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Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

Author

Listed:
  • Gytis Dudas

    (Gothenburg Global Biodiversity Centre
    Vilnius University Hospital Santaros Klinikos)

  • Samuel L. Hong

    (Immunology and Transplantation, Rega Institute, KU Leuven)

  • Barney I. Potter

    (Immunology and Transplantation, Rega Institute, KU Leuven)

  • Sébastien Calvignac-Spencer

    (Robert Koch Institute
    Robert Koch Institute)

  • Frédéric S. Niatou-Singa

    (WWF Central African Republic Programme Office)

  • Thais B. Tombolomako

    (WWF Central African Republic Programme Office)

  • Terence Fuh-Neba

    (WWF Central African Republic Programme Office)

  • Ulrich Vickos

    (Amitié Hospital
    Children’s Hospital Bambino Gesù, IRCCS)

  • Markus Ulrich

    (Robert Koch Institute)

  • Fabian H. Leendertz

    (Robert Koch Institute)

  • Kamran Khan

    (BlueDot
    St. Michael’s Hospital
    University of Toronto)

  • Carmen Huber

    (BlueDot)

  • Alexander Watts

    (BlueDot)

  • Ingrida Olendraitė

    (Vilnius University Hospital Santaros Klinikos
    University of Cambridge, Addenbrooke’s Hospital Lab)

  • Joost Snijder

    (Utrecht University)

  • Kim N. Wijnant

    (Utrecht University)

  • Alexandre M.J.J. Bonvin

    (Utrecht University)

  • Pascale Martres

    (Microbiology, Centre Hospitalier René Dubos)

  • Sylvie Behillil

    (CNRS UMR 3569, Université de Paris, Institut Pasteur
    Institut Pasteur)

  • Ahidjo Ayouba

    (TransVIHMI, Université de Montpellier, IRD, INSERM)

  • Martin Foudi Maidadi

    (Institut de Recherches Médicales et D’études des Plantes Médicinales)

  • Dowbiss Meta Djomsi

    (Institut de Recherches Médicales et D’études des Plantes Médicinales)

  • Celestin Godwe

    (Institut de Recherches Médicales et D’études des Plantes Médicinales)

  • Christelle Butel

    (TransVIHMI, Université de Montpellier, IRD, INSERM)

  • Aistis Šimaitis

    (The Office of the Government of the Republic of Lithuania)

  • Miglė Gabrielaitė

    (Center for Genomic Medicine, Rigshospitalet)

  • Monika Katėnaitė

    (Vilnius University Hospital Santaros Klinikos)

  • Rimvydas Norvilas

    (Vilnius University Hospital Santaros Klinikos
    State Research Institute Centre for Innovative Medicine)

  • Ligita Raugaitė

    (Vilnius University Hospital Santaros Klinikos)

  • Giscard Wilfried Koyaweda

    (Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP))

  • Jephté Kaleb Kandou

    (Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP))

  • Rimvydas Jonikas

    (Hospital of Lithuanian University of Health Sciences Kauno Klinikos)

  • Inga Nasvytienė

    (Hospital of Lithuanian University of Health Sciences Kauno Klinikos)

  • Živilė Žemeckienė

    (Hospital of Lithuanian University of Health Sciences Kauno Klinikos)

  • Dovydas Gečys

    (Lithuanian University of Health Sciences)

  • Kamilė Tamušauskaitė

    (Lithuanian University of Health Sciences)

  • Milda Norkienė

    (Vilnius University)

  • Emilija Vasiliūnaitė

    (Vilnius University)

  • Danguolė Žiogienė

    (Vilnius University)

  • Albertas Timinskas

    (Vilnius University)

  • Marius Šukys

    (Hospital of Lithuanian University of Health Sciences Kauno Klinikos
    Lithuanian University of Health Sciences)

  • Mantas Šarauskas

    (Hospital of Lithuanian University of Health Sciences Kauno Klinikos)

  • Gediminas Alzbutas

    (Lithuanian University of Health Sciences)

  • Adrienne Amuri Aziza

    (National Institute for Biomedical Research (INRB)
    University of Kinshasa (UNIKIN))

  • Eddy Kinganda Lusamaki

    (National Institute for Biomedical Research (INRB)
    University of Kinshasa (UNIKIN))

  • Jean-Claude Makangara Cigolo

    (National Institute for Biomedical Research (INRB)
    University of Kinshasa (UNIKIN))

  • Francisca Muyembe Mawete

    (National Institute for Biomedical Research (INRB)
    University of Kinshasa (UNIKIN))

  • Emmanuel Lokilo Lofiko

    (National Institute for Biomedical Research (INRB))

  • Placide Mbala Kingebeni

    (National Institute for Biomedical Research (INRB)
    University of Kinshasa (UNIKIN))

  • Jean-Jacques Muyembe Tamfum

    (National Institute for Biomedical Research (INRB)
    University of Kinshasa (UNIKIN))

  • Marie Roseline Darnycka Belizaire

    (World Health Organization, Central African Republic Office)

  • René Ghislain Essomba

    (Ministry of Public Health
    University of Yaoundé I)

  • Marie Claire Okomo Assoumou

    (Ministry of Public Health
    University of Yaoundé I)

  • Akenji Blaise Mboringong

    (Ministry of Public Health)

  • Alle Baba Dieng

    (Cameroon Office)

  • Dovilė Juozapaitė

    (Vilnius University Hospital Santaros Klinikos)

  • Salome Hosch

    (Swiss Tropical and Public Health Institute)

  • Justino Obama

    (Ministry of Health and Social Welfare)

  • Mitoha Ondo’o Ayekaba

    (Ministry of Health and Social Welfare)

  • Daniel Naumovas

    (Vilnius University Hospital Santaros Klinikos)

  • Arnoldas Pautienius

    (Lithuanian University of Health Sciences)

  • Clotaire Donatien Rafaï

    (Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP))

  • Astra Vitkauskienė

    (Lithuanian University of Health Sciences)

  • Rasa Ugenskienė

    (Hospital of Lithuanian University of Health Sciences Kauno Klinikos
    Lithuanian University of Health Sciences)

  • Alma Gedvilaitė

    (Vilnius University)

  • Darius Čereškevičius

    (Hospital of Lithuanian University of Health Sciences Kauno Klinikos
    Lithuanian University of Health Sciences)

  • Vaiva Lesauskaitė

    (Lithuanian University of Health Sciences)

  • Lukas Žemaitis

    (Lithuanian University of Health Sciences
    National Public Health Surveillance Laboratory)

  • Laimonas Griškevičius

    (Vilnius University Hospital Santaros Klinikos)

  • Guy Baele

    (Immunology and Transplantation, Rega Institute, KU Leuven)

Abstract

Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers.

Suggested Citation

  • Gytis Dudas & Samuel L. Hong & Barney I. Potter & Sébastien Calvignac-Spencer & Frédéric S. Niatou-Singa & Thais B. Tombolomako & Terence Fuh-Neba & Ulrich Vickos & Markus Ulrich & Fabian H. Leendertz, 2021. "Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26055-8
    DOI: 10.1038/s41467-021-26055-8
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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.

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