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; Nadine Rujeni

doi:10.1038/s41467-021-25985-7

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

Research output: Contribution to journal › Article › peer-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 language	English
Article number	5705
Journal	Nature Communications
Volume	12
Issue number	1
DOIs	https://doi.org/10.1038/s41467-021-25985-7
Publication status	Published - 29 Sept 2021

Access to Document

10.1038/s41467-021-25985-7Licence: Creative Commons: Attribution (CC-BY)

RujeniEtalNC2021GenomicSequencingOfSARS-CoV-2InRwandaFinal published version, 9.23 MBLicence: Creative Commons: Attribution (CC-BY)

The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control
Rambaut, A. (Principal Investigator)
EU government bodies
1/08/17 → 31/07/23
Project: Research
Putting genomic surveillance at the heart of viral epidemic response.
Rambaut, A. (Principal Investigator)
UK-based charities
1/08/17 → 31/07/24
Project: Research
Wellcome Trust Four-Year PhD Studentship (Ms Aine O'Toole)
Matthews, K. (Principal Investigator) & Woolhouse, M. (Co-investigator)
UK-based charities
1/10/16 → 1/10/21
Project: Research

Cite this

Butera, Y., Mukantwari, E., Artesi, M., Umuringa, J. D., O’Toole, Á. N., Hill, V., Rooke, S., Hong, S. L., Dellicour, S., Majyambere, O., Bontems, S., Boujemla, B., Quick, J., Resende, P. C., Loman, N., Umumararungu, E., Kabanda, A., Murindahabi, M. M., Tuyisenge, P., ... Rujeni, N. (2021). Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity. Nature Communications, 12(1), Article 5705. https://doi.org/10.1038/s41467-021-25985-7

@article{94226d86da3147d69acce64b6da94cfd,

title = "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.",

author = "Yvan Butera and Enatha Mukantwari and Maria Artesi and Umuringa, {Jeanne D{\textquoteright}arc} and O{\textquoteright}Toole, {{\'A}ine Niamh} and Verity Hill and Stefan Rooke and Hong, {Samuel Leandro} and Simon Dellicour and Onesphore Majyambere and Sebastien Bontems and Bouchra Boujemla and Josh Quick and Resende, {Paola Cristina} and Nick Loman and Esperance Umumararungu and Alice Kabanda and Murindahabi, {Marylin Milumbu} and Patrick Tuyisenge and Misbah Gashegu and Rwabihama, {Jean Paul} and Reuben Sindayiheba and Djordje Gikic and Jacob Souopgui and Wilfred Ndifon and Robert Rutayisire and Swaibu Gatare and Tharcisse Mpunga and Daniel Ngamije and Vincent Bours and Andrew Rambaut and Sabin Nsanzimana and Guy Baele and Keith Durkin and Leon Mutesa and Nadine Rujeni",

year = "2021",

month = sep,

day = "29",

doi = "10.1038/s41467-021-25985-7",

language = "English",

volume = "12",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

number = "1",

}

Butera, Y, Mukantwari, E, Artesi, M, Umuringa, JD, O’Toole, ÁN, Hill, V, Rooke, S, Hong, SL, Dellicour, S, Majyambere, O, Bontems, S, Boujemla, B, Quick, J, Resende, PC, Loman, N, Umumararungu, E, Kabanda, A, Murindahabi, MM, Tuyisenge, P, Gashegu, M, Rwabihama, JP, Sindayiheba, R, Gikic, D, Souopgui, J, Ndifon, W, Rutayisire, R, Gatare, S, Mpunga, T, Ngamije, D, Bours, V, Rambaut, A, Nsanzimana, S, Baele, G, Durkin, K, Mutesa, L & Rujeni, N 2021, 'Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity', Nature Communications, vol. 12, no. 1, 5705. https://doi.org/10.1038/s41467-021-25985-7

TY - JOUR

T1 - Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity

AU - Butera, Yvan

AU - Mukantwari, Enatha

AU - Artesi, Maria

AU - Umuringa, Jeanne D’arc

AU - O’Toole, Áine Niamh

AU - Hill, Verity

AU - Rooke, Stefan

AU - Hong, Samuel Leandro

AU - Dellicour, Simon

AU - Majyambere, Onesphore

AU - Bontems, Sebastien

AU - Boujemla, Bouchra

AU - Quick, Josh

AU - Resende, Paola Cristina

AU - Loman, Nick

AU - Umumararungu, Esperance

AU - Kabanda, Alice

AU - Murindahabi, Marylin Milumbu

AU - Tuyisenge, Patrick

AU - Gashegu, Misbah

AU - Rwabihama, Jean Paul

AU - Sindayiheba, Reuben

AU - Gikic, Djordje

AU - Souopgui, Jacob

AU - Ndifon, Wilfred

AU - Rutayisire, Robert

AU - Gatare, Swaibu

AU - Mpunga, Tharcisse

AU - Ngamije, Daniel

AU - Bours, Vincent

AU - Rambaut, Andrew

AU - Nsanzimana, Sabin

AU - Baele, Guy

AU - Durkin, Keith

AU - Mutesa, Leon

AU - Rujeni, Nadine

PY - 2021/9/29

Y1 - 2021/9/29

N2 - 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.

AB - 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.

U2 - 10.1038/s41467-021-25985-7

DO - 10.1038/s41467-021-25985-7

M3 - Article

SN - 2041-1723

VL - 12

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 5705

ER -

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

Abstract

Access to Document

Fingerprint

Projects

The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control

Putting genomic surveillance at the heart of viral epidemic response.

Wellcome Trust Four-Year PhD Studentship (Ms Aine O'Toole)

Cite this