Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics.
SARS-CoV-2
classification
epidemics
mutant
pandemics
travel
variant
zoonosis
Journal
Frontiers in microbiology
ISSN: 1664-302X
Titre abrégé: Front Microbiol
Pays: Switzerland
ID NLM: 101548977
Informations de publication
Date de publication:
2021
2021
Historique:
received:
30
09
2021
accepted:
15
12
2021
entrez:
24
2
2022
pubmed:
25
2
2022
medline:
25
2
2022
Statut:
epublish
Résumé
After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on ≥5 hallmark mutations along the whole genome shared by ≥30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47 and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analyzing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from farm minks. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.
Identifiants
pubmed: 35197938
doi: 10.3389/fmicb.2021.786233
pmc: PMC8859183
doi:
Types de publication
Journal Article
Langues
eng
Pagination
786233Informations de copyright
Copyright © 2022 Colson, Fournier, Chaudet, Delerce, Giraud-Gatineau, Houhamdi, Andrieu, Brechard, Bedotto, Prudent, Gazin, Beye, Burel, Dudouet, Tissot-Dupont, Gautret, Lagier, Million, Brouqui, Parola, Fenollar, Drancourt, La Scola, Levasseur and Raoult.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
Clin Microbiol Infect. 2021 Jul;27(7):1040.e7-1040.e10
pubmed: 33887469
Science. 1974 Sep 27;185(4157):1115-23
pubmed: 17835456
Nucleic Acids Res. 2009 Mar;37(4):1011-34
pubmed: 19213802
Clin Microbiol Infect. 2021 Sep;27(9):1352.e1-1352.e5
pubmed: 33991677
J Med Virol. 2021 Apr;93(4):2177-2195
pubmed: 33095454
Bioinformatics. 2018 Dec 1;34(23):4121-4123
pubmed: 29790939
Lancet Infect Dis. 2020 May;20(5):533-534
pubmed: 32087114
Arch Virol. 2008;153(4):783-821
pubmed: 18256781
Bioinformatics. 2008 Mar 1;24(5):719-20
pubmed: 18024473
Trends Microbiol. 1996 Jun;4(6):216-8
pubmed: 8795155
Nature. 2021 Jul;595(7869):713-717
pubmed: 34192736
PLoS Genet. 2019 Oct 17;15(10):e1008271
pubmed: 31622336
Sci Am. 1993 Jul;269(1):42-9
pubmed: 8337597
Infect Genet Evol. 2007 Jan;7(1):133-44
pubmed: 16713373
Infect Genet Evol. 2021 Nov;95:105038
pubmed: 34403832
J Clin Virol. 2021 Jun;139:104814
pubmed: 33836314
Gene. 1976;1(1):3-25
pubmed: 1052322
Science. 2021 Jan 8;371(6525):172-177
pubmed: 33172935
Arch Virol. 2013 Dec;158(12):2633-9
pubmed: 23836393
Proc Natl Acad Sci U S A. 2021 Jul 20;118(29):
pubmed: 34292871
Travel Med Infect Dis. 2021 Jul-Aug;42:102085
pubmed: 34029710
Nat Rev Microbiol. 2021 Jul;19(7):409-424
pubmed: 34075212
Virology. 2015 May;479-480:46-51
pubmed: 25824477
J Infect. 2021 Aug;83(2):197-206
pubmed: 34089757
Viruses. 2021 Oct 28;13(11):
pubmed: 34834983
Clin Microbiol Infect. 2021 Oct;27(10):1516.e1-1516.e6
pubmed: 34044152
JAMA. 2021 Sep 21;326(11):1001-1002
pubmed: 34406361
Nature. 2021 Jul;595(7869):707-712
pubmed: 34098568
Proc Natl Acad Sci U S A. 2021 Jun 22;118(25):
pubmed: 34083352
Euro Surveill. 2020 Aug;25(32):
pubmed: 32794443
Nat Commun. 2020 Nov 25;11(1):5986
pubmed: 33239633
Int J Infect Dis. 2021 May;106:228-236
pubmed: 33785459
Cell Mol Life Sci. 2021 Dec;78(24):7967-7989
pubmed: 34731254
J Clin Virol. 2021 Jul;140:104868
pubmed: 34029990
Acta Biomed. 2020 Mar 19;91(1):157-160
pubmed: 32191675
Arch Virol. 2022 Feb;167(2):583-589
pubmed: 35083577
Arch Virol. 2005 Oct;150(10):2151-79
pubmed: 16132185
Proc Natl Acad Sci U S A. 2021 Mar 2;118(9):
pubmed: 33571105
Travel Med Infect Dis. 2021 Mar-Apr;40:101980
pubmed: 33535105
Eur J Clin Microbiol Infect Dis. 2020 Aug;39(8):1601-1603
pubmed: 32270412
Nat Microbiol. 2021 Oct;6(10):1233-1244
pubmed: 34548634
J Vet Diagn Invest. 2021 Sep;33(5):939-942
pubmed: 34109885
Arch Virol. 2013 Jun;158(6):1425-32
pubmed: 23358612
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Evol Bioinform Online. 2020 Oct 23;16:1176934320965149
pubmed: 33149541
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Front Microbiol. 2021 Apr 01;12:663815
pubmed: 33868218
Q Rev Biophys. 1971 Aug;4(2):149-212
pubmed: 5134461
Nat Rev Genet. 2004 Jan;5(1):52-61
pubmed: 14708016
Science. 2020 Apr 24;368(6489):395-400
pubmed: 32144116
Nat Microbiol. 2020 Nov;5(11):1403-1407
pubmed: 32669681
BMJ. 2020 Jun 3;369:m1924
pubmed: 32493767