#Pathogenetic #profiling of #COVID19 and #SARS-like viruses (Brief Bioinformat., abstract)

[Source: Briefings in Bioinformatics, full page: (LINK). Abstract, edited.]

Pathogenetic profiling of COVID-19 and SARS-like viruses

Zulkar Nain, Humayan Kabir Rana, Pietro Liò, Sheikh Mohammed Shariful Islam, Matthew A Summers, Mohammad Ali Moni

Briefings in Bioinformatics, bbaa173, https://doi.org/10.1093/bib/bbaa173

Published: 11 August 2020



The novel coronavirus (2019-nCoV) has recently emerged, causing COVID-19 outbreaks and significant societal/global disruption. Importantly, COVID-19 infection resembles SARS-like complications. However, the lack of knowledge about the underlying genetic mechanisms of COVID-19 warrants the development of prospective control measures. In this study, we employed whole-genome alignment and digital DNA–DNA hybridization analyses to assess genomic linkage between 2019-nCoV and other coronaviruses. To understand the pathogenetic behavior of 2019-nCoV, we compared gene expression datasets of viral infections closest to 2019-nCoV with four COVID-19 clinical presentations followed by functional enrichment of shared dysregulated genes. Potential chemical antagonists were also identified using protein–chemical interaction analysis. Based on phylogram analysis, the 2019-nCoV was found genetically closest to SARS-CoVs. In addition, we identified 562 upregulated and 738 downregulated genes (adj. P ≤ 0.05) with SARS-CoV infection. Among the dysregulated genes, SARS-CoV shared ≤19 upregulated and ≤22 downregulated genes with each of different COVID-19 complications. Notably, upregulation of BCL6 and PFKFB3 genes was common to SARS-CoV, pneumonia and severe acute respiratory syndrome, while they shared CRIP2, NSG1 and TNFRSF21 genes in downregulation. Besides, 14 genes were common to different SARS-CoV comorbidities that might influence COVID-19 disease. We also observed similarities in pathways that can lead to COVID-19 and SARS-CoV diseases. Finally, protein–chemical interactions suggest cyclosporine, resveratrol and quercetin as promising drug candidates against COVID-19 as well as other SARS-like viral infections. The pathogenetic analyses, along with identified biomarkers, signaling pathways and chemical antagonists, could prove useful for novel drug development in the fight against the current global 2019-nCoV pandemic.

2019-nCoV, coronavirus, COVID-19, microarray, SARS-CoV-2, comorbidities

Issue Section: Case study

Keywords: SARS-CoV-2; COVID-19; Viral pathogenesis.


A #molecular #pore spans the double #membrane of the #coronavirus replication #organelle (Science, abstract)

[Source: Science, full page: (LINK). Abstract, edited.]

A molecular pore spans the double membrane of the coronavirus replication organelle

Georg Wolff1, Ronald W. A. L. Limpens1, Jessika C. Zevenhoven-Dobbe2, Ulrike Laugks3, Shawn Zheng4, Anja W. M. de Jong1, Roman I. Koning1, David A. Agard5, Kay Grünewald3,6, Abraham J. Koster1, Eric J. Snijder2, Montserrat Bárcena1,*

1 Department of Cell and Chemical Biology, Section Electron Microscopy, Leiden University Medical Center, Leiden 2333 ZC, Netherlands. 2 Department of Medical Microbiology, Molecular Virology Laboratory, Leiden University Medical Center, Leiden 2333 ZA, Netherlands. 3 Department of Structural Cell Biology of Viruses, Centre for Structural Systems Biology, Heinrich Pette Institute, Leibnitz Institute of Experimental Virology, Hamburg, Germany. 4 Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94143, USA. 5 Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA. 6 Department of Chemistry, MIN Faculty, Universität Hamburg, Hamburg, Germany.

*Corresponding author. Email: m.barcena@lumc.nl

Science  06 Aug 2020: eabd3629 | DOI: DOI: 10.1126/science.abd3629



Coronavirus genome replication is associated with virus-induced cytosolic double-membrane vesicles, which may provide a tailored micro-environment for viral RNA synthesis in the infected cell. However, it is unclear how newly synthesized genomes and mRNAs can travel from these sealed replication compartments to the cytosol to ensure their translation and the assembly of progeny virions. Here, we used cellular electron cryo-microscopy to visualize a molecular pore complex that spans both membranes of the double-membrane vesicle and would allow export of RNA to the cytosol. A hexameric assembly of a large viral transmembrane protein was found to form the core of the crown-shaped complex. This coronavirus-specific structure likely plays a critical role in coronavirus replication and thus constitutes a potential drug target.

Keywords: SARS-CoV-2; COVID-19; Viral pathogenesis.


#Coronavirus #RNA #proofreading: molecular basis and therapeutic targeting (Mol Cell., abstract)

[Source: Molecular Cell, full page: (LINK). Abstract, edited.]

Coronavirus RNA proofreading: molecular basis and therapeutic targeting

Fran Robson †, Khadija Shahed Khan †, Thi Khanh Le, Clément Paris, Sinem Demirbag, Peter Barfuss, Palma Rocchi, Wai-Lung Ng

Published: August 04, 2020 | DOI: https://doi.org/10.1016/j.molcel.2020.07.027



The coronavirus disease 2019 (COVID-19) that is wreaking havoc on global public health and economies has heightened awareness about the lack of effective antiviral treatments for human coronaviruses (CoVs). Many current antivirals, notably nucleoside analogues (NA), exert their effect by incorporation into viral genomes and subsequent disruption of viral replication and fidelity. The development of anti-CoV drugs has long been hindered by the capacity of CoVs to proofread and remove mismatched nucleotides during genome replication and transcription. Here, we review the molecular basis of the CoV proofreading complex and evaluate its potential as a drug target. We also consider existing nucleoside analogues and novel genomic techniques as potential anti-CoV therapeutics that could be used individually or in combination to target the proofreading mechanism.

Publication stage In Press Accepted Manuscript

Identification DOI: https://doi.org/10.1016/j.molcel.2020.07.027

Copyright © 2020 Elsevier Inc.

Keywords: SARS-CoV-2; COVID-19; Viral pathogenesis.


#SARS-CoV-2 infects #human #neural progenitor #cells and brain #organoids (Cell Res., summary)

[Source: Cell Research, full page: (LINK). Summary, edited.]

SARS-CoV-2 infects human neural progenitor cells and brain organoids

Bao-Zhong Zhang, Hin Chu, Shuo Han, Huiping Shuai, Jian Deng, Ye-fan Hu, Hua-rui Gong, Andrew Chak-Yiu Lee, Zijiao Zou, Thomas Yau, Wutian Wu, Ivan Fan-Ngai Hung, Jasper Fuk-Woo Chan, Kwok-Yung Yuen & Jian-Dong Huang

Cell Research (2020)


ùDear Editor, Coronavirus disease 2019 (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)1 has resulted in over 13 million confirmed cases and more than 580,045 deaths across 218 countries and geographical regions as of July 16, 2020. This novel coronavirus primarily causes respiratory illness with clinical manifestations largely resembling those of SARS. However, neurological symptoms including headache, anosmia, ageusia, confusion, seizure, and encephalopathy have also been frequently reported in COVID-19 patients.2,3 In a study of 214 hospitalized COVID-19 patients in Wuhan, China, neurologic findings were reported in 36.4% of patients, and were more commonly observed in patients with severe infections (45.5%).2 Similarly, a study from France reported neurologic findings in 84.5% (49/58) of COVID-19 patients admitted to hospital.3 Importantly, a recent study in Germany demonstrated that SARS-CoV-2 RNA could be detected in brain biopsies in 36.4% (8/22) of fatal COVID-19 cases,4 which highlights the potential for viral infections in the human brain. To date, there has been no direct experimental evidence of SARS-CoV-2 infection in the human central nervous system (CNS). We recently demonstrated that SARS-CoV-2 could infect and replicate in cells of neuronal origin.5 In line with this finding, we showed that SARS-CoV-2 could infect and damage the olfactory sensory neurons of hamsters.6 In addition, angiotensin-converting enzyme 2 (ACE2), the entry receptor of SARS-CoV-2, is widely detected in the brain and is highly concentrated in a number of locations including substantia nigra, middle temporal gyrus, and posterior cingulate cortex.7 Together, these findings suggest that the human brain might be an extra-pulmonary target of SARS-CoV-2 infection.


Keywords: SARS-CoV-2; COVID-19; Viral pathogenesis.


#Papain-like #protease regulates #SARS-CoV-2 viral spread and innate #immunity (Nature, abstract)

[Source: Nature, full page: (LINK). Abstract, edited.]

This is an unedited manuscript that has been accepted for publication. Nature Research are providing this early version of the manuscript as a service to our authors and readers. The manuscript will undergo copyediting, typesetting and a proof review before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers apply.

Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity

Donghyuk Shin, Rukmini Mukherjee, Diana Grewe, Denisa Bojkova, Kheewoong Baek, Anshu Bhattacharya, Laura Schulz, Marek Widera, Ahmad Reza Mehdipour, Georg Tascher, Paul P. Geurink, Alexander Wilhelm, Gerbrand J. van der Heden van Noort, Huib Ovaa, Stefan Müller, Klaus-Peter Knobeloch, Krishnaraj Rajalingam, Brenda A. Schulman, Jindrich Cinatl, Gerhard Hummer, Sandra Ciesek & Ivan Dikic

Nature (2020)



The papain-like protease PLpro is an essential coronavirus enzyme required for processing viral polyproteins to generate a functional replicase complex and enable viral spread1,2. PLpro is also implicated in cleaving proteinaceous post-translational modifications on host proteins as an evasion mechanism against host anti-viral immune responses3–5. Here, we provide biochemical, structural and functional characterization of the SARS-CoV-2 PLpro (SCoV2-PLpro) and outline differences to SARS-CoV PLpro (SCoV-PLpro) in controlling host interferon (IFN) and NF-κB pathways. While SCoV2-PLpro and SCoV-PLpro share 83% sequence identity, they exhibit different host substrate preferences. In particular, SCoV2-PLpro preferentially cleaves the ubiquitin-like protein ISG15, whereas SCoV-PLpro predominantly targets ubiquitin chains. The crystal structure of SCoV2-PLpro in complex with ISG15 reveals distinctive interactions with the amino-terminal ubiquitin-like domain of ISG15, highlighting this high affinity and specificity. Furthermore, upon infection, SCoV2-PLpro contributes to the cleavage of ISG15 from interferon responsive factor 3 (IRF3) and attenuates type I interferon responses. Importantly, inhibition of SCoV2-PLpro with GRL-0617 impairs the virus-induced cytopathogenic effect, fosters the anti-viral interferon pathway and reduces viral replication in infected cells. These results highlight a dual therapeutic strategy in which targeting of SCoV2-PLpro can suppress SARS-CoV-2 infection and promote anti-viral immunity.

Keywords: SARS-CoV-2; COVID-19; Viral pathogenesis.


#Structural #basis for #helicase-polymerase coupling in the #SARS-CoV-2 replication-transcription complex (Cell, abstract)

[Source: Cell, full page: (LINK). Abstract, edited.]

Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex

James Chen, Brandon Malone, Eliza Llewellyn, Michael Grasso, Patrick M.M. Shelton, Paul Dominic B. Olinares, Kashyap Maruthi, Ed T. Eng, Hasan Vatandaslar, Brian T. Chait, Tarun Kapoor, Seth A. Darst, Elizabeth A. Campbell

Published: July 28, 2020 | DOI: https://doi.org/10.1016/j.cell.2020.07.033



  • Structure of SARS-CoV-2 replication-transcription complex (RTC) with nsp13 helicases
  • The nsp13 NTPase domains sit in front of the RCT, constraining functional models
  • Nsp13 may drive RTC backtracking, thus impacting proofreading and template-switching
  • Structural analysis of ADP-Mg2+-bound NiRAN domain, a potential antiviral target



SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated and transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with a cast of accessory factors. One of these factors is the nsp13 helicase. Both the holo-RdRp and nsp13 are essential for viral replication and are targets for treating the disease COVID-19. Here we present cryo-electron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template-product in complex with two molecules of the nsp13 helicase. The Nidovirus-order-specific N-terminal domains of each nsp13 interact with the N-terminal extension of each copy of nsp8. One nsp13 also contacts the nsp12-thumb. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. We also observe ADP-Mg2+ bound in the nsp12 N-terminal nidovirus RdRp-associated nucleotidyltransferase domain, detailing a new pocket for anti-viral therapeutic development.

Accepted: July 22, 2020 – Received in revised form: July 10, 2020 – Received: June 22, 2020

Publication stage In Press Accepted Manuscript

Identification DOI: https://doi.org/10.1016/j.cell.2020.07.033

Copyright © 2020 Elsevier Inc.

Keywords: SARS-CoV-2; COVID-19; Viral pathogenesis.


#Cytoskeleton—a crucial #key in host #cell for #coronavirus infection (J Mol Cell Biol., abstract)

[Source: Journal of Molecular Cell Biology, full page: (LINK). Abstract, edited.]

Cytoskeleton—a crucial key in host cell for coronavirus infection

Zeyu Wen, Yue Zhang, Zhekai Lin, Kun Shi, Yaming Jiu

Journal of Molecular Cell Biology, mjaa042, https://doi.org/10.1093/jmcb/mjaa042

Published: 27 July 2020



The emerging coronavirus pandemic is threatening the public health all over the world. Cytoskeleton is an intricate network involved in controlling cell shape, cargo transport, signal transduction, and cell division. Infection biology studies have illuminated essential roles for cytoskeleton in mediating the outcome of host‒virus interactions. In this review, we discuss the dynamic interactions between actin filaments, microtubules, intermediate filaments, and coronaviruses. In one round of viral life cycle, coronaviruses surf along filopodia on the host membrane to the entry sites, utilize specific intermediate filament protein as co-receptor to enter target cells, hijack microtubules for transportation to replication and assembly sites, and promote actin filaments polymerization to provide forces for egress. During coronavirus infection, disruption of host cytoskeleton homeostasis and modification state is tightly connected to pathological processes, such as defective cytokinesis, demyelinating, cilia loss, and neuron necrosis. There are increasing mechanistic studies on cytoskeleton upon coronavirus infection, such as viral protein‒cytoskeleton interaction, changes in the expression and post-translation modification, related signaling pathways, and incorporation with other host factors. Collectively, these insights provide new concepts for fundamental virology and the control of coronavirus infection.

coronavirus, host cytoskeleton, actin filaments, microtubules, intermediate filaments, pathology

Issue Section: Review

This content is only available as a PDF.

© The Author(s) 2020. Published by Oxford University Press on behalf of Journal of Molecular Cell Biology, IBCB, SIBS, CAS.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Keywords: SARS-CoV-2; COVID-19; Viral pathogenesis.


LY6E impairs #coronavirus #fusion and confers #immune #control of viral disease (Nat Microbiol., abstract)

[Source: Nature Microbiology, full page: (LINK). Abstract, edited.]

LY6E impairs coronavirus fusion and confers immune control of viral disease

Stephanie Pfaender, Katrina B. Mar, […] Volker Thiel

Nature Microbiology (2020)



Zoonotic coronaviruses (CoVs) are substantial threats to global health, as exemplified by the emergence of two severe acute respiratory syndrome CoVs (SARS-CoV and SARS-CoV-2) and Middle East respiratory syndrome CoV (MERS-CoV) within two decades1,2,3. Host immune responses to CoVs are complex and regulated in part through antiviral interferons. However, interferon-stimulated gene products that inhibit CoVs are not well characterized4. Here, we show that lymphocyte antigen 6 complex, locus E (LY6E) potently restricts infection by multiple CoVs, including SARS-CoV, SARS-CoV-2 and MERS-CoV. Mechanistic studies revealed that LY6E inhibits CoV entry into cells by interfering with spike protein-mediated membrane fusion. Importantly, mice lacking Ly6e in immune cells were highly susceptible to a murine CoV—mouse hepatitis virus. Exacerbated viral pathogenesis in Ly6e knockout mice was accompanied by loss of hepatic immune cells, higher splenic viral burden and reduction in global antiviral gene pathways. Accordingly, we found that constitutive Ly6e directly protects primary B cells from murine CoV infection. Our results show that LY6E is a critical antiviral immune effector that controls CoV infection and pathogenesis. These findings advance our understanding of immune-mediated control of CoV in vitro and in vivo—knowledge that could help inform strategies to combat infection by emerging CoVs.

Keywords: SARS-CoV-2; COVID-19; MERS-CoV; SARS-CoV; Coronavirus; Viral pathogenesis; Immunology.


Presence of #Genetic #Variants Among Young #Men With #Severe #COVID19 (JAMA, abstract)

[Source: JAMA, full page: (LINK). Abstract, edited.]

Presence of Genetic Variants Among Young Men With Severe COVID-19

Caspar I. van der Made, MD1,2,3,4; Annet Simons, PhD1; Janneke Schuurs-Hoeijmakers, MD, PhD1; Guus van den Heuvel, MD5; Tuomo Mantere, PhD1; Simone Kersten, MSc1,2,3; Rosanne C. van Deuren, MSc1,2,3; Marloes Steehouwer, BSc1; Simon V. van Reijmersdal, BSc1; Martin Jaeger, PhD2,3; Tom Hofste, BSc1; Galuh Astuti, PhD1; Jordi Corominas Galbany, PhD1; Vyne van der Schoot, MD, PhD6; Hans van der Hoeven, MD, PhD7; Wanda Hagmolen of ten Have, MD, PhD5; Eva Klijn, MD, PhD8; Catrien van den Meer, MD9; Jeroen Fiddelaers, MD10; Quirijn de Mast, MD, PhD2,3,4; Chantal P. Bleeker-Rovers, MD, PhD2,4,11; Leo A. B. Joosten, PhD2,3,4; Helger G. Yntema, PhD1,12; Christian Gilissen, PhD1,3; Marcel Nelen, PhD1; Jos W. M. van der Meer, MD, PhD2,3,4; Han G. Brunner, MD, PhD1,6,12,13; Mihai G. Netea, MD, PhD2,3,4,14; Frank L. van de Veerdonk, MD, PhD2,3,4; Alexander Hoischen, PhD1,2,3,4

Author Affiliations: 1 Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; 2 Radboud University Medical Center Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; 3 Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; 4 Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, the Netherlands; 5 Pulmonology Department, Radboud University Medical Center, Nijmegen, the Netherlands; 6 Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands; 7 Department of Intensive Care, Radboud University Medical Center Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands; 8 Department of Intensive Care, Erasmus Medical Center, Rotterdam, the Netherlands; 9 Department of Intensive Care, Ziekenhuis Rivierenland, Tiel, the Netherlands; 10 Department of Pulmonology, Admiraal de Ruyter Ziekenhuis, Goes, the Netherlands; 11 Radboud Institute Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; 12 Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; 13 GROW School of Oncology and developmental biology, and MHeNs School of Mental Health and Neuroscience, Maastricht University, the Netherlands; 14 Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany

JAMA. Published online July 24, 2020. doi:10.1001/jama.2020.13719


Key Points

  • Question  – Are genetic variants associated with severe coronavirus disease 2019 (COVID-19) in young male patients?
  • Findings  – In a case series that included 4 young male patients with severe COVID-19 from 2 families, rare loss-of-function variants of the X-chromosomal TLR7 were identified, with immunological defects in type I and II interferon production.
  • Meaning  – These findings provide insights into the pathogenesis of COVID-19.




Severe coronavirus disease 2019 (COVID-19) can occur in younger, predominantly male, patients without preexisting medical conditions. Some individuals may have primary immunodeficiencies that predispose to severe infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).


To explore the presence of genetic variants associated with primary immunodeficiencies among young patients with COVID-19.

Design, Setting, and Participants  

Case series of pairs of brothers without medical history meeting the selection criteria of young (age <35 years) brother pairs admitted to the intensive care unit (ICU) due to severe COVID-19. Four men from 2 unrelated families were admitted to the ICUs of 4 hospitals in the Netherlands between March 23 and April 12, 2020. The final date of follow-up was May 16, 2020. Available family members were included for genetic variant segregation analysis and as controls for functional experiments.


Severe COVID-19.

Main Outcome and Measures  

Results of rapid clinical whole-exome sequencing, performed to identify a potential monogenic cause. Subsequently, basic genetic and immunological tests were performed in primary immune cells isolated from the patients and family members to characterize any immune defects.


The 4 male patients had a mean age of 26 years (range, 21-32), with no history of major chronic disease. They were previously well before developing respiratory insufficiency due to severe COVID-19, requiring mechanical ventilation in the ICU. The mean duration of ventilatory support was 10 days (range, 9-11); the mean duration of ICU stay was 13 days (range, 10-16). One patient died. Rapid clinical whole-exome sequencing of the patients and segregation in available family members identified loss-of-function variants of the X-chromosomal TLR7. In members of family 1, a maternally inherited 4-nucleotide deletion was identified (c.2129_2132del; p.[Gln710Argfs*18]); the affected members of family 2 carried a missense variant (c.2383G>T; p.[Val795Phe]). In primary peripheral blood mononuclear cells from the patients, downstream type I interferon (IFN) signaling was transcriptionally downregulated, as measured by significantly decreased mRNA expression of IRF7, IFNB1, and ISG15 on stimulation with the TLR7 agonist imiquimod as compared with family members and controls. The production of IFN-γ, a type II IFN, was decreased in patients in response to stimulation with imiquimod.

Conclusions and Relevance  

In this case series of 4 young male patients with severe COVID-19, rare putative loss-of-function variants of X-chromosomal TLR7 were identified that were associated with impaired type I and II IFN responses. These preliminary findings provide insights into the pathogenesis of COVID-19.

Keywords: SARS-CoV-2; COVID-19; Genetics; Immunodeficiency; Viral pathogenesis; Interferons.


Type I and Type III #IFN Restrict #SARS-CoV-2 Infection of Human #Airway #Epithelial Cultures (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Type I and Type III IFN Restrict SARS-CoV-2 Infection of Human Airway Epithelial Cultures

Abigail Vanderheiden, Philipp Ralfs, Tatiana Chirkova, Amit A. Upadhyay, Matthew G. Zimmerman, Shamika Bedoya, Hadj Aoued, Gregory M. Tharp, Kathryn L. Pellegrini, Candela Manfredi, Eric Sorscher, Bernardo Mainou, Jenna L. Lobby, Jacob E. Kohlmeier, Anice C. Lowen, Pei-Yong Shi, Vineet D. Menachery, Larry J. Anderson, Arash Grakoui, Steven E. Bosinger, Mehul S. Suthar

DOI: 10.1128/JVI.00985-20



The newly emerged human coronavirus, SARS-CoV-2, has caused a pandemic of respiratory illness. Current evidence suggests that severe cases of SARS-CoV-2 are associated with a dysregulated immune response. However, little is known about how the innate immune system responds to SARS-CoV-2. Here, we modeled SARS-CoV-2 infection using primary human airway epithelial (pHAE) cultures, which are maintained in an air-liquid interface. We found that SARS-CoV-2 infects and replicates in pHAE cultures and is directionally released on the apical, but not basolateral surface. Transcriptional profiling studies found that infected pHAE cultures had a molecular signature dominated by pro-inflammatory cytokines and chemokine induction, including IL-6, TNFα, CXCL8, and identified NF-κB and ATF-4 as key drivers of this pro-inflammatory cytokine response. Surprisingly, we observed a complete lack of a type I or III interferon (IFN) response to SARS-CoV-2 infection. However, pre-treatment and post-treatment with type I and III IFNs significantly reduced virus replication in pHAE cultures that correlated with upregulation of antiviral effector genes. Combined, our findings demonstrate that SARS-CoV-2 does not trigger an IFN response but is sensitive to the effects of type I and III IFNs. Our studies demonstrate the utility of pHAE cultures to model SARS-CoV-2 infection and that both type I and III IFNs can serve as therapeutic options to treat COVID-19 patients.



The current pandemic of respiratory illness, COVID-19, is caused by a recently emerged coronavirus named SARS-CoV-2. This virus infects airway and lung cells causing fever, dry cough, and shortness of breath. Severe cases of COVID-19 can result in lung damage, low blood oxygen levels, and even death. As there are currently no vaccines approved for use in humans, studies of the mechanisms of SARS-CoV-2 infection are urgently needed. Our research identifies an excellent system to model SARS-CoV-2 infection of the human airways, that can be used to test various treatments. Analysis of infection in this model system found that human airway epithelial cultures induce a strong pro-inflammatory cytokine response yet block the production of type I and III IFNs. to SARS-CoV-2. However, treatment of airway cultures with the immune molecules, type I or type III interferon (IFN) was able to inhibit SARS-CoV-2 infection. Thus, our model system identified type I or type III IFN as potential antiviral treatments for COVID-19 patients.

Copyright © 2020 American Society for Microbiology. All Rights Reserved.

This article is made available via the PMC Open Access Subset for unrestricted noncommercial re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

Keywords: SARS-CoV-2; COVID-19; Viral pathogenesis; Interferons.