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

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; Kamran Khan; Carmen Huber; Alexander Watts; Ingrida Olendraitė; Joost Snijder; Kim N Wijnant; Alexandre M J J Bonvin; Pascale Martres; Sylvie Behillil; Ahidjo Ayouba; Martin Foudi Maidadi; Dowbiss Meta Djomsi; Celestin Godwe; Christelle Butel; Aistis Šimaitis; Miglė Gabrielaitė; Monika Katėnaitė; Rimvydas Norvilas; Ligita Raugaitė; Giscard Wilfried Koyaweda; Jephté Kaleb Kandou; Rimvydas Jonikas; Inga Nasvytienė; Živilė Žemeckienė; Dovydas Gečys; Kamilė Tamušauskaitė; Milda Norkienė; Emilija Vasiliūnaitė; Danguolė Žiogienė; Albertas Timinskas; Marius Šukys; Mantas Šarauskas; Gediminas Alzbutas; Adrienne Amuri Aziza; Eddy Kinganda Lusamaki; Jean-Claude Makangara Cigolo; Francisca Muyembe Mawete; Emmanuel Lokilo Lofiko; Placide Mbala Kingebeni; Jean-Jacques Muyembe Tamfum; Marie Roseline Darnycka Belizaire; René Ghislain Essomba; Marie Claire Okomo Assoumou; Akenji Blaise Mboringong; Alle Baba Dieng; Dovilė Juozapaitė; Salome Hosch; Justino Obama; Mitoha Ondo'o Ayekaba; Daniel Naumovas; Arnoldas Pautienius; Clotaire Donatien Rafaï; Astra Vitkauskienė; Rasa Ugenskienė; Alma Gedvilaitė; Darius Čereškevičius; Vaiva Lesauskaitė; Lukas Žemaitis; Laimonas Griškevičius; Guy Baele

doi:10.1038/s41467-021-26055-8

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

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, Kamran Khan, Carmen Huber, Alexander Watts, Ingrida Olendraitė, Joost Snijder, Kim N Wijnant, Alexandre M J J Bonvin, Pascale Martres, Sylvie Behillil, Ahidjo AyoubaMartin Foudi Maidadi, Dowbiss Meta Djomsi, Celestin Godwe, Christelle Butel, Aistis Šimaitis, Miglė Gabrielaitė, Monika Katėnaitė, Rimvydas Norvilas, Ligita Raugaitė, Giscard Wilfried Koyaweda, Jephté Kaleb Kandou, Rimvydas Jonikas, Inga Nasvytienė, Živilė Žemeckienė, Dovydas Gečys, Kamilė Tamušauskaitė, Milda Norkienė, Emilija Vasiliūnaitė, Danguolė Žiogienė, Albertas Timinskas, Marius Šukys, Mantas Šarauskas, Gediminas Alzbutas, Adrienne Amuri Aziza, Eddy Kinganda Lusamaki, Jean-Claude Makangara Cigolo, Francisca Muyembe Mawete, Emmanuel Lokilo Lofiko, Placide Mbala Kingebeni, Jean-Jacques Muyembe Tamfum, Marie Roseline Darnycka Belizaire, René Ghislain Essomba, Marie Claire Okomo Assoumou, Akenji Blaise Mboringong, Alle Baba Dieng, Dovilė Juozapaitė, Salome Hosch, Justino Obama, Mitoha Ondo'o Ayekaba, Daniel Naumovas, Arnoldas Pautienius, Clotaire Donatien Rafaï, Astra Vitkauskienė, Rasa Ugenskienė, Alma Gedvilaitė, Darius Čereškevičius, Vaiva Lesauskaitė, Lukas Žemaitis, Laimonas Griškevičius, Guy Baele

Afdeling for Genomisk Medicin DIA

44 Citationer (Scopus)

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.

Originalsprog	Engelsk
Artikelnummer	5769
Tidsskrift	Nature Communications
Vol/bind	12
Udgave nummer	1
Sider (fra-til)	5769
Antal sider	12
ISSN	2041-1722
DOI	https://doi.org/10.1038/s41467-021-26055-8
Status	Udgivet - 1 okt. 2021

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Dudas, G., Hong, S. L., Potter, B. I., Calvignac-Spencer, S., Niatou-Singa, F. S., Tombolomako, T. B., Fuh-Neba, T., Vickos, U., Ulrich, M., Leendertz, F. H., Khan, K., Huber, C., Watts, A., Olendraitė, I., Snijder, J., Wijnant, K. N., Bonvin, A. M. J. J., Martres, P., Behillil, S., ... Baele, G. (2021). Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Nature Communications, 12(1), 5769. Artikel 5769. https://doi.org/10.1038/s41467-021-26055-8

Dudas, G, Hong, SL, Potter, BI, Calvignac-Spencer, S, Niatou-Singa, FS, Tombolomako, TB, Fuh-Neba, T, Vickos, U, Ulrich, M, Leendertz, FH, Khan, K, Huber, C, Watts, A, Olendraitė, I, Snijder, J, Wijnant, KN, Bonvin, AMJJ, Martres, P, Behillil, S, Ayouba, A, Maidadi, MF, Djomsi, DM, Godwe, C, Butel, C, Šimaitis, A, Gabrielaitė, M, Katėnaitė, M, Norvilas, R, Raugaitė, L, Koyaweda, GW, Kandou, JK, Jonikas, R, Nasvytienė, I, Žemeckienė, Ž, Gečys, D, Tamušauskaitė, K, Norkienė, M, Vasiliūnaitė, E, Žiogienė, D, Timinskas, A, Šukys, M, Šarauskas, M, Alzbutas, G, Aziza, AA, Lusamaki, EK, Cigolo, J-CM, Mawete, FM, Lofiko, EL, Kingebeni, PM, Tamfum, J-JM, Belizaire, MRD, Essomba, RG, Assoumou, MCO, Mboringong, AB, Dieng, AB, Juozapaitė, D, Hosch, S, Obama, J, Ayekaba, MO, Naumovas, D, Pautienius, A, Rafaï, CD, Vitkauskienė, A, Ugenskienė, R, Gedvilaitė, A, Čereškevičius, D, Lesauskaitė, V, Žemaitis, L, Griškevičius, L & Baele, G 2021, 'Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions', Nature Communications, bind 12, nr. 1, 5769, s. 5769. https://doi.org/10.1038/s41467-021-26055-8

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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.",

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T1 - Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

AU - Dudas, Gytis

AU - Hong, Samuel L

AU - Potter, Barney I

AU - Calvignac-Spencer, Sébastien

AU - Niatou-Singa, Frédéric S

AU - Tombolomako, Thais B

AU - Fuh-Neba, Terence

AU - Vickos, Ulrich

AU - Ulrich, Markus

AU - Leendertz, Fabian H

AU - Khan, Kamran

AU - Huber, Carmen

AU - Watts, Alexander

AU - Olendraitė, Ingrida

AU - Snijder, Joost

AU - Wijnant, Kim N

AU - Bonvin, Alexandre M J J

AU - Martres, Pascale

AU - Behillil, Sylvie

AU - Ayouba, Ahidjo

AU - Maidadi, Martin Foudi

AU - Djomsi, Dowbiss Meta

AU - Godwe, Celestin

AU - Butel, Christelle

AU - Šimaitis, Aistis

AU - Gabrielaitė, Miglė

AU - Katėnaitė, Monika

AU - Norvilas, Rimvydas

AU - Raugaitė, Ligita

AU - Koyaweda, Giscard Wilfried

AU - Kandou, Jephté Kaleb

AU - Jonikas, Rimvydas

AU - Nasvytienė, Inga

AU - Žemeckienė, Živilė

AU - Gečys, Dovydas

AU - Tamušauskaitė, Kamilė

AU - Norkienė, Milda

AU - Vasiliūnaitė, Emilija

AU - Žiogienė, Danguolė

AU - Timinskas, Albertas

AU - Šukys, Marius

AU - Šarauskas, Mantas

AU - Alzbutas, Gediminas

AU - Aziza, Adrienne Amuri

AU - Lusamaki, Eddy Kinganda

AU - Cigolo, Jean-Claude Makangara

AU - Mawete, Francisca Muyembe

AU - Lofiko, Emmanuel Lokilo

AU - Kingebeni, Placide Mbala

AU - Tamfum, Jean-Jacques Muyembe

AU - Belizaire, Marie Roseline Darnycka

AU - Essomba, René Ghislain

AU - Assoumou, Marie Claire Okomo

AU - Mboringong, Akenji Blaise

AU - Dieng, Alle Baba

AU - Juozapaitė, Dovilė

AU - Hosch, Salome

AU - Obama, Justino

AU - Ayekaba, Mitoha Ondo'o

AU - Naumovas, Daniel

AU - Pautienius, Arnoldas

AU - Rafaï, Clotaire Donatien

AU - Vitkauskienė, Astra

AU - Ugenskienė, Rasa

AU - Gedvilaitė, Alma

AU - Čereškevičius, Darius

AU - Lesauskaitė, Vaiva

AU - Žemaitis, Lukas

AU - Griškevičius, Laimonas

AU - Baele, Guy

PY - 2021/10/1

Y1 - 2021/10/1

N2 - 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.

AB - 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.

KW - Africa, Central/epidemiology

KW - Antibodies, Neutralizing/immunology

KW - COVID-19/epidemiology

KW - Europe/epidemiology

KW - Humans

KW - Immune Evasion/genetics

KW - Mutation

KW - Phylogeny

KW - Phylogeography

KW - SARS-CoV-2/classification

KW - Spike Glycoprotein, Coronavirus/genetics

KW - Travel/statistics & numerical data

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U2 - 10.1038/s41467-021-26055-8

DO - 10.1038/s41467-021-26055-8

M3 - Journal article

C2 - 34599175

SN - 2041-1722

VL - 12

SP - 5769

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 5769

ER -

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

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