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Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data

BACKGROUND: Advances in SARS-CoV-2 sequencing have enabled identification of new variants, tracking of its evolution, and monitoring of its spread. We aimed to use whole genome sequencing to describe the molecular epidemiology of the SARS-CoV-2 outbreak and to inform the implementation of effective...

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Autores principales: Mashe, Tapfumanei, Takawira, Faustinos Tatenda, de Oliveira Martins, Leonardo, Gudza-Mugabe, Muchaneta, Chirenda, Joconiah, Munyanyi, Manes, Chaibva, Blessmore V, Tarupiwa, Andrew, Gumbo, Hlanai, Juru, Agnes, Nyagupe, Charles, Ruhanya, Vurayai, Phiri, Isaac, Manangazira, Portia, Goredema, Alexander, Danda, Sydney, Chabata, Israel, Jonga, Janet, Munharira, Rutendo, Masunda, Kudzai, Mukeredzi, Innocent, Mangwanya, Douglas, Trotter, Alex, Le Viet, Thanh, Rudder, Steven, Kay, Gemma, Baker, David, Thilliez, Gaetan, Gutierrez, Ana Victoria, O'Grady, Justin, Hove, Maxwell, Mutapuri-Zinyowera, Sekesai, Page, Andrew J, Kingsley, Robert A, Mhlanga, Gibson
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Author(s). Published by Elsevier Ltd. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8536247/
https://www.ncbi.nlm.nih.gov/pubmed/34695371
http://dx.doi.org/10.1016/S2214-109X(21)00434-4
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author Mashe, Tapfumanei
Takawira, Faustinos Tatenda
de Oliveira Martins, Leonardo
Gudza-Mugabe, Muchaneta
Chirenda, Joconiah
Munyanyi, Manes
Chaibva, Blessmore V
Tarupiwa, Andrew
Gumbo, Hlanai
Juru, Agnes
Nyagupe, Charles
Ruhanya, Vurayai
Phiri, Isaac
Manangazira, Portia
Goredema, Alexander
Danda, Sydney
Chabata, Israel
Jonga, Janet
Munharira, Rutendo
Masunda, Kudzai
Mukeredzi, Innocent
Mangwanya, Douglas
Trotter, Alex
Le Viet, Thanh
Rudder, Steven
Kay, Gemma
Baker, David
Thilliez, Gaetan
Gutierrez, Ana Victoria
O'Grady, Justin
Hove, Maxwell
Mutapuri-Zinyowera, Sekesai
Page, Andrew J
Kingsley, Robert A
Mhlanga, Gibson
author_facet Mashe, Tapfumanei
Takawira, Faustinos Tatenda
de Oliveira Martins, Leonardo
Gudza-Mugabe, Muchaneta
Chirenda, Joconiah
Munyanyi, Manes
Chaibva, Blessmore V
Tarupiwa, Andrew
Gumbo, Hlanai
Juru, Agnes
Nyagupe, Charles
Ruhanya, Vurayai
Phiri, Isaac
Manangazira, Portia
Goredema, Alexander
Danda, Sydney
Chabata, Israel
Jonga, Janet
Munharira, Rutendo
Masunda, Kudzai
Mukeredzi, Innocent
Mangwanya, Douglas
Trotter, Alex
Le Viet, Thanh
Rudder, Steven
Kay, Gemma
Baker, David
Thilliez, Gaetan
Gutierrez, Ana Victoria
O'Grady, Justin
Hove, Maxwell
Mutapuri-Zinyowera, Sekesai
Page, Andrew J
Kingsley, Robert A
Mhlanga, Gibson
author_sort Mashe, Tapfumanei
collection PubMed
description BACKGROUND: Advances in SARS-CoV-2 sequencing have enabled identification of new variants, tracking of its evolution, and monitoring of its spread. We aimed to use whole genome sequencing to describe the molecular epidemiology of the SARS-CoV-2 outbreak and to inform the implementation of effective public health interventions for control in Zimbabwe. METHODS: We performed a retrospective study of nasopharyngeal samples collected from nine laboratories in Zimbabwe between March 20 and Oct 16, 2020. Samples were taken as a result of quarantine procedures for international arrivals or to test for infection in people who were symptomatic or close contacts of positive cases. Samples that had a cycle threshold of less than 30 in the diagnostic PCR test were processed for sequencing. We began our analysis in July, 2020 (120 days since the first case), with a follow-up in October, 2020 (at 210 days since the first case). The phylogenetic relationship of the genome sequences within Zimbabwe and global samples was established using maximum likelihood and Bayesian methods. FINDINGS: Of 92 299 nasopharyngeal samples collected during the study period, 8099 were PCR-positive and 328 were available for sequencing, with 156 passing sequence quality control. 83 (53%) of 156 were from female participants. At least 26 independent introductions of SARS-CoV-2 into Zimbabwe in the first 210 days were associated with 12 global lineages. 151 (97%) of 156 had the Asp614Gly mutation in the spike protein. Most cases, 93 (60%), were imported from outside Zimbabwe. Community transmission was reported 6 days after the onset of the outbreak. INTERPRETATION: Initial public health interventions delayed onset of SARS-CoV-2 community transmission after the introduction of the virus from international and regional migration in Zimbabwe. Global whole genome sequence data are essential to reveal major routes of spread and guide intervention strategies. FUNDING: WHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limited.
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spelling pubmed-85362472021-10-25 Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data Mashe, Tapfumanei Takawira, Faustinos Tatenda de Oliveira Martins, Leonardo Gudza-Mugabe, Muchaneta Chirenda, Joconiah Munyanyi, Manes Chaibva, Blessmore V Tarupiwa, Andrew Gumbo, Hlanai Juru, Agnes Nyagupe, Charles Ruhanya, Vurayai Phiri, Isaac Manangazira, Portia Goredema, Alexander Danda, Sydney Chabata, Israel Jonga, Janet Munharira, Rutendo Masunda, Kudzai Mukeredzi, Innocent Mangwanya, Douglas Trotter, Alex Le Viet, Thanh Rudder, Steven Kay, Gemma Baker, David Thilliez, Gaetan Gutierrez, Ana Victoria O'Grady, Justin Hove, Maxwell Mutapuri-Zinyowera, Sekesai Page, Andrew J Kingsley, Robert A Mhlanga, Gibson Lancet Glob Health Articles BACKGROUND: Advances in SARS-CoV-2 sequencing have enabled identification of new variants, tracking of its evolution, and monitoring of its spread. We aimed to use whole genome sequencing to describe the molecular epidemiology of the SARS-CoV-2 outbreak and to inform the implementation of effective public health interventions for control in Zimbabwe. METHODS: We performed a retrospective study of nasopharyngeal samples collected from nine laboratories in Zimbabwe between March 20 and Oct 16, 2020. Samples were taken as a result of quarantine procedures for international arrivals or to test for infection in people who were symptomatic or close contacts of positive cases. Samples that had a cycle threshold of less than 30 in the diagnostic PCR test were processed for sequencing. We began our analysis in July, 2020 (120 days since the first case), with a follow-up in October, 2020 (at 210 days since the first case). The phylogenetic relationship of the genome sequences within Zimbabwe and global samples was established using maximum likelihood and Bayesian methods. FINDINGS: Of 92 299 nasopharyngeal samples collected during the study period, 8099 were PCR-positive and 328 were available for sequencing, with 156 passing sequence quality control. 83 (53%) of 156 were from female participants. At least 26 independent introductions of SARS-CoV-2 into Zimbabwe in the first 210 days were associated with 12 global lineages. 151 (97%) of 156 had the Asp614Gly mutation in the spike protein. Most cases, 93 (60%), were imported from outside Zimbabwe. Community transmission was reported 6 days after the onset of the outbreak. INTERPRETATION: Initial public health interventions delayed onset of SARS-CoV-2 community transmission after the introduction of the virus from international and regional migration in Zimbabwe. Global whole genome sequence data are essential to reveal major routes of spread and guide intervention strategies. FUNDING: WHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limited. The Author(s). Published by Elsevier Ltd. 2021-12 2021-10-22 /pmc/articles/PMC8536247/ /pubmed/34695371 http://dx.doi.org/10.1016/S2214-109X(21)00434-4 Text en © 2021 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Articles
Mashe, Tapfumanei
Takawira, Faustinos Tatenda
de Oliveira Martins, Leonardo
Gudza-Mugabe, Muchaneta
Chirenda, Joconiah
Munyanyi, Manes
Chaibva, Blessmore V
Tarupiwa, Andrew
Gumbo, Hlanai
Juru, Agnes
Nyagupe, Charles
Ruhanya, Vurayai
Phiri, Isaac
Manangazira, Portia
Goredema, Alexander
Danda, Sydney
Chabata, Israel
Jonga, Janet
Munharira, Rutendo
Masunda, Kudzai
Mukeredzi, Innocent
Mangwanya, Douglas
Trotter, Alex
Le Viet, Thanh
Rudder, Steven
Kay, Gemma
Baker, David
Thilliez, Gaetan
Gutierrez, Ana Victoria
O'Grady, Justin
Hove, Maxwell
Mutapuri-Zinyowera, Sekesai
Page, Andrew J
Kingsley, Robert A
Mhlanga, Gibson
Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data
title Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data
title_full Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data
title_fullStr Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data
title_full_unstemmed Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data
title_short Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data
title_sort genomic epidemiology and the role of international and regional travel in the sars-cov-2 epidemic in zimbabwe: a retrospective study of routinely collected surveillance data
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8536247/
https://www.ncbi.nlm.nih.gov/pubmed/34695371
http://dx.doi.org/10.1016/S2214-109X(21)00434-4
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