Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

George Githinji; Zaydah R de Laurent; Khadija Said Mohammed; Donwilliams O Omuoyo; Peter M Macharia; John M Morobe; Edward Otieno; Samson M Kinyanjui; Ambrose Agweyu; Eric Maitha; Ben Kitole; Thani Suleiman; Mohamed Mwakinangu; John Nyambu; John Otieno; Barke Salim; Kadondi Kasera; John Kiiru; Rashid Aman; Edwine Barasa; George Warimwe; Philip Bejon; Benjamin Tsofa; Lynette Isabella Ochola-Oyier; D James Nokes; Charles N Agoti

doi:10.1038/s41467-021-25137-x

Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

George Githinji, Zaydah R de Laurent, Khadija Said Mohammed, Donwilliams O Omuoyo, Peter M Macharia, John M Morobe, Edward Otieno, Samson M Kinyanjui, Ambrose Agweyu, Eric Maitha, Ben Kitole, Thani Suleiman, Mohamed Mwakinangu, John Nyambu, John Otieno, Barke Salim, Kadondi Kasera, John Kiiru, Rashid Aman, Edwine BarasaGeorge Warimwe, Philip Bejon, Benjamin Tsofa, Lynette Isabella Ochola-Oyier, D James Nokes, Charles N Agoti

Reproductive and Maternal Health

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Abstract

Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission. Here, we generated 311 SARS-CoV-2 genomes from samples collected in coastal Kenya between 17th March and 31st July 2020. We estimated multiple independent SARS-CoV-2 introductions into the region were primarily of European origin, although introductions could have come through neighbouring countries. Lineage B.1 accounted for 74% of sequenced cases. Lineages A, B and B.4 were detected in screened individuals at the Kenya-Tanzania border or returning travellers. Though multiple lineages were introduced into coastal Kenya following the initial confirmed case, none showed extensive local expansion other than lineage B.1. International points of entry were important conduits of SARS-CoV-2 importations into coastal Kenya and early public health responses prevented established transmission of some lineages. Undetected introductions through points of entry including imports from elsewhere in the country gave rise to the local epidemic at the Kenyan coast.

Original language	English
Article number	4809
Journal	Nature Communications
Volume	12
Issue number	1
ISSN	2041-1723
DOIs	https://doi.org/10.1038/s41467-021-25137-x
Publication status	Published - 2021

Keywords

Adolescent
Adult
Aged
Aged, 80 and over
COVID-19/diagnosis
Child
Child, Preschool
Female
Genetic Variation
Genome, Viral
Humans
Infant
Kenya/epidemiology
Male
Middle Aged
Pandemics
Phylogeny
Public Health
SARS-CoV-2/classification
Sequence Analysis
Tanzania
Travel
Young Adult

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10.1038/s41467-021-25137-xLicence: CC BY

2021ncom4809Final published version, 2.89 MBLicence: CC BY

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Githinji, G., de Laurent, Z. R., Mohammed, K. S., Omuoyo, D. O., Macharia, P. M., Morobe, J. M., Otieno, E., Kinyanjui, S. M., Agweyu, A., Maitha, E., Kitole, B., Suleiman, T., Mwakinangu, M., Nyambu, J., Otieno, J., Salim, B., Kasera, K., Kiiru, J., Aman, R., ... Agoti, C. N. (2021). Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya. Nature Communications, 12(1), Article 4809. https://doi.org/10.1038/s41467-021-25137-x

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Githinji, G, de Laurent, ZR, Mohammed, KS, Omuoyo, DO, Macharia, PM, Morobe, JM, Otieno, E, Kinyanjui, SM, Agweyu, A, Maitha, E, Kitole, B, Suleiman, T, Mwakinangu, M, Nyambu, J, Otieno, J, Salim, B, Kasera, K, Kiiru, J, Aman, R, Barasa, E, Warimwe, G, Bejon, P, Tsofa, B, Ochola-Oyier, LI, Nokes, DJ & Agoti, CN 2021, 'Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya', Nature Communications, vol. 12, no. 1, 4809. https://doi.org/10.1038/s41467-021-25137-x

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T1 - Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

AU - Githinji, George

AU - de Laurent, Zaydah R

AU - Mohammed, Khadija Said

AU - Omuoyo, Donwilliams O

AU - Macharia, Peter M

AU - Morobe, John M

AU - Otieno, Edward

AU - Kinyanjui, Samson M

AU - Agweyu, Ambrose

AU - Maitha, Eric

AU - Kitole, Ben

AU - Suleiman, Thani

AU - Mwakinangu, Mohamed

AU - Nyambu, John

AU - Otieno, John

AU - Salim, Barke

AU - Kasera, Kadondi

AU - Kiiru, John

AU - Aman, Rashid

AU - Barasa, Edwine

AU - Warimwe, George

AU - Bejon, Philip

AU - Tsofa, Benjamin

AU - Ochola-Oyier, Lynette Isabella

AU - Nokes, D James

AU - Agoti, Charles N

PY - 2021

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N2 - Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission. Here, we generated 311 SARS-CoV-2 genomes from samples collected in coastal Kenya between 17th March and 31st July 2020. We estimated multiple independent SARS-CoV-2 introductions into the region were primarily of European origin, although introductions could have come through neighbouring countries. Lineage B.1 accounted for 74% of sequenced cases. Lineages A, B and B.4 were detected in screened individuals at the Kenya-Tanzania border or returning travellers. Though multiple lineages were introduced into coastal Kenya following the initial confirmed case, none showed extensive local expansion other than lineage B.1. International points of entry were important conduits of SARS-CoV-2 importations into coastal Kenya and early public health responses prevented established transmission of some lineages. Undetected introductions through points of entry including imports from elsewhere in the country gave rise to the local epidemic at the Kenyan coast.

AB - Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission. Here, we generated 311 SARS-CoV-2 genomes from samples collected in coastal Kenya between 17th March and 31st July 2020. We estimated multiple independent SARS-CoV-2 introductions into the region were primarily of European origin, although introductions could have come through neighbouring countries. Lineage B.1 accounted for 74% of sequenced cases. Lineages A, B and B.4 were detected in screened individuals at the Kenya-Tanzania border or returning travellers. Though multiple lineages were introduced into coastal Kenya following the initial confirmed case, none showed extensive local expansion other than lineage B.1. International points of entry were important conduits of SARS-CoV-2 importations into coastal Kenya and early public health responses prevented established transmission of some lineages. Undetected introductions through points of entry including imports from elsewhere in the country gave rise to the local epidemic at the Kenyan coast.

KW - Adolescent

KW - Adult

KW - Aged

KW - Aged, 80 and over

KW - COVID-19/diagnosis

KW - Child

KW - Child, Preschool

KW - Female

KW - Genetic Variation

KW - Genome, Viral

KW - Humans

KW - Infant

KW - Kenya/epidemiology

KW - Male

KW - Middle Aged

KW - Pandemics

KW - Phylogeny

KW - Public Health

KW - SARS-CoV-2/classification

KW - Sequence Analysis

KW - Tanzania

KW - Travel

KW - Young Adult

U2 - 10.1038/s41467-021-25137-x

DO - 10.1038/s41467-021-25137-x

M3 - A1: Web of Science-article

C2 - 34376689

SN - 2041-1723

VL - 12

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 4809

ER -

Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

Abstract

Keywords

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