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 COVID-19 Genomics UK (COG-UK) Consortium, SARS-CoV-2 Research Group, Tapfumanei Mashe*, Faustinos Tatenda Takawira, Leonardo De Oliveira Martins, Muchaneta Gudza-Mugabe, Joconiah Chirenda, Manes Munyanyi, Blessmore V Chaibva, Andrew Tarupiwa, Hlanai Gumbo, Agnes Juru, Charles Nyagupe, Vurayai Ruhanya, Isaac Phiri, Portia Manangazira, Alexander Goredema, Sydney Danda, Israel Chabata, Janet JongaRutendo Munharira, Kudzai Masunda, Innocent Mukeredzi, Douglas Mangwanya, Alex Trotter, Thanh Le-Viet, Steven Rudder, Gemma Kay, David Baker, Gaetan Thilliez, Ana Victoria Gutierrez, Justin O'Grady, Maxwell Hove, Sekesai Mutapuri-Zinyowera, Andrew J Page, Robert A Kingsley, Gibson Mhlanga, Matthew Bashton, Andrew Nelson, Clare McCann, Darren Smith, Greg Young

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

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.
Original languageEnglish
Pages (from-to)e1658-e1666
Number of pages9
JournalThe Lancet Global Health
Volume9
Issue number12
Early online date22 Oct 2021
DOIs
Publication statusE-pub ahead of print - 22 Oct 2021

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