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

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.

Figure 1

Study profile

Figure 2

Epidemic curve of SARS-CoV-2 confirmed cases as of Oct 16, 2020 (A) Cumulative number of positive tests for SARS-CoV-2 in individuals reporting travel in the previous 2 weeks (probable imported cases) or domestic cases by day. (B) Number of reported positive tests for SARS-CoV-2 by day.

Figure 3

Phylogenetic relationship of SARS-CoV-2 genomes from Zimbabwe and closely related genomes from global cases Maximum likelihood phylogenetic tree of 156 SARS-CoV-2 genomes from Zimbabwe together with their closest 316 genomes from global samples. Lineages connecting Zimbabwe clusters (red) and global lineages (black) are indicated.

Figure 4

SNP differences between genomes from the cluster containing the B.1.446 lineage and the ancestral sequence The sequences classified by Pangolin as B.1.446 are in red, while the others were classified as B.1. The plot was created with the software snipit.