The study aimed to understand the introduction and spread of SARS-CoV-2 in coastal Kenya, a significant international tourism hub and gateway to East and Central Africa. The first confirmed case in Kenya was on March 13th, 2020, shortly after the WHO declared COVID-19 a pandemic. Kenya implemented containment measures, including border closures, curfews, and restrictions on gatherings. Despite these measures, cases increased steadily, indicating established local transmission. Coastal Kenya, with its multiple international entry points (airports, seaports, and land borders), posed a particular risk. Mombasa, a major city in the region, emerged as an early epicenter. Understanding the early importation and spread of SARS-CoV-2 was crucial for evaluating the effectiveness of early interventions and for designing future control measures. Previous research had examined travel history and transmission patterns in East Africa, but a large-scale genomic epidemiology study for Kenya was lacking. This study aimed to fill that gap by sequencing and analyzing SARS-CoV-2 positive samples collected in coastal Kenya between March and July 2020 to understand the introduction and spread patterns of the virus in the region.

Several studies have investigated SARS-CoV-2 transmission patterns in East Africa, including examining travel history and overall transmission dynamics. However, there was a lack of comprehensive genomic epidemiology data specific to Kenya, particularly during the early stages of the pandemic. This study aimed to address this gap by providing the first large-scale genomic epidemiology study of SARS-CoV-2 for coastal Kenya, informing our understanding of the virus's introduction and spread.

SARS-CoV-2 RT-PCR testing was established in mid-March 2020, with samples collected from various sources, including returning citizens, individuals with symptoms, and contacts of confirmed cases. A total of 406 RT-PCR positive samples were collected between March 17th and July 31st, 2020, with 311 used for phylogenetic analysis. The sequences were generated using the ARTIC nCoV-2019 sequencing protocol, involving RNA purification, RT-PCR, library preparation, and sequencing via an Oxford Nanopore platform. Demographic data, including age, sex, and travel history, were collected. Lineage assignment was performed using Pangolin and Nextclade tools. Phylogenetic analysis was conducted using a modified Nextstrain Augur pipeline, including alignment using MAFFT, tree construction using Treetime, and time-scaled tree inference. To infer the number of introductions, two approaches were used: 1) Observing fresh lineages during the early epidemic phase along with epidemiological data; 2) A computational phylogeographic approach using PastML and ancestral trait reconstruction. A global dataset of sequences (n=2077) collected before July 31st, 2020, was used for context.

The study identified multiple independent introductions of SARS-CoV-2 into coastal Kenya, primarily from Europe. Lineage B.1 was the dominant lineage (74%), exhibiting rapid expansion, while other lineages (A, B, B.4) were detected mainly in returning travelers or at border points. The median age of sequenced individuals was 37 years, with 66% being male and over half asymptomatic. Approximately 26% of individuals had a history of recent international travel. Early public health interventions (border control, screening, quarantine, isolation, and contact tracing) appear to have limited the spread of some lineages. Undetected introductions, however, contributed to local epidemics, particularly of lineage B.1 in Mombasa. Phylogenetic analysis revealed at least 3 independent introductions, and computational methods estimated a higher number (34-37) of introductions into coastal Kenya and its surrounding regions. The study also highlighted the importance of border control and early interventions in preventing widespread transmission, and provided evidence for the effectiveness of these measures despite the potential for undetected introductions.

The findings demonstrate the importance of genomic surveillance in understanding SARS-CoV-2 introduction and transmission dynamics. The dominance of lineage B.1 and the limited spread of other lineages suggest the effectiveness of early public health interventions in containing the virus. However, undetected introductions highlight the need for continued vigilance and improved surveillance strategies. The study's findings have direct implications for informing public health policy and resource allocation in Kenya and the East African region. The results emphasize the need for continued genomic surveillance and collaboration across countries to effectively control the pandemic.

This study provides the first large-scale genomic epidemiology analysis of SARS-CoV-2 in coastal Kenya, revealing multiple introductions, primarily from Europe. Early public health interventions were partially successful in limiting spread but undetected introductions led to sustained transmission. Continued genomic surveillance is vital to monitor the virus's evolution and inform public health responses.

The study acknowledges limitations, including incomplete epidemiological data for some individuals, incomplete genomes due to low viral load, and a non-systematic testing strategy. The findings might not be fully generalizable to the entire East African region due to regional variations. The sampling bias may also affect the observed lineage distributions.