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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...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Author(s). Published by Elsevier Ltd.
2021
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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. |
format | Online Article Text |
id | pubmed-8536247 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | The Author(s). Published by Elsevier Ltd. |
record_format | MEDLINE/PubMed |
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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