Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination.
BA.1
Delta
Omicron
RNA virus
SARS-CoV-2
Translation to patients
alternative allele fraction
breakpoint
co-infection
recombination
sequencing
Journal
Med (New York, N.Y.)
ISSN: 2666-6340
Titre abrégé: Med
Pays: United States
ID NLM: 101769215
Informations de publication
Date de publication:
09 Dec 2022
09 Dec 2022
Historique:
received:
25
04
2022
revised:
14
06
2022
accepted:
07
10
2022
pubmed:
5
11
2022
medline:
15
12
2022
entrez:
4
11
2022
Statut:
ppublish
Résumé
Between November 2021 and February 2022, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events. We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant. We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5' end of the viral genome was from the Delta genome and the 3' end from Omicron, including the majority of the spike protein gene, though the breakpoints were different. Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared with the circulating Omicron lineages. This research was supported by the NIH RADx initiative and by the Centers for Disease Control Contract 75D30121C12730 (Helix).
Sections du résumé
BACKGROUND
BACKGROUND
Between November 2021 and February 2022, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events.
METHODS
METHODS
We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant.
FINDINGS
RESULTS
We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5' end of the viral genome was from the Delta genome and the 3' end from Omicron, including the majority of the spike protein gene, though the breakpoints were different.
CONCLUSIONS
CONCLUSIONS
Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared with the circulating Omicron lineages.
FUNDING
BACKGROUND
This research was supported by the NIH RADx initiative and by the Centers for Disease Control Contract 75D30121C12730 (Helix).
Identifiants
pubmed: 36332633
pii: S2666-6340(22)00449-4
doi: 10.1016/j.medj.2022.10.002
pmc: PMC9581791
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
848-859.e4Informations de copyright
Copyright © 2022 Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declarations of interests A.B., T.B., S.W., A.D.R., D.W., H.D., J.T.M., E.K., T.C., K.T., J.N., J.R., S.C., E.T.C., K.S.B., N.L.W., P.B.-F., S.J., E.S., D.B., J.T.L., M.I., W.L., and S.L. are all employees of Helix.
Références
Cell Host Microbe. 2021 Jul 14;29(7):1093-1110
pubmed: 34242582
Cell. 2021 Sep 30;184(20):5179-5188.e8
pubmed: 34499854
Signal Transduct Target Ther. 2022 Apr 26;7(1):138
pubmed: 35474215
Nature. 2022 Mar;603(7902):679-686
pubmed: 35042229
Virus Evol. 2022 Jun 14;8(2):veac054
pubmed: 35814334
Nat Rev Microbiol. 2011 Jul 04;9(8):617-26
pubmed: 21725337
Virus Evol. 2015 May 26;1(1):vev003
pubmed: 27774277
Cell Rep Med. 2022 Mar 11;3(4):100583
pubmed: 35480627
Innovation (Camb). 2021 Aug 28;2(3):100128
pubmed: 34124706
Virology. 2013 Sep 1;443(2):197-207
pubmed: 23763770
J Med Virol. 2022 Oct;94(10):4830-4838
pubmed: 35705528
Microbiol Spectr. 2022 Jun 29;10(3):e0060522
pubmed: 35502920
Nat Commun. 2022 May 18;13(1):2745
pubmed: 35585202
Nat Microbiol. 2020 Nov;5(11):1403-1407
pubmed: 32669681
Genetics. 2021 Jul 14;218(3):
pubmed: 33983397
Virus Evol. 2022 Aug 11;8(2):veac050
pubmed: 35996593
Nature. 2022 Feb;602(7895):19
pubmed: 35058630
Bioinformatics. 2018 Dec 1;34(23):4121-4123
pubmed: 29790939
Nat Rev Microbiol. 2015 Jul;13(7):414-25
pubmed: 26052661
Euro Surveill. 2022 Apr;27(16):
pubmed: 35451361
J Clin Microbiol. 2022 Jul 20;60(7):e0034222
pubmed: 35766514
Wellcome Open Res. 2021 Nov 10;6:305
pubmed: 35634532
Bioinformatics. 2022 May 26;38(11):3118-3120
pubmed: 35451456
J Infect Dis. 2009 Feb 15;199(4):580-9
pubmed: 19143562
Emerg Infect Dis. 2022 Jul;28(7):1442-1445
pubmed: 35551714
Nat Biotechnol. 2011 Jan;29(1):24-6
pubmed: 21221095