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

Article scientifique 2021 Anglais

Résumé

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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Dudas, G., Hong, S., Potter, B., Calvignac‐Spencer, S., Niatou-Singa, F., Tombolomako, T., Fuh-Neba, T., Vickos, U., Ulrich, M., Leendertz, F., Khan, K., Huber, C., Watts, A., Olendraitė, I., Snijder, J., Wijnant, K., Bonvin, A., Martres, P., Behillil, S., Ayouba, A., Maïdadi‐Foudi, M., Djomsi, D., Godwe, C., Butel, C., Šimaitis, A., Gabrielaitė, M., Katėnaitė, M., Norvilas, R., Raugaitė, L., Koyaweda, G., Kandou, J., Jonikas, R., Nasvytienė, I., Žemeckienė, Ž., Gečys, D., Tamušauskaitė, K., Norkienė, M., Vasiliūnaitė, E., Žiogienė, D., Timinskas, A., Šukys, M., Šarauskas, M., Alzbutas, G., Amuri-Aziza, A., Kinganda-Lusamaki, E., Makangara-Cigolo, J., Mawete, F., Lofiko, E., Kingebeni, P., Tamfum, J., Bélizaire, M., Essomba, R., Assoumou, M., Mboringong, A., Dieng, A., Juozapaitė, D., Hosch, S., Obama, J., Ayekaba, M., Naumovas, D., Pautienius, A., Rafaï, C., 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. https://doi.org/10.1038/s41467-021-26055-8

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Auteur(s)

Gytis Dudas Samuel L. Hong Barney 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 Maïdadi‐Foudi Dowbiss Meta Djomsi Célestin 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 Bélizaire René Ghislain Essomba Marie Claire Okomo Assoumou Akenji Blaise Mboringong Allé 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

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