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Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study

BACKGROUND: Detailed understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic. METHODS: Here, we analysed 1139 SARS-CoV-2 genomes from positive samp...

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Autores principales: Agoti, Charles N, Ochola-Oyier, Lynette Isabella, Dellicour, Simon, Mohammed, Khadija Said, Lambisia, Arnold W, de Laurent, Zaydah R, Morobe, John M, Mburu, Maureen W, Omuoyo, Donwilliams O, Ongera, Edidah M, Ndwiga, Leonard, Maitha, Eric, Kitole, Benson, Suleiman, Thani, Mwakinangu, Mohamed, Nyambu, John K, Otieno, John, Salim, Barke, Musyoki, Jennifer, Murunga, Nickson, Otieno, Edward, Kiiru, John N, Kasera, Kadondi, Amoth, Patrick, Mwangangi, Mercy, Aman, Rashid, Kinyanjui, Samson, Warimwe, George, Phan, My, Agweyu, Ambrose, Cotten, Matthew, Barasa, Edwine, Tsofa, Benjamin, Nokes, D James, Bejon, Philip, Githinji, George
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9282859/
https://www.ncbi.nlm.nih.gov/pubmed/35699426
http://dx.doi.org/10.7554/eLife.71703
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author Agoti, Charles N
Ochola-Oyier, Lynette Isabella
Dellicour, Simon
Mohammed, Khadija Said
Lambisia, Arnold W
de Laurent, Zaydah R
Morobe, John M
Mburu, Maureen W
Omuoyo, Donwilliams O
Ongera, Edidah M
Ndwiga, Leonard
Maitha, Eric
Kitole, Benson
Suleiman, Thani
Mwakinangu, Mohamed
Nyambu, John K
Otieno, John
Salim, Barke
Musyoki, Jennifer
Murunga, Nickson
Otieno, Edward
Kiiru, John N
Kasera, Kadondi
Amoth, Patrick
Mwangangi, Mercy
Aman, Rashid
Kinyanjui, Samson
Warimwe, George
Phan, My
Agweyu, Ambrose
Cotten, Matthew
Barasa, Edwine
Tsofa, Benjamin
Nokes, D James
Bejon, Philip
Githinji, George
author_facet Agoti, Charles N
Ochola-Oyier, Lynette Isabella
Dellicour, Simon
Mohammed, Khadija Said
Lambisia, Arnold W
de Laurent, Zaydah R
Morobe, John M
Mburu, Maureen W
Omuoyo, Donwilliams O
Ongera, Edidah M
Ndwiga, Leonard
Maitha, Eric
Kitole, Benson
Suleiman, Thani
Mwakinangu, Mohamed
Nyambu, John K
Otieno, John
Salim, Barke
Musyoki, Jennifer
Murunga, Nickson
Otieno, Edward
Kiiru, John N
Kasera, Kadondi
Amoth, Patrick
Mwangangi, Mercy
Aman, Rashid
Kinyanjui, Samson
Warimwe, George
Phan, My
Agweyu, Ambrose
Cotten, Matthew
Barasa, Edwine
Tsofa, Benjamin
Nokes, D James
Bejon, Philip
Githinji, George
author_sort Agoti, Charles N
collection PubMed
description BACKGROUND: Detailed understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic. METHODS: Here, we analysed 1139 SARS-CoV-2 genomes from positive samples collected between March 2020 and February 2021 across six counties of Coastal Kenya (Mombasa, Kilifi, Taita Taveta, Kwale, Tana River, and Lamu) to infer virus introductions and local transmission patterns during the first two waves of infections. Virus importations were inferred using ancestral state reconstruction, and virus dispersal between counties was estimated using discrete phylogeographic analysis. RESULTS: During Wave 1, 23 distinct Pango lineages were detected across the six counties, while during Wave 2, 29 lineages were detected; 9 of which occurred in both waves and 4 seemed to be Kenya specific (B.1.530, B.1.549, B.1.596.1, and N.8). Most of the sequenced infections belonged to lineage B.1 (n = 723, 63%), which predominated in both Wave 1 (73%, followed by lineages N.8 [6%] and B.1.1 [6%]) and Wave 2 (56%, followed by lineages B.1.549 [21%] and B.1.530 [5%]). Over the study period, we estimated 280 SARS-CoV-2 virus importations into Coastal Kenya. Mombasa City, a vital tourist and commercial centre for the region, was a major route for virus imports, most of which occurred during Wave 1, when many Coronavirus Disease 2019 (COVID-19) government restrictions were still in force. In Wave 2, inter-county transmission predominated, resulting in the emergence of local transmission chains and diversity. CONCLUSIONS: Our analysis supports moving COVID-19 control strategies in the region from a focus on international travel to strategies that will reduce local transmission. FUNDING: This work was funded by The Wellcome (grant numbers: 220985, 203077/Z/16/Z, 220977/Z/20/Z, and 222574/Z/21/Z) and the National Institute for Health and Care Research (NIHR), project references: 17/63/and 16/136/33 using UK Aid from the UK government to support global health research, The UK Foreign, Commonwealth and Development Office. The views expressed in this publication are those of the author(s) and not necessarily those of the funding agencies.
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spelling pubmed-92828592022-07-15 Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study Agoti, Charles N Ochola-Oyier, Lynette Isabella Dellicour, Simon Mohammed, Khadija Said Lambisia, Arnold W de Laurent, Zaydah R Morobe, John M Mburu, Maureen W Omuoyo, Donwilliams O Ongera, Edidah M Ndwiga, Leonard Maitha, Eric Kitole, Benson Suleiman, Thani Mwakinangu, Mohamed Nyambu, John K Otieno, John Salim, Barke Musyoki, Jennifer Murunga, Nickson Otieno, Edward Kiiru, John N Kasera, Kadondi Amoth, Patrick Mwangangi, Mercy Aman, Rashid Kinyanjui, Samson Warimwe, George Phan, My Agweyu, Ambrose Cotten, Matthew Barasa, Edwine Tsofa, Benjamin Nokes, D James Bejon, Philip Githinji, George eLife Epidemiology and Global Health BACKGROUND: Detailed understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic. METHODS: Here, we analysed 1139 SARS-CoV-2 genomes from positive samples collected between March 2020 and February 2021 across six counties of Coastal Kenya (Mombasa, Kilifi, Taita Taveta, Kwale, Tana River, and Lamu) to infer virus introductions and local transmission patterns during the first two waves of infections. Virus importations were inferred using ancestral state reconstruction, and virus dispersal between counties was estimated using discrete phylogeographic analysis. RESULTS: During Wave 1, 23 distinct Pango lineages were detected across the six counties, while during Wave 2, 29 lineages were detected; 9 of which occurred in both waves and 4 seemed to be Kenya specific (B.1.530, B.1.549, B.1.596.1, and N.8). Most of the sequenced infections belonged to lineage B.1 (n = 723, 63%), which predominated in both Wave 1 (73%, followed by lineages N.8 [6%] and B.1.1 [6%]) and Wave 2 (56%, followed by lineages B.1.549 [21%] and B.1.530 [5%]). Over the study period, we estimated 280 SARS-CoV-2 virus importations into Coastal Kenya. Mombasa City, a vital tourist and commercial centre for the region, was a major route for virus imports, most of which occurred during Wave 1, when many Coronavirus Disease 2019 (COVID-19) government restrictions were still in force. In Wave 2, inter-county transmission predominated, resulting in the emergence of local transmission chains and diversity. CONCLUSIONS: Our analysis supports moving COVID-19 control strategies in the region from a focus on international travel to strategies that will reduce local transmission. FUNDING: This work was funded by The Wellcome (grant numbers: 220985, 203077/Z/16/Z, 220977/Z/20/Z, and 222574/Z/21/Z) and the National Institute for Health and Care Research (NIHR), project references: 17/63/and 16/136/33 using UK Aid from the UK government to support global health research, The UK Foreign, Commonwealth and Development Office. The views expressed in this publication are those of the author(s) and not necessarily those of the funding agencies. eLife Sciences Publications, Ltd 2022-06-14 /pmc/articles/PMC9282859/ /pubmed/35699426 http://dx.doi.org/10.7554/eLife.71703 Text en © 2022, Agoti et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Epidemiology and Global Health
Agoti, Charles N
Ochola-Oyier, Lynette Isabella
Dellicour, Simon
Mohammed, Khadija Said
Lambisia, Arnold W
de Laurent, Zaydah R
Morobe, John M
Mburu, Maureen W
Omuoyo, Donwilliams O
Ongera, Edidah M
Ndwiga, Leonard
Maitha, Eric
Kitole, Benson
Suleiman, Thani
Mwakinangu, Mohamed
Nyambu, John K
Otieno, John
Salim, Barke
Musyoki, Jennifer
Murunga, Nickson
Otieno, Edward
Kiiru, John N
Kasera, Kadondi
Amoth, Patrick
Mwangangi, Mercy
Aman, Rashid
Kinyanjui, Samson
Warimwe, George
Phan, My
Agweyu, Ambrose
Cotten, Matthew
Barasa, Edwine
Tsofa, Benjamin
Nokes, D James
Bejon, Philip
Githinji, George
Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study
title Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study
title_full Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study
title_fullStr Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study
title_full_unstemmed Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study
title_short Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study
title_sort transmission networks of sars-cov-2 in coastal kenya during the first two waves: a retrospective genomic study
topic Epidemiology and Global Health
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9282859/
https://www.ncbi.nlm.nih.gov/pubmed/35699426
http://dx.doi.org/10.7554/eLife.71703
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