Mashe, Tapfumanei, Takawira, Faustinos Tatenda, de Oliveira Martins, Leonardo 
ORCID: 0000-0001-5247-1320, Gudza-Mugabe, Muchaneta, Chirenda, Joconiah, Munyanyi, Manes, Chaibva, Blessmore V, Tarupiwa, Andrew, Gumbo, Hlanai, Juru, Agnes et al (show 27 more authors)
(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, 2214-109X
Abstract
<h4>Background</h4>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.<h4>Methods</h4>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.<h4>Findings</h4>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.<h4>Interpretation</h4>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.<h4>Funding</h4>WHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limited.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | COVID-19 Genomics UK Consortium, SARS-CoV-2 Research Group, Humans, Retrospective Studies, Genome, Viral, Adolescent, Adult, Middle Aged, Child, Child, Preschool, Infant, Zimbabwe, Female, Male, Young Adult, Molecular Epidemiology, Epidemics, Public Health Surveillance, Whole Genome Sequencing, Travel-Related Illness, COVID-19, SARS-CoV-2 |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 09 May 2022 09:00 |
| Last Modified: | 07 Dec 2024 23:18 |
| DOI: | 10.1016/s2214-109x(21)00434-4 |
| Open Access URL: | https://doi.org/10.1016/S2214-109X(21)00434-4 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3154487 |
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