Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion.
Journal
Memorias do Instituto Oswaldo Cruz
ISSN: 1678-8060
Titre abrégé: Mem Inst Oswaldo Cruz
Pays: Brazil
ID NLM: 7502619
Informations de publication
Date de publication:
2022
2022
Historique:
received:
15
08
2021
accepted:
03
11
2021
entrez:
12
1
2022
pubmed:
13
1
2022
medline:
14
1
2022
Statut:
epublish
Résumé
Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in non-structural, structural, and accessory open reading frames (ORFs) or genes. We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological links between outbreaks. Genomes from Coronavirus disease 2019 (COVID-19) case-patients were Illumina sequenced using ARTIC_V3. The assembled genomes were analysed to detect substitutions and indels. We reported the emergence and spread of a unique 4-nucleotide deletion in the accessory ORF6, an interesting gene with immune modulation activity. The deletion in ORF6 removes one repeat unit of a two 4-nucleotide repeat, which shows that directly repeated sequences in the SARS-CoV-2 genome are associated with indels, even outside the context of extended repeat regions. The 4-nucleotide deletion produces a frameshifting change that results in a protein with two inserted amino acids, increasing the coding information of this accessory ORF. Epidemiological and genomic data indicate that the deletion variant has a single common ancestor and was initially detected in a health care outbreak and later in other COVID-19 cases, establishing a transmission cluster in the Uruguayan population. Our findings provide evidence for the origin and spread of deletion variants and emphasise indels' importance in epidemiological studies, including differentiating consecutive outbreaks occurring in the same health facility.
Sections du résumé
BACKGROUND
BACKGROUND
Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in non-structural, structural, and accessory open reading frames (ORFs) or genes.
OBJECTIVES
OBJECTIVE
We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological links between outbreaks.
METHODS
METHODS
Genomes from Coronavirus disease 2019 (COVID-19) case-patients were Illumina sequenced using ARTIC_V3. The assembled genomes were analysed to detect substitutions and indels.
FINDINGS
RESULTS
We reported the emergence and spread of a unique 4-nucleotide deletion in the accessory ORF6, an interesting gene with immune modulation activity. The deletion in ORF6 removes one repeat unit of a two 4-nucleotide repeat, which shows that directly repeated sequences in the SARS-CoV-2 genome are associated with indels, even outside the context of extended repeat regions. The 4-nucleotide deletion produces a frameshifting change that results in a protein with two inserted amino acids, increasing the coding information of this accessory ORF. Epidemiological and genomic data indicate that the deletion variant has a single common ancestor and was initially detected in a health care outbreak and later in other COVID-19 cases, establishing a transmission cluster in the Uruguayan population.
MAIN CONCLUSIONS
CONCLUSIONS
Our findings provide evidence for the origin and spread of deletion variants and emphasise indels' importance in epidemiological studies, including differentiating consecutive outbreaks occurring in the same health facility.
Identifiants
pubmed: 35019072
pii: S0074-02762021000101107
doi: 10.1590/0074-02760210275
pmc: PMC8752050
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e210275Références
Infect Genet Evol. 2021 Apr;89:104736
pubmed: 33516969
Euro Surveill. 2020 Jan;25(3):
pubmed: 31992387
Emerg Microbes Infect. 2020 Dec;9(1):1418-1428
pubmed: 32529952
Biochem Biophys Res Commun. 2021 Jan 29;538:116-124
pubmed: 33685621
Transbound Emerg Dis. 2021 Nov;68(6):3075-3082
pubmed: 33501730
Virus Res. 2021 Jan 2;291:198222
pubmed: 33166565
Infect Genet Evol. 2020 Sep;83:104353
pubmed: 32387562
Cell Death Differ. 2020 Dec;27(12):3209-3225
pubmed: 33037393
J Virol. 2020 Jul 1;94(14):
pubmed: 32357959
Infect Genet Evol. 2020 Nov;85:104557
pubmed: 32950697
Nat Commun. 2020 Jul 30;11(1):3810
pubmed: 32733001
J Mol Evol. 2020 Sep;88(7):549-561
pubmed: 32617614
Nature. 2020 Mar;579(7798):270-273
pubmed: 32015507
Nat Med. 2021 Apr;27(4):622-625
pubmed: 33654292
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Euro Surveill. 2021 Jan;26(3):
pubmed: 33478625
Clin Microbiol Infect. 2020 Jul;26(7):960-962
pubmed: 32234449
Virus Res. 2008 Apr;133(1):113-21
pubmed: 18045721
Euro Surveill. 2017 Mar 30;22(13):
pubmed: 28382917
Sci Rep. 2021 Feb 10;11(1):3487
pubmed: 33568759
Lancet. 2021 Feb 6;397(10273):452-455
pubmed: 33515491
Sci Rep. 2021 Feb 18;11(1):4108
pubmed: 33602998
Int J Mol Sci. 2020 Oct 24;21(21):
pubmed: 33114322
Emerg Microbes Infect. 2020 Dec;9(1):837-842
pubmed: 32301390
Emerg Microbes Infect. 2021 Dec;10(1):167-177
pubmed: 33399033
PLoS Pathog. 2020 May 14;16(5):e1008421
pubmed: 32407364
Virus Res. 2010 Nov;153(2):299-304
pubmed: 20800627
Science. 2020 Sep 4;369(6508):1255-1260
pubmed: 32703910
Infect Genet Evol. 2020 Nov;85:104471
pubmed: 32707288
mBio. 2020 Jul 21;11(4):
pubmed: 32694143
Virus Res. 2020 Sep;286:198074
pubmed: 32589897
Proc Natl Acad Sci U S A. 2020 Nov 10;117(45):28344-28354
pubmed: 33097660
Emerg Microbes Infect. 2020 Dec;9(1):1457-1466
pubmed: 32543353
J Transl Med. 2020 Aug 31;18(1):329
pubmed: 32867854
J Med Virol. 2021 Mar;93(3):1702-1721
pubmed: 32970329
Front Microbiol. 2021 Feb 17;11:615280
pubmed: 33679622
Mol Biol Evol. 2009 Jul;26(7):1641-50
pubmed: 19377059
Mol Syst Biol. 2009;5:311
pubmed: 19888206
Science. 2021 Mar 12;371(6534):1139-1142
pubmed: 33536258
Nat Microbiol. 2020 Nov;5(11):1403-1407
pubmed: 32669681
J Virol. 2007 Sep;81(18):9812-24
pubmed: 17596301
Virus Evol. 2021 Aug 14;7(2):veab069
pubmed: 34532067