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

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 re-