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Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients

Abstract : 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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Submitted on : Tuesday, October 20, 2020 - 2:58:54 PM
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Pierre Bost, Amir Giladi, Yang Liu, Yanis Bendjelal, Gang Xu, et al.. Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients. Cell, Elsevier, 2020, 181 (7), pp.1475-1488.e12. ⟨10.1016/j.cell.2020.05.006⟩. ⟨pasteur-02965299⟩

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