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, The COVID-19 Genomics UK (COG-UK) Consortium, , SARS-CoV-2 Research Group, , Bashton, Matthew, Nelson, Andrew, McCann, Clare, Smith, Darren and Young, Greg (2021) 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. The Lancet Global Health, 9 (12). e1658-e1666. ISSN 2214-109X

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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.

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.

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.

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.

WHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limited.

Item Type: Article
Additional Information: Matthew Bashton, Andrew Nelson, Clare McCann, Greg Young and Darren Smith are members of the COVID-19 Genomics UK (COG-UK) consortium. Funding information: This work was supported by a combination of routine work of scientists at the National Microbiology Reference Laboratory, Biomedical Research and Training Institute, Beatrice Road Infectious Diseases Hospital, National Virology Laboratory, and National TB Reference Laboratory (Zimbabwe). The authors gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC); this research was funded in part by the BBSRC Institute Strategic Programme Microbes in the Food Chain (BB/R012504/1) and its constituent projects (BBS/E/F/000PR10348, BBS/E/F/000PR10349, BBS/E/F/000PR10351, and BBS/E/F/000PR10352) and by the Quadram Institute Bioscience BBSRC funded Core Capability Grant (project number BB/CCG1860/1). The COVID-19 Genomics UK Consortium is supported by funding from the Medical Research Council, part of UK Research & Innovation, the National Institutes of Health Research and Genome Research Limited, operating as the Wellcome Sanger Institute. The authors thank all local clinical and laboratory staff for their contribution and dedication to the SARS-CoV-2 surveillance network. Special thanks go to Elizabeth Tabitha Abbew, for all her expert advice and proofreading of the Article. The authors acknowledge the Epidemiology and Diseases Control Department of the Ministry of Health and Child Care who provided full access to all the COVID-19 datasets used in this study. We thank members of the COVID-19 Genomics UK Consortium for their contributions in generating some of the data used in this study. We thank the laboratories who submitted their data to the GISAID; full details are listed in the appendix 1 (p 14).
Subjects: B100 Anatomy, Physiology and Pathology
C500 Microbiology
C700 Molecular Biology, Biophysics and Biochemistry
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: Elena Carlaw
Date Deposited: 19 Nov 2021 16:28
Last Modified: 19 Nov 2021 16:30

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