# Longitudinal Epidemiology and Variant Dynamics of SARS-CoV-2 in Coastal Kenya (2020–2025): Clinical Features and Wave Patterns

## TL;DR

This study tracks SARS-CoV-2 infections in coastal Kenya from 2020 to 2025, showing how the virus's symptoms and variants changed over time.

## Contribution

The study provides detailed longitudinal data on SARS-CoV-2 in Kenya, highlighting local variant dynamics and symptom shifts during Omicron waves.

## Key findings

- Nine SARS-CoV-2 infection waves were recorded, with increasing intervals between waves over time.
- Locally dominant variants like AY.116 and BQ.1.8 were rare globally during their detection periods.
- Symptoms like loss of smell predicted infection pre-Omicron, while body malaise and sore throat were more predictive during Omicron waves.

## Abstract

SARS-CoV-2 is a major cause of outpatient-attended acute respiratory infections (ARIs). Data from Africa are limited on SARS-CoV-2 infection, variants, symptom profile, and longitudinal trends for outpatient presentation.

Starting December 2020, we established ARI surveillance at 5 outpatient clinics in coastal Kenya, recruiting ∼15 participants (any age) per week per clinic for SARS-CoV-2 testing and genome analysis. Participants provided respiratory samples, demographic details, and vaccination and symptom data. We compared SARS-CoV-2 clinical and molecular epidemiology before and during Omicron waves using multivariate logistic regression.

By February 2025, we had recruited 14 562 ARI cases, with 1053 (7.2%) testing positive for SARS-CoV-2. The median age of cases was 25 years (IQR, 15–41) and 65.0% were female. Nine infection waves were recorded, with positivity ranging 8.2% to 25.6%. Interwave intervals increased from ≤3 months in 2021 to ≥6 months in 2024. Sixty-eight PANGO lineages were identified from 782 (74.2%) sequenced cases, with 4 predominating local waves (AY.116, BQ.1.8, FY.4.1, LF.7.3.2), which were rare globally (<0.5%) during their detection period. Overall, common symptoms among positive cases were cough (91.5%), nasal discharge (76.7%), and fever (53.1%). Loss of sense of smell was strongly predictive of COVID-19 in the pre–Omicron era, but body malaise, sore throat, joint pain, and nasal discharge were predictive during the Omicron period.

SARS-CoV-2 increasingly shows seasonal annual patterns in coastal Kenya, with its clinical features resembling established endemic respiratory viruses. Its case burden is most pronounced in young adults. Locally dominant genetic variants may differ from those globally.

Clinical and genomic analysis of SARS-CoV-2 outpatient infections in coastal Kenya (2020–2025) revealed widening interwave intervals, repeated predominance of locally distinct PANGO lineages, and shifting of predictive symptoms following Omicron emergence, thereby underscoring the importance of continued local SARS-CoV-2/respiratory virus surveillance.