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Kerr CM, Pfannenstiel JJ, Alhammad YM, Roy A, O’Connor JJ, Ghimire R, Khattabi R, Shrestha R, McDonald PR, Gao P, Johnson DK, More S, Channappanavar R, Fehr AR. Mutation of highly conserved residues in loop 2 of the coronavirus macrodomain demonstrates that enhanced ADP-ribose binding is detrimental to infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574082. [PMID: 38260573 PMCID: PMC10802294 DOI: 10.1101/2024.01.03.574082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
All coronaviruses (CoVs) encode for a conserved macrodomain (Mac1) located in nonstructural protein 3 (nsp3). Mac1 is an ADP-ribosylhydrolase that binds and hydrolyzes mono-ADP-ribose from target proteins. Previous work has shown that Mac1 is important for virus replication and pathogenesis. Within Mac1, there are several regions that are highly conserved across CoVs, including the GIF (glycine-isoleucine-phenylalanine) motif. To determine how the biochemical activities of these residues impact CoV replication, the isoleucine and the phenylalanine residues were mutated to alanine (I-A/F-A) in both recombinant Mac1 proteins and recombinant CoVs, including murine hepatitis virus (MHV), Middle East respiratory syndrome coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The F-A mutant proteins had ADP-ribose binding and/or hydrolysis defects that led to attenuated replication and pathogenesis in cell culture and mice. In contrast, the I-A mutations had normal enzyme activity and enhanced ADP-ribose binding. Despite increased ADP-ribose binding, I-A mutant MERS-CoV and SARS-CoV-2 were highly attenuated in both cell culture and mice, indicating that this isoleucine residue acts as a gate that controls ADP-ribose binding for efficient virus replication. These results highlight the function of this highly conserved residue and provide unique insight into how macrodomains control ADP-ribose binding and hydrolysis to promote viral replication and pathogenesis.
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Affiliation(s)
- Catherine M. Kerr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | | | - Yousef M. Alhammad
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Anuradha Roy
- High Throughput Screening Laboratory, University of Kansas, Lawrence, Kansas 66047, USA
| | - Joseph J. O’Connor
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Roshan Ghimire
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Reem Khattabi
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Rakshya Shrestha
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Peter R. McDonald
- High Throughput Screening Laboratory, University of Kansas, Lawrence, Kansas 66047, USA
| | - Philip Gao
- Protein Production Group, University of Kansas, Lawrence, Kansas 66047, USA
| | - David K. Johnson
- Molecular Graphics and Modeling Laboratory and the Computational Chemical Biology Core, University of Kansas, Lawrence, Kansas 66047, USA
| | - Sunil More
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, College of Veterinary Medicine, Stillwater, Oklahoma 74078, USA
| | - Rudragouda Channappanavar
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, College of Veterinary Medicine, Stillwater, Oklahoma 74078, USA
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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Irún P, Gracia R, Piazuelo E, Pardo J, Morte E, Paño JR, Boza J, Carrera-Lasfuentes P, Higuera GA, Lanas A. Serum lipid mediator profiles in COVID-19 patients and lung disease severity: a pilot study. Sci Rep 2023; 13:6497. [PMID: 37081104 PMCID: PMC10118224 DOI: 10.1038/s41598-023-33682-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/17/2023] [Indexed: 04/22/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 infection is highly heterogeneous, ranging from asymptomatic to severe and fatal cases. COVID-19 has been characterized by an increase of serum pro-inflammatory cytokine levels which seems to be associated with fatal cases. By contrast, the role of pro-resolving lipid mediators (SPMs), involved in the attenuation of inflammatory responses, has been scarcely investigated, so further studies are needed to understand SPMs metabolism in COVID-19 and other infectious diseases. Our aim was to analyse the lipid mediator metabolome, quantifying pro- and anti-inflammatory serum bioactive lipids by LC-MS/MS in 7 non-infected subjects and 24 COVID-19 patients divided into mild, moderate, and severe groups according to the pulmonary involvement, to better understand the disease outcome and the severity of the pulmonary manifestations. Statistical analysis was performed with the R programming language (R Foundation for Statistical Computing, Vienna, Austria). All COVID-19 patients had increased levels of Prostaglandin E2. Severe patients showed a significant increase versus controls, mild- and moderate-affected patients, expressed as median (interquartile range), in resolvin E1 [112.6 (502.7) vs 0.0 (0.0) pg/ml in the other groups], as well as in maresin 2 [14.5 (7.0) vs 8.1 (4.2), 5.5 (4.3), and 3.0 (4.0) pg/ml, respectively]. Moreover, 14-hydroxy docosahexaenoic acid (14-HDHA) levels were also increased in severe vs control and mild-affected patients [24.7 (38.2) vs 2.4 (2.2) and 3.7 (6.4) ng/mL, respectively]. Resolvin D5 was also significantly elevated in both moderate [15.0 (22.4) pg/ml] and severe patients [24.0 (24.1) pg/ml] versus controls [0.0 (0.0) pg/ml]. These results were confirmed by sparse partial least squares discriminant analysis which highlighted the contribution of these mediators to the separation between each of the groups. In conclusion, the potent inflammatory response to SARS-CoV-2 infection involves not only pro- but also anti-inflammatory lipid mediators that can be quantified in easily accessible serum samples, suggesting the need to perform future research on their generation pathways that will help us to discover new therapeutic targets.
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Affiliation(s)
- Pilar Irún
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain.
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain.
| | | | - Elena Piazuelo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS Aragón), Zaragoza, Spain
- Departamento de Farmacología y Fisiología, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Julián Pardo
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
- Departamento de Microbiología, Medicina Preventiva y Salud, Universidad de Zaragoza, Zaragoza, Spain
- Aragón I + D Foundation (ARAID), Government of Aragon, Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain
| | - Elena Morte
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain
- Infectious Disease Department, University Hospital Lozano Blesa, Zaragoza, Spain
| | - José Ramon Paño
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain
- Infectious Disease Department, University Hospital Lozano Blesa, Zaragoza, Spain
| | | | - Patricia Carrera-Lasfuentes
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | | | - Angel Lanas
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
- Service of Digestive Diseases, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
- Departamento de Medicina, Psiquiatría y Dermatología, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
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Acquisition of Furin Cleavage Site and Further SARS-CoV-2 Evolution Change the Mechanisms of Viral Entry, Infection Spread, and Cell Signaling. J Virol 2022; 96:e0075322. [PMID: 35876526 PMCID: PMC9364789 DOI: 10.1128/jvi.00753-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the human population leads to further viral evolution. The new variants that arise during this evolution are more infectious. Our data suggest that newer variants have shifted from utilizing both cathepsin/endosome- and TMPRSS2-mediated entry mechanisms to rely on a TMPRSS2-dependent entry pathway. Accordingly, only the early lineages of SARS-CoV-2 are capable of infecting and forming syncytia in Vero/ACE2 cells which lack TMPRSS2 expression. The presence of an intact multibasic furin cleavage site (FCS) in the S protein was a key requirement for cell-to-cell fusion. Deletion of FCS makes SARS-CoV-2 more infectious in vitro but renders it incapable of syncytium formation. Cell-to-cell fusion likely represents an alternative means of virus spread and is resistant to the presence of high levels of neutralizing monoclonal antibodies (MAbs) and immune sera in the media. In this study, we also noted that cells infected with SARS-CoV-2 with an intact FCS or alphavirus replicon expressing S protein (VEErep/S) released high levels of free S1 subunit. The released S1 is capable of activating the TLR4 receptor and inducing a pro-inflammatory response. Thus, S1 activation of TLR4 may be an important contributor to SARS-CoV-2-induced COVID-19 disease and needs to be considered in the design of COVID mRNA vaccines. Lastly, a VEErep/S-replicon was shown to produce large amounts of infectious, syncytium-forming pseudoviruses and thus could represent alternative experimental system for screening inhibitors of virus entry and syncytium formation. IMPORTANCE The results of this study demonstrate that the late lineages of SARS-CoV-2 evolved to more efficient use of the TMPRSS2-mediated entry pathway and gradually lost an ability to employ the cathepsins/endosome-mediated entry. The acquisition of a furin cleavage site (FCS) by SARS-CoV-2-specific S protein made the virus a potent producer of syncytia. Their formation is also determined by expression of ACE2 and TMPRSS2 and is resistant to neutralizing human MAbs and immune sera. Syncytium formation appears to be an alternative means of infection spread following the development of an adaptive immune response. Cells infected with SARS-CoV-2 with an intact FCS secrete high levels of the S1 subunit. The released S1 demonstrates an ability to activate the TLR4 receptor and induce pro-inflammatory cytokines, which represent a hallmark of SARS-CoV-2 pathogenesis. Alphavirus replicons encoding SARS-CoV-2 S protein cause spreading, syncytium-forming infection, and they can be applied as an experimental tool for studying the mechanism of syncytium formation.
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Kibler KV, Szczerba M, Lake D, Roeder AJ, Rahman M, Hogue BG, Roy Wong LY, Perlman S, Li Y, Jacobs BL. Intranasal Immunization with a Vaccinia Virus Vaccine Vector Expressing Pre-Fusion Stabilized SARS-CoV-2 Spike Fully Protected Mice against Lethal Challenge with the Heavily Mutated Mouse-Adapted SARS2-N501Y MA30 Strain of SARS-CoV-2. Vaccines (Basel) 2022; 10:vaccines10081172. [PMID: 35893821 PMCID: PMC9394475 DOI: 10.3390/vaccines10081172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/24/2022] Open
Abstract
The Omicron SARS-CoV-2 variant has been designated as a variant of concern because its spike protein is heavily mutated. In particular, the Omicron spike is mutated at five positions (K417, N440, E484, Q493, and N501) that have been associated with escape from neutralizing antibodies induced by either infection with or immunization against the early Washington strain of SARS-CoV-2. The mouse-adapted strain of SARS-CoV-2, SARS2-N501YMA30, contains a spike that is also heavily mutated, with mutations at four of the five positions in the Omicron spike associated with neutralizing antibody escape (K417, E484, Q493, and N501). In this manuscript, we show that intranasal immunization with a pre-fusion stabilized Washington strain spike, expressed from a highly attenuated, replication-competent vaccinia virus construct, NYVAC-KC, fully protected mice against symptoms and death from SARS2-N501YMA30. Similarly, immunization by scarification on the skin fully protected against death, but not from mild disease. This data demonstrates that the Washington strain spike, when expressed from a highly attenuated, replication-competent poxvirus—administered without parenteral injection—can fully protect against the heavily mutated mouse-adapted SARS2-N501YMA30.
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Affiliation(s)
- Karen V. Kibler
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85287, USA; (M.S.); (M.R.); (B.G.H.); (Y.L.); (B.L.J.)
- Correspondence:
| | - Mateusz Szczerba
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85287, USA; (M.S.); (M.R.); (B.G.H.); (Y.L.); (B.L.J.)
| | - Douglas Lake
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (D.L.); (A.J.R.)
| | - Alexa J. Roeder
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (D.L.); (A.J.R.)
| | - Masmudur Rahman
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85287, USA; (M.S.); (M.R.); (B.G.H.); (Y.L.); (B.L.J.)
| | - Brenda G. Hogue
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85287, USA; (M.S.); (M.R.); (B.G.H.); (Y.L.); (B.L.J.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (D.L.); (A.J.R.)
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA; (L.-Y.R.W.); (S.P.)
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA; (L.-Y.R.W.); (S.P.)
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Yize Li
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85287, USA; (M.S.); (M.R.); (B.G.H.); (Y.L.); (B.L.J.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (D.L.); (A.J.R.)
| | - Bertram L. Jacobs
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85287, USA; (M.S.); (M.R.); (B.G.H.); (Y.L.); (B.L.J.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (D.L.); (A.J.R.)
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Abstract
The cytokine storm (CS) in hyperinflammation is characterized by high levels of cytokines, extreme activation of innate as well as adaptive immune cells and initiation of apoptosis. High levels of apoptotic cells overwhelm the proper recognition and removal system of these cells. Phosphatidylserine on the apoptotic cell surface, which normally provides a recognition signal for removal, becomes a target for hemostatic proteins and secretory phospholipase A2. The dysregulation of these normal pathways in hemostasis and the inflammasome result in a prothrombotic state, cellular death, and end-organ damage. In this review, we provide the argument that this imbalance in recognition and removal is a common denominator regardless of the inflammatory trigger. The complex reaction of the immune defense system in hyperinflammation leads to self-inflicted damage. This common endpoint may provide additional options to monitor the progression of the inflammatory syndrome, predict severity, and may add to possible treatment strategies.
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Zhu Y, Zhou W, Niu Z, Sun J, Zhang Z, Li Q, Zheng Y, Wang C, Gao L, Sun Q. Long-range enhancement of N501Y-endowed mouse infectivity of SARS-CoV-2 by the non-RBD mutations of Ins215KLRS and H655Y. Biol Direct 2022; 17:14. [PMID: 35658928 PMCID: PMC9167559 DOI: 10.1186/s13062-022-00325-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/13/2022] [Indexed: 11/28/2022] Open
Abstract
Background Rodents, such as mice, are vulnerable targets, and potential intermediate hosts, of SARS-CoV-2 variants of concern, including Alpha, Beta, Gamma, and Omicron. N501Y in the receptor-binding domain (RBD) of Spike protein is the key mutation dictating the mouse infectivity, on which the neighboring mutations within RBD have profound impacts. However, the impacts of mutations outside RBD on N501Y-mediated mouse infectivity remain to be explored. Results Herein, we report that two non-RBD mutations derived from mouse-adapted strain, Ins215KLRS in the N-terminal domain (NTD) and H655Y in the subdomain linking S1 to S2, enhance mouse infectivity in the presence of N501Y mutation, either alone or together. This is associated with increased interaction of Spike with mouse ACE2 and mutations-induced local conformation changes in Spike protein. Mechanistically, the H655Y mutation disrupts interaction with N657, resulting in a less tight loop that wraps the furin-cleavage finger; and the insertion of 215KLRS in NTD increases its intramolecular interaction with a peptide chain that interfaced with the RBD-proximal region of the neighboring protomer, leading to a more flexible RBD that facilitates receptor binding. Moreover, the Omicron Spike that contains Ins214EPE and H655Y mutations confer mouse infectivity > 50 times over the N501Y mutant, which could be effectively suppressed by mutating them back to wild type. Conclusions Collectively, our study sheds light on the cooperation between distant Spike mutations in promoting virus infectivity, which may undermine the high infectiousness of Omicron variants towards mice. Supplementary information The online version contains supplementary material available at 10.1186/s13062-022-00325-x.
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Zhang C, Cui H, Li E, Guo Z, Wang T, Yan F, Liu L, Li Y, Chen D, Meng K, Li N, Qin C, Liu J, Gao Y, Zhang C. The SARS-CoV-2 B.1.351 Variant Can Transmit in Rats But Not in Mice. Front Immunol 2022; 13:869809. [PMID: 35572504 PMCID: PMC9095975 DOI: 10.3389/fimmu.2022.869809] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 04/05/2022] [Indexed: 11/23/2022] Open
Abstract
Previous studies have shown that B.1.351 and other variants have extended the host range of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to mice. Sustained transmission is a prerequisite for viral maintenance in a population. However, no evidence of natural transmission of SARS-CoV-2 in wild mice has been documented to date. Here, we evaluated the replication and contact transmission of the B.1.351 variant in mice and rats. The B.1.351 variant could infect and replicate efficiently in the airways of mice and rats. Furthermore, the B.1.351 variant could not be transmitted in BALB/c or C57BL/6 mice but could be transmitted with moderate efficiency in rats by direct contact. Additionally, the B.1.351 variant did not transmit from inoculated Syrian hamsters to BALB/c mice. Moreover, the mouse-adapted SARS-CoV-2 strain C57MA14 did not transmit in mice. In summary, the risk of B.1.351 variant transmission in mice is extremely low, but the transmission risk in rats should not be neglected. We should pay more attention to the potential natural transmission of SARS-CoV-2 variants in rats and their possible spillback to humans.
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Affiliation(s)
- Cheng Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Huan Cui
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - Entao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Zhendong Guo
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Tiecheng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Fang Yan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Lina Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yuanguo Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Di Chen
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Keyin Meng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Nan Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Chengfeng Qin
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Juxiang Liu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Yuwei Gao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Chunmao Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
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SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters. Nature 2022; 603:687-692. [PMID: 35062015 PMCID: PMC8942849 DOI: 10.1038/s41586-022-04441-6] [Citation(s) in RCA: 393] [Impact Index Per Article: 196.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/19/2022] [Indexed: 11/09/2022]
Abstract
The recent emergence of B.1.1.529, the Omicron variant1,2, has raised concerns of escape from protection by vaccines and therapeutic antibodies. A key test for potential countermeasures against B.1.1.529 is their activity in preclinical rodent models of respiratory tract disease. Here, using the collaborative network of the SARS-CoV-2 Assessment of Viral Evolution (SAVE) programme of the National Institute of Allergy and Infectious Diseases (NIAID), we evaluated the ability of several B.1.1.529 isolates to cause infection and disease in immunocompetent and human ACE2 (hACE2)-expressing mice and hamsters. Despite modelling data indicating that B.1.1.529 spike can bind more avidly to mouse ACE2 (refs. 3,4), we observed less infection by B.1.1.529 in 129, C57BL/6, BALB/c and K18-hACE2 transgenic mice than by previous SARS-CoV-2 variants, with limited weight loss and lower viral burden in the upper and lower respiratory tracts. In wild-type and hACE2 transgenic hamsters, lung infection, clinical disease and pathology with B.1.1.529 were also milder than with historical isolates or other SARS-CoV-2 variants of concern. Overall, experiments from the SAVE/NIAID network with several B.1.1.529 isolates demonstrate attenuated lung disease in rodents, which parallels preliminary human clinical data. A collaborative study demonstrates that, compared with previous SARS-CoV-2 variants, B.1.1.529 isolates cause less infection and disease in mice and hamsters, in agreement with preliminary data from studies in humans.
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Origin and evolutionary analysis of the SARS-CoV-2 Omicron variant. JOURNAL OF BIOSAFETY AND BIOSECURITY 2022; 4:33-37. [PMID: 35005525 PMCID: PMC8718870 DOI: 10.1016/j.jobb.2021.12.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/16/2021] [Accepted: 12/19/2021] [Indexed: 12/14/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved rapidly into new variants throughout the pandemic. The Omicron variant has more than 50 mutations when compared with the original wild-type strain and has been identified globally in numerous countries. In this report, we analyzed the mutational profiles of several variants, including the per-site mutation rate, to determine evolutionary relationships. The Omicron variant was found to have a unique mutation profile when compared with that of other SARS-CoV-2 variants, containing mutations that are rare in clinical samples. Moreover, the presence of five mouse-adapted mutation sites suggests that Omicron may have evolved in a mouse host. Mutations in the Omicron receptor-binding domain (RBD) region, in particular, have potential implications for the ongoing pandemic.
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10
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Wong LYR, Perlman S. Immune dysregulation and immunopathology induced by SARS-CoV-2 and related coronaviruses - are we our own worst enemy? Nat Rev Immunol 2022; 22:47-56. [PMID: 34837062 PMCID: PMC8617551 DOI: 10.1038/s41577-021-00656-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 02/04/2023]
Abstract
Human coronaviruses cause a wide spectrum of disease, ranging from mild common colds to acute respiratory distress syndrome and death. Three highly pathogenic human coronaviruses - severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus and SARS-CoV-2 - have illustrated the epidemic and pandemic potential of human coronaviruses, and a better understanding of their disease-causing mechanisms is urgently needed for the rational design of therapeutics. Analyses of patients have revealed marked dysregulation of the immune system in severe cases of human coronavirus infection, and there is ample evidence that aberrant immune responses to human coronaviruses are typified by impaired induction of interferons, exuberant inflammatory responses and delayed adaptive immune responses. In addition, various viral proteins have been shown to impair interferon induction and signalling and to induce inflammasome activation. This suggests that severe disease associated with human coronaviruses is mediated by both dysregulated host immune responses and active viral interference. Here we discuss our current understanding of the mechanisms involved in each of these scenarios.
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Affiliation(s)
- Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA.
- Department of Paediatrics, University of Iowa, Iowa City, IA, USA.
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11
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Kibler KV, Szczerba M, Lake D, Roeder AJ, Rahman M, Hogue BG, Roy Wong LY, Perlman S, Li Y, Jacobs BL. Intranasal immunization with a vaccinia virus vaccine vector expressing pre-fusion stabilized SARS-CoV-2 spike fully protected mice against lethal challenge with the heavily mutated mouse-adapted SARS2-N501Y MA30 strain of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34909775 DOI: 10.1101/2021.07.28.454201] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
The Omicron SARS-CoV-2 variant has been designated a variant of concern because its spike protein is heavily mutated. In particular, Omicron spike is mutated at 5 positions (K417, N440, E484, Q493 and N501) that have been associated with escape from neutralizing antibodies induced by either infection with or immunization against the early Washington strain of SARS-CoV-2. The mouse-adapted strain of SARS-CoV-2, SARS2-N501Y MA30 , contains a spike that is also heavily mutated, with mutations at 4 of the 5 positions in Omicron spike associated with neutralizing antibody escape (K417, E484, Q493 and N501). In this manuscript we show that intranasal immunization with a pre-fusion stabilized Washington strain spike, expressed from a highly attenuated, replication-competent vaccinia virus construct, NYVAC-KC, fully protected mice against disease and death from SARS2-N501Y MA30 . Similarly, immunization by scarification on the skin fully protected against death, but not from mild disease. This data demonstrates that Washington strain spike, when expressed from a highly attenuated, replication-competent poxvirus, administered without parenteral injection can fully protect against the heavily mutated mouse-adapted SARS2-N501Y MA30 .
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Affiliation(s)
- Karen V Kibler
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
| | - Mateusz Szczerba
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
| | - Douglas Lake
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Alexa J Roeder
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Masmudur Rahman
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
| | - Brenda G Hogue
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | - Yize Li
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Bertram L Jacobs
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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Kibler KV, Szczerba M, Lake D, Roeder AJ, Rahman M, Hogue BG, Roy Wong LY, Perlman S, Li Y, Jacobs BL. Intranasal immunization with a vaccinia virus vaccine vector expressing pre-fusion stabilized SARS-CoV-2 spike fully protected mice against lethal challenge with the heavily mutated mouse-adapted SARS2-N501Y MA30 strain of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.06.471483. [PMID: 34909775 PMCID: PMC8669842 DOI: 10.1101/2021.12.06.471483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The Omicron SARS-CoV-2 variant has been designated a variant of concern because its spike protein is heavily mutated. In particular, Omicron spike is mutated at 5 positions (K417, N440, E484, Q493 and N501) that have been associated with escape from neutralizing antibodies induced by either infection with or immunization against the early Washington strain of SARS-CoV-2. The mouse-adapted strain of SARS-CoV-2, SARS2-N501Y MA30 , contains a spike that is also heavily mutated, with mutations at 4 of the 5 positions in Omicron spike associated with neutralizing antibody escape (K417, E484, Q493 and N501). In this manuscript we show that intranasal immunization with a pre-fusion stabilized Washington strain spike, expressed from a highly attenuated, replication-competent vaccinia virus construct, NYVAC-KC, fully protected mice against disease and death from SARS2-N501Y MA30 . Similarly, immunization by scarification on the skin fully protected against death, but not from mild disease. This data demonstrates that Washington strain spike, when expressed from a highly attenuated, replication-competent poxvirus, administered without parenteral injection can fully protect against the heavily mutated mouse-adapted SARS2-N501Y MA30 .
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Affiliation(s)
- Karen V. Kibler
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
| | - Mateusz Szczerba
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
| | - Douglas Lake
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Alexa J. Roeder
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Masmudur Rahman
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
| | - Brenda G. Hogue
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | - Yize Li
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Bertram L. Jacobs
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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Kant R, Kareinen L, Smura T, Freitag TL, Jha SK, Alitalo K, Meri S, Sironen T, Saksela K, Strandin T, Kipar A, Vapalahti O. Common Laboratory Mice Are Susceptible to Infection with the SARS-CoV-2 Beta Variant. Viruses 2021; 13:2263. [PMID: 34835069 PMCID: PMC8619350 DOI: 10.3390/v13112263] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 01/25/2023] Open
Abstract
Small animal models are of crucial importance for assessing COVID-19 countermeasures. Common laboratory mice would be well-suited for this purpose but are not susceptible to infection with wild-type SARS-CoV-2. However, the development of mouse-adapted virus strains has revealed key mutations in the SARS-CoV-2 spike protein that increase infectivity, and interestingly, many of these mutations are also present in naturally occurring SARS-CoV-2 variants of concern. This suggests that these variants might have the ability to infect common laboratory mice. Herein we show that the SARS-CoV-2 beta variant attains infectibility to BALB/c mice and causes pulmonary changes within 2-3 days post infection, consistent with results seen in other murine models of COVID-19, at a reasonable virus dose (2 × 105 PFU). The findings suggest that common laboratory mice can serve as the animal model of choice for testing the effectiveness of antiviral drugs and vaccines against SARS-CoV-2.
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Affiliation(s)
- Ravi Kant
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
| | - Lauri Kareinen
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
| | - Teemu Smura
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
| | - Tobias L. Freitag
- Research Programs Unit, Immunobiology, University of Helsinki, 00290 Helsinki, Finland;
| | - Sawan Kumar Jha
- Translational Cancer Medicine Program, Faculty of Medicine and Helsinki Institute of Life Science, University of Helsinki, 00290 Helsinki, Finland; (S.K.J.); (K.A.)
| | - Kari Alitalo
- Translational Cancer Medicine Program, Faculty of Medicine and Helsinki Institute of Life Science, University of Helsinki, 00290 Helsinki, Finland; (S.K.J.); (K.A.)
| | - Seppo Meri
- Department of Bacteriology and Immunology and Translational Immunology Research Program, University of Helsinki, 00290 Helsinki, Finland;
| | - Tarja Sironen
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
| | - Kalle Saksela
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
| | - Tomas Strandin
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
| | - Anja Kipar
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 3RF, UK
| | - Olli Vapalahti
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, Helsinki University Hospital, 00290 Helsinki, Finland
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are of concern, with the P.1 variants dominating in Brazil. Brazil is now seeing a record number of deaths. Here, we report that the pathogenicity in hamsters of a P.1 variant is similar to that of nonvariant SARS-CoV-2. However, it has an expanded host range as shown by its replication in mice. Prior infection with nonvariant SARS-CoV-2 strains efficiently prevented replication of the P.1 variant in the lower respiratory tract of hamsters upon reinfection. Convalescent sera from patients infected with nonvariants or sera from messenger RNA vaccinees showed comparable neutralization titers among the P.1 and previously circulating strains. These results suggest that previous SARS-CoV-2 infection and vaccines based on the original SARS-CoV-2 will provide some protection against P.1 infection. The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a key role in viral infectivity. It is also the major antigen stimulating the host's protective immune response, specifically, the production of neutralizing antibodies. Recently, a new variant of SARS-CoV-2 possessing multiple mutations in the S protein, designated P.1, emerged in Brazil. Here, we characterized a P.1 variant isolated in Japan by using Syrian hamsters, a well-established small animal model for the study of SARS-CoV-2 disease (COVID-19). In hamsters, the variant showed replicative abilities and pathogenicity similar to those of early and contemporary strains (i.e., SARS-CoV-2 bearing aspartic acid [D] or glycine [G] at position 614 of the S protein). Sera and/or plasma from convalescent patients and BNT162b2 messenger RNA vaccinees showed comparable neutralization titers across the P.1 variant, S-614D, and S-614G strains. In contrast, the S-614D and S-614G strains were less well recognized than the P.1 variant by serum from a P.1-infected patient. Prior infection with S-614D or S-614G strains efficiently prevented the replication of the P.1 variant in the lower respiratory tract of hamsters upon reinfection. In addition, passive transfer of neutralizing antibodies to hamsters infected with the P.1 variant or the S-614G strain led to reduced virus replication in the lower respiratory tract. However, the effect was less pronounced against the P.1 variant than the S-614G strain. These findings suggest that the P.1 variant may be somewhat antigenically different from the early and contemporary strains of SARS-CoV-2.
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