Tracking down the origin and subsequent spread of SARS-CoV-2 lineage B.1.619

Nena Bollen; Samuel L. Hong; Barney I. Potter; Reto Lienhard; Marie-Lise Tritten; Nicolas Sierro; Emmanuel Guedj; R. mi Dulize; David Bornand; Mehdi Auberson; Maxime Berthouzoz; Pauline Duvoisin; Nikolai V. Ivanov; Manuel C. Peitsch; Verity Hill; Veerle Matheeussen; S. bastien Bontems; Bruno Verhasselt; Jonathan Degosserie; Luc Waumans; Guillaume Bayon-Vicente; Marijke Reynders; Lien Cattoir; Valentin Coste; Hanne Valgaeren; Johan van Weyenbergh; Lize Cuypers; Emmanuel André; Keith Durkin; Piet Maes; Kamran Khan; Carmen Huber; Marc A. Suchard; Martin Maidadi Foudi; C. lestin Godwe; Moise Henri Moumbeket Yifomnjou; Messanga Landry; Richard Njouom; Placide Mbala Kingebeni; Paul Oluniyi; Idowu B. Olawoye; Christian Happi; Ahidjo Ayouba; Martine Peeters; Sylvie Behillil; Etienne Simon-Lorière; Martin Hölzer; Simon Dellicour; Gytis Dudas; Guy Baele; COVID-19 Genomics Belgium Consortium

doi:10.1093/ve/veaf017

Tracking down the origin and subsequent spread of SARS-CoV-2 lineage B.1.619

Nena Bollen^*
, Samuel L. Hong
, Barney I. Potter
, Reto Lienhard
, Marie-Lise Tritten
, Nicolas Sierro
, Emmanuel Guedj
, R. mi Dulize
, David Bornand
, Mehdi Auberson
, Maxime Berthouzoz
, Pauline Duvoisin
, Nikolai V. Ivanov
, Manuel C. Peitsch
, Verity Hill
, Veerle Matheeussen
, S. bastien Bontems
, Bruno Verhasselt
, Jonathan Degosserie
, Luc Waumans

Guillaume Bayon-Vicente, Marijke Reynders, Lien Cattoir, Valentin Coste, Hanne Valgaeren, Johan van Weyenbergh, Lize Cuypers, Emmanuel André, Keith Durkin, Piet Maes, Kamran Khan, Carmen Huber, Marc A. Suchard, Martin Maidadi Foudi, C. lestin Godwe, Moise Henri Moumbeket Yifomnjou, Messanga Landry, Richard Njouom, Placide Mbala Kingebeni, Paul Oluniyi, Idowu B. Olawoye, Christian Happi, Ahidjo Ayouba, Martine Peeters, Sylvie Behillil, Etienne Simon-Lorière, Martin Hölzer, Simon Dellicour, Gytis Dudas, Guy Baele, COVID-19 Genomics Belgium Consortium

^*Corresponding author for this work

KU Leuven
ADMED Microbiologie
Philip Morris Products S.A.
University of Edinburgh
University of Antwerp
University of Liege
Ghent University
Université catholique de Louvain
Jessa Hospital
Universite de Mons
OLV Hospital Aalst
Imelda Hospital
BlueDot Inc.
University of Toronto
University of California at Los Angeles
Institute of Medical Research and Medicinal Plant Studies Yaounde
Centre Pasteur du Cameroun
Ministère de la Santé Publique
L’Hôpital Général de Référence de Kole
Redeemer's University
African Centre of Excellence for Genomics of Infectious Diseases (ACEGID)
Recherches Translationnelles sur le VIH et les Maladies Infectieuses
Institut Pasteur Paris
Robert Koch-Institut
Université libre de Bruxelles
Vilnius University

Research output: Contribution to journal › Article › Academic › peer-review

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Abstract

Since late 2020, the emergence of variants of concern (VOCs) of SARS-CoV-2 has been of concern to public health, researchers and policymakers. Mutations in the SARS-CoV-2 genome—for which clear evidence is available indicating a significant impact on transmissibility, severity and/or immunity—illustrate the importance of genomic surveillance and monitoring the evolution and geographic spread of novel lineages. Lineage B.1.619 was first detected in Switzerland in January 2021, in international travellers returning from Cameroon. This lineage was subsequently also detected in Rwanda, Belgium, Cameroon, France, and many other countries and is characterised by spike protein amino acid mutations N440K and E484K in the receptor binding domain, which are associated with immune escape and higher infectiousness. In this study, we perform a phylogeographic analysis to track the geographic origin and subsequent dispersal of SARS-CoV-2 lineage B.1.619. We employ a recently developed travel history-aware phylogeographic model, enabling us to incorporate genomic sequences with associated travel information. We estimate that B.1.619 most likely originated in Cameroon, in November 2020. We estimate the influence of the number of air-traffic passengers on the dispersal of B.1.619 but find no significant effect, illustrative of the complex dispersal patterns of SARS-CoV-2 lineages. Finally, we examine the metadata associated with infected Belgian patients and report a wide range of symptoms and medical interventions.

Original language	English
Article number	veaf017
Journal	Virus evolution
Volume	11
Issue number	1
DOIs	https://doi.org/10.1093/ve/veaf017
Publication status	Published - 2025

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

B.1.619
Bayesian inference
COVID-19
GLM
Markov chain Monte Carlo
SARS-CoV-2
air traffic
phylogenetics
phylogeography

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10.1093/ve/veaf017

Tracking-down-the-origin-and-subsequent-spread-of-sars-cov-2-lineage-b1619.pdfFinal published version, 2.28 MBLicence: Taverne

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Bollen, N., Hong, S. L., Potter, B. I., Lienhard, R., Tritten, M.-L., Sierro, N., Guedj, E., Dulize, R. M., Bornand, D., Auberson, M., Berthouzoz, M., Duvoisin, P., Ivanov, N. V., Peitsch, M. C., Hill, V., Matheeussen, V., Bontems, S. B., Verhasselt, B., Degosserie, J., ... COVID-19 Genomics Belgium Consortium (2025). Tracking down the origin and subsequent spread of SARS-CoV-2 lineage B.1.619. Virus evolution, 11(1), Article veaf017. https://doi.org/10.1093/ve/veaf017

@article{000fae3b86324a15b2c20ba6b2bd6b00,

title = "Tracking down the origin and subsequent spread of SARS-CoV-2 lineage B.1.619",

abstract = "Since late 2020, the emergence of variants of concern (VOCs) of SARS-CoV-2 has been of concern to public health, researchers and policymakers. Mutations in the SARS-CoV-2 genome—for which clear evidence is available indicating a significant impact on transmissibility, severity and/or immunity—illustrate the importance of genomic surveillance and monitoring the evolution and geographic spread of novel lineages. Lineage B.1.619 was first detected in Switzerland in January 2021, in international travellers returning from Cameroon. This lineage was subsequently also detected in Rwanda, Belgium, Cameroon, France, and many other countries and is characterised by spike protein amino acid mutations N440K and E484K in the receptor binding domain, which are associated with immune escape and higher infectiousness. In this study, we perform a phylogeographic analysis to track the geographic origin and subsequent dispersal of SARS-CoV-2 lineage B.1.619. We employ a recently developed travel history-aware phylogeographic model, enabling us to incorporate genomic sequences with associated travel information. We estimate that B.1.619 most likely originated in Cameroon, in November 2020. We estimate the influence of the number of air-traffic passengers on the dispersal of B.1.619 but find no significant effect, illustrative of the complex dispersal patterns of SARS-CoV-2 lineages. Finally, we examine the metadata associated with infected Belgian patients and report a wide range of symptoms and medical interventions.",

keywords = "B.1.619, Bayesian inference, COVID-19, GLM, Markov chain Monte Carlo, SARS-CoV-2, air traffic, phylogenetics, phylogeography",

author = "Nena Bollen and Hong, \{Samuel L.\} and Potter, \{Barney I.\} and Reto Lienhard and Marie-Lise Tritten and Nicolas Sierro and Emmanuel Guedj and Dulize, \{R. mi\} and David Bornand and Mehdi Auberson and Maxime Berthouzoz and Pauline Duvoisin and Ivanov, \{Nikolai V.\} and Peitsch, \{Manuel C.\} and Verity Hill and Veerle Matheeussen and Bontems, \{S. bastien\} and Bruno Verhasselt and Jonathan Degosserie and Luc Waumans and Guillaume Bayon-Vicente and Marijke Reynders and Lien Cattoir and Valentin Coste and Hanne Valgaeren and \{van Weyenbergh\}, Johan and Lize Cuypers and Emmanuel Andr{\'e} and Keith Durkin and Piet Maes and Kamran Khan and Carmen Huber and Suchard, \{Marc A.\} and Foudi, \{Martin Maidadi\} and Godwe, \{C. lestin\} and Yifomnjou, \{Moise Henri Moumbeket\} and Messanga Landry and Richard Njouom and Kingebeni, \{Placide Mbala\} and Paul Oluniyi and Olawoye, \{Idowu B.\} and Christian Happi and Ahidjo Ayouba and Martine Peeters and Sylvie Behillil and Etienne Simon-Lori{\`e}re and Martin H{\"o}lzer and Simon Dellicour and Gytis Dudas and Guy Baele and \{COVID-19 Genomics Belgium Consortium\} and Emmanuel Andr{\'e} and Simon Dellicour and \{van Ranst\}, Marc and Barney Potter and Samuel Hong and Dufrasne, \{Fran{\c c}ois E.\} and Ruddy Wattiez and Carl Vael and Lynsey Berckmans and Philippe Selhorst and Ari{\"e}n, \{Kevin K.\} and Arnaud Marchant and Coralie Henin and Benoit Haerlingen and \{de Mendonca\}, Ricardo and Marie-Luce Delforge and \{van Dooren\}, Sonia and Bruno Hinckel and Hideo Imamura and Toon Janssen and Ben Caljon and Oriane Soetens and Denis Pi{\'e}rard and Thomas Demuyser and Charlotte Michel and Olivier Vandenberg and \{van den Wijngaert\}, Sigi and Giulia Zorzi and Jean Ruelle and Mukadi, \{Benoit Kabamba\} and Jean-Luc Gala and Bertrand Bearzatto and Ambroise, \{J. r{\^o}me\} and \{van Lint\}, Philippe and Walter Verstrepen and Reinout Naesens and Michael Peeters and Kate Bakelants and Sarah Denayer and Sofieke Klamer and Pascale Hilbert and Sylvain Broh{\'e}e and Pierre-Emmanuel l{\'e}onard and Deniz Karadurmus and Jeremie Gras and Damien F{\'e}ret and Barbara Lambert and Anne Vankeerberghen and Astrid Holderbeke and \{de Beenhouwer\}, Hans and Christine Lammens and Xavier, \{Basil Britto\} and \{le Mercier\}, Marie and Jasmine Coppens and Herman Goossens and Martens, \{Geert A.\} and Koen Swaert and \{van Hoecke\}, Frederik and Dieter Desmet and Pierre Bogaerts and Olivier Denis and TeDin Huang and Dagmar Obbels and Johan Frans and Annick Smismans and Paul-Emile Claus and Truus Goegebuer and Ann Lemmens and \{van den Poel\}, Bea and \{de Bock\}, Sonja and Wim Laffut and \{van Even\}, Ellen and \{van Acker\}, Jos and Charlotte Verfaillie and Elke Vanlaere and \{de Rauw\}, Klara and Brigitte Maes and Guy Froyen and Bert Cruys and Ellen Geerdens and \{van Meensel\}, Britt and Reinoud Cartuyvels and Severine Berden and Marijke Raymaekers and Meex, \{C. cile\} and Laurent Gillet and Maria Artesi and Marie-Pierre Hayette and Vincent Bours and Claire Gourzon{\`e}s and Olivier Ek and Fabrice Bureau and Jorn Hellemans and Patrick Descheemaeker and Marijke Reynders",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2025. Published by Oxford University Press.",

year = "2025",

doi = "10.1093/ve/veaf017",

language = "English",

volume = "11",

journal = "Virus evolution",

issn = "2057-1577",

publisher = "Oxford University Press",

number = "1",

}

Bollen, N, Hong, SL, Potter, BI, Lienhard, R, Tritten, M-L, Sierro, N, Guedj, E, Dulize, RM, Bornand, D, Auberson, M, Berthouzoz, M, Duvoisin, P, Ivanov, NV, Peitsch, MC, Hill, V, Matheeussen, V, Bontems, SB, Verhasselt, B, Degosserie, J, Waumans, L, Bayon-Vicente, G, Reynders, M, Cattoir, L, Coste, V, Valgaeren, H, van Weyenbergh, J, Cuypers, L, André, E, Durkin, K, Maes, P, Khan, K, Huber, C, Suchard, MA, Foudi, MM, Godwe, CL, Yifomnjou, MHM, Landry, M, Njouom, R, Kingebeni, PM, Oluniyi, P, Olawoye, IB, Happi, C, Ayouba, A, Peeters, M, Behillil, S, Simon-Lorière, E, Hölzer, M, Dellicour, S, Dudas, G, Baele, G & COVID-19 Genomics Belgium Consortium 2025, 'Tracking down the origin and subsequent spread of SARS-CoV-2 lineage B.1.619', Virus evolution, vol. 11, no. 1, veaf017. https://doi.org/10.1093/ve/veaf017

TY - JOUR

T1 - Tracking down the origin and subsequent spread of SARS-CoV-2 lineage B.1.619

AU - Bollen, Nena

AU - Hong, Samuel L.

AU - Potter, Barney I.

AU - Lienhard, Reto

AU - Tritten, Marie-Lise

AU - Sierro, Nicolas

AU - Guedj, Emmanuel

AU - Dulize, R. mi

AU - Bornand, David

AU - Auberson, Mehdi

AU - Berthouzoz, Maxime

AU - Duvoisin, Pauline

AU - Ivanov, Nikolai V.

AU - Peitsch, Manuel C.

AU - Hill, Verity

AU - Matheeussen, Veerle

AU - Bontems, S. bastien

AU - Verhasselt, Bruno

AU - Degosserie, Jonathan

AU - Waumans, Luc

AU - Bayon-Vicente, Guillaume

AU - Reynders, Marijke

AU - Cattoir, Lien

AU - Coste, Valentin

AU - Valgaeren, Hanne

AU - van Weyenbergh, Johan

AU - Cuypers, Lize

AU - André, Emmanuel

AU - Durkin, Keith

AU - Maes, Piet

AU - Khan, Kamran

AU - Huber, Carmen

AU - Suchard, Marc A.

AU - Foudi, Martin Maidadi

AU - Godwe, C. lestin

AU - Yifomnjou, Moise Henri Moumbeket

AU - Landry, Messanga

AU - Njouom, Richard

AU - Kingebeni, Placide Mbala

AU - Oluniyi, Paul

AU - Olawoye, Idowu B.

AU - Happi, Christian

AU - Ayouba, Ahidjo

AU - Peeters, Martine

AU - Behillil, Sylvie

AU - Simon-Lorière, Etienne

AU - Hölzer, Martin

AU - Dellicour, Simon

AU - Dudas, Gytis

AU - Baele, Guy

AU - COVID-19 Genomics Belgium Consortium

AU - André, Emmanuel

AU - Dellicour, Simon

AU - van Ranst, Marc

AU - Potter, Barney

AU - Hong, Samuel

AU - Dufrasne, François E.

AU - Wattiez, Ruddy

AU - Vael, Carl

AU - Berckmans, Lynsey

AU - Selhorst, Philippe

AU - Ariën, Kevin K.

AU - Marchant, Arnaud

AU - Henin, Coralie

AU - Haerlingen, Benoit

AU - de Mendonca, Ricardo

AU - Delforge, Marie-Luce

AU - van Dooren, Sonia

AU - Hinckel, Bruno

AU - Imamura, Hideo

AU - Janssen, Toon

AU - Caljon, Ben

AU - Soetens, Oriane

AU - Piérard, Denis

AU - Demuyser, Thomas

AU - Michel, Charlotte

AU - Vandenberg, Olivier

AU - van den Wijngaert, Sigi

AU - Zorzi, Giulia

AU - Ruelle, Jean

AU - Mukadi, Benoit Kabamba

AU - Gala, Jean-Luc

AU - Bearzatto, Bertrand

AU - Ambroise, J. rôme

AU - van Lint, Philippe

AU - Verstrepen, Walter

AU - Naesens, Reinout

AU - Peeters, Michael

AU - Bakelants, Kate

AU - Denayer, Sarah

AU - Klamer, Sofieke

AU - Hilbert, Pascale

AU - Brohée, Sylvain

AU - léonard, Pierre-Emmanuel

AU - Karadurmus, Deniz

AU - Gras, Jeremie

AU - Féret, Damien

AU - Lambert, Barbara

AU - Vankeerberghen, Anne

AU - Holderbeke, Astrid

AU - de Beenhouwer, Hans

AU - Lammens, Christine

AU - Xavier, Basil Britto

AU - le Mercier, Marie

AU - Coppens, Jasmine

AU - Goossens, Herman

AU - Martens, Geert A.

AU - Swaert, Koen

AU - van Hoecke, Frederik

AU - Desmet, Dieter

AU - Bogaerts, Pierre

AU - Denis, Olivier

AU - Huang, TeDin

AU - Obbels, Dagmar

AU - Frans, Johan

AU - Smismans, Annick

AU - Claus, Paul-Emile

AU - Goegebuer, Truus

AU - Lemmens, Ann

AU - van den Poel, Bea

AU - de Bock, Sonja

AU - Laffut, Wim

AU - van Even, Ellen

AU - van Acker, Jos

AU - Verfaillie, Charlotte

AU - Vanlaere, Elke

AU - de Rauw, Klara

AU - Maes, Brigitte

AU - Froyen, Guy

AU - Cruys, Bert

AU - Geerdens, Ellen

AU - van Meensel, Britt

AU - Cartuyvels, Reinoud

AU - Berden, Severine

AU - Raymaekers, Marijke

AU - Meex, C. cile

AU - Gillet, Laurent

AU - Artesi, Maria

AU - Hayette, Marie-Pierre

AU - Bours, Vincent

AU - Gourzonès, Claire

AU - Ek, Olivier

AU - Bureau, Fabrice

AU - Hellemans, Jorn

AU - Descheemaeker, Patrick

AU - Reynders, Marijke

PY - 2025

Y1 - 2025

N2 - Since late 2020, the emergence of variants of concern (VOCs) of SARS-CoV-2 has been of concern to public health, researchers and policymakers. Mutations in the SARS-CoV-2 genome—for which clear evidence is available indicating a significant impact on transmissibility, severity and/or immunity—illustrate the importance of genomic surveillance and monitoring the evolution and geographic spread of novel lineages. Lineage B.1.619 was first detected in Switzerland in January 2021, in international travellers returning from Cameroon. This lineage was subsequently also detected in Rwanda, Belgium, Cameroon, France, and many other countries and is characterised by spike protein amino acid mutations N440K and E484K in the receptor binding domain, which are associated with immune escape and higher infectiousness. In this study, we perform a phylogeographic analysis to track the geographic origin and subsequent dispersal of SARS-CoV-2 lineage B.1.619. We employ a recently developed travel history-aware phylogeographic model, enabling us to incorporate genomic sequences with associated travel information. We estimate that B.1.619 most likely originated in Cameroon, in November 2020. We estimate the influence of the number of air-traffic passengers on the dispersal of B.1.619 but find no significant effect, illustrative of the complex dispersal patterns of SARS-CoV-2 lineages. Finally, we examine the metadata associated with infected Belgian patients and report a wide range of symptoms and medical interventions.

AB - Since late 2020, the emergence of variants of concern (VOCs) of SARS-CoV-2 has been of concern to public health, researchers and policymakers. Mutations in the SARS-CoV-2 genome—for which clear evidence is available indicating a significant impact on transmissibility, severity and/or immunity—illustrate the importance of genomic surveillance and monitoring the evolution and geographic spread of novel lineages. Lineage B.1.619 was first detected in Switzerland in January 2021, in international travellers returning from Cameroon. This lineage was subsequently also detected in Rwanda, Belgium, Cameroon, France, and many other countries and is characterised by spike protein amino acid mutations N440K and E484K in the receptor binding domain, which are associated with immune escape and higher infectiousness. In this study, we perform a phylogeographic analysis to track the geographic origin and subsequent dispersal of SARS-CoV-2 lineage B.1.619. We employ a recently developed travel history-aware phylogeographic model, enabling us to incorporate genomic sequences with associated travel information. We estimate that B.1.619 most likely originated in Cameroon, in November 2020. We estimate the influence of the number of air-traffic passengers on the dispersal of B.1.619 but find no significant effect, illustrative of the complex dispersal patterns of SARS-CoV-2 lineages. Finally, we examine the metadata associated with infected Belgian patients and report a wide range of symptoms and medical interventions.

KW - B.1.619

KW - Bayesian inference

KW - COVID-19

KW - GLM

KW - Markov chain Monte Carlo

KW - SARS-CoV-2

KW - air traffic

KW - phylogenetics

KW - phylogeography

UR - https://www.scopus.com/pages/publications/105017639082

U2 - 10.1093/ve/veaf017

DO - 10.1093/ve/veaf017

M3 - Article

C2 - 41031290

SN - 2057-1577

VL - 11

JO - Virus evolution

JF - Virus evolution

IS - 1

M1 - veaf017

ER -

Tracking down the origin and subsequent spread of SARS-CoV-2 lineage B.1.619

Abstract

UN SDGs

Keywords

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