| Title: |
Longitudinal Epidemiology and Variant Dynamics of SARS-CoV-2 in Coastal Kenya (2020–2025): Clinical Features and Wave Patterns |
| Authors: |
Lambisia, Arnold W; Nyiro, Joyce; Githinji, George; Katama, Esther N; Moraa, Edidah; Mwita, John M; Mutunga, Martin; Maina, Grace; Bejon, Philip; Phan, My V T; Cotten, Matthew; Dellicour, Simon; Ochola-Oyier, L Isabella; Sande, Charles; Holmes, Edward C; Nyagwange, James; Agoti, Charles N |
| Contributors: |
Research Foundation; Flanders; European Union |
| Source: |
Open Forum Infectious Diseases ; volume 13, issue 3 ; ISSN 2328-8957 |
| Publisher Information: |
Oxford University Press (OUP) |
| Publication Year: |
2026 |
| Description: |
Background 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. Methods 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. Results 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 ( |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| DOI: |
10.1093/ofid/ofag084 |
| DOI: |
10.1093/ofid/ofag084/67004393/ofag084.pdf |
| Availability: |
https://doi.org/10.1093/ofid/ofag084; https://academic.oup.com/ofid/advance-article-pdf/doi/10.1093/ofid/ofag084/67004393/ofag084.pdf; https://academic.oup.com/ofid/article-pdf/13/3/ofag084/67004393/ofag084.pdf |
| Rights: |
https://creativecommons.org/licenses/by/4.0/ |
| Accession Number: |
edsbas.6BCBD190 |
| Database: |
BASE |