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Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity.


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.

SUBMITTER: Butera Y 

PROVIDER: S-EPMC8481346 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity.

Butera Yvan Y   Mukantwari Enatha E   Artesi Maria M   Umuringa Jeanne d'arc JD   O'Toole Áine Niamh ÁN   Hill Verity V   Rooke Stefan S   Hong Samuel Leandro SL   Dellicour Simon S   Majyambere Onesphore O   Bontems Sebastien S   Boujemla Bouchra B   Quick Josh J   Resende Paola Cristina PC   Loman Nick N   Umumararungu Esperance E   Kabanda Alice A   Murindahabi Marylin Milumbu MM   Tuyisenge Patrick P   Gashegu Misbah M   Rwabihama Jean Paul JP   Sindayiheba Reuben R   Gikic Djordje D   Souopgui Jacob J   Ndifon Wilfred W   Rutayisire Robert R   Gatare Swaibu S   Mpunga Tharcisse T   Ngamije Daniel D   Bours Vincent V   Rambaut Andrew A   Nsanzimana Sabin S   Baele Guy G   Durkin Keith K   Mutesa Leon L   Rujeni Nadine N  

Nature communications 20210929 1


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 Kigal  ...[more]

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