeted sequencing of the Spike gene. Forty samples were analyzed, of which 50% (n = 20) tested positive for SARS-CoV-2 by real-time RT-qPCR. Of these, 45% (n = 9) were successfully amplified by RT-PCR and sequenced. The majority (78%, 7/9) of the viruses belonged to the Delta (B.1.617.2) lineage of SARS-CoV-2, while a minority (22%) belonged to the Alpha (B.1.1.7) and Alpha-Delta lineages. Phylogenetic analysis of the SARS-COV-2 delta lineage strains revealed scattered clustering of the Kenyan viruses among the global strains included in the analysis, suggesting different introductory routes into the country. On the whole, our results confirm previous clinical findings that SARS-CoV-2 variants belonging to the Alpha (B.1.1.7) and Delta (B.1.617.2) lineages circulated in Nairobi County, Kenya during the study period, with the latter predominating. This is the first study to describe the diversity of SARS-CoV-2 variants circulating in Kenya, through wastewater analysis.

关键词： Wastewater Surveillance SARS-CoV-2 Delta Variants Spike Gene COVID-19 Kenya

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