Culture and identification of a "Deltamicron" SARS-CoV-2 in a three cases cluster in southern France.
Omicron
SARS-CoV-2
delta
deltamicron
epidemic
lineage
recombinant
variant
Journal
Journal of medical virology
ISSN: 1096-9071
Titre abrégé: J Med Virol
Pays: United States
ID NLM: 7705876
Informations de publication
Date de publication:
08 2022
08 2022
Historique:
revised:
11
04
2022
received:
07
03
2022
accepted:
12
04
2022
pubmed:
26
4
2022
medline:
16
6
2022
entrez:
25
4
2022
Statut:
ppublish
Résumé
Multiple SARS-CoV-2 variants have successively, or concomitantly spread worldwide since the summer of 2020. A few co-infections with different variants were reported and genetic recombinations, common among coronaviruses, were reported or suspected based on co-detection of signature mutations of different variants in a given genome. Here we report three infections in southern France with a Delta 21J_AY.4-Omicron 21K/BA.1 "Deltamicron" recombinant. The hybrid genome harbors signature mutations of the two lineages, supported by a mean sequencing depth of 1163-1421 reads and a mean nucleotide diversity of 0.1%-0.6%. It is composed of the near full-length spike gene (from codons 156-179) of an Omicron 21K/BA.1 variant in a Delta 21J/AY.4 lineage backbone. Importantly, we cultured an isolate of this recombinant and sequenced its genome. It was observed by scanning electron microscopy. As it is misidentified with current variant screening quantitative polymerase chain reaction (qPCR), we designed and implemented for routine diagnosis a specific duplex qPCR. Finally, structural analysis of the recombinant spike suggested its hybrid content could optimize viral binding to the host cell membrane. These findings prompt further studies of the virological, epidemiological, and clinical features of this recombinant.
Identifiants
pubmed: 35467028
doi: 10.1002/jmv.27789
pmc: PMC9088576
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3739-3749Informations de copyright
© 2022 Wiley Periodicals LLC.
Références
Genetics. 2021 Jul 14;218(3):
pubmed: 33983397
Virus Evol. 2021 Jul 15;7(2):veab059
pubmed: 36793768
J Infect. 2015 Jun;70(6):641-50
pubmed: 25530469
J Infect. 2021 Aug;83(2):197-206
pubmed: 34089757
Virology. 2021 Oct;562:63-73
pubmed: 34265628
Nat Rev Genet. 2012 Mar 16;13(4):283-96
pubmed: 22421730
Eur J Clin Microbiol Infect Dis. 2011 Aug;30(8):935-6
pubmed: 21618022
Front Cell Infect Microbiol. 2012 Aug 28;2:113
pubmed: 22973559
Eur J Clin Microbiol Infect Dis. 2020 Jun;39(6):1059-1061
pubmed: 32342252
Eur J Clin Microbiol Infect Dis. 2021 Mar;40(3):477-484
pubmed: 33389257
J Med Virol. 2022 Jul;94(7):3421-3430
pubmed: 35243660
Nat Microbiol. 2020 Nov;5(11):1403-1407
pubmed: 32669681
Nature. 2021 Jul;595(7869):713-717
pubmed: 34192736
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549
pubmed: 29722887
J Med Virol. 2022 Aug;94(8):3739-3749
pubmed: 35467028
Clin Infect Dis. 2020 Jul 28;71(15):884-887
pubmed: 32130405
Cell. 2021 Sep 30;184(20):5179-5188.e8
pubmed: 34499854
J Med Virol. 2022 May;94(5):2019-2025
pubmed: 34997962
Med J Aust. 2020 Jul;213(1):44-44.e1
pubmed: 32506536
J Virol. 2019 Nov 13;93(23):
pubmed: 31534035
Infect Genet Evol. 2013 Mar;14:29-38
pubmed: 23178317
Nucleic Acids Res. 2002 Jul 15;30(14):3059-66
pubmed: 12136088
Arch Virol. 2020 Oct;165(10):2341-2348
pubmed: 32737584
Nat Commun. 2013;4:2700
pubmed: 24193254
Mol Biol Evol. 2022 Feb 3;39(2):
pubmed: 35106601
Nature. 2021 Jul;595(7869):707-712
pubmed: 34098568
J Virol. 1999 Jan;73(1):152-60
pubmed: 9847317
Nature. 2022 Feb;602(7895):19
pubmed: 35058630
Bioinformatics. 2018 Dec 1;34(23):4121-4123
pubmed: 29790939
Pathog Immun. 2021 Aug 20;6(2):27-49
pubmed: 34541432
Nucleic Acids Res. 2022 Jan 7;50(D1):D161-D164
pubmed: 34850943
Biotechnol Lett. 2022 Mar;44(3):399-414
pubmed: 35037234
J Clin Virol. 2021 Jul;140:104868
pubmed: 34029990
PLoS One. 2021 May 25;16(5):e0251368
pubmed: 34033650
PLoS Pathog. 2021 Jan 19;17(1):e1009226
pubmed: 33465137
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
BMC Ecol Evol. 2021 Jan 21;21(1):5
pubmed: 33514319
Cell Host Microbe. 2017 Sep 13;22(3):420
pubmed: 28910639
J Gen Virol. 2018 Oct;99(10):1345-1356
pubmed: 30156526
Virus Res. 2021 Apr 15;296:198345
pubmed: 33631222
Cell. 2019 May 2;177(4):1010-1021.e32
pubmed: 30981557
J Med Virol. 2022 May;94(5):2290-2295
pubmed: 35060146
Eur J Clin Microbiol Infect Dis. 2020 Aug;39(8):1601-1603
pubmed: 32270412
Nat Commun. 2022 May 18;13(1):2745
pubmed: 35585202
Front Microbiol. 2022 Feb 07;12:786233
pubmed: 35197938
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712