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

Author

Listed:
  • Yvan Butera

    (University of Rwanda
    Ministry of Health
    GIGA Research Institute)

  • 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
    Université Libre de Bruxelles)

  • 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
    Oswaldo Cruz Institute, FIOCRUZ)

  • Nick Loman

    (University of Birmingham)

  • Esperance Umumararungu

    (Rwanda Biomedical Center)

  • Alice Kabanda

    (Rwanda Biomedical Center)

  • Marylin Milumbu Murindahabi

    (Ministry of Health
    University of Rwanda)

  • 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
    IBMM, Université Libre de)

  • Wilfred Ndifon

    (African Institute for Mathematical Sciences)

  • Robert Rutayisire

    (Ministry of Health
    Rwanda Biomedical Center)

  • Swaibu Gatare

    (Ministry of Health
    Rwanda Biomedical Center)

  • Tharcisse Mpunga

    (Ministry of Health)

  • Daniel Ngamije

    (Ministry of Health)

  • Vincent Bours

    (GIGA Research Institute
    University Hospital of Liège)

  • 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
    Ministry of Health)

  • Nadine Rujeni

    (Ministry of Health
    University of Rwanda)

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.

Suggested Citation

  • 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 Bont, 2021. "Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25985-7
    DOI: 10.1038/s41467-021-25985-7
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    Cited by:

    1. Edyth Parker & Catelyn Anderson & Mark Zeller & Ahmad Tibi & Jennifer L. Havens & Geneviève Laroche & Mehdi Benlarbi & Ardeshir Ariana & Refugio Robles-Sikisaka & Alaa Abdel Latif & Alexander Watts & , 2022. "Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. Jordan Douglas & David Winter & Andrea McNeill & Sam Carr & Michael Bunce & Nigel French & James Hadfield & Joep Ligt & David Welch & Jemma L. Geoghegan, 2022. "Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    3. Philemon Lindagato & Yongjun Li & Gaoxue Yang, 2023. "Save the giants: demand beyond production capacity of tantalum raw materials," Mineral Economics, Springer;Raw Materials Group (RMG);Luleå University of Technology, vol. 36(3), pages 535-541, September.
    4. Idowu B. Olawoye & Paul E. Oluniyi & Judith U. Oguzie & Jessica N. Uwanibe & Tolulope A. Kayode & Testimony J. Olumade & Fehintola V. Ajogbasile & Edyth Parker & Philomena E. Eromon & Priscilla Abechi, 2023. "Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    5. Tamara Kaleta & Lisa Kern & Samuel Leandro Hong & Martin Hölzer & Georg Kochs & Julius Beer & Daniel Schnepf & Martin Schwemmle & Nena Bollen & Philipp Kolb & Magdalena Huber & Svenja Ulferts & Sebast, 2022. "Antibody escape and global spread of SARS-CoV-2 lineage A.27," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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