Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication.
Coronaviruses are of veterinary and medical importance and include highly pathogenic zoonotic viruses, such as SARS-CoV and MERS-CoV. They are known to efficiently evade early innate immune responses, manifesting in almost negligible expression of type-I interferons (IFN-I). This evasion strategy suggests an evolutionary conserved viral function that has evolved to prevent RNA-based sensing of infection in vertebrate hosts. Here we show that the coronavirus endonuclease (EndoU) activity is key to prevent early induction of double-stranded RNA (dsRNA) host cell responses. Replication of EndoU-deficient coronaviruses is greatly attenuated in vivo and severely restricted in primary cells even during the early phase of the infection. In macrophages we found immediate induction of IFN-I expression and RNase L-mediated breakdown of ribosomal RNA. Accordingly, EndoU-deficient viruses can retain replication only in cells that are deficient in IFN-I expression or sensing, and in cells lacking both RNase L and PKR. Collectively our results demonstrate that the coronavirus EndoU efficiently prevents simultaneous activation of host cell dsRNA sensors, such as Mda5, OAS and PKR. The localization of the EndoU activity at the site of viral RNA synthesis-within the replicase complex-suggests that coronaviruses have evolved a viral RNA decay pathway to evade early innate and intrinsic antiviral host cell responses.
Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland.|Federal Department of Home Affairs, Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland.
Eveline
E
Kindler
Institute of Immunobiology, Kantonsspital St.Gallen, St.Gallen, Switzerland.
Cristina
C
Gil-Cruz
Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany.
Julia
J
Spanier
Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America.
Yize
Y
Li
Universities Giessen & Marburg Lung Center (UGMLC), Deutsches Zentrum für Lungenforschung (DZL), Giessen, Germany.
Jochen
J
Wilhelm
Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
Huib H
HH
Rabouw
Singapore Immunology Network, Singapore.
Roland
R
Züst
Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America.
Mihyun
0000-0003-2639-0265
M
Hwang
Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland.|Federal Department of Home Affairs, Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland.|Graduate School for Biomedical Science, University of Bern, Bern, Switzerland.
Philip
0000-0002-8366-1220
P
V'kovski
Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland.|Federal Department of Home Affairs, Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland.
Hanspeter
0000-0003-0763-6469
H
Stalder
Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland.|Federal Department of Home Affairs, Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland.
Sabrina
S
Marti
Max-Planck-Institute of Biochemistry, Martinsried, Germany.
Matthias
M
Habjan
Washington University School of Medicine, St. Louis, MO, USA.
Luisa
L
Cervantes-Barragan
Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America.
Ruth
R
Elliot
Institute for Medical Virology, Justus-Liebig-University, Giessen, Germany.
Nadja
N
Karl
Department of Cancer Biology, Lerner Research Institute, Cleveland, Ohio, United States of America.
Christina
C
Gaughan
Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
Frank J M
0000-0001-5800-749X
FJ
van Kuppeveld
Department of Cancer Biology, Lerner Research Institute, Cleveland, Ohio, United States of America.
Robert H
RH
Silverman
Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
Markus
M
Keller
Institute of Immunobiology, Kantonsspital St.Gallen, St.Gallen, Switzerland.
Burkhard
B
Ludewig
Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America.
Cornelia C
CC
Bergmann
Institute for Medical Virology, Justus-Liebig-University, Giessen, Germany.
John
J
Ziebuhr
Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America.
Susan R
0000-0002-8155-4528
SR
Weiss
Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany.
Ulrich
U
Kalinke
Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland.|Federal Department of Home Affairs, Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland.
Volker
0000-0002-5783-0887
V
Thiel
D000818:Animals; D003332:Coronaviridae / Q000201:enzymology* / Q000276:immunology; D018352:Coronavirus Infections / Q000276:immunology*; D004720:Endonucleases / Q000276:immunology*; D004797:Enzyme-Linked Immunosorbent Assay; D005434:Flow Cytometry; D054884:Host-Pathogen Interactions / Q000276:immunology; D006801:Humans; D057131:Immune Evasion / Q000502:physiology*; D007113:Immunity, Innate / Q000276:immunology; D051379:Mice; D008810:Mice, Inbred C57BL; D060888:Real-Time Polymerase Chain Reaction; D014764:Viral Proteins / Q000276:immunology*
D014764:Viral Proteins; D004720:Endonucleases