Accès ouvert

Temporal lineage replacements and dominance of imported variants of concern during the COVID-19 pandemic in Kenya

Article scientifique 2022 Anglais

Résumé

Background: Kenya's COVID-19 epidemic was seeded early in March 2020 and did not peak until early August 2020 (wave 1), late-November 2020 (wave 2), mid-April 2021 (wave 3), late August 2021 (wave 4), and mid-January 2022 (wave 5). Methods: Here, we present SARS-CoV-2 lineages associated with the five waves through analysis of 1034 genomes, which included 237 non-variants of concern and 797 variants of concern (VOC) that had increased transmissibility, disease severity or vaccine resistance. Results: In total 40 lineages were identified. The early European lineages (B.1 and B.1.1) were the first to be seeded. The B.1 lineage continued to expand and remained dominant, accounting for 60% (72/120) and 57% (45/79) in waves 1 and 2 respectively. Waves three, four and five respectively were dominated by VOCs that were distributed as follows: Alpha 58.5% (166/285), Delta 92.4% (327/354), Omicron 95.4% (188/197) and Beta at 4.2% (12/284) during wave 3 and 0.3% (1/354) during wave 4. Phylogenetic analysis suggests multiple introductions of variants from outside Kenya, more so during the first, third, fourth and fifth waves, as well as subsequent lineage diversification. Conclusions: The data highlights the importance of genome surveillance in determining circulating variants to aid interpretation of phenotypes such as transmissibility, virulence and/or resistance to therapeutics/vaccines.

Citer ce document

Kimita, G., Nyataya, J., Omuseni, E., Sigei, F., Lemtudo, A., Muthanje, E., Andika, B., Liyai, R., Githii, R., Masakwe, C., Ochola, S., Awinda, G., Kifude, C., Mutai, B., Gatata, R., Waitumbi, J. (2022). Temporal lineage replacements and dominance of imported variants of concern during the COVID-19 pandemic in Kenya. https://doi.org/10.1038/s43856-022-00167-8

Accès au document

Voir sur le dépôt source

Ce document est hébergé sur son dépôt institutionnel d'origine.

Auteur(s)

Gathii Kimita Josphat Nyataya Esther Omuseni Faith Sigei Allan Lemtudo Eric M. Muthanje Brian Andika Rehema Liyai Rachel Githii Clement Masakwe Stephen Ochola George Awinda Carol Kifude Beth Mutai Robert M. Gatata John Waitumbi

Statistiques

Consultations : 1

Téléchargements : 0