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

Yvan Butera, Enatha Mukantwari, Maria Artesi, Jeanne d’arc Umuringa, Áine Niamh O’Toole, Verity Hill, Stefan Rooke, Samuel Leandro Hong, Simon Dellicour, Onesphore Majyambere, Sebastien Bontems, Bouchra Boujemla, Josh Quick, Paola Cristina Resende, Nick Loman, Esperance Umumararungu, Alice Kabanda, Marylin Milumbu Murindahabi, Patrick Tuyisenge, Misbah Gashegu, Jean Paul Rwabihama, Reuben Sindayiheba, Djordje Gikic, Jacob Souopgui, Wilfred Ndifon, Robert Rutayisire, Swaibu Gatare, Tharcisse Mpunga, Daniel Ngamije, Vincent Bours, Andrew Rambaut, Sabin Nsanzimana, Guy Baele (), Keith Durkin (), Leon Mutesa () and Nadine Rujeni ()
Additional contact information
Yvan Butera: University of Rwanda
Enatha Mukantwari: Rwanda Biomedical Center
Maria Artesi: GIGA Research Institute
Jeanne d’arc Umuringa: Rwanda Biomedical Center
Áine Niamh O’Toole: University of Edinburgh
Verity Hill: University of Edinburgh
Stefan Rooke: University of Edinburgh
Samuel Leandro Hong: Immunology and Transplantation, Rega Institute KU Leuven
Simon Dellicour: Immunology and Transplantation, Rega Institute KU Leuven
Onesphore Majyambere: Rwanda Biomedical Center
Sebastien Bontems: University Hospital of Liège
Bouchra Boujemla: GIGA Research Institute
Josh Quick: University of Birmingham
Paola Cristina Resende: University College London
Nick Loman: University of Birmingham
Esperance Umumararungu: Rwanda Biomedical Center
Alice Kabanda: Rwanda Biomedical Center
Marylin Milumbu Murindahabi: Ministry of Health
Patrick Tuyisenge: Rwanda Biomedical Center
Misbah Gashegu: Ministry of Health
Jean Paul Rwabihama: Ministry of Health
Reuben Sindayiheba: Rwanda Biomedical Center
Djordje Gikic: Ministry of Health
Jacob Souopgui: University of Rwanda
Wilfred Ndifon: African Institute for Mathematical Sciences
Robert Rutayisire: Ministry of Health
Swaibu Gatare: Ministry of Health
Tharcisse Mpunga: Ministry of Health
Daniel Ngamije: Ministry of Health
Vincent Bours: GIGA Research Institute
Andrew Rambaut: University of Edinburgh
Sabin Nsanzimana: Ministry of Health
Guy Baele: Immunology and Transplantation, Rega Institute KU Leuven
Keith Durkin: GIGA Research Institute
Leon Mutesa: University of Rwanda
Nadine Rujeni: Ministry of Health

Nature Communications, 2021, vol. 12, issue 1, 1-11

Abstract: 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.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25985-7

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DOI: 10.1038/s41467-021-25985-7

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