Wastewater-Based Genomic Surveillance of SARS-CoV-2 Variant Circulation in Two Informal Urban Settlements in Nairobi, Kenya

Abstract Background SARS-CoV-2 genomic surveillance data remain limited in most low and middle-income countries (LMICs), resulting in significant gaps in the understanding of variant circulation and evolution. Wastewater-based epidemiology (WBE) presents a non-invasive, cost-effective, and population-representative surveillance approach that can complement clinical testing, particularly in densely populated urban informal settlements with limited healthcare access. This study aimed to pilot wastewater-based genomic surveillance as a multifaceted public health tool in Kenya. Methods A prospective study was conducted using wastewater samples collected from two WHO-validated environmental surveillance sites — Eastleigh A (Kamukunji sub-county) and Mathare (Starehe sub-county) — in Nairobi, Kenya, between December 2022 and October 2023. A total of 272 samples were collected using Moore swabs at a frequency of two to three times per week. Samples were concentrated using Nanotrap® Magnetic Virus Particles, and nucleic acid was extracted using the Qiagen QIAamp Viral RNA Mini Kit. SARS-CoV-2 was detected using RT-PCR (TaqPath™ COVID-19 CE-IVD RT-PCR Kit). Library preparation for whole-genome sequencing was performed using the Illumina COVIDSeq kit, and sequencing was conducted on the Illumina MiSeq platform. Bioinformatic analysis was performed using Terra.bio and RStudio, and phylogenetic analysis included sequences abstracted from GISAID. Results Of 272 samples, 238 (87.5%) tested positive with a cycle threshold (Ct) value of less than 36. Genomic analysis of 181 sequences identified Omicron as the predominant circulating variant, detected in 59% of samples. Other variants included XBB (16%), XBB.2.3(10%), XBB.1.9.X (5%), and additional minor variants. These findings were concordant with clinical sequencing data from Kenya over the same period. Conclusions Wastewater-based genomic surveillance reliably reflected SARS-CoV-2 variant trends observed in clinical data. This approach provides early signals of variant emergence and evolution, offering a cost-effective complement to clinical surveillance in resource-limited settings.