Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients
Open accessAbstract
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.
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Viral RNA was also detected in a subset of macrophages (SPP1+ macrophages).
“Viral RNA was also detected in a subset of macrophages (SPP1 + macrophages) (Bost et al., 2020; Chua et al., 2020).”
From COVID-19 and the human innate immune system (2021) · cites this paper as Bost et al., 2020
Viral RNA was detected in single-cell transcriptomes of bronchoalveolar lavage fluid from COVID-19 patients with severe but not mild disease.
“By applying a newly developed computational pipeline called Viral-Track, viral RNA was detected in single-cell transcriptomes of bronchoalveolar lavage fluid (BALF) samples from COVID-19 patients with severe, but not mild, disease course (Bost et al., 2020), suggestive of a differential progression of infection in the lung.”
From COVID-19 and the human innate immune system (2021) · cites this paper as Bost et al., 2020
Co-infection of monocytes in bronchoalveolar lavage fluid with human metapneumovirus was identified in one severe COVID-19 patient.
“co-infection of monocytes in the BALF with human metapneumovirus was identified in one of the severe COVID-19 patients (Bost et al., 2020)”
From COVID-19 and the human innate immune system (2021) · cites this paper as Bost et al., 2020
The strongest enrichment of SARS-CoV-2 viral RNA was observed in ciliated and epithelial progenitor cells.
“The strongest enrichment of viral RNA was observed in ciliated and epithelial progenitors.”
From COVID-19 and the human innate immune system (2021) · cites this paper as Bost et al., 2020
CD147 is widely expressed and receptor expression does not seem to correlate with viral load, arguing against CD147 as a major entry receptor for SARS-CoV-2.
“CD147 is widely expressed and receptor expression and viral load does not seem to correlate (Bost et al., 2020) arguing against CD147 as a major entry receptor for SARS-CoV-2.”
From COVID-19 and the human innate immune system (2021) · cites this paper as Bost et al., 2020
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Dysregulation of brain and choroid plexus cell types in severe COVID-19
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SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids
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- Authors
- Bost, P., Giladi, A., Liu, Y., Bendjelal, Y., Xu, G., David, E., Blecher-Gonen, R., Cohen, M., Medaglia, C., Li, H., Deczkowska, A., Zhang, S., Schwikowski, B., Zhang, Z., & Amit, I.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Weizmann Institute of Science (IL)
- Southern University of Science and Technology (CN)
- Shanghai Medical College of Fudan University (CN)
- Corresponding author
- Schwikowski, Benno
- Zhang, Zheng
- Amit, Ido
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2020-06
- Volume
- 181
- Issue
- 7
- Pages
- 1475-1488.e12
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC7205692
- OpenAlex
- W3022248657
- Cited by
- 471
- References
- 76
- Citations by year
- 2026: 13 · 2025: 34 · 2024: 51 · 2023: 58 · 2022: 95 · 2021: 142 · 2020: 77 · 2019: 1
- FWCI
- 30.14
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- Funders
- Weizmann Institute of Science
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Keywords
- COVID-19 pandemic, SARS-CoV-2, host-virus interaction, viral RNA detection, single-cell RNA sequencing, severe COVID-19, bronchoalveolar lavage, type I interferon signaling, monocytes, hepatitis B virus, immune response
- MeSH terms
- Betacoronavirus, COVID-19, SARS-CoV-2, Animals, Humans, Interferons, Lung, Pneumonia, Viral, Sensitivity and Specificity, Severity of Illness Index, Software, Sequence Analysis, RNA, Coronavirus Infections, Host-Pathogen Interactions, Pandemics, Single-Cell Analysis, Coinfection
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