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.

Autor:	Mashe T; National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe. Electronic address: mashet2006@yahoo.co.uk., Takawira FT; National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe., de Oliveira Martins L; Quadram Institute Bioscience, Norwich, UK., Gudza-Mugabe M; WHO, Harare, Zimbabwe., Chirenda J; Department of Surgical Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe., Munyanyi M; Department of Health Information and Surveilance, Ministry of Health and Child Care, Harare, Zimbabwe., Chaibva BV; Department of Pharmacy Services, Ministry of Health and Child Care, Harare, Zimbabwe., Tarupiwa A; National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe., Gumbo H; National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe., Juru A; National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe., Nyagupe C; National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe., Ruhanya V; Department of Surgical Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe., Phiri I; Department of Epidemiology and Disease Control, Ministry of Health and Child Care, Harare, Zimbabwe., Manangazira P; Department of Epidemiology and Disease Control, Ministry of Health and Child Care, Harare, Zimbabwe., Goredema A; Department of Epidemiology and Disease Control, Ministry of Health and Child Care, Harare, Zimbabwe., Danda S; Department of Epidemiology and Disease Control, Ministry of Health and Child Care, Harare, Zimbabwe., Chabata I; Department of Epidemiology and Disease Control, Ministry of Health and Child Care, Harare, Zimbabwe., Jonga J; Department of Epidemiology and Disease Control, Ministry of Health and Child Care, Harare, Zimbabwe., Munharira R; Department of Epidemiology and Disease Control, Ministry of Health and Child Care, Harare, Zimbabwe., Masunda K; Harare City Health Department, Beatrice Road Infectious Diseases Hospital, Harare, Zimbabwe., Mukeredzi I; Harare City Health Department, Beatrice Road Infectious Diseases Hospital, Harare, Zimbabwe., Mangwanya D; Department of Epidemiology and Disease Control, Ministry of Health and Child Care, Harare, Zimbabwe., Trotter A; Quadram Institute Bioscience, Norwich, UK., Le Viet T; Quadram Institute Bioscience, Norwich, UK., Rudder S; Quadram Institute Bioscience, Norwich, UK., Kay G; Quadram Institute Bioscience, Norwich, UK., Baker D; Quadram Institute Bioscience, Norwich, UK., Thilliez G; Quadram Institute Bioscience, Norwich, UK., Gutierrez AV; Quadram Institute Bioscience, Norwich, UK., O'Grady J; Quadram Institute Bioscience, Norwich, UK., Hove M; Department of Curative Services, Ministry of Health and Child Care, Harare, Zimbabwe., Mutapuri-Zinyowera S; National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe., Page AJ; Quadram Institute Bioscience, Norwich, UK., Kingsley RA; Quadram Institute Bioscience, Norwich, UK; School of Biological Sciences, University of East Anglia, Norwich, UK. Electronic address: rob.kingsley@quadram.ac.uk., Mhlanga G; Department of Epidemiology and Disease Control, Ministry of Health and Child Care, Harare, Zimbabwe.
Jazyk:	angličtina
Zdroj:	The Lancet. Global health [Lancet Glob Health] 2021 Dec; Vol. 9 (12), pp. e1658-e1666. Date of Electronic Publication: 2021 Oct 22.
DOI:	10.1016/S2214-109X(21)00434-4
Abstrakt:	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. Competing Interests: Declaration of interests We declare no competing interests. (Copyright © 2021 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)
Databáze:	MEDLINE
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