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
Summary: 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...
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2021
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oai:doaj.org-article:10a344c6de104c8aafbf987f42c0abc72021-11-18T04:48:37ZGenomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data2214-109X10.1016/S2214-109X(21)00434-4https://doaj.org/article/10a344c6de104c8aafbf987f42c0abc72021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2214109X21004344https://doaj.org/toc/2214-109XSummary: 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.Tapfumanei Mashe, MScFaustinos Tatenda Takawira, MScLeonardo de Oliveira Martins, PhDMuchaneta Gudza-Mugabe, PhDJoconiah Chirenda, PhDManes Munyanyi, MScBlessmore V Chaibva, MPHAndrew Tarupiwa, MScHlanai Gumbo, MScAgnes Juru, MScCharles Nyagupe, MScVurayai Ruhanya, MScIsaac Phiri, MPHPortia Manangazira, MPHAlexander Goredema, MScSydney Danda, MScIsrael Chabata, MScJanet Jonga, MScRutendo Munharira, MScKudzai Masunda, MPHInnocent Mukeredzi, MScDouglas Mangwanya, MScAlex Trotter, PhDThanh Le Viet, PhDSteven Rudder, MScGemma Kay, PhDDavid Baker, BScGaetan Thilliez, PhDAna Victoria Gutierrez, PhDJustin O'Grady, PhDMaxwell Hove, PhDSekesai Mutapuri-Zinyowera, PhDAndrew J Page, PhDRobert A Kingsley, ProfPhDGibson Mhlanga, MPHElsevierarticlePublic aspects of medicineRA1-1270ENThe Lancet Global Health, Vol 9, Iss 12, Pp e1658-e1666 (2021) |
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Public aspects of medicine RA1-1270 |
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Public aspects of medicine RA1-1270 Tapfumanei Mashe, MSc Faustinos Tatenda Takawira, MSc Leonardo de Oliveira Martins, PhD Muchaneta Gudza-Mugabe, PhD Joconiah Chirenda, PhD Manes Munyanyi, MSc Blessmore V Chaibva, MPH Andrew Tarupiwa, MSc Hlanai Gumbo, MSc Agnes Juru, MSc Charles Nyagupe, MSc Vurayai Ruhanya, MSc Isaac Phiri, MPH Portia Manangazira, MPH Alexander Goredema, MSc Sydney Danda, MSc Israel Chabata, MSc Janet Jonga, MSc Rutendo Munharira, MSc Kudzai Masunda, MPH Innocent Mukeredzi, MSc Douglas Mangwanya, MSc Alex Trotter, PhD Thanh Le Viet, PhD Steven Rudder, MSc Gemma Kay, PhD David Baker, BSc Gaetan Thilliez, PhD Ana Victoria Gutierrez, PhD Justin O'Grady, PhD Maxwell Hove, PhD Sekesai Mutapuri-Zinyowera, PhD Andrew J Page, PhD Robert A Kingsley, ProfPhD Gibson Mhlanga, MPH 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 |
| description |
Summary: 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 |
article |
| author |
Tapfumanei Mashe, MSc Faustinos Tatenda Takawira, MSc Leonardo de Oliveira Martins, PhD Muchaneta Gudza-Mugabe, PhD Joconiah Chirenda, PhD Manes Munyanyi, MSc Blessmore V Chaibva, MPH Andrew Tarupiwa, MSc Hlanai Gumbo, MSc Agnes Juru, MSc Charles Nyagupe, MSc Vurayai Ruhanya, MSc Isaac Phiri, MPH Portia Manangazira, MPH Alexander Goredema, MSc Sydney Danda, MSc Israel Chabata, MSc Janet Jonga, MSc Rutendo Munharira, MSc Kudzai Masunda, MPH Innocent Mukeredzi, MSc Douglas Mangwanya, MSc Alex Trotter, PhD Thanh Le Viet, PhD Steven Rudder, MSc Gemma Kay, PhD David Baker, BSc Gaetan Thilliez, PhD Ana Victoria Gutierrez, PhD Justin O'Grady, PhD Maxwell Hove, PhD Sekesai Mutapuri-Zinyowera, PhD Andrew J Page, PhD Robert A Kingsley, ProfPhD Gibson Mhlanga, MPH |
| author_facet |
Tapfumanei Mashe, MSc Faustinos Tatenda Takawira, MSc Leonardo de Oliveira Martins, PhD Muchaneta Gudza-Mugabe, PhD Joconiah Chirenda, PhD Manes Munyanyi, MSc Blessmore V Chaibva, MPH Andrew Tarupiwa, MSc Hlanai Gumbo, MSc Agnes Juru, MSc Charles Nyagupe, MSc Vurayai Ruhanya, MSc Isaac Phiri, MPH Portia Manangazira, MPH Alexander Goredema, MSc Sydney Danda, MSc Israel Chabata, MSc Janet Jonga, MSc Rutendo Munharira, MSc Kudzai Masunda, MPH Innocent Mukeredzi, MSc Douglas Mangwanya, MSc Alex Trotter, PhD Thanh Le Viet, PhD Steven Rudder, MSc Gemma Kay, PhD David Baker, BSc Gaetan Thilliez, PhD Ana Victoria Gutierrez, PhD Justin O'Grady, PhD Maxwell Hove, PhD Sekesai Mutapuri-Zinyowera, PhD Andrew J Page, PhD Robert A Kingsley, ProfPhD Gibson Mhlanga, MPH |
| author_sort |
Tapfumanei Mashe, MSc |
| 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_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_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_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 |
| publisher |
Elsevier |
| publishDate |
2021 |
| url |
https://doaj.org/article/10a344c6de104c8aafbf987f42c0abc7 |
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