Shiloh
Editor, Senior Moderator
Source: https://www.cell.com/cell/fulltext/S0092-8674(20)30568-7
Host-viral infection maps reveal signatures of severe COVID-19 patients
Pierre Bost ∗ Amir Giladi ∗ Yang Liu ∗ Benno Schwikowski
Zheng Zhang Ido Amit #
Published:May 07, 2020DOI:https://doi.org/10.1016/j.cell.2020.05.006
Highlights
Viral-track: a computational framework to analyze host-viral infection maps
Viral-track sorts infected from bystander cells and reveals virus-induced expression
SARS-CoV-2 infects epithelial cells and alters immune landscape in severe patients
Coinfection of SARS-Cov-2 and hMPV affects monocytes and dampen interferon response
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 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 IFN-signaling. Viral-Track provides a robust technology for dissecting the mechanisms of viral-infection and pathology...
Host-viral infection maps reveal signatures of severe COVID-19 patients
Pierre Bost ∗ Amir Giladi ∗ Yang Liu ∗ Benno Schwikowski
Zheng Zhang Ido Amit #
Published:May 07, 2020DOI:https://doi.org/10.1016/j.cell.2020.05.006
Highlights
Viral-track: a computational framework to analyze host-viral infection maps
Viral-track sorts infected from bystander cells and reveals virus-induced expression
SARS-CoV-2 infects epithelial cells and alters immune landscape in severe patients
Coinfection of SARS-Cov-2 and hMPV affects monocytes and dampen interferon response
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 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 IFN-signaling. Viral-Track provides a robust technology for dissecting the mechanisms of viral-infection and pathology...