The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, has spread globally, with the arising of new variants (e.g., alpha, delta, and omicron) affecting infection control, leading to policy changes in social restrictions, and impacts on the efficacy of vaccines. An understanding of the genetic diversity, phylogeny and lineages of SAR-CoV-2 provides insights into circulating infections, and insights into the robustness and design of vaccines and other infection control tools. To date, there have been more than 11 million reported infections and 239,000 reported deaths caused by the novel coronavirus in Africa . In the early months of the COVID-19 pandemic, Africa’s rapid and coordinated response, informed by emerging data, led to infection control which mitigated effects of a first-wave and to a lesser degree a second wave . This included rapid response through genomic surveillance to curb the spread of SARS-CoV-2. Nigeria took three days to sequence SARS-CoV-2 genome after the identification of the novel virus in the country . Within the same period, the Network for Genomic Surveillance in South Africa (NGS-SA) was established to facilitate case confirmation and sequencing of the positive cases for phylogenetic and lineage updates . Public and health officers in Uganda also set a sequencing program to facilitate genomic sequencing of the confirmed positive samples from the rapid contact tracing and international arrivals . However, now in 2022, as vast vaccination campaigns have enabled the global north to gain some control over the pandemic, the vaccine roll-out in Africa lags because of inequities in accessing them. Kenya has vaccinated 12,652,991 people at a rate of 23.89% doses per 100 people .
Kenya joined the genomic surveillance of the SARS-CoV-2 pandemic after reporting the first case on 13th March, 2020 (Health, 2020). Most of the earlier cases were dominated by the lineage B.1, which was introduced into African countries from the international arrivals, particularly from European origin. Early public health measures in Kenya included restricted movements through limitation of social interactions and gatherings, but these failed to prevent transmission . By the end of July 2020, the Kenyan Ministry of Health had reported 20,636 PCR confirmed cases and 341 SARS-CoV-2 associated deaths. Most of the cases were from Nairobi and Mombasa, which were exposed to cross-border interactions and international arrivals, with individuals who did not undergo rapid testing procedures at the points of border control. At the time, seroprevalence surveillance of the national blood bank revealed the existence of SARS-CoV-2 in the population before the published 13th March 2020 . The growing prevalence was confirmed by the community-based modelling teams  who relied solely on the seroprevalence, PCR confirmed cases, and genomic data that were able to present different variants for each wave in the country.
Genomic surveillance is an essential approach to characterise the transmission dynamics and the prevalence of SARS-CoV-2 within a population. Most of the sequences published in Kenya have been closely related to the Wuhan reference sequences clustered between 4 and 16 nucleotide substitutions . The predominant nucleotide substitutions were associated with mutations at positions A23403G (S:D614G), P970L, P314L, R203K and G204R . However, genomic surveillance revealed D614G to dominate the prevalence across the country and across the borders despite its initial appearance in the earlier stages of the pandemic .
Here, we sequenced RT-PCR confirmed SARS-CoV-2 positive samples, sourced from Nairobi and Kiambu County, collected between September 2020 and March 2021, spanning in between the severe alpha and delta variants of concern within the country and across borders. This work led to 52 SARS-CoV-2 isolate sequences for the phylo-genomic analyses across Nairobi and Kiambu County, one of the largest genomic epidemiology studies in the Nairobi metropolitan.