دورية أكاديمية
أعرض في EDS

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

التفاصيل البيبلوغرافية
العنوان: Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions.
المؤلفون: Dudas G; Gothenburg Global Biodiversity Centre, Gothenburg, Sweden. gytisdudas@gmail.com.; Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania. gytisdudas@gmail.com., Hong SL; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium., Potter BI; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium., Calvignac-Spencer S; Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany.; Viral Evolution, Robert Koch Institute, 13353, Berlin, Germany., Niatou-Singa FS; WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic., Tombolomako TB; WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic., Fuh-Neba T; WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic., Vickos U; Infectious and Tropical Diseases Unit, Department of medicine, Amitié Hospital, Bangui, Central African Republic.; Academic Department of Pediatrics, Clinical immunology and vaccinology, Children's Hospital Bambino Gesù, IRCCS, Rome, Italy., Ulrich M; Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany., Leendertz FH; Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany., Khan K; BlueDot, Toronto, ON, M5J 1A7, Canada.; Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, M5B 1A6, Canada.; Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, M5S 3H2, Canada., Huber C; BlueDot, Toronto, ON, M5J 1A7, Canada., Watts A; BlueDot, Toronto, ON, M5J 1A7, Canada., Olendraitė I; Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania.; Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Lab, CB2 2QQ, Cambridge, UK., Snijder J; Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands., Wijnant KN; Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands., Bonvin AMJJ; Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands., Martres P; Microbiology, Centre Hospitalier René Dubos, Cergy Pontoise, France., Behillil S; Molecular Genetics of RNA viruses, CNRS UMR 3569, Université de Paris, Institut Pasteur, Paris, France.; National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France., Ayouba A; TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, 34394, Montpellier cedex, France., Maidadi MF; Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon., Djomsi DM; Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon., Godwe C; Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon., Butel C; TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, 34394, Montpellier cedex, France., Šimaitis A; The Office of the Government of the Republic of Lithuania, Vilnius, Lithuania., Gabrielaitė M; Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark., Katėnaitė M; Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania., Norvilas R; Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania.; Department of Experimental, Preventive and Clinical Medicine, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania., Raugaitė L; Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania., Koyaweda GW; Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic., Kandou JK; Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic., Jonikas R; Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania., Nasvytienė I; Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania., Žemeckienė Ž; Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania., Gečys D; Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania., Tamušauskaitė K; Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania., Norkienė M; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Vasiliūnaitė E; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Žiogienė D; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Timinskas A; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Šukys M; Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania.; Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania., Šarauskas M; Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania., Alzbutas G; Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania., Aziza AA; National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo.; University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo., Lusamaki EK; National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo.; University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo., Cigolo JM; National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo.; University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo., Mawete FM; National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo.; University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo., Lofiko EL; National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo., Kingebeni PM; National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo.; University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo., Tamfum JM; National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo.; University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo., Belizaire MRD; World Health Organization, Central African Republic Office, Bangui, Central African Republic., Essomba RG; National Public Health Laboratory, Ministry of Public Health, Yaoundé, Cameroon.; Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon., Assoumou MCO; National Public Health Laboratory, Ministry of Public Health, Yaoundé, Cameroon.; Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon., Mboringong AB; National Public Health Laboratory, Ministry of Public Health, Yaoundé, Cameroon., Dieng AB; World Health Organization, Cameroon Office, Yaoundé, Cameroon., Juozapaitė D; Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania., Hosch S; Swiss Tropical and Public Health Institute, Basel, Switzerland., Obama J; Ministry of Health and Social Welfare, Malabo, Equatorial Guinea., Ayekaba MO; Ministry of Health and Social Welfare, Malabo, Equatorial Guinea., Naumovas D; Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania., Pautienius A; Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania., Rafaï CD; Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic., Vitkauskienė A; Department of Laboratory Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania., Ugenskienė R; Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania.; Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania., Gedvilaitė A; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Čereškevičius D; Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania.; Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania., Lesauskaitė V; Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania., Žemaitis L; Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania.; National Public Health Surveillance Laboratory, Vilnius, Lithuania., Griškevičius L; Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania., Baele G; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium. guy.baele@kuleuven.be.
المصدر: Nature communications [Nat Commun] 2021 Oct 01; Vol. 12 (1), pp. 5769. Date of Electronic Publication: 2021 Oct 01.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Pub. Group
مواضيع طبية MeSH: COVID-19/*transmission , COVID-19/*virology , SARS-CoV-2/*genetics, Africa, Central/epidemiology ; Antibodies, Neutralizing/immunology ; COVID-19/epidemiology ; Europe/epidemiology ; Humans ; Immune Evasion/genetics ; Mutation ; Phylogeny ; Phylogeography ; SARS-CoV-2/classification ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus/genetics ; Travel/statistics & numerical data
مستخلص: 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.
(© 2021. The Author(s).)
References: Mol Biol Evol. 2013 Apr;30(4):772-80. (PMID: 23329690)
Nat Med. 2020 Sep;26(9):1405-1410. (PMID: 32678356)
Cell. 2020 Apr 16;181(2):281-292.e6. (PMID: 32155444)
PLoS Biol. 2006 May;4(5):e88. (PMID: 16683862)
Curr Protoc. 2021 Apr;1(4):e98. (PMID: 33836121)
Syst Biol. 2012 May;61(3):539-42. (PMID: 22357727)
Cell. 2020 Sep 3;182(5):1295-1310.e20. (PMID: 32841599)
Ann Intern Med. 2020 May 05;172(9):577-582. (PMID: 32150748)
Viruses. 2020 Aug 15;12(8):. (PMID: 32824272)
Cell. 2020 Oct 29;183(3):739-751.e8. (PMID: 32991842)
Nat Microbiol. 2020 Nov;5(11):1403-1407. (PMID: 32669681)
Syst Biol. 2016 Mar;65(2):250-64. (PMID: 26526428)
Virus Evol. 2020 Apr 10;6(1):veaa027. (PMID: 32296544)
Nat Microbiol. 2021 Aug;6(8):1094-1101. (PMID: 34163035)
Lancet Infect Dis. 2021 Apr;21(4):e80. (PMID: 32791042)
Wellcome Open Res. 2020 Mar 30;5:53. (PMID: 32923688)
Virus Evol. 2018 Jun 08;4(1):vey016. (PMID: 29942656)
Nat Commun. 2021 Dec 13;12(1):7251. (PMID: 34903718)
J Mol Evol. 1985;22(2):160-74. (PMID: 3934395)
Syst Biol. 2018 Sep 1;67(5):901-904. (PMID: 29718447)
BMJ Open. 2020 Aug 5;10(8):e039856. (PMID: 32759252)
J Infect Dis. 2014 Jul 1;210(1):121-5. (PMID: 24446525)
Mol Cell. 2020 May 21;78(4):779-784.e5. (PMID: 32362314)
Cell. 2019 Aug 22;178(5):1057-1071.e11. (PMID: 31442400)
Mol Biol Evol. 2013 Mar;30(3):713-24. (PMID: 23180580)
Nature. 2021 Jul;595(7869):707-712. (PMID: 34098568)
Cell Host Microbe. 2021 Mar 10;29(3):477-488.e4. (PMID: 33535027)
Bioinformatics. 2018 Dec 1;34(23):4121-4123. (PMID: 29790939)
Cell Host Microbe. 2021 May 12;29(5):747-751.e4. (PMID: 33887205)
Science. 2021 May 21;372(6544):815-821. (PMID: 33853970)
J Mol Biol. 2016 Feb 22;428(4):720-725. (PMID: 26410586)
Euro Surveill. 2017 Mar 30;22(13):. (PMID: 28382917)
J Mol Evol. 1994 Sep;39(3):306-14. (PMID: 7932792)
Virus Evol. 2021 Jul 30;7(2):veab064. (PMID: 34527285)
Sci Rep. 2021 Feb 22;11(1):4320. (PMID: 33619331)
Mol Biol Evol. 2020 May 1;37(5):1530-1534. (PMID: 32011700)
Bioinformatics. 2021 Jul 19;37(12):1673-1680. (PMID: 33471068)
Virus Evol. 2016 Apr 09;2(1):vew007. (PMID: 27774300)
Nature. 2021 Apr;592(7853):277-282. (PMID: 33545711)
Nat Commun. 2020 Oct 9;11(1):5110. (PMID: 33037213)
Bull Math Biol. 2020 Apr 8;82(4):52. (PMID: 32270376)
N Engl J Med. 2020 Dec 3;383(23):2291-2293. (PMID: 33176080)
Nature. 2020 May;581(7807):215-220. (PMID: 32225176)
PLoS Comput Biol. 2009 Sep;5(9):e1000520. (PMID: 19779555)
J Mol Biol. 1990 Oct 5;215(3):403-10. (PMID: 2231712)
Protein Sci. 2018 Jan;27(1):14-25. (PMID: 28710774)
Syst Biol. 2010 May;59(3):307-21. (PMID: 20525638)
معلومات مُعتمدة: 001 International WHO_ World Health Organization
المشرفين على المادة: 0 (Antibodies, Neutralizing)
0 (Spike Glycoprotein, Coronavirus)
0 (spike protein, SARS-CoV-2)
تواريخ الأحداث: Date Created: 20211002 Date Completed: 20211018 Latest Revision: 20240403
رمز التحديث: 20240403
مُعرف محوري في PubMed: PMC8486757
DOI: 10.1038/s41467-021-26055-8
PMID: 34599175
قاعدة البيانات: MEDLINE
الوصف
تدمد:2041-1723
DOI:10.1038/s41467-021-26055-8