Hepatitis C and HIV detection by blood RNA-sequencing in cohort of smokers.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
24 01 2023
24 01 2023
Historique:
received:
10
05
2022
accepted:
13
01
2023
entrez:
24
1
2023
pubmed:
25
1
2023
medline:
27
1
2023
Statut:
epublish
Résumé
Detection of viruses by RNA and DNA sequencing has improved the understanding of the human virome. We sought to identify blood viral signatures through secondary use of RNA-sequencing (RNA-seq) data in a large study cohort. The ability to reveal undiagnosed infections with public health implications among study subjects with available sequencing data could enable epidemiologic surveys and may lead to diagnosis and therapeutic interventions, leveraging existing research data in a clinical context. We detected viral RNA in peripheral blood RNA-seq data from a COPD-enriched population of current and former smokers. Correlation between viral detection and both reported infections and relevant disease outcomes was evaluated. We identified Hepatitis C virus RNA in 228 subjects and HIV RNA in 30 subjects. Overall, we observed 31 viral species, including Epstein-Barr virus and Cytomegalovirus. We observed an enrichment of Hepatitis C and HIV infections among subjects reporting liver disease and HIV infections, respectively. Higher interferon expression scores were observed in the subjects with Hepatitis C and HIV infections. Through secondary use of RNA-seq from a cohort of current and former smokers, we detected peripheral blood viral signatures. We identified HIV and Hepatitis C virus (HCV), highlighting potential public health implications for the approach described this study. We observed correlations with reported infections, chronic infection outcomes and the host transcriptomic response, providing evidence to support the validity of the approach.
Identifiants
pubmed: 36693932
doi: 10.1038/s41598-023-28156-4
pii: 10.1038/s41598-023-28156-4
pmc: PMC9873751
doi:
Substances chimiques
RNA
63231-63-0
RNA, Viral
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1357Subventions
Organisme : NHLBI NIH HHS
ID : U01 HL089856
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL147326
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL130512
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL125583
Pays : United States
Organisme : NHLBI NIH HHS
ID : K25 HL136846
Pays : United States
Organisme : NHLBI NIH HHS
ID : U01 HL089897
Pays : United States
Organisme : NHLBI NIH HHS
ID : K08 HL146972
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL124233
Pays : United States
Informations de copyright
© 2023. The Author(s).
Références
J Interferon Cytokine Res. 2013 Jan;33(1):15-23
pubmed: 23067362
Nucleic Acids Res. 2013 May 1;41(10):e108
pubmed: 23558742
Nat Genet. 2013 Jun;45(6):580-5
pubmed: 23715323
Hepatology. 2019 Mar;69(3):1020-1031
pubmed: 30398671
Nat Rev Genet. 2019 Jun;20(6):341-355
pubmed: 30918369
BMC Bioinformatics. 2013 Jan 16;14:7
pubmed: 23323831
Annu Rev Microbiol. 2016 Sep 8;70:125-41
pubmed: 27607550
COPD. 2010 Feb;7(1):32-43
pubmed: 20214461
Immunity. 2015 May 19;42(5):805-13
pubmed: 25992857
Bioinformatics. 2018 Dec 15;34(24):4287-4289
pubmed: 29982281
Wellcome Open Res. 2019 Oct 14;4:155
pubmed: 32055707
Pathog Immun. 2016 Spring;1(1):107-116
pubmed: 27500281
Front Immunol. 2014 Jan 13;4:498
pubmed: 24454311
PLoS Pathog. 2017 Mar 22;13(3):e1006292
pubmed: 28328962
Lab Invest. 2004 Sep;84(9):1148-59
pubmed: 15208644
Ann Med. 2022 Dec;54(1):314-325
pubmed: 35068272
BMC Med Genomics. 2017 Oct 6;10(1):58
pubmed: 28985737
Sci Rep. 2021 Oct 6;11(1):19875
pubmed: 34615932
Nucleic Acids Res. 2016 Jan 4;44(D1):D574-80
pubmed: 26578574
J Infect Dis. 2005 Jun 15;191(12):2064-74
pubmed: 15897992
BMC Pulm Med. 2020 Apr 3;20(1):81
pubmed: 32245461
BMC Biol. 2020 Jun 4;18(1):55
pubmed: 32493363
PLoS One. 2014 Dec 16;9(12):e114438
pubmed: 25514500
Cell Syst. 2015 Dec 23;1(6):417-425
pubmed: 26771021
J Infect Dis. 2013 Mar;207 Suppl 1:S1-6
pubmed: 23390299
J Hepatol. 2014 Nov;61(1 Suppl):S58-68
pubmed: 25443346
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Hepatology. 1996 Oct;24(4):759-65
pubmed: 8855173