Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe
Open accessPreprint — published as 10.1038/s41467-021-26055-8
Abstract
Many high-income countries have met the SARS-CoV-2 pandemic with overwhelming sequencing resources and have identified numerous distinct lineages, including some with notably altered biology. Over a year into the pandemic following unprecedented reductions in worldwide human mobility, distinct introduced lineages of SARS-CoV-2 without sequenced antecedents are increasingly discovered in high-income countries as a result of ongoing SARS-CoV-2 genomic surveillance initiatives. We here describe one such SARS-CoV-2 lineage, 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. This lineage – designated B.1.620 – is known to circulate in Lithuania and has now been found in several European states, but also in increasing numbers in central Africa owing to important recent increases in genome sequencing efforts on the continent. We provide evidence of likely ongoing local transmission of B.1.620 in Lithuania, France, Germany, Spain, Belgium and the Central African Republic. We describe the suite of mutations this lineage carries, its potential to be resistant to neutralising antibodies, travel histories for a subset of the European cases, and evidence of local B.1.620 transmission in Europe. We make a case for the likely Central African origin of this lineage by providing travel records as well as the outcomes of carefully crafted phylogenetic and phylogeographic inference methodologies, the latter of which is able to exploit individual travel histories recorded for infected travellers having entered different European countries.
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All sequences in the study were manually verified for phylogenetic location.
“This is in line with recent concerns regarding misclassifications of Pangolin 37 , and led us to manually verify the phylogenetic location of all sequences in our study.”
From Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals (2021) · cites this paper as [37]
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Wolday, D., Ndungu, F. M., Gómez-Pérez, G. P., & de Wit, T. F. R. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.693269 · Cited by 17 · see citing works
Pirnay, J., Selhorst, P., Hong, S. L., Cochez, C., Potter, B. I., Maes, P., Petrillo, M., Dudas, G., Claes, V., der Beken, Y. V., et al. (2021) · Viruses · doi:10.3390/v13071359 · Cited by 8 · see citing works
Self-citationRapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peak PCR Platform
Bechtold, P., Wagner, P., Hosch, S., Siegrist, D., Ruiz‐Serrano, A., Gregorini, M., Mpina, M., Ndoho, F. A. O., Obama, J., Ayekaba, M. O., et al. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c02368 · Cited by 25 · see citing works
Helle, K. B., Sadiku, A., Zelleke, G. M., Bouba, A., Ibrahim, T. B., Obama, H. C. J. T., Appiah, V., Ngwa, G. A., Teboh-Ewungkem, M. I., & Schneider, K. A. (2021) · PLoS ONE · doi:10.1371/journal.pone.0253758 · Cited by 13 · see citing works
SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise
Duerr, R., Crosse, K. M., Valero-Jimenez, A. M., & Dittmann, M. (2021) · Microorganisms · doi:10.3390/microorganisms9071389 · Cited by 12 · see citing works
“620, first identified in Lithuania, Europe, is spreading in different European countries and traces back to its probable origin Cameroon and surrounding West-Central African countries [426].”
BackgroundSARS-CoV-2 convergent evolution as a guide to explore adaptive advantagePreprint
Zahradník, J., Nunvář, J., & Schreiber, G. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.24.445534 · Cited by 6 · see citing works
Characterizing the Severity of SARS-CoV-2 Variants at a Single Pediatric Center
Khan, A., Ichura, C., Wang, H., de Rezende, I. M., Sahoo, M. K., Huang, C., Solis, D., Sibai, M., Yamamoto, F. F., Nyathi, S., et al. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.896352 · Cited by 3 · see citing works
An investigation of multivariate data-driven deep learning models for predicting COVID-19 variants
Baihaqi, A. D., Yudistira, N., & Santoso, E. (2024) · Healthcare Analytics · doi:10.1016/j.health.2024.100331 · Cited by 2 · see citing works
SARS-CoV-2 vaccines from A to Z: A Review of the current challenges
Albalaty, J. M., Forsan, F. H., Awad, S., et al. (2023) · Global NEST Journal · doi:10.30955/gnj.004651 · Cited by 1 · see citing works
“This lineage was deemed to have plenty of mutations and deletions that affect antibody-mediated immunity (Dudas et al ., 2021).”
BackgroundHIV and SARS-CoV-2: the interplay of two wicked problems
Kiekens, A., Bwire, G., Decouttere, C., et al. (2022) · BMJ Global Health · doi:10.1136/bmjgh-2022-009105 · Cited by 1
Prediction of COVID-19 by Its Variants using Multivariate Data-driven Deep Learning Models
Baihaqi, A. D., Yudistira, N., & Santoso, E. (2023) · arXiv.org · doi:10.48550/arxiv.2301.10616
- Authors
- Dudas, G., Hong, S. L., Potter, B., Calvignac-Spencer, S., Niatou-Singa, F. S., Tombolomako, T. B., Fuh-Neba, T., Vickos, U., Ulrich, M., Leendertz, F. H., Khan, K., Watts, A., Olendraitė, I., Snijder, J., Wijnant, K. N., Bonvin, A. M. J. J., Martres, P., Behillil, S., Ayouba, A., Maidadi, M. F., Djomsi, D. M., Godwe, C., Butel, C., Šimaitis, A., Gabrielaitė, M., Katėnaitė, M., Norvilas, R., Raugaitė, L., Jonikas, R., Nasvytienė, I., Žemeckienė, Ž., Gečys, D., Tamušauskaitė, K., Norkienė, M., Vasiliūnaitė, E., Žiogienė, D., Timinskas, A., Šukys, M., Šarauskas, M., Alzbutas, G., Juozapaitė, D., Naumovas, D., Pautienius, A., Vitkauskienė, A., Ugenskienė, R., Gedvilaitė, A., Čereškevičius, D., Lesauskaitė, V., Žemaitis, L., Griškevičius, L., & Baele, G.
- Affiliations
- Vilnius University Hospital Santariskiu Klinikos (LT)
- Rega Institute for Medical Research (BE)
- University of Bangui (CF)
- Robert Koch Institute (DE)
- St. Michael's Hospital (CA)
- BlueDot (Canada) (CA)
- University of Cambridge (GB)
- Utrecht University (NL)
- Hôpital NOVO (FR)
- Centre National de la Recherche Scientifique (FR)
- Inserm (FR)
- Institut de Recherches Médicales et d’Etudes des Plantes Médicinales (CM)
- Rigshospitalet (DK)
- State Research Institute Centre for Innovative Medicine (LT)
- Lithuanian University of Health Sciences (LT)
- Vilnius University (LT)
- Corresponding author
- Dudas, Gytis
- Baele, Guy
- ORCID
- Dudas, Gytis
- Hong, Samuel L.
- Potter, Barney
- Calvignac-Spencer, Sébastien
- Vickos, Ulrich
- Ulrich, Markus
- Leendertz, Fabian H.
- Khan, Kamran
- Watts, Alexander
- Olendraitė, Ingrida
- Snijder, Joost
- Wijnant, Kim N.
- Bonvin, Alexandre M.J.J.
- Martres, Pascale
- Behillil, Sylvie
- Ayouba, Ahidjo
- Djomsi, Dowbiss Meta
- Šimaitis, Aistis
- Gabrielaitė, Miglė
- Norvilas, Rimvydas
- Žemeckienė, Živilė
- Gečys, Dovydas
- Tamušauskaitė, Kamilė
- Norkienė, Milda
- Vasiliūnaitė, Emilija
- Žiogienė, Danguolė
- Šukys, Marius
- Alzbutas, Gediminas
- Juozapaitė, Dovilė
- Naumovas, Daniel
- Pautienius, Arnoldas
- Vitkauskienė, Astra
- Ugenskienė, Rasa
- Gedvilaitė, Alma
- Lesauskaitė, Vaiva
- Žemaitis, Lukas
- Griškevičius, Laimonas
- Baele, Guy
- Venue
- Nature Communications
- Publisher
- openRxiv
- Published
- 2021-05-08
- Volume
- 12
- Issue
- 1
- Pages
- 5769-5769
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC8486757
- OpenAlex
- W3204551635
- Cited by
- 76
- References
- 45
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 14 · 2023: 10 · 2022: 33 · 2021: 14
- FWCI
- 5.62
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Nature Communications (publishedVersion, cc-by)
- medRxiv (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- edoc (University of Basel) (acceptedVersion)
- HAL (submittedVersion, cc-by)
- Publication server of the Robert Koch Institute (Robert Kock Institute) (submittedVersion, cc-by)
- Lirias (KU Leuven) (submittedVersion, cc-by)
- Lithuanian University of Health Sciences (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo
- Apollo (cc-by)
- Funders
- World Health Organization
- Institut de Recherche pour le Développement
- European Commission (823830, HORIZON2020, 777536)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (823830, ICI 024.002.009, 024.002.009))
- KU Leuven (C14/18/094)
- Vlaamse regering (G098321N, C14/18/094)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Keywords
- spike protein mutations, E484K, phylogeography, travel history, local transmission, Lithuania, genomic surveillance
- MeSH terms
- COVID-19, SARS-CoV-2, Africa, Central, Europe, Humans, Mutation, Phylogeny, Travel, Immune Evasion, Antibodies, Neutralizing, Phylogeography, Spike Glycoprotein, Coronavirus
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