Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients.
Animals
Betacoronavirus
/ isolation & purification
COVID-19
Coinfection
/ immunology
Coronavirus Infections
/ immunology
Host-Pathogen Interactions
Humans
Interferons
/ immunology
Lung
/ pathology
Pandemics
Pneumonia, Viral
/ immunology
SARS-CoV-2
Sensitivity and Specificity
Sequence Analysis, RNA
Severity of Illness Index
Single-Cell Analysis
Software
COVID-19
Viral-Track
single-cell RNA-seq
virus host interactions
Journal
Cell
ISSN: 1097-4172
Titre abrégé: Cell
Pays: United States
ID NLM: 0413066
Informations de publication
Date de publication:
25 06 2020
25 06 2020
Historique:
received:
30
03
2020
revised:
16
04
2020
accepted:
01
05
2020
pubmed:
2
6
2020
medline:
11
7
2020
entrez:
2
6
2020
Statut:
ppublish
Résumé
Viruses are a constant threat to global health as highlighted by the current COVID-19 pandemic. Currently, lack of data underlying how the human host interacts with viruses, including the SARS-CoV-2 virus, limits effective therapeutic intervention. We introduce Viral-Track, a computational method that globally scans unmapped single-cell RNA sequencing (scRNA-seq) data for the presence of viral RNA, enabling transcriptional cell sorting of infected versus bystander cells. We demonstrate the sensitivity and specificity of Viral-Track to systematically detect viruses from multiple models of infection, including hepatitis B virus, in an unsupervised manner. Applying Viral-Track to bronchoalveloar-lavage samples from severe and mild COVID-19 patients reveals a dramatic impact of the virus on the immune system of severe patients compared to mild cases. Viral-Track detects an unexpected co-infection of the human metapneumovirus, present mainly in monocytes perturbed in type-I interferon (IFN)-signaling. Viral-Track provides a robust technology for dissecting the mechanisms of viral-infection and pathology.
Identifiants
pubmed: 32479746
pii: S0092-8674(20)30568-7
doi: 10.1016/j.cell.2020.05.006
pmc: PMC7205692
pii:
doi:
Substances chimiques
Interferons
9008-11-1
Types de publication
Evaluation Study
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1475-1488.e12Informations de copyright
Copyright © 2020 Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Interests The authors declare no competing interests.
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