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 GasheguJean 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*, Nadine Rujeni

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Article number5705
JournalNature Communications
Volume12
Issue number1
DOIs
Publication statusPublished - Dec 2021
Externally publishedYes

Bibliographical note

Funding Information:
This research was commissioned by the National Institute of Health Research (NIHR) Global Health Research programme (16/136/33) using UK aid from the UK Government (funding to E.M. and N.R. through TIBA partnership) and additional funds from the Government of Rwanda through RBC/National Reference Laboratory in collaboration with the Belgian Development Agency (ENABEL) for additional genomic sequencing at the GIGA Research Institute-Liege/Belgium. The views expressed in this publication are those of the authors and not necessarily those of the NIHR, the National Institute of Health Research, the Department of Health and Social Care, or the Rwandan Government. G.B. acknowledges support from the Internal Fondsen KU Leuven/Internal Funds KU Leuven (Grant No. C14/18/094) and the Research Foundation–Flanders (“Fonds voor Wetenschappelijk Onderzoek - Vlaanderen,” G0E1420N, G098321N). S.L.H. acknowledges support from the Research Foundation-Flanders (“Fonds voor Weten-schappelijk Onderzoek - Vlaanderen,” G0D5117N). S.D. is supported by the Fonds National de la Recherche Scientifique (FNRS, Belgium). VH was supported by the Bi otechnology and Biological Sciences Research Council (BBSRC) [grant number BB/ M010996/1]. A.O.T. is supported by the Wellcome Trust Hosts, Pathogens & Global Health Programme [grant number: grant.203783/Z/16/Z] and Fast Grants [award number: 2236]. A.R. acknowledges the support of the Wellcome Trust (Collaborators Award 206298/Z/17/Z – ARTIC network) and the European Research Council (grant agreement no. 725422 – ReservoirDOCS).

Publisher Copyright:
© 2021, The Author(s).

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