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GENOMIC SEQUENCING OF SARS-COV-2 IN RWANDA REVEALS THE IMPORTANCE OF INCOMING TRAVELERS ON LINEAGE DIVERSITY
Butera, Yvan et al. | Date Issued: 2021
Author
Butera, Yvan
Mukantwari, Enatha
Artesi, Maria
Umuringa, Jeanne d´arc
O`Toole, Áine Niamh
Hill, Verity
Rooke, Stefan
Hong, Samuel Leandro
Dellicou, Simon
Majyambere, Onesphore
Bontems, Sebastien
Boujemla, Bouchra
Quick, Josh
Resende, Paola Cristina
Loman, NIck
Umumararungu, Esperance
Kabanda, Alice
Murindahabi, Marylin Milumbu
Tuyisenge, Patrick
Gashegu, Misbah
Rwabihama, Jean Paul
Sindayiheba, Reuben
Gikic, Djordje
Souopgui, Jacob
Ndifon, Wilfred
Rutayisire, Robert
Gatare, Swaibu
Mpunga, Tharcisse
Ngamije, Daniel
Bours, Vincent
Rambaut, Andrew
Nsanzimana, Sabin
Baele, Guy
Durkin, Keith
Mutesa, Leon
Rujeni, Nadine
Affilliation
Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda. Kigali, Rwanda / Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health. Kigali, Rwanda / Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium.
National Reference Laboratory, Rwanda Biomedical Center, Kigali, Rwanda.
Laboratory of Human Genetics, GIGA Research Institute. Liège, Belgium.
National Reference Laboratory, Rwanda Biomedical Center, Kigali, Rwanda.
Institute of Evolutionary Biology, University of Edinburgh. Edinburgh, Scotland.
Institute of Evolutionary Biology, University of Edinburgh. Edinburgh, Scotland.
Institute of Evolutionary Biology, University of Edinburgh. Edinburgh, Scotland.
Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven. Leuven, Belgium.
Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven. Leuven, Belgium / Spatial Epidemiology Laboratory, Université Libre de Bruxelles. Brussels, Belgium.
National Reference Laboratory, Rwanda Biomedical Center, Kigali, Rwanda.
Department of Clinical Microbiology, University Hospital of Liège., Liège, Belgium.
Laboratory of Human Genetics, GIGA Research Institute. Liège, Belgium.
University of Birmingham. Birmingham, England.
University College London. London, England / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Vírus Respiratório e do Sarampo. Rio de Janeiro, RJ, Brasil.
University of Birmingham. Birmingham, England.
National Reference Laboratory, Rwanda Biomedical Center. Kigali, Rwanda.
National Reference Laboratory, Rwanda Biomedical Center. Kigali, Rwanda.
Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda / School of Science, College of Science and Technology, University of Rwanda. Kigali, Rwanda.
National Reference Laboratory, Rwanda Biomedical Center. Kigali, Rwanda.
Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda.
Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda.
National Reference Laboratory, Rwanda Biomedical Center. Kigali, Rwanda.
Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda.
Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda / Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de, Bruxelles. Gosselies, Belgium.
African Institute for Mathematical Sciences. Kigali, Rwanda.
Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda / National Reference Laboratory, Rwanda Biomedical Center. Kigali, Rwanda.
Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda / National Reference Laboratory, Rwanda Biomedical Center. Kigali, Rwanda.
Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium / Department of Human Genetics, University Hospital of Liège, Liège, Belgium.
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland.
Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health. Kigali, Rwanda.
Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven. Leuven, Belgium.
Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium.
Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda / Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda.
Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda / Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, Leuven, Belgium.
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.
Keywords in Portuguese
SARS-CoV-2
Sequenciamento genômico
Ruanda, África
Importância dos viajantes
Com diversidade de linhagem
Taxas de transmissão
 
Keywords
SARS-CoV-2
Rwanda
Genomic sequencing
Importance of incoming travelers
Lineage diversity
Transmission rates
 
Publisher
Nature
Citation
BUTERA, Yvan et al. Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity. Nature Communications, v. 12, 5705, p. 1-11, 2021.
DOI
10.1038/s41467-021-25985-7
ISSN
2041-1723