Abstract
COVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Here we describe 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in Rwanda from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the B.1.1.7 and B.1.351 variants of concern among incoming travelers tested at Kigali International Airport. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences were available. Our results highlight the importance of systematic genomic surveillance and regional collaborations for a durable response towards combating COVID-19.
Highlights
3,17 ✉, 1234567890():,; COVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2
We report the detection of the first Rwandan cases of the B.1.1.7 and B.1.351 variants of concern among incoming travelers tested at Kigali International Airport
We show the origin of these collected travel cases for which we have genomic data in Fig. 2, with a focus on neighboring countries, which reveals that most travel cases originated in Tanzania, a country that has not yet made any genomic data available
Summary
3,17 ✉, 1234567890():,; COVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Despite continued massive testing[6], contact tracing, hotspot mapping, and preventive measures[7], the number of cases continued to increase (Fig. 1 and Supplementary Figure S1), mainly associated with cross-border land travels through truck drivers[8] and imported cases (Supplementary Fig. S2). This culminated in a ‘first wave’ of local transmission between July and September 2020. Given the importance of these findings on regional surveillance of SARS-CoV-2, we emphasize the need for strengthening genomic surveillance at the country’s points of entry following the detection of the first cases of the B.1.1.7 and B.1.351 VOCs among travelers arriving at KIA
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