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Kirk NM, Liang Y, Ly H. Pathogenesis and virulence of coronavirus disease: Comparative pathology of animal models for COVID-19. Virulence 2024; 15:2316438. [PMID: 38362881 PMCID: PMC10878030 DOI: 10.1080/21505594.2024.2316438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/04/2024] [Indexed: 02/17/2024] Open
Abstract
Animal models that can replicate clinical and pathologic features of severe human coronavirus infections have been instrumental in the development of novel vaccines and therapeutics. The goal of this review is to summarize our current understanding of the pathogenesis of coronavirus disease 2019 (COVID-19) and the pathologic features that can be observed in several currently available animal models. Knowledge gained from studying these animal models of SARS-CoV-2 infection can help inform appropriate model selection for disease modelling as well as for vaccine and therapeutic developments.
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Affiliation(s)
- Natalie M. Kirk
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
| | - Yuying Liang
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
| | - Hinh Ly
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
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2
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Gong Q, Jiang R, Ji L, Lin H, Liu M, Tang X, Yang Y, Han W, Chen J, Guo Z, Wang Q, Li Q, Wang X, Jiang T, Xie S, Yang X, Zhou P, Shi Z, Lin X. Establishment of a human organoid-based evaluation system for assessing interspecies infection risk of animal-borne coronaviruses. Emerg Microbes Infect 2024; 13:2327368. [PMID: 38531008 DOI: 10.1080/22221751.2024.2327368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/01/2024] [Indexed: 03/28/2024]
Abstract
The COVID-19 pandemic presents a major threat to global public health. Several lines of evidence have shown that the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), along with two other highly pathogenic coronaviruses, SARS-CoV and Middle East Respiratory Syndrome (MERS-CoV) originated from bats. To prevent and control future coronavirus outbreaks, it is necessary to investigate the interspecies infection and pathogenicity risks of animal-related coronaviruses. Currently used infection models, including in vitro cell lines and in vivo animal models, fail to fully mimic the primary infection in human tissues. Here, we employed organoid technology as a promising new model for studying emerging pathogens and their pathogenic mechanisms. We investigated the key host-virus interaction patterns of five human coronaviruses (SARS-CoV-2 original strain, Omicron BA.1, MERS-CoV, HCoV-229E, and HCoV-OC43) in different human respiratory organoids. Five indicators, including cell tropism, invasion preference, replication activity, host response and virus-induced cell death, were developed to establish a comprehensive evaluation system to predict coronavirus interspecies infection and pathogenicity risks. Using this system, we further examined the pathogenicity and interspecies infection risks of three SARS-related coronaviruses (SARSr-CoV), including WIV1 and rRsSHC014S from bats, and MpCoV-GX from pangolins. Moreover, we found that cannabidiol, a non-psychoactive plant extract, exhibits significant inhibitory effects on various coronaviruses in human lung organoid. Cannabidiol significantly enhanced interferon-stimulated gene expression but reduced levels of inflammatory cytokines. In summary, our study established a reliable comprehensive evaluation system to analyse infection and pathogenicity patterns of zoonotic coronaviruses, which could aid in prevention and control of potentially emerging coronavirus diseases.
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Affiliation(s)
- Qianchun Gong
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
- Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu, People's Republic of China
| | - Rendi Jiang
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Lina Ji
- School of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China
| | - Haofeng Lin
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Meiqin Liu
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Xiaofang Tang
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Yong Yang
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Wei Han
- School of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China
| | - Jing Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Zishuo Guo
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Qi Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, People's Republic of China
| | - Qian Li
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Xi Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Tingting Jiang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Shizhe Xie
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Xinglou Yang
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People's Republic of China
| | - Peng Zhou
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People's Republic of China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, People's Republic of China
| | - Zhengli Shi
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
- Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu, People's Republic of China
- School of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China
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3
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Qiao S, Wang X. Structural determinants of spike infectivity in bat SARS-like coronaviruses RsSHC014 and WIV1. J Virol 2024; 98:e0034224. [PMID: 39028202 PMCID: PMC11334503 DOI: 10.1128/jvi.00342-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
The recurrent spillovers of coronaviruses (CoVs) have posed severe threats to public health and the global economy. Bat severe acute respiratory syndrome (SARS)-like CoVs RsSHC014 and WIV1, currently circulating in bat populations, are poised for human emergence. The trimeric spike (S) glycoprotein, responsible for receptor recognition and membrane fusion, plays a critical role in cross-species transmission and infection. Here, we determined the cryo-electron microscopy (EM) structures of the RsSHC014 S protein in the closed state at 2.9 Å, the WIV1 S protein in the closed state at 2.8 Å, and the intermediate state at 4.0 Å. In the intermediate state, one receptor-binding domain (RBD) is in the "down" position, while the other two RBDs exhibit poor density. We also resolved the complex structure of the WIV1 S protein bound to human ACE2 (hACE2) at 4.5 Å, which provides structural basis for the future emergence of WIV1 in humans. Through biochemical experiments, we found that despite strong binding affinities between the RBDs and both human and civet ACE2, the pseudoviruses of RsSHC014, but not WIV1, failed to infect 293T cells overexpressing either human or civet ACE2. Mutagenesis analysis revealed that the Y623H substitution, located in the SD2 region, significantly improved the cell entry efficiency of RsSHC014 pseudoviruses, which is likely accomplished by promoting the open conformation of spike glycoproteins. Our findings emphasize the necessity of both efficient RBD lifting and tight RBD-hACE2 binding for viral infection and underscore the significance of the 623 site of the spike glycoprotein for the infectivity of bat SARS-like CoVs. IMPORTANCE The bat SARS-like CoVs RsSHC014 and WIV1 can use hACE2 for cell entry without further adaptation, indicating their potential risk of emergence in human populations. The S glycoprotein, responsible for receptor recognition and membrane fusion, plays a crucial role in cross-species transmission and infection. In this study, we determined the cryo-EM structures of the S glycoproteins of RsSHC014 and WIV1. Detailed comparisons revealed dynamic structural variations within spike proteins. We also elucidated the complex structure of WIV1 S-hACE2, providing structural evidence for the potential emergence of WIV1 in humans. Although RsSHC014 and WIV1 had similar hACE2-binding affinities, they exhibited distinct pseudovirus cell entry behavior. Through mutagenesis and cryo-EM analysis, we revealed that besides the structural variations, the 623 site in the SD2 region is another important structural determinant of spike infectivity.
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Affiliation(s)
- Shuyuan Qiao
- The Ministry of Education Key Laboratory of Protein Science, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
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4
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Leist SR, Schäfer A, Risemberg EL, Bell TA, Hock P, Zweigart MR, Linnertz CL, Miller DR, Shaw GD, de Villena FPM, Ferris MT, Valdar W, Baric RS. Sarbecovirus disease susceptibility is conserved across viral and host models. Virus Res 2024; 346:199399. [PMID: 38823688 PMCID: PMC11225686 DOI: 10.1016/j.virusres.2024.199399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 04/15/2024] [Accepted: 05/15/2024] [Indexed: 06/03/2024]
Abstract
Coronaviruses have caused three severe epidemics since the start of the 21st century: SARS, MERS and COVID-19. The severity of the ongoing COVID-19 pandemic and increasing likelihood of future coronavirus outbreaks motivates greater understanding of factors leading to severe coronavirus disease. We screened ten strains from the Collaborative Cross mouse genetic reference panel and identified strains CC006/TauUnc (CC006) and CC044/Unc (CC044) as coronavirus-susceptible and resistant, respectively, as indicated by variable weight loss and lung congestion scores four days post-infection. We generated a genetic mapping population of 755 CC006xCC044 F2 mice and exposed the mice to one of three genetically distinct mouse-adapted coronaviruses: clade 1a SARS-CoV MA15 (n=391), clade 1b SARS-CoV-2 MA10 (n=274), and clade 2 HKU3-CoV MA (n=90). Quantitative trait loci (QTL) mapping in SARS-CoV MA15- and SARS-CoV-2 MA10-infected F2 mice identified genetic loci associated with disease severity. Specifically, we identified seven loci associated with variation in outcome following infection with either virus, including one, HrS43, that is present in both groups. Three of these QTL, including HrS43, were also associated with HKU3-CoV MA outcome. HrS43 overlaps with a QTL previously reported by our lab that is associated with SARS-CoV MA15 outcome in CC011xCC074 F2 mice and is also syntenic with a human chromosomal region associated with severe COVID-19 outcomes in humans GWAS. The results reported here provide: (a) additional support for the involvement of this locus in SARS-CoV MA15 infection, (b) the first conclusive evidence that this locus is associated with susceptibility across the Sarbecovirus subgenus, and (c) demonstration of the relevance of mouse models in the study of coronavirus disease susceptibility in humans.
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Affiliation(s)
- Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, United States
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, United States
| | - Ellen L Risemberg
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, United States; Department of Genetics, University of North Carolina at Chapel Hill, United States
| | - Timothy A Bell
- Department of Genetics, University of North Carolina at Chapel Hill, United States
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, United States
| | - Mark R Zweigart
- Department of Epidemiology, University of North Carolina at Chapel Hill, United States
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, United States
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, United States
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, United States
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, United States
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, United States.
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, United States.
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, United States; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, United States.
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5
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Peña-Hernández MA, Alfajaro MM, Filler RB, Moriyama M, Keeler EL, Ranglin ZE, Kong Y, Mao T, Menasche BL, Mankowski MC, Zhao Z, Vogels CBF, Hahn AM, Kalinich CC, Zhang S, Huston N, Wan H, Araujo-Tavares R, Lindenbach BD, Homer R, Pyle AM, Martinez DR, Grubaugh ND, Israelow B, Iwasaki A, Wilen CB. SARS-CoV-2-related bat viruses evade human intrinsic immunity but lack efficient transmission capacity. Nat Microbiol 2024:10.1038/s41564-024-01765-z. [PMID: 39075235 DOI: 10.1038/s41564-024-01765-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/19/2024] [Indexed: 07/31/2024]
Abstract
Circulating bat coronaviruses represent a pandemic threat. However, our understanding of bat coronavirus pathogenesis and transmission potential is limited by the lack of phenotypically characterized strains. We created molecular clones for the two closest known relatives of SARS-CoV-2, BANAL-52 and BANAL-236. We demonstrated that BANAL-CoVs and SARS-CoV-2 have similar replication kinetics in human bronchial epithelial cells. However, BANAL-CoVs have impaired replication in human nasal epithelial cells and in the upper airway of mice. We also observed reduced pathogenesis in mice and diminished transmission in hamsters. Further, we observed that diverse bat coronaviruses evade interferon and downregulate major histocompatibility complex class I. Collectively, our study demonstrates that despite high genetic similarity across bat coronaviruses, prediction of pandemic potential of a virus necessitates functional characterization. Finally, the restriction of bat coronavirus replication in the upper airway highlights that transmission potential and innate immune restriction can be uncoupled in this high-risk family of emerging viruses.
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Affiliation(s)
- Mario A Peña-Hernández
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Miyu Moriyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Emma L Keeler
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Zara E Ranglin
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Yong Kong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Bridget L Menasche
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Madeleine C Mankowski
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Zhe Zhao
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Shuo Zhang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Nicholas Huston
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Han Wan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Rafael Araujo-Tavares
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Robert Homer
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - David R Martinez
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Benjamin Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.
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6
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Tse AL, Acreman CM, Ricardo-Lax I, Berrigan J, Lasso G, Balogun T, Kearns FL, Casalino L, McClain GL, Chandran AM, Lemeunier C, Amaro RE, Rice CM, Jangra RK, McLellan JS, Chandran K, Miller EH. Distinct pathway for evolution of enhanced receptor binding and cell entry in SARS-like bat coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600393. [PMID: 38979151 PMCID: PMC11230278 DOI: 10.1101/2024.06.24.600393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Understanding the zoonotic risks posed by bat coronaviruses (CoVs) is critical for pandemic preparedness. Herein, we generated recombinant vesicular stomatitis viruses (rVSVs) bearing spikes from divergent bat CoVs to investigate their cell entry mechanisms. Unexpectedly, the successful recovery of rVSVs bearing the spike from SHC014, a SARS-like bat CoV, was associated with the acquisition of a novel substitution in the S2 fusion peptide-proximal region (FPPR). This substitution enhanced viral entry in both VSV and coronavirus contexts by increasing the availability of the spike receptor-binding domain to recognize its cellular receptor, ACE2. A second substitution in the spike N-terminal domain, uncovered through forward-genetic selection, interacted epistatically with the FPPR substitution to synergistically enhance spike:ACE2 interaction and viral entry. Our findings identify genetic pathways for adaptation by bat CoVs during spillover and host-to-host transmission, fitness trade-offs inherent to these pathways, and potential Achilles' heels that could be targeted with countermeasures.
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7
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Heo CK, Lim WH, Moon KB, Yang J, Kim SJ, Kim HS, Kim DJ, Cho EW. S2 Peptide-Conjugated SARS-CoV-2 Virus-like Particles Provide Broad Protection against SARS-CoV-2 Variants of Concern. Vaccines (Basel) 2024; 12:676. [PMID: 38932406 PMCID: PMC11209314 DOI: 10.3390/vaccines12060676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Approved COVID-19 vaccines primarily induce neutralizing antibodies targeting the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein. However, the emergence of variants of concern with RBD mutations poses challenges to vaccine efficacy. This study aimed to design a next-generation vaccine that provides broader protection against diverse coronaviruses, focusing on glycan-free S2 peptides as vaccine candidates to overcome the low immunogenicity of the S2 domain due to the N-linked glycans on the S antigen stalk, which can mask S2 antibody responses. Glycan-free S2 peptides were synthesized and attached to SARS-CoV-2 virus-like particles (VLPs) lacking the S antigen. Humoral and cellular immune responses were analyzed after the second booster immunization in BALB/c mice. Enzyme-linked immunosorbent assay revealed the reactivity of sera against SARS-CoV-2 variants, and pseudovirus neutralization assay confirmed neutralizing activities. Among the S2 peptide-conjugated VLPs, the S2.3 (N1135-K1157) and S2.5 (A1174-L1193) peptide-VLP conjugates effectively induced S2-specific serum immunoglobulins. These antisera showed high reactivity against SARS-CoV-2 variant S proteins and effectively inhibited pseudoviral infections. S2 peptide-conjugated VLPs activated SARS-CoV-2 VLP-specific T-cells. The SARS-CoV-2 vaccine incorporating conserved S2 peptides and CoV-2 VLPs shows promise as a universal vaccine capable of generating neutralizing antibodies and T-cell responses against SARS-CoV-2 variants.
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Affiliation(s)
- Chang-Kyu Heo
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Youseong-gu, Daejeon 34141, Republic of Korea; (C.-K.H.); (W.-H.L.)
| | - Won-Hee Lim
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Youseong-gu, Daejeon 34141, Republic of Korea; (C.-K.H.); (W.-H.L.)
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34141, Republic of Korea
| | - Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (K.-B.M.); (H.-S.K.)
| | - Jihyun Yang
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea;
| | - Sang Jick Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea;
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (K.-B.M.); (H.-S.K.)
| | - Doo-Jin Kim
- Chungbuk National University College of Medicine, 194-15 Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si 28160, Republic of Korea;
| | - Eun-Wie Cho
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Youseong-gu, Daejeon 34141, Republic of Korea; (C.-K.H.); (W.-H.L.)
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34141, Republic of Korea
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8
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Schäfer A, Gralinski LE, Leist SR, Hampton BK, Mooney MA, Jensen KL, Graham RL, Agnihothram S, Jeng S, Chamberlin S, Bell TA, Scobey DT, Linnertz CL, VanBlargan LA, Thackray LB, Hock P, Miller DR, Shaw GD, Diamond MS, de Villena FPM, McWeeney SK, Heise MT, Menachery VD, Ferris MT, Baric RS. Genetic loci regulate Sarbecovirus pathogenesis: A comparison across mice and humans. Virus Res 2024; 344:199357. [PMID: 38508400 PMCID: PMC10981091 DOI: 10.1016/j.virusres.2024.199357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/15/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
Coronavirus (CoV) cause considerable morbidity and mortality in humans and other mammals, as evidenced by the emergence of Severe Acute Respiratory CoV (SARS-CoV) in 2003, Middle East Respiratory CoV (MERS-CoV) in 2012, and SARS-CoV-2 in 2019. Although poorly characterized, natural genetic variation in human and other mammals modulate virus pathogenesis, as reflected by the spectrum of clinical outcomes ranging from asymptomatic infections to lethal disease. Using multiple human epidemic and zoonotic Sarbecoviruses, coupled with murine Collaborative Cross genetic reference populations, we identify several dozen quantitative trait loci that regulate SARS-like group-2B CoV pathogenesis and replication. Under a Chr4 QTL, we deleted a candidate interferon stimulated gene, Trim14 which resulted in enhanced SARS-CoV titers and clinical disease, suggesting an antiviral role during infection. Importantly, about 60 % of the murine QTL encode susceptibility genes identified as priority candidates from human genome-wide association studies (GWAS) studies after SARS-CoV-2 infection, suggesting that similar selective forces have targeted analogous genes and pathways to regulate Sarbecovirus disease across diverse mammalian hosts. These studies provide an experimental platform in rodents to investigate the molecular-genetic mechanisms by which potential cross mammalian susceptibility loci and genes regulate type-specific and cross-SARS-like group 2B CoV replication, immunity, and pathogenesis in rodent models. Our study also provides a paradigm for identifying susceptibility loci for other highly heterogeneous and virulent viruses that sporadically emerge from zoonotic reservoirs to plague human and animal populations.
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Affiliation(s)
- Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael A Mooney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Kara L Jensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rachel L Graham
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sudhakar Agnihothram
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sophia Jeng
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Steven Chamberlin
- Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Timothy A Bell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - D Trevor Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology & Immunology2, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology3, Washington University School of Medicine, St. Louis, MO, USA
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shannon K McWeeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Mark T Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill NC, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA; Department of Pathology and Center for Biodefense & Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill NC, USA.
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9
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Cohen AA, Keeffe JR, Schiepers A, Dross SE, Greaney AJ, Rorick AV, Gao H, Gnanapragasam PNP, Fan C, West AP, Ramsingh AI, Erasmus JH, Pata JD, Muramatsu H, Pardi N, Lin PJC, Baxter S, Cruz R, Quintanar-Audelo M, Robb E, Serrano-Amatriain C, Magneschi L, Fotheringham IG, Fuller DH, Victora GD, Bjorkman PJ. Mosaic sarbecovirus nanoparticles elicit cross-reactive responses in pre-vaccinated animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.08.576722. [PMID: 38370696 PMCID: PMC10871317 DOI: 10.1101/2024.02.08.576722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Immunization with mosaic-8b [60-mer nanoparticles presenting 8 SARS-like betacoronavirus (sarbecovirus) receptor-binding domains (RBDs)] elicits more broadly cross-reactive antibodies than homotypic SARS-CoV-2 RBD-only nanoparticles and protects against sarbecoviruses. To investigate original antigenic sin (OAS) effects on mosaic-8b efficacy, we evaluated effects of prior COVID-19 vaccinations in non-human primates and mice on anti-sarbecovirus responses elicited by mosaic-8b, admix-8b (8 homotypics), or homotypic SARS-CoV-2 immunizations, finding greatest cross-reactivity for mosaic-8b. As demonstrated by molecular fate-mapping in which antibodies from specific cohorts of B cells are differentially detected, B cells primed by WA1 spike mRNA-LNP dominated antibody responses after RBD-nanoparticle boosting. While mosaic-8b- and homotypic-nanoparticles boosted cross-reactive antibodies, de novo antibodies were predominantly induced by mosaic-8b, and these were specific for variant RBDs with increased identity to RBDs on mosaic-8b. These results inform OAS mechanisms and support using mosaic-8b to protect COVID-19 vaccinated/infected humans against as-yet-unknown SARS-CoV-2 variants and animal sarbecoviruses with human spillover potential.
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Affiliation(s)
- Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- These authors contributed equally
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- These authors contributed equally
| | - Ariën Schiepers
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, 10065, USA
| | - Sandra E Dross
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- National Primate Research Center, Seattle, WA 98121, USA
| | - Allison J Greaney
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Annie V Rorick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | - Janice D Pata
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, University at Albany, Albany, NY, 12201, USA
| | - Hiromi Muramatsu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Scott Baxter
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Rita Cruz
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Martina Quintanar-Audelo
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
- Present address: Centre for Inflammation Research and Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Ellis Robb
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | | | - Leonardo Magneschi
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Ian G Fotheringham
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Deborah H Fuller
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- National Primate Research Center, Seattle, WA 98121, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, 10065, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Lead contact
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10
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Martinez DR, Moreira FR, Catanzaro NJ, Diefenbacher MV, Zweigart MR, Gully KL, De la Cruz G, Brown AJ, Adams LE, Yount B, Baric TJ, Mallory ML, Conrad H, May SR, Dong S, Scobey DT, Nguyen C, Montgomery SA, Perry J, Babusis D, Barrett KT, Nguyen AH, Nguyen AQ, Kalla R, Bannister R, Feng JY, Cihlar T, Baric RS, Mackman RL, Bilello JP, Schäfer A, Sheahan TP. The oral nucleoside prodrug GS-5245 is efficacious against SARS-CoV-2 and other endemic, epidemic, and enzootic coronaviruses. Sci Transl Med 2024; 16:eadj4504. [PMID: 38776389 PMCID: PMC11333937 DOI: 10.1126/scitranslmed.adj4504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Despite the wide availability of several safe and effective vaccines that prevent severe COVID-19, the persistent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) that can evade vaccine-elicited immunity remains a global health concern. In addition, the emergence of SARS-CoV-2 VOCs that can evade therapeutic monoclonal antibodies underscores the need for additional, variant-resistant treatment strategies. Here, we characterize the antiviral activity of GS-5245, obeldesivir (ODV), an oral prodrug of the parent nucleoside GS-441524, which targets the highly conserved viral RNA-dependent RNA polymerase (RdRp). We show that GS-5245 is broadly potent in vitro against alphacoronavirus HCoV-NL63, SARS-CoV, SARS-CoV-related bat-CoV RsSHC014, Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 WA/1, and the highly transmissible SARS-CoV-2 BA.1 Omicron variant. Moreover, in mouse models of SARS-CoV, SARS-CoV-2 (WA/1 and Omicron B1.1.529), MERS-CoV, and bat-CoV RsSHC014 pathogenesis, we observed a dose-dependent reduction in viral replication, body weight loss, acute lung injury, and pulmonary function with GS-5245 therapy. Last, we demonstrate that a combination of GS-5245 and main protease (Mpro) inhibitor nirmatrelvir improved outcomes in vivo against SARS-CoV-2 compared with the single agents. Together, our data support the clinical evaluation of GS-5245 against coronaviruses that cause or have the potential to cause human disease.
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Affiliation(s)
- David R. Martinez
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
- Yale Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Fernando R. Moreira
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Nicholas J. Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Meghan V. Diefenbacher
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Mark R. Zweigart
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kendra L. Gully
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Gabriela De la Cruz
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Ariane J. Brown
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Lily E. Adams
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Thomas J. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Michael L. Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Helen Conrad
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Samantha R. May
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephanie Dong
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - D. Trevor Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Cameron Nguyen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephanie A. Montgomery
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Jason Perry
- Gilead Sciences, Inc, Foster City, CA, 94404, USA
| | | | | | | | | | - Rao Kalla
- Gilead Sciences, Inc, Foster City, CA, 94404, USA
| | | | - Joy Y. Feng
- Gilead Sciences, Inc, Foster City, CA, 94404, USA
| | - Tomas Cihlar
- Gilead Sciences, Inc, Foster City, CA, 94404, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
- Rapidly Emerging Antiviral Drug Development Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Rapidly Emerging Antiviral Drug Development Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Timothy P. Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
- Rapidly Emerging Antiviral Drug Development Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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11
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Dillard JA, Taft-Benz SA, Knight AC, Anderson EJ, Pressey KD, Parotti B, Martinez SA, Diaz JL, Sarkar S, Madden EA, De la Cruz G, Adams LE, Dinnon KH, Leist SR, Martinez DR, Schäfer A, Powers JM, Yount BL, Castillo IN, Morales NL, Burdick J, Evangelista MKD, Ralph LM, Pankow NC, Linnertz CL, Lakshmanane P, Montgomery SA, Ferris MT, Baric RS, Baxter VK, Heise MT. Adjuvant-dependent impact of inactivated SARS-CoV-2 vaccines during heterologous infection by a SARS-related coronavirus. Nat Commun 2024; 15:3738. [PMID: 38702297 PMCID: PMC11068739 DOI: 10.1038/s41467-024-47450-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 04/02/2024] [Indexed: 05/06/2024] Open
Abstract
Whole virus-based inactivated SARS-CoV-2 vaccines adjuvanted with aluminum hydroxide have been critical to the COVID-19 pandemic response. Although these vaccines are protective against homologous coronavirus infection, the emergence of novel variants and the presence of large zoonotic reservoirs harboring novel heterologous coronaviruses provide significant opportunities for vaccine breakthrough, which raises the risk of adverse outcomes like vaccine-associated enhanced respiratory disease. Here, we use a female mouse model of coronavirus disease to evaluate inactivated vaccine performance against either homologous challenge with SARS-CoV-2 or heterologous challenge with a bat-derived coronavirus that represents a potential emerging disease threat. We show that inactivated SARS-CoV-2 vaccines adjuvanted with aluminum hydroxide can cause enhanced respiratory disease during heterologous infection, while use of an alternative adjuvant does not drive disease and promotes heterologous viral clearance. In this work, we highlight the impact of adjuvant selection on inactivated vaccine safety and efficacy against heterologous coronavirus infection.
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Affiliation(s)
- Jacob A Dillard
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sharon A Taft-Benz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Audrey C Knight
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth J Anderson
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katia D Pressey
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Breantié Parotti
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sabian A Martinez
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jennifer L Diaz
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sanjay Sarkar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily A Madden
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gabriela De la Cruz
- Pathology Services Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lily E Adams
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth H Dinnon
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John M Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Izabella N Castillo
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Noah L Morales
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jane Burdick
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Lauren M Ralph
- Pathology Services Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas C Pankow
- Pathology Services Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Premkumar Lakshmanane
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephanie A Montgomery
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Dallas Tissue Research, Farmers Branch, TX, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ralph S Baric
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Victoria K Baxter
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Mark T Heise
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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12
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Hills FR, Eruera AR, Hodgkinson-Bean J, Jorge F, Easingwood R, Brown SHJ, Bouwer JC, Li YP, Burga LN, Bostina M. Variation in structural motifs within SARS-related coronavirus spike proteins. PLoS Pathog 2024; 20:e1012158. [PMID: 38805567 PMCID: PMC11236199 DOI: 10.1371/journal.ppat.1012158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 07/10/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
SARS-CoV-2 is the third known coronavirus (CoV) that has crossed the animal-human barrier in the last two decades. However, little structural information exists related to the close genetic species within the SARS-related coronaviruses. Here, we present three novel SARS-related CoV spike protein structures solved by single particle cryo-electron microscopy analysis derived from bat (bat SL-CoV WIV1) and civet (cCoV-SZ3, cCoV-007) hosts. We report complex glycan trees that decorate the glycoproteins and density for water molecules which facilitated modeling of the water molecule coordination networks within structurally important regions. We note structural conservation of the fatty acid binding pocket and presence of a linoleic acid molecule which are associated with stabilization of the receptor binding domains in the "down" conformation. Additionally, the N-terminal biliverdin binding pocket is occupied by a density in all the structures. Finally, we analyzed structural differences in a loop of the receptor binding motif between coronaviruses known to infect humans and the animal coronaviruses described in this study, which regulate binding to the human angiotensin converting enzyme 2 receptor. This study offers a structural framework to evaluate the close relatives of SARS-CoV-2, the ability to inform pandemic prevention, and aid in the development of pan-neutralizing treatments.
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Affiliation(s)
- Francesca R. Hills
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alice-Roza Eruera
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James Hodgkinson-Bean
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Fátima Jorge
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
| | - Richard Easingwood
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
| | - Simon H. J. Brown
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, New South Wales, Australia
| | - James C. Bouwer
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, New South Wales, Australia
| | - Yi-Ping Li
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Laura N. Burga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
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13
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Basil MC, Alysandratos KD, Kotton DN, Morrisey EE. Lung repair and regeneration: Advanced models and insights into human disease. Cell Stem Cell 2024; 31:439-454. [PMID: 38492572 PMCID: PMC11070171 DOI: 10.1016/j.stem.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/18/2024]
Abstract
The respiratory system acts as both the primary site of gas exchange and an important sensor and barrier to the external environment. The increase in incidences of respiratory disease over the past decades has highlighted the importance of developing improved therapeutic approaches. This review will summarize recent research on the cellular complexity of the mammalian respiratory system with a focus on gas exchange and immunological defense functions of the lung. Different models of repair and regeneration will be discussed to help interpret human and animal data and spur the investigation of models and assays for future drug development.
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Affiliation(s)
- Maria C Basil
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn, Children's Hospital of Philadelphia (CHOP) Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA.
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA.
| | - Edward E Morrisey
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn, Children's Hospital of Philadelphia (CHOP) Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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14
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Sun L, Man Q, Zhang H, Xia S, Lu L, Wang X, Xiong L, Jiang S. Strong cross immune responses against sarbecoviruses but not merbecoviruses in SARS-CoV-2 BA.5/BF.7-infected individuals with or without inactivated COVID-19 vaccination. J Infect 2024; 88:106138. [PMID: 38490275 DOI: 10.1016/j.jinf.2024.106138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/04/2024] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Affiliation(s)
- Lujia Sun
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Qiuhong Man
- Department of Laboratory Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Hui Zhang
- Department of Laboratory Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Shuai Xia
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Lu Lu
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xinling Wang
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Lize Xiong
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China
| | - Shibo Jiang
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
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15
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Rexhepaj M, Park YJ, Perruzza L, Asarnow D, Mccallum M, Culap K, Saliba C, Leoni G, Balmelli A, Yoshiyama CN, Dickinson MS, Quispe J, Brown JT, Tortorici MA, Sprouse KR, Taylor AL, Starr TN, Corti D, Benigni F, Veesler D. Broadly neutralizing antibodies against emerging delta-coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.586411. [PMID: 38617231 PMCID: PMC11014491 DOI: 10.1101/2024.03.27.586411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Porcine deltacoronavirus (PDCoV) spillovers were recently detected in children with acute undifferentiated febrile illness, underscoring recurrent zoonoses of divergent coronaviruses. To date, no vaccines or specific therapeutics are approved for use in humans against PDCoV. To prepare for possible future PDCoV epidemics, we isolated human spike (S)-directed monoclonal antibodies from transgenic mice and found that two of them, designated PD33 and PD41, broadly neutralized a panel of PDCoV variants. Cryo-electron microscopy structures of PD33 and PD41 in complex with the PDCoV receptor-binding domain and S ectodomain trimer provide a blueprint of the epitopes recognized by these mAbs, rationalizing their broad inhibitory activity. We show that both mAbs inhibit PDCoV by competitively interfering with host APN binding to the PDCoV receptor-binding loops, explaining the mechanism of viral neutralization. PD33 and PD41 are candidates for clinical advancement, which could be stockpiled to prepare for possible future PDCoV outbreaks.
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Affiliation(s)
- Megi Rexhepaj
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Lisa Perruzza
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Mathew Mccallum
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Katja Culap
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Giada Leoni
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Alessio Balmelli
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Miles S. Dickinson
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Jack Taylor Brown
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - M. Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Kaitlin R. Sprouse
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ashley L. Taylor
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Tyler N Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Davide Corti
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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16
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Chao CW, Sprouse KR, Miranda MC, Catanzaro NJ, Hubbard ML, Addetia A, Stewart C, Brown JT, Dosey A, Valdez A, Ravichandran R, Hendricks GG, Ahlrichs M, Dobbins C, Hand A, Treichel C, Willoughby I, Walls AC, McGuire AT, Leaf EM, Baric RS, Schäfer A, Veesler D, King NP. Protein nanoparticle vaccines induce potent neutralizing antibody responses against MERS-CoV. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584735. [PMID: 38558973 PMCID: PMC10979991 DOI: 10.1101/2024.03.13.584735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic betacoronavirus that causes severe and often lethal respiratory illness in humans. The MERS-CoV spike (S) protein is the viral fusogen and the target of neutralizing antibodies, and has therefore been the focus of vaccine design efforts. Currently there are no licensed vaccines against MERS-CoV and only a few candidates have advanced to Phase I clinical trials. Here we developed MERS-CoV vaccines utilizing a computationally designed protein nanoparticle platform that has generated safe and immunogenic vaccines against various enveloped viruses, including a licensed vaccine for SARS-CoV-2. Two-component protein nanoparticles displaying MERS-CoV S-derived antigens induced robust neutralizing antibody responses and protected mice against challenge with mouse-adapted MERS-CoV. Electron microscopy polyclonal epitope mapping and serum competition assays revealed the specificities of the dominant antibody responses elicited by immunogens displaying the prefusion-stabilized S-2P trimer, receptor binding domain (RBD), or N-terminal domain (NTD). An RBD nanoparticle vaccine elicited antibodies targeting multiple non-overlapping epitopes in the RBD, whereas anti-NTD antibodies elicited by the S-2P- and NTD-based immunogens converged on a single antigenic site. Our findings demonstrate the potential of two-component nanoparticle vaccine candidates for MERS-CoV and suggest that this platform technology could be broadly applicable to betacoronavirus vaccine development.
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Affiliation(s)
- Cara W Chao
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Marcos C Miranda
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Miranda L Hubbard
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack T Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Annie Dosey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Adian Valdez
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Grace G Hendricks
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Craig Dobbins
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexis Hand
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Catherine Treichel
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Isabelle Willoughby
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Andrew T McGuire
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth M Leaf
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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17
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Halfmann PJ, Loeffler K, Duffy A, Kuroda M, Yang JE, Wright ER, Kawaoka Y, Kane RS. Broad protection against clade 1 sarbecoviruses after a single immunization with cocktail spike-protein-nanoparticle vaccine. Nat Commun 2024; 15:1284. [PMID: 38346966 PMCID: PMC10861510 DOI: 10.1038/s41467-024-45495-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/25/2024] [Indexed: 02/15/2024] Open
Abstract
The 2002 SARS outbreak, the 2019 emergence of COVID-19, and the continuing evolution of immune-evading SARS-CoV-2 variants together highlight the need for a broadly protective vaccine against ACE2-utilizing sarbecoviruses. While updated variant-matched formulations are a step in the right direction, protection needs to extend beyond SARS-CoV-2 and its variants to include SARS-like viruses. Here, we introduce bivalent and trivalent vaccine formulations using our spike protein nanoparticle platform that completely protect female hamsters against BA.5 and XBB.1 challenges with no detectable virus in the lungs. The trivalent cocktails elicit highly neutralizing responses against all tested Omicron variants and the bat sarbecoviruses SHC014 and WIV1. Finally, our 614D/SHC014/XBB trivalent spike formulation completely protects human ACE2-transgenic female hamsters against challenges with WIV1 and SHC014 with no detectable virus in the lungs. Collectively, these results illustrate that our trivalent protein-nanoparticle cocktail can provide broad protection against SARS-CoV-2-like and SARS-CoV-1-like sarbecoviruses.
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Affiliation(s)
- Peter J Halfmann
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Kathryn Loeffler
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Augustine Duffy
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Makoto Kuroda
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Cryo-EM Research Center, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Midwest Center for Cryo-Electron Tomography, University of Wisconsin, Madison, WI, 53706, USA
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Cryo-EM Research Center, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Midwest Center for Cryo-Electron Tomography, University of Wisconsin, Madison, WI, 53706, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA.
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan.
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, 162-8655, Japan.
| | - Ravi S Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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18
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Chen Z, Yuan Y, Hu Q, Zhu A, Chen F, Li S, Guan X, Lv C, Tang T, He Y, Cheng J, Zheng J, Hu X, Zhao J, Zhao J, Sun J. SARS-CoV-2 immunity in animal models. Cell Mol Immunol 2024; 21:119-133. [PMID: 38238440 PMCID: PMC10806257 DOI: 10.1038/s41423-023-01122-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
The COVID-19 pandemic, which was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a worldwide health crisis due to its transmissibility. SARS-CoV-2 infection results in severe respiratory illness and can lead to significant complications in affected individuals. These complications encompass symptoms such as coughing, respiratory distress, fever, infectious shock, acute respiratory distress syndrome (ARDS), and even multiple-organ failure. Animal models serve as crucial tools for investigating pathogenic mechanisms, immune responses, immune escape mechanisms, antiviral drug development, and vaccines against SARS-CoV-2. Currently, various animal models for SARS-CoV-2 infection, such as nonhuman primates (NHPs), ferrets, hamsters, and many different mouse models, have been developed. Each model possesses distinctive features and applications. In this review, we elucidate the immune response elicited by SARS-CoV-2 infection in patients and provide an overview of the characteristics of various animal models mainly used for SARS-CoV-2 infection, as well as the corresponding immune responses and applications of these models. A comparative analysis of transcriptomic alterations in the lungs from different animal models revealed that the K18-hACE2 and mouse-adapted virus mouse models exhibited the highest similarity with the deceased COVID-19 patients. Finally, we highlighted the current gaps in related research between animal model studies and clinical investigations, underscoring lingering scientific questions that demand further clarification.
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Affiliation(s)
- Zhao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Yaochang Yuan
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Qingtao Hu
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 510000, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Fenghua Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Shu Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Xin Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Chao Lv
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Tian Tang
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Yiyun He
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Jinling Cheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Jie Zheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Xiaoyu Hu
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China.
- Guangzhou National Laboratory, Guangzhou, Guangdong, 510005, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China.
- Guangzhou National Laboratory, Guangzhou, Guangdong, 510005, China.
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518005, China.
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, National Centre for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China.
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19
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Wang Y, Ye M, Zhang F, Freeman ZT, Yu H, Ye X, He Y. Ontology-based taxonomical analysis of experimentally verified natural and laboratory human coronavirus hosts and its implication for COVID-19 virus origination and transmission. PLoS One 2024; 19:e0295541. [PMID: 38252647 PMCID: PMC10802970 DOI: 10.1371/journal.pone.0295541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/26/2023] [Indexed: 01/24/2024] Open
Abstract
To fully understand COVID-19, it is critical to study all possible hosts of SARS-CoV-2 (the pathogen of COVID-19). In this work, we collected, annotated, and performed ontology-based taxonomical analysis of all the reported and verified hosts for all human coronaviruses including SARS-CoV, MERS-CoV, SARS-CoV-2, HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1. A total of 37 natural hosts and 19 laboratory animal hosts of human coronaviruses were identified based on experimental evidence. Our analysis found that all the verified susceptible natural and laboratory animals belong to therian mammals. Specifically, these 37 natural therian hosts include one wildlife marsupial mammal (i.e., Virginia opossum) and 36 Eutheria mammals (a.k.a. placental mammals). The 19 laboratory animal hosts are also classified as therian mammals. The mouse models with genetically modified human ACE2 or DPP4 were more susceptible to virulent human coronaviruses with clear symptoms, suggesting the critical role of ACE2 and DPP4 to coronavirus virulence. Coronaviruses became more virulent and adaptive in the mouse hosts after a series of viral passages in the mice, providing clue to the possible coronavirus origination. The Huanan Seafood Wholesale Market animals identified early in the COVID-19 outbreak were also systematically analyzed as possible COVID-19 hosts. To support knowledge standardization and query, the annotated host knowledge was modeled and represented in the Coronavirus Infectious Disease Ontology (CIDO). Based on our and others' findings, we further propose a MOVIE model (i.e., Multiple-Organism viral Variations and Immune Evasion) to address how viral variations in therian animal hosts and the host immune evasion might have led to dynamic COVID-19 pandemic outcomes.
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Affiliation(s)
- Yang Wang
- Guizhou University School of Medicine, Guiyang, Guizhou, China
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital and NHC Key Laboratory of Immunological Diseases, People’s Hospital of Guizhou University, Guiyang, Guizhou, China
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States of America
| | - Muhui Ye
- Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong, China
| | - Fengwei Zhang
- Guizhou University School of Medicine, Guiyang, Guizhou, China
| | - Zachary Thomas Freeman
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States of America
| | - Hong Yu
- Guizhou University School of Medicine, Guiyang, Guizhou, China
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital and NHC Key Laboratory of Immunological Diseases, People’s Hospital of Guizhou University, Guiyang, Guizhou, China
| | - Xianwei Ye
- Guizhou University School of Medicine, Guiyang, Guizhou, China
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital and NHC Key Laboratory of Immunological Diseases, People’s Hospital of Guizhou University, Guiyang, Guizhou, China
| | - Yongqun He
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States of America
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States of America
- Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, United States of America
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20
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Lee J, Zepeda SK, Park YJ, Taylor AL, Quispe J, Stewart C, Leaf EM, Treichel C, Corti D, King NP, Starr TN, Veesler D. Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus. Cell Host Microbe 2023; 31:1961-1973.e11. [PMID: 37989312 PMCID: PMC10913562 DOI: 10.1016/j.chom.2023.10.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/12/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
Although Rhinolophus bats harbor diverse clade 3 sarbecoviruses, the structural determinants of receptor tropism along with the antigenicity of their spike (S) glycoproteins remain uncharacterized. Here, we show that the African Rhinolophus bat clade 3 sarbecovirus PRD-0038 S has a broad angiotensin-converting enzyme 2 (ACE2) usage and that receptor-binding domain (RBD) mutations further expand receptor promiscuity and enable human ACE2 utilization. We determine a cryo-EM structure of the PRD-0038 RBD bound to Rhinolophus alcyone ACE2, explaining receptor tropism and highlighting differences with SARS-CoV-1 and SARS-CoV-2. Characterization of PRD-0038 S using cryo-EM and monoclonal antibody reactivity reveals its distinct antigenicity relative to SARS-CoV-2 and identifies PRD-0038 cross-neutralizing antibodies for pandemic preparedness. PRD-0038 S vaccination elicits greater titers of antibodies cross-reacting with vaccine-mismatched clade 2 and clade 1a sarbecoviruses compared with SARS-CoV-2 S due to broader antigenic targeting, motivating the inclusion of clade 3 antigens in next-generation vaccines for enhanced resilience to viral evolution.
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Affiliation(s)
- Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ashley L Taylor
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Elizabeth M Leaf
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Tyler N Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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21
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Guo H, Cho B, Hinton PR, He S, Yu Y, Ramesh AK, Sivaccumar JP, Ku Z, Campo K, Holland S, Sachdeva S, Mensch C, Dawod M, Whitaker A, Eisenhauer P, Falcone A, Honce R, Botten JW, Carroll SF, Keyt BA, Womack AW, Strohl WR, Xu K, Zhang N, An Z, Ha S, Shiver JW, Fu TM. An ACE2 decamer viral trap as a durable intervention solution for current and future SARS-CoV. Emerg Microbes Infect 2023; 12:2275598. [PMID: 38078382 PMCID: PMC10768737 DOI: 10.1080/22221751.2023.2275598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/19/2023] [Indexed: 12/18/2023]
Abstract
The capacity of SARS-CoV-2 to evolve poses challenges to conventional prevention and treatment options such as vaccination and monoclonal antibodies, as they rely on viral receptor binding domain (RBD) sequences from previous strains. Additionally, animal CoVs, especially those of the SARS family, are now appreciated as a constant pandemic threat. We present here a new antiviral approach featuring inhalation delivery of a recombinant viral trap composed of ten copies of angiotensin-converting enzyme 2 (ACE2) fused to the IgM Fc. This ACE2 decamer viral trap is designed to inhibit SARS-CoV-2 entry function, regardless of viral RBD sequence variations as shown by its high neutralization potency against all known SARS-CoV-2 variants, including Omicron BQ.1, BQ.1.1, XBB.1 and XBB.1.5. In addition, it demonstrates potency against SARS-CoV-1, human NL63, as well as bat and pangolin CoVs. The multivalent trap is effective in both prophylactic and therapeutic settings since a single intranasal dosing confers protection in human ACE2 transgenic mice against viral challenges. Lastly, this molecule is stable at ambient temperature for more than twelve weeks and can sustain physical stress from aerosolization. These results demonstrate the potential of a decameric ACE2 viral trap as an inhalation solution for ACE2-dependent coronaviruses of current and future pandemic concerns.
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Affiliation(s)
| | | | | | - Sijia He
- IGM Biosciences, Mountain View, CA, USA
| | | | - Ashwin Kumar Ramesh
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jwala Priyadarsini Sivaccumar
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | | | | | | | | | - Annalis Whitaker
- Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT, USA
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Philip Eisenhauer
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Allison Falcone
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Rebekah Honce
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Jason W. Botten
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | | | | | | | | | - Kai Xu
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sha Ha
- IGM Biosciences, Mountain View, CA, USA
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22
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Kapingidza AB, Marston DJ, Harris C, Wrapp D, Winters K, Mielke D, Xiaozhi L, Yin Q, Foulger A, Parks R, Barr M, Newman A, Schäfer A, Eaton A, Flores JM, Harner A, Catanzaro NJ, Mallory ML, Mattocks MD, Beverly C, Rhodes B, Mansouri K, Van Itallie E, Vure P, Dunn B, Keyes T, Stanfield-Oakley S, Woods CW, Petzold EA, Walter EB, Wiehe K, Edwards RJ, Montefiori DC, Ferrari G, Baric R, Cain DW, Saunders KO, Haynes BF, Azoitei ML. Engineered immunogens to elicit antibodies against conserved coronavirus epitopes. Nat Commun 2023; 14:7897. [PMID: 38036525 PMCID: PMC10689493 DOI: 10.1038/s41467-023-43638-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Immune responses to SARS-CoV-2 primarily target the receptor binding domain of the spike protein, which continually mutates to escape acquired immunity. Other regions in the spike S2 subunit, such as the stem helix and the segment encompassing residues 815-823 adjacent to the fusion peptide, are highly conserved across sarbecoviruses and are recognized by broadly reactive antibodies, providing hope that vaccines targeting these epitopes could offer protection against both current and emergent viruses. Here we employ computational modeling to design scaffolded immunogens that display the spike 815-823 peptide and the stem helix epitopes without the distracting and immunodominant receptor binding domain. These engineered proteins bind with high affinity and specificity to the mature and germline versions of previously identified broadly protective human antibodies. Epitope scaffolds interact with both sera and isolated monoclonal antibodies with broadly reactivity from individuals with pre-existing SARS-CoV-2 immunity. When used as immunogens, epitope scaffolds elicit sera with broad betacoronavirus reactivity and protect as "boosts" against live virus challenge in mice, illustrating their potential as components of a future pancoronavirus vaccine.
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Affiliation(s)
- A Brenda Kapingidza
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Daniel J Marston
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Caitlin Harris
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Daniel Wrapp
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Kaitlyn Winters
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Dieter Mielke
- Department of Surgery, Duke University, Durham, NC, USA
- Center for Human Systems Immunology, Duke University, Durham, NC, USA
| | - Lu Xiaozhi
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Qi Yin
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Andrew Foulger
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Rob Parks
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amanda Eaton
- Department of Surgery, Duke University, Durham, NC, USA
| | - Justine Mae Flores
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Austin Harner
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael L Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa D Mattocks
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christopher Beverly
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Brianna Rhodes
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | | | - Elizabeth Van Itallie
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Pranay Vure
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Brooke Dunn
- Department of Surgery, Duke University, Durham, NC, USA
| | - Taylor Keyes
- Department of Surgery, Duke University, Durham, NC, USA
| | | | - Christopher W Woods
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
- Center for Infectious Diseases and Diagnostic Innovation, Duke University Medical Center, Durham, NC, USA
| | - Elizabeth A Petzold
- Center for Infectious Diseases and Diagnostic Innovation, Duke University Medical Center, Durham, NC, USA
| | - Emmanuel B Walter
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Robert J Edwards
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | | | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Surgery, Duke University, Durham, NC, USA
- Center for Human Systems Immunology, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Surgery, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Department of Immunology, Duke University, Durham, NC, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
- Department of Immunology, Duke University, Durham, NC, USA
| | - Mihai L Azoitei
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA.
- Department of Medicine, Duke University, Durham, NC, USA.
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23
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Smits P, Cambourieu C, Ouimet M. Connections between health research systems and decision-making spaces: lessons from the COVID-19 pandemic in the province of Québec, Canada. Health Res Policy Syst 2023; 21:116. [PMID: 37919781 PMCID: PMC10621227 DOI: 10.1186/s12961-023-01053-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 09/23/2023] [Indexed: 11/04/2023] Open
Abstract
The coronavirus 2019 (COVID-19) pandemic allowed for exceptional decision-making power to be placed in the hands of public health departments. Data and information were widely disseminated in the media and on websites. While the improvement of pandemic management is still a learning curve, the ecosystem perspective - that is, the interconnection of academic health research systems and decision-making spaces - has received little attention. In this commentary, we look at the mechanisms in place, or not, in Canada for ensuring decision-making spheres can "speak" to academic research systems. We look at the thick walls that are still in place between health research systems and decision-making spaces. More precisely, we discuss three organizational flaws that we identified in the evidence-informed decision-making ecosystem of Québec and, more broadly, Canada. We introduce some inspiring measures that other countries have implemented to better link evidence and public health decision-making during health crises. The observed flaws and options are related to the vitality of early information sharing relays, the cross-sectional capacity to issue opinions, and the collection and integration of hard and soft data.
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Affiliation(s)
- Pernelle Smits
- Departement de Management, Université Laval, Québec, Canada.
| | | | - Mathieu Ouimet
- Departement de Sciences Politiques, Université Laval, Québec, Canada
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24
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Rabaan AA, Alenazy MF, Alshehri AA, Alshahrani MA, Al-Subaie MF, Alrasheed HA, Al Kaabi NA, Thakur N, Bouafia NA, Alissa M, Alsulaiman AM, AlBaadani AM, Alhani HM, Alhaddad AH, Alfouzan WA, Ali BMA, Al-Abdulali KH, Khamis F, Bayahya A, Al Fares MA, Sharma M, Dhawan M. An updated review on pathogenic coronaviruses (CoVs) amid the emergence of SARS-CoV-2 variants: A look into the repercussions and possible solutions. J Infect Public Health 2023; 16:1870-1883. [PMID: 37839310 DOI: 10.1016/j.jiph.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
SARS-CoV-2, responsible for COVID-19, shares 79% and 50% of its identity with SARS-CoV-1 and MERS-CoV, respectively. It uses the same main cell attachment and entry receptor as SARS-CoV-1, which is the ACE-2 receptor. However, key residues in the receptor-binding domain of its S-protein seem to give it a stronger affinity for the receptor and a better ability to hide from the host immune system. Like SARS-CoV-1 and MERS-CoV, cytokine storms in critically ill COVID-19 patients cause ARDS, neurological pathology, multiorgan failure, and increased death. Though many issues remain, the global research effort and lessons from SARS-CoV-1 and MERS-CoV are hopeful. The emergence of novel SARS-CoV-2 variants and subvariants raised serious concerns among the scientific community amid the emergence of other viral diseases like monkeypox and Marburg virus, which are major concerns for healthcare settings worldwide. Hence, an updated review on the comparative analysis of various coronaviruses (CoVs) has been developed, which highlights the evolution of CoVs and their repercussions.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan.
| | - Maha Fahad Alenazy
- Department of Physiology, College of Medicine, King Khalid university hospital, King Saud University, Riyadh 4545, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Mohammed Abdulrahman Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Maha F Al-Subaie
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Research Center, Dr. Sulaiman Alhabib Medical Group, Riyadh 13328, Saudi Arabia; Department of Infectious Diseases, Dr. Sulaiman Alhabib Medical Group, Riyadh 13328, Saudi Arabia
| | - Hayam A Alrasheed
- Department of pharmacy Practice, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia; Pharmacy Department, King Abdullah Bin Abdulaziz University Hospital, Riyadh 11671, Saudi Arabia
| | - Nawal A Al Kaabi
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi, 51900, United Arab Emirates; College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Nanamika Thakur
- University Institute of Biotechnology, Department of Biotechnology, Chandigarh University, Mohali 140413, India
| | - Nabiha A Bouafia
- Infection prevention and control centre of Excellence, Prince Sultan Medical Military City, Riyadh 12233, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | | | - Abeer M AlBaadani
- Internal Medicine Department, Infectious Disease Division, London health science Center, London, Ontario N6G0X2, Canada
| | - Hatem M Alhani
- Department of Pediatric Infectious Disease, Maternity and Children Hospital, Dammam 31176, Saudi Arabia; Department of Infection Control, Maternity and Children Hospital, Dammam 31176, Saudi Arabia; Preventive Medicine and Infection Prevention and Control Department, Directorate of Ministry of Health, Dammam 32245, Saudi Arabia
| | - Ali H Alhaddad
- Assistant Agency for Hospital Affairs, Ministry of Health, Riyadh 12382, Saudi Arabia
| | - Wadha A Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait; Microbiology Unit, Department of Laboratories, Farwania Hospital, Farwania 85000, Kuwait
| | - Batool Mohammed Abu Ali
- Infectious disease section, Department of internal medicine, King Fahad Hospital Hofuf, Hofuf 36365, Saudi Arabia
| | - Khadija H Al-Abdulali
- Nursing Department, Home health care, Qatif Health Network, Qatif 31911, Saudi Arabia
| | - Faryal Khamis
- Infection Diseases unit, Department of Internal Medicine, Royal Hospital, Muscat 1331, Oman
| | - Ali Bayahya
- Microbiology Department, Alqunfudah General Hospital, Alqunfudah 28813, Saudi Arabia
| | - Mona A Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia.
| | - Manish Sharma
- University Institute of Biotechnology, Department of Biotechnology, Chandigarh University, Mohali 140413, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, India; Trafford College, Altrincham, Manchester WA14 5PQ, UK.
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25
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Martinez DR, Schäfer A, Gavitt TD, Mallory ML, Lee E, Catanzaro NJ, Chen H, Gully K, Scobey T, Korategere P, Brown A, Smith L, Parks R, Barr M, Newman A, Bowman C, Powers JM, Soderblom EJ, Mansouri K, Edwards RJ, Baric RS, Haynes BF, Saunders KO. Vaccine-mediated protection against Merbecovirus and Sarbecovirus challenge in mice. Cell Rep 2023; 42:113248. [PMID: 37858337 PMCID: PMC10842144 DOI: 10.1016/j.celrep.2023.113248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/30/2023] [Accepted: 09/26/2023] [Indexed: 10/21/2023] Open
Abstract
The emergence of three highly pathogenic human coronaviruses-severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003, Middle Eastern respiratory syndrome (MERS)-CoV in 2012, and SARS-CoV-2 in 2019-underlines the need to develop broadly active vaccines against the Merbecovirus and Sarbecovirus betacoronavirus subgenera. While SARS-CoV-2 vaccines protect against severe COVID-19, they do not protect against other sarbecoviruses or merbecoviruses. Here, we vaccinate mice with a trivalent sortase-conjugate nanoparticle (scNP) vaccine containing the SARS-CoV-2, RsSHC014, and MERS-CoV receptor-binding domains (RBDs), which elicited live-virus neutralizing antibody responses. The trivalent RBD scNP elicited serum neutralizing antibodies against bat zoonotic Wuhan Institute of Virology-1 (WIV-1)-CoV, SARS-CoV, SARS-CoV-2 BA.1, SARS-CoV-2 XBB.1.5, and MERS-CoV live viruses. The monovalent SARS-CoV-2 RBD scNP vaccine only protected against Sarbecovirus challenge, whereas the trivalent RBD scNP vaccine protected against both Merbecovirus and Sarbecovirus challenge in highly pathogenic and lethal mouse models. This study demonstrates proof of concept for a single pan-sarbecovirus/pan-merbecovirus vaccine that protects against three highly pathogenic human coronaviruses spanning two betacoronavirus subgenera.
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Affiliation(s)
- David R Martinez
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Center for Infection and Immunity, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tyler D Gavitt
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Michael L Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Esther Lee
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Haiyan Chen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kendra Gully
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Trevor Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pooja Korategere
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alecia Brown
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lena Smith
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cindy Bowman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - John M Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Erik J Soderblom
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC 27710, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert J Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.
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26
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Heise M, Dillard J, Taft-Benz S, Knight A, Anderson E, Pressey K, Parotti B, Martinez S, Diaz J, Sarkar S, Madden E, De la Cruz G, Adams L, Dinnon K, Leist S, Martinez D, Schaefer A, Powers J, Yount B, Castillo I, Morales N, Burdick J, Evangelista MK, Ralph L, Pankow N, Linnertz C, Lakshmanane P, Montgomery S, Ferris M, Baric R, Baxter V. Adjuvant-dependent effects on the safety and efficacy of inactivated SARS-CoV-2 vaccines during heterologous infection by a SARS-related coronavirus. RESEARCH SQUARE 2023:rs.3.rs-3401539. [PMID: 37961507 PMCID: PMC10635311 DOI: 10.21203/rs.3.rs-3401539/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Inactivated whole virus SARS-CoV-2 vaccines adjuvanted with aluminum hydroxide (Alum) are among the most widely used COVID-19 vaccines globally and have been critical to the COVID-19 pandemic response. Although these vaccines are protective against homologous virus infection in healthy recipients, the emergence of novel SARS-CoV-2 variants and the presence of large zoonotic reservoirs provide significant opportunities for vaccine breakthrough, which raises the risk of adverse outcomes including vaccine-associated enhanced respiratory disease (VAERD). To evaluate this possibility, we tested the performance of an inactivated SARS-CoV-2 vaccine (iCoV2) in combination with Alum against either homologous or heterologous coronavirus challenge in a mouse model of coronavirus-induced pulmonary disease. Consistent with human results, iCoV2 + Alum protected against homologous challenge. However, challenge with a heterologous SARS-related coronavirus, Rs-SHC014-CoV (SHC014), up to at least 10 months post-vaccination, resulted in VAERD in iCoV2 + Alum-vaccinated animals, characterized by pulmonary eosinophilic infiltrates, enhanced pulmonary pathology, delayed viral clearance, and decreased pulmonary function. In contrast, vaccination with iCoV2 in combination with an alternative adjuvant (RIBI) did not induce VAERD and promoted enhanced SHC014 clearance. Further characterization of iCoV2 + Alum-induced immunity suggested that CD4+ T cells were a major driver of VAERD, and these responses were partially reversed by re-boosting with recombinant Spike protein + RIBI adjuvant. These results highlight potential risks associated with vaccine breakthrough in recipients of Alum-adjuvanted inactivated vaccines and provide important insights into factors affecting both the safety and efficacy of coronavirus vaccines in the face of heterologous virus infections.
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Affiliation(s)
- Mark Heise
- University of North Carolina at Chapel Hill
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Boyd Yount
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill
| | | | | | | | | | | | | | | | - Prem Lakshmanane
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC
| | | | | | | | - Victoria Baxter
- Texas Biomedical Research Institute, San Antonio, Texas, USA
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27
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Fritch EJ, Mordant AL, Gilbert TSK, Wells CI, Yang X, Barker NK, Madden EA, Dinnon KH, Hou YJ, Tse LV, Castillo IN, Sims AC, Moorman NJ, Lakshmanane P, Willson TM, Herring LE, Graves LM, Baric RS. Investigation of the Host Kinome Response to Coronavirus Infection Reveals PI3K/mTOR Inhibitors as Betacoronavirus Antivirals. J Proteome Res 2023; 22:3159-3177. [PMID: 37634194 DOI: 10.1021/acs.jproteome.3c00182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Host kinases play essential roles in the host cell cycle, innate immune signaling, the stress response to viral infection, and inflammation. Previous work has demonstrated that coronaviruses specifically target kinase cascades to subvert host cell responses to infection and rely upon host kinase activity to phosphorylate viral proteins to enhance replication. Given the number of kinase inhibitors that are already FDA approved to treat cancers, fibrosis, and other human disease, they represent an attractive class of compounds to repurpose for host-targeted therapies against emerging coronavirus infections. To further understand the host kinome response to betacoronavirus infection, we employed multiplex inhibitory bead mass spectrometry (MIB-MS) following MERS-CoV and SARS-CoV-2 infection of human lung epithelial cell lines. Our MIB-MS analyses revealed activation of mTOR and MAPK signaling following MERS-CoV and SARS-CoV-2 infection, respectively. SARS-CoV-2 host kinome responses were further characterized using paired phosphoproteomics, which identified activation of MAPK, PI3K, and mTOR signaling. Through chemogenomic screening, we found that clinically relevant PI3K/mTOR inhibitors were able to inhibit coronavirus replication at nanomolar concentrations similar to direct-acting antivirals. This study lays the groundwork for identifying broad-acting, host-targeted therapies to reduce betacoronavirus replication that can be rapidly repurposed during future outbreaks and epidemics. The proteomics, phosphoproteomics, and MIB-MS datasets generated in this study are available in the Proteomics Identification Database (PRIDE) repository under project identifiers PXD040897 and PXD040901.
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Affiliation(s)
- Ethan J Fritch
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7290, United States
| | - Angie L Mordant
- UNC Michael Hooker Proteomics Core, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Thomas S K Gilbert
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7365, United States
| | - Carrow I Wells
- Structural Genomics Consortium, Department of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Xuan Yang
- Structural Genomics Consortium, Department of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Natalie K Barker
- UNC Michael Hooker Proteomics Core, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Emily A Madden
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7290, United States
| | - Kenneth H Dinnon
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7290, United States
| | - Yixuan J Hou
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7400, United States
| | - Longping V Tse
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7400, United States
| | - Izabella N Castillo
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7290, United States
| | - Amy C Sims
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7400, United States
| | - Nathaniel J Moorman
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7290, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Premkumar Lakshmanane
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7290, United States
| | - Timothy M Willson
- Structural Genomics Consortium, Department of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States
| | - Laura E Herring
- UNC Michael Hooker Proteomics Core, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7365, United States
| | - Lee M Graves
- UNC Michael Hooker Proteomics Core, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7365, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Ralph S Baric
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7290, United States
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7400, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, United States
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28
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Hou YJ, Chiba S, Leist SR, Meganck RM, Martinez DR, Schäfer A, Catanzaro NJ, Sontake V, West A, Edwards CE, Yount B, Lee RE, Gallant SC, Zost SJ, Powers J, Adams L, Kong EF, Mattocks M, Tata A, Randell SH, Tata PR, Halfmann P, Crowe JE, Kawaoka Y, Baric RS. Host range, transmissibility and antigenicity of a pangolin coronavirus. Nat Microbiol 2023; 8:1820-1833. [PMID: 37749254 PMCID: PMC10522490 DOI: 10.1038/s41564-023-01476-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 08/14/2023] [Indexed: 09/27/2023]
Abstract
The pathogenic and cross-species transmission potential of SARS-CoV-2-related coronaviruses (CoVs) remain poorly characterized. Here we recovered a wild-type pangolin (Pg) CoV GD strain including derivatives encoding reporter genes using reverse genetics. In primary human cells, PgCoV replicated efficiently but with reduced fitness and showed less efficient transmission via airborne route compared with SARS-CoV-2 in hamsters. PgCoV was potently inhibited by US Food and Drug Administration approved drugs, and neutralized by COVID-19 patient sera and SARS-CoV-2 therapeutic antibodies in vitro. A pan-Sarbecovirus antibody and SARS-CoV-2 S2P recombinant protein vaccine protected BALB/c mice from PgCoV infection. In K18-hACE2 mice, PgCoV infection caused severe clinical disease, but mice were protected by a SARS-CoV-2 human antibody. Efficient PgCoV replication in primary human cells and hACE2 mice, coupled with a capacity for airborne spread, highlights an emergence potential. However, low competitive fitness, pre-immune humans and the benefit of COVID-19 countermeasures should impede its ability to spread globally in human populations.
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Affiliation(s)
- Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Moderna Inc., Cambridge, MA, USA
| | - Shiho Chiba
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rita M Meganck
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vishwaraj Sontake
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Catlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rhianna E Lee
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel C Gallant
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Seth J Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lily Adams
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Edgar F Kong
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa Mattocks
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aleksandra Tata
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Purushothama R Tata
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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29
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Lin HF, Liu MQ, Jiang RD, Gong QC, Su J, Guo ZS, Chen Y, Jia JK, Dong TY, Zhu Y, Li A, Shen XR, Wang Y, Li B, Xie TT, Yang XL, Hu B, Shi ZL. Characterization of a mouse-adapted strain of bat severe acute respiratory syndrome-related coronavirus. J Virol 2023; 97:e0079023. [PMID: 37607058 PMCID: PMC10537601 DOI: 10.1128/jvi.00790-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 06/18/2023] [Indexed: 08/24/2023] Open
Abstract
Bats carry genetically diverse severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs). Some of them utilize human angiotensin-converting enzyme 2 (hACE2) as a receptor and cannot efficiently replicate in wild-type mice. Our previous study demonstrated that the bat SARSr-CoV rRsSHC014S induces respiratory infection and lung damage in hACE2 transgenic mice but not wild-type mice. In this study, we generated a mouse-adapted strain of rRsSHC014S, which we named SMA1901, by serial passaging of wild-type virus in BALB/c mice. SMA1901 showed increased infectivity in mouse lungs and induced interstitial lung pneumonia in both young and aged mice after intranasal inoculation. Genome sequencing revealed mutations in not only the spike protein but the whole genome, which may be responsible for the enhanced pathogenicity of SMA1901 in wild-type BALB/c mice. SMA1901 induced age-related mortality similar to that observed in SARS and COVID-19. Drug testing using antibodies and antiviral molecules indicated that this mouse-adapted virus strain can be used to test prophylactic and therapeutic drug candidates against SARSr-CoVs. IMPORTANCE The genetic diversity of SARSr-CoVs in wildlife and their potential risk of cross-species infection highlights the importance of developing a powerful animal model to evaluate the antibodies and antiviral drugs. We acquired the mouse-adapted strain of a bat-origin coronavirus named SMA1901 by natural serial passaging of rRsSHC014S in BALB/c mice. The SMA1901 infection caused interstitial pneumonia and inflammatory immune responses in both young and aged BALB/c mice after intranasal inoculation. Our model exhibited age-related mortality similar to SARS and COVID-19. Therefore, our model will be of high value for investigating the pathogenesis of bat SARSr-CoVs and could serve as a prospective test platform for prophylactic and therapeutic candidates.
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Affiliation(s)
- Hao-Feng Lin
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Qin Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ren-Di Jiang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Qian-Chun Gong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jia Su
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Shuo Guo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing-Kun Jia
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tian-Yi Dong
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ang Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xu-Rui Shen
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
| | - Yi Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ting-Ting Xie
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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30
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Lee J, Zepeda SK, Park YJ, Taylor AL, Quispe J, Stewart C, Leaf EM, Treichel C, Corti D, King NP, Starr TN, Veesler D. Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557371. [PMID: 37745523 PMCID: PMC10515872 DOI: 10.1101/2023.09.12.557371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Although Rhinolophus bats harbor diverse clade 3 sarbecoviruses, the structural determinants of receptor tropism along with the antigenicity of their spike (S) glycoproteins remain uncharacterized. Here, we show that the African Rinolophus bat clade 3 sarbecovirus PRD-0038 S has a broad ACE2 usage and that RBD mutations further expand receptor promiscuity and enable human ACE2 utilization. We determined a cryoEM structure of the PRD-0038 RBD bound to R. alcyone ACE2, explaining receptor tropism and highlighting differences with SARS-CoV-1 and SARS-CoV-2. Characterization of PRD-0038 S using cryoEM and monoclonal antibody reactivity revealed its distinct antigenicity relative to SARS-CoV-2 and identified PRD-0038 cross-neutralizing antibodies for pandemic preparedness. PRD-0038 S vaccination elicited greater titers of antibodies cross-reacting with vaccine-mismatched clade 2 and clade 1a sarbecoviruses compared to SARS-CoV-2 S due to broader antigenic targeting, motivating the inclusion of clade 3 antigens in next-generation vaccines for enhanced resilience to viral evolution.
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Affiliation(s)
- Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Samantha K. Zepeda
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Ashley L. Taylor
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Elizabeth M. Leaf
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Tyler N. Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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31
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Su X, Huang Z, Xu W, Wang Q, Xing L, Lu L, Jiang S, Xia S. IgG Fc-Binding Peptide-Conjugated Pan-CoV Fusion Inhibitor Exhibits Extended In Vivo Half-Life and Synergistic Antiviral Effect When Combined with Neutralizing Antibodies. Biomolecules 2023; 13:1283. [PMID: 37759683 PMCID: PMC10526447 DOI: 10.3390/biom13091283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/13/2023] [Accepted: 08/16/2023] [Indexed: 09/29/2023] Open
Abstract
The peptide-based pan-coronavirus fusion inhibitor EK1 is in phase III clinical trials, and it has, thus far, shown good clinical application prospects against SARS-CoV-2 and its variants. To further improve its in vivo long-acting property, we herein developed an Fc-binding strategy by conjugating EK1 with human immunoglobulin G Fc-binding peptide (IBP), which can exploit the long half-life advantage of IgG in vivo. The newly engineered peptide IBP-EK1 showed potent and broad-spectrum inhibitory activity against SARS-CoV-2 and its variants, including various Omicron sublineages and other human coronaviruses (HCoVs) with low cytotoxicity. In mouse models, IBP-EK1 possessed potent prophylactic and therapeutic efficacy against lethal HCoV-OC43 challenge, and it showed good safety profile and low immunogenicity. More importantly, IBP-EK1 exhibited a significantly extended in vivo half-life in rhesus monkeys of up to 37.7 h, which is about 20-fold longer than that reported for EK1. Strikingly, IBP-EK1 displayed strong in vitro or ex vivo synergistic anti-HCoV effect when combined with monoclonal neutralizing antibodies, including REGN10933 or S309, suggesting that IBP-conjugated EK1 can be further developed as a long-acting, broad-spectrum anti-HCoV agent, either alone or in combination with neutralizing antibodies, to combat the current COVID-19 pandemic or future outbreaks caused by emerging and re-emerging highly pathogenic HCoVs.
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Affiliation(s)
| | | | | | | | | | | | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai 200032, China; (X.S.); (Z.H.); (W.X.); (Q.W.); (L.X.); (L.L.)
| | - Shuai Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai 200032, China; (X.S.); (Z.H.); (W.X.); (Q.W.); (L.X.); (L.L.)
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32
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Halfmann PJ, Loeffler K, Duffy A, Kuroda M, Kawaoka Y, Kane RS. Broad Protection Against Clade 1 Sarbecoviruses After a Single Immunization with Cocktail Spike-Protein-Nanoparticle Vaccine. RESEARCH SQUARE 2023:rs.3.rs-3088907. [PMID: 37461652 PMCID: PMC10350183 DOI: 10.21203/rs.3.rs-3088907/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The 2002 SARS outbreak, the 2019 emergence of COVID-19, and the continuing evolution of immune-evading SARS-CoV-2 variants together highlight the need for a broadly protective vaccine against ACE2-utilizing sarbecoviruses. While updated variant-matched formulations such as Pfizer-BioNTech's bivalent vaccine are a step in the right direction, protection needs to extend beyond SARS-CoV-2 and its variants to include SARS-like viruses. Here, we introduce bivalent and trivalent vaccine formulations using our spike protein nanoparticle platform that completely protected hamsters against BA.5 and XBB.1 challenges with no detectable virus in the lungs. The trivalent cocktails elicited highly neutralizing responses against all tested Omicron variants and the bat sarbecoviruses SHC014 and WIV1. Finally, our 614D/SHC014/XBB trivalent spike formulation completely protected human ACE2-transgenic hamsters against challenges with WIV1 and SHC014 with no detectable virus in the lungs. Collectively, these results illustrate that our trivalent protein-nanoparticle cocktail can provide broad protection against SARS-CoV-2-like and SARS-CoV-1-like sarbecoviruses.
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Affiliation(s)
- Peter J. Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Kathryn Loeffler
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Augustine Duffy
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo 162-8655, Japan
| | - Ravi S. Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
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33
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Ma C, Liu C, Xiong Q, Gu M, Shi L, Wang C, Si J, Tong F, Liu P, Huang M, Yan H. Broad host tropism of ACE2-using MERS-related coronaviruses and determinants restricting viral recognition. Cell Discov 2023; 9:57. [PMID: 37321999 DOI: 10.1038/s41421-023-00566-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/14/2023] [Indexed: 06/17/2023] Open
Abstract
Recently, two Middle East respiratory syndrome coronavirus (MERS-CoV) closely related to bat merbecoviruses, NeoCoV and PDF-2180, were discovered to use angiotensin-converting enzyme 2 (ACE2) for entry. The two viruses cannot use human ACE2 efficiently, and their host range and cross-species transmissibility across a wide range of mammalian species remain unclear. Herein, we characterized the species-specific receptor preference of these viruses by testing ACE2 orthologues from 49 bats and 53 non-bat mammals through receptor-binding domain (RBD)-binding and pseudovirus entry assays. Results based on bat ACE2 orthologues revealed that the two viruses were unable to use most, but not all, ACE2 from Yinpterochiropteran bats (Yin-bats), which is distinct from NL63 and SARS-CoV-2. Besides, both viruses exhibited broad receptor recognition spectra across non-bat mammals. Genetic and structural analyses of bat ACE2 orthologues highlighted four crucial host range determinants, all confirmed by subsequent functional assays in human and bat cells. Notably, residue 305, participating in a critical viral receptor interaction, plays a crucial role in host tropism determination, particularly in non-bat mammals. Furthermore, NeoCoV and PDF-2180 mutants with enhanced human ACE2 recognition expanded the potential host range, especially by enhancing their interaction with an evolutionarily conserved hydrophobic pocket. Our results elucidate the molecular basis for the species-specific ACE2 usage of MERS-related viruses and shed light on their zoonotic risks.
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Affiliation(s)
- Chengbao Ma
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Chen Liu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Qing Xiong
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Mengxue Gu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Lulu Shi
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Chunli Wang
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Junyu Si
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Fei Tong
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Peng Liu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Meiling Huang
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Huan Yan
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China.
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34
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Martinez DR, Schafer A, Gavitt TD, Mallory ML, Lee E, Catanzaro NJ, Chen H, Gully K, Scobey T, Korategere P, Brown A, Smith L, Parks R, Barr M, Newman A, Bowman C, Powers JM, Mansouri K, Edwards RJ, Baric RS, Haynes BF, Saunders KO. Vaccine-mediated protection against merbecovirus and sarbecovirus challenge in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.540829. [PMID: 37293083 PMCID: PMC10245799 DOI: 10.1101/2023.05.22.540829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The emergence of three distinct highly pathogenic human coronaviruses - SARS-CoV in 2003, MERS-CoV in 2012, and SARS-CoV-2 in 2019 - underlines the need to develop broadly active vaccines against the Merbecovirus and Sarbecovirus betacoronavirus subgenera. While SARS-CoV-2 vaccines are highly protective against severe COVID-19 disease, they do not protect against other sarbecoviruses or merbecoviruses. Here, we vaccinate mice with a trivalent sortase-conjugate nanoparticle (scNP) vaccine containing the SARS-CoV-2, RsSHC014, and MERS-CoV receptor binding domains (RBDs), which elicited live-virus neutralizing antibody responses and broad protection. Specifically, a monovalent SARS-CoV-2 RBD scNP vaccine only protected against sarbecovirus challenge, whereas the trivalent RBD scNP vaccine protected against both merbecovirus and sarbecovirus challenge in highly pathogenic and lethal mouse models. Moreover, the trivalent RBD scNP elicited serum neutralizing antibodies against SARS-CoV, MERS-CoV and SARS-CoV-2 BA.1 live viruses. Our findings show that a trivalent RBD nanoparticle vaccine displaying merbecovirus and sarbecovirus immunogens elicits immunity that broadly protects mice against disease. This study demonstrates proof-of-concept for a single pan-betacoronavirus vaccine to protect against three highly pathogenic human coronaviruses spanning two betacoronavirus subgenera.
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Affiliation(s)
- David R. Martinez
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
- Yale Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Alexandra Schafer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tyler D. Gavitt
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Michael L. Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Esther Lee
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Nicholas J. Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Haiyan Chen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kendra Gully
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Trevor Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Pooja Korategere
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Alecia Brown
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Lena Smith
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Rob Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Cindy Bowman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - John M. Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
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35
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Havranek B, Lindsey GW, Higuchi Y, Itoh Y, Suzuki T, Okamoto T, Hoshino A, Procko E, Islam SM. A computationally designed ACE2 decoy has broad efficacy against SARS-CoV-2 omicron variants and related viruses in vitro and in vivo. Commun Biol 2023; 6:513. [PMID: 37173421 PMCID: PMC10177734 DOI: 10.1038/s42003-023-04860-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity-enhanced soluble ACE2 (sACE2) is an alternative strategy that works by binding the SARS-CoV-2 S protein, acting as a 'decoy' to block the interaction between the S and human ACE2. Using a computational design strategy, we designed an affinity-enhanced ACE2 decoy, FLIF, that exhibited tight binding to SARS-CoV-2 delta and omicron variants. Our computationally calculated absolute binding free energies (ABFE) between sACE2:SARS-CoV-2 S proteins and their variants showed excellent agreement to binding experiments. FLIF displayed robust therapeutic utility against a broad range of SARS-CoV-2 variants and sarbecoviruses, and neutralized omicron BA.5 in vitro and in vivo. Furthermore, we directly compared the in vivo therapeutic efficacy of wild-type ACE2 (non-affinity enhanced ACE2) against FLIF. A few wild-type sACE2 decoys have shown to be effective against early circulating variants such as Wuhan in vivo. Our data suggest that moving forward, affinity-enhanced ACE2 decoys like FLIF may be required to combat evolving SARS-CoV-2 variants. The approach described herein emphasizes how computational methods have become sufficiently accurate for the design of therapeutics against viral protein targets. Affinity-enhanced ACE2 decoys remain highly effective at neutralizing omicron subvariants.
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Affiliation(s)
- Brandon Havranek
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, 19107, USA
- ComputePharma, LLC., Chicago, IL, USA
| | | | - Yusuke Higuchi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tatsuya Suzuki
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Atsushi Hoshino
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801, USA
- Cyrus Biotechnology, Inc., Seattle, WA, USA
| | - Shahidul M Islam
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- ComputePharma, LLC., Chicago, IL, USA.
- Department of Chemistry, Delaware State University, Dover, DE, 19901, USA.
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36
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Feng Y, Yuan M, Powers JM, Hu M, Munt JE, Arunachalam PS, Leist SR, Bellusci L, Kim J, Sprouse KR, Adams LE, Sundaramurthy S, Zhu X, Shirreff LM, Mallory ML, Scobey TD, Moreno A, O’Hagan DT, Kleanthous H, Villinger FJ, Veesler D, King NP, Suthar MS, Khurana S, Baric RS, Wilson IA, Pulendran B. Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine. Sci Transl Med 2023; 15:eadg7404. [PMID: 37163615 PMCID: PMC11032722 DOI: 10.1126/scitranslmed.adg7404] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/11/2023] [Indexed: 05/12/2023]
Abstract
The rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that evade immunity elicited by vaccination has placed an imperative on the development of countermeasures that provide broad protection against SARS-CoV-2 and related sarbecoviruses. Here, we identified extremely potent monoclonal antibodies (mAbs) that neutralized multiple sarbecoviruses from macaques vaccinated with AS03-adjuvanted monovalent subunit vaccines. Longitudinal analysis revealed progressive accumulation of somatic mutation in the immunoglobulin genes of antigen-specific memory B cells (MBCs) for at least 1 year after primary vaccination. Antibodies generated from these antigen-specific MBCs at 5 to 12 months after vaccination displayed greater potency and breadth relative to those identified at 1.4 months. Fifteen of the 338 (about 4.4%) antibodies isolated at 1.4 to 6 months after the primary vaccination showed potency against SARS-CoV-2 BA.1, despite the absence of serum BA.1 neutralization. 25F9 and 20A7 neutralized authentic clade 1 sarbecoviruses (SARS-CoV, WIV-1, SHC014, SARS-CoV-2 D614G, BA.1, and Pangolin-GD) and vesicular stomatitis virus-pseudotyped clade 3 sarbecoviruses (BtKY72 and PRD-0038). 20A7 and 27A12 showed potent neutralization against all SARS-CoV-2 variants and multiple Omicron sublineages, including BA.1, BA.2, BA.3, BA.4/5, BQ.1, BQ.1.1, and XBB. Crystallography studies revealed the molecular basis of broad and potent neutralization through targeting conserved sites within the RBD. Prophylactic protection of 25F9, 20A7, and 27A12 was confirmed in mice, and administration of 25F9 particularly provided complete protection against SARS-CoV-2, BA.1, SARS-CoV, and SHC014 challenge. These data underscore the extremely potent and broad activity of these mAbs against sarbecoviruses.
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Affiliation(s)
- Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University; Stanford, CA 94305, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - John M. Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | - Mengyun Hu
- Institute for Immunity, Transplantation and Infection, Stanford University; Stanford, CA 94305, USA
| | - Jennifer E. Munt
- Department of Epidemiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | - Prabhu S. Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University; Stanford, CA 94305, USA
| | - Sarah R. Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | - Lorenza Bellusci
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA); Silver Spring, MD 20993, USA
| | - JungHyun Kim
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA); Silver Spring, MD 20993, USA
| | - Kaitlin R. Sprouse
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Lily E. Adams
- Department of Epidemiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | | | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Lisa M. Shirreff
- New Iberia Research Center, University of Louisiana at Lafayette; New Iberia, LA 70560, USA
| | - Michael L. Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | - Trevor D. Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | - Alberto Moreno
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, GA 30322, USA
| | | | | | - Francois J. Villinger
- New Iberia Research Center, University of Louisiana at Lafayette; New Iberia, LA 70560, USA
| | - David Veesler
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington; Seattle, WA 98195, USA
| | - Neil P. King
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington; Seattle, WA 98195, USA
| | - Mehul S. Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center; Atlanta, GA 30329, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA); Silver Spring, MD 20993, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University; Stanford, CA 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford University; Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University; Stanford, CA 94305, USA
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37
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Song G, Yuan M, Liu H, Capozzola T, Lin RN, Torres JL, He WT, Musharrafieh R, Dueker K, Zhou P, Callaghan S, Mishra N, Yong P, Anzanello F, Avillion G, Vo AL, Li X, Makhdoomi M, Feng Z, Zhu X, Peng L, Nemazee D, Safonova Y, Briney B, Ward AB, Burton DR, Wilson IA, Andrabi R. Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538488. [PMID: 37162858 PMCID: PMC10168401 DOI: 10.1101/2023.04.26.538488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Developing broad coronavirus vaccines requires identifying and understanding the molecular basis of broadly neutralizing antibody (bnAb) spike sites. In our previous work, we identified sarbecovirus spike RBD group 1 and 2 bnAbs. We have now shown that many of these bnAbs can still neutralize highly mutated SARS-CoV-2 variants, including the XBB.1.5. Structural studies revealed that group 1 bnAbs use recurrent germline-encoded CDRH3 features to interact with a conserved RBD region that overlaps with class 4 bnAb site. Group 2 bnAbs recognize a less well-characterized "site V" on the RBD and destabilize spike trimer. The site V has remained largely unchanged in SARS-CoV-2 variants and is highly conserved across diverse sarbecoviruses, making it a promising target for broad coronavirus vaccine development. Our findings suggest that targeted vaccine strategies may be needed to induce effective B cell responses to escape resistant subdominant spike RBD bnAb sites.
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Affiliation(s)
- Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan N. Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wan-ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rami Musharrafieh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Katharina Dueker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sean Callaghan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nitesh Mishra
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fabio Anzanello
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Avillion
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anh Lina Vo
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xuduo Li
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Muzamil Makhdoomi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ziqi Feng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yana Safonova
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Ian A. Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Lead Contact
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38
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Adams LE, Leist SR, Dinnon KH, West A, Gully KL, Anderson EJ, Loome JF, Madden EA, Powers JM, Schäfer A, Sarkar S, Castillo IN, Maron JS, McNamara RP, Bertera HL, Zweigert MR, Higgins JS, Hampton BK, Premkumar L, Alter G, Montgomery SA, Baxter VK, Heise MT, Baric RS. Fc-mediated pan-sarbecovirus protection after alphavirus vector vaccination. Cell Rep 2023; 42:112326. [PMID: 37000623 PMCID: PMC10063157 DOI: 10.1016/j.celrep.2023.112326] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/21/2022] [Accepted: 03/17/2023] [Indexed: 04/01/2023] Open
Abstract
Group 2B β-coronaviruses (sarbecoviruses) have caused regional and global epidemics in modern history. Here, we evaluate the mechanisms of cross-sarbecovirus protective immunity, currently less clear yet important for pan-sarbecovirus vaccine development, using a panel of alphavirus-vectored vaccines covering bat to human strains. While vaccination does not prevent virus replication, it protects against lethal heterologous disease outcomes in both severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and clade 2 bat sarbecovirus challenge models. The spike vaccines tested primarily elicit a highly S1-specific homologous neutralizing antibody response with no detectable cross-virus neutralization. Rather, non-neutralizing antibody functions, mechanistically linked to FcgR4 and spike S2, mediate cross-protection in wild-type mice. Protection is lost in FcR knockout mice, further supporting a model for non-neutralizing, protective antibodies. These data highlight the importance of FcR-mediated cross-protective immune responses in universal pan-sarbecovirus vaccine designs.
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Affiliation(s)
- Lily E Adams
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth H Dinnon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kendra L Gully
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth J Anderson
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jennifer F Loome
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily A Madden
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John M Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sanjay Sarkar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Izabella N Castillo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jenny S Maron
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, USA
| | - Ryan P McNamara
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, USA
| | - Harry L Bertera
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, USA
| | - Mark R Zweigert
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jaclyn S Higgins
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, USA
| | - Stephanie A Montgomery
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Dallas Tissue Research, Dallas, TX, USA
| | - Victoria K Baxter
- Division of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark T Heise
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Ralph S Baric
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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39
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Allen JD, Ivory DP, Song SG, He WT, Capozzola T, Yong P, Burton DR, Andrabi R, Crispin M. The diversity of the glycan shield of sarbecoviruses related to SARS-CoV-2. Cell Rep 2023; 42:112307. [PMID: 36972173 PMCID: PMC10015101 DOI: 10.1016/j.celrep.2023.112307] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/16/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023] Open
Abstract
Animal reservoirs of sarbecoviruses represent a significant risk of emergent pandemics, as evidenced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Vaccines remain successful at limiting severe disease and death, but the potential for further coronavirus zoonosis motivates the search for pan-coronavirus vaccines. This necessitates a better understanding of the glycan shields of coronaviruses, which can occlude potential antibody epitopes on spike glycoproteins. Here, we compare the structure of 12 sarbecovirus glycan shields. Of the 22 N-linked glycan attachment sites present on SARS-CoV-2, 15 are shared by all 12 sarbecoviruses. However, there are significant differences in the processing state at glycan sites in the N-terminal domain, such as N165. Conversely, glycosylation sites in the S2 domain are highly conserved and contain a low abundance of oligomannose-type glycans, suggesting a low glycan shield density. The S2 domain may therefore provide a more attractive target for immunogen design efforts aiming to generate a pan-coronavirus antibody response.
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Affiliation(s)
- Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
| | - Dylan P Ivory
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sophie Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wan-Ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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40
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Clever S, Volz A. Mouse models in COVID-19 research: analyzing the adaptive immune response. Med Microbiol Immunol 2023; 212:165-183. [PMID: 35661253 PMCID: PMC9166226 DOI: 10.1007/s00430-022-00735-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/15/2022] [Indexed: 11/29/2022]
Abstract
The emergence of SARS-CoV-2, the severe acute respiratory syndrome coronavirus type 2 causing the COVID-19 pandemic, resulted in a major necessity for scientific countermeasures. Investigations revealing the exact mechanisms of the SARS-CoV-2 pathogenesis provide the basis for the development of therapeutic measures and protective vaccines against COVID-19. Animal models are inevitable for infection and pre-clinical vaccination studies as well as therapeutic testing. A well-suited animal model, mimicking the pathology seen in human COVID-19 patients, is an important basis for these investigations. Several animal models were already used during SARS-CoV-2 studies with different clinical outcomes after SARS-CoV-2 infection. Here, we give an overview of different animal models used in SARS-CoV-2 infection studies with a focus on the mouse model. Mice provide a well-established animal model for laboratory use and several different mouse models have been generated and are being used in SARS-CoV-2 studies. Furthermore, the analysis of SARS-CoV-2-specific T cells during infection and in vaccination studies in mice is highlighted.
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Affiliation(s)
- Sabrina Clever
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Asisa Volz
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
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Zhou P, Song G, Liu H, Yuan M, He WT, Beutler N, Zhu X, Tse LV, Martinez DR, Schäfer A, Anzanello F, Yong P, Peng L, Dueker K, Musharrafieh R, Callaghan S, Capozzola T, Limbo O, Parren M, Garcia E, Rawlings SA, Smith DM, Nemazee D, Jardine JG, Safonova Y, Briney B, Rogers TF, Wilson IA, Baric RS, Gralinski LE, Burton DR, Andrabi R. Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease. Immunity 2023; 56:669-686.e7. [PMID: 36889306 PMCID: PMC9933850 DOI: 10.1016/j.immuni.2023.02.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/10/2022] [Accepted: 02/10/2023] [Indexed: 02/18/2023]
Abstract
Pan-betacoronavirus neutralizing antibodies may hold the key to developing broadly protective vaccines against novel pandemic coronaviruses and to more effectively respond to SARS-CoV-2 variants. The emergence of Omicron and subvariants of SARS-CoV-2 illustrates the limitations of solely targeting the receptor-binding domain (RBD) of the spike (S) protein. Here, we isolated a large panel of broadly neutralizing antibodies (bnAbs) from SARS-CoV-2 recovered-vaccinated donors, which targets a conserved S2 region in the betacoronavirus spike fusion machinery. Select bnAbs showed broad in vivo protection against all three deadly betacoronaviruses, SARS-CoV-1, SARS-CoV-2, and MERS-CoV, which have spilled over into humans in the past two decades. Structural studies of these bnAbs delineated the molecular basis for their broad reactivity and revealed common antibody features targetable by broad vaccination strategies. These bnAbs provide new insights and opportunities for antibody-based interventions and for developing pan-betacoronavirus vaccines.
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Affiliation(s)
- Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wan-Ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Longping V Tse
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David R Martinez
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexandra Schäfer
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Fabio Anzanello
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Katharina Dueker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rami Musharrafieh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sean Callaghan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oliver Limbo
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elijah Garcia
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stephen A Rawlings
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Davey M Smith
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joseph G Jardine
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yana Safonova
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thomas F Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Ralph S Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Departments of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Lisa E Gralinski
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA.
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.
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Wang D, Yuan Y, Liu B, Epstein ND, Yang Y. Protein-based nano-vaccines against SARS-CoV-2: Current design strategies and advances of candidate vaccines. Int J Biol Macromol 2023; 236:123979. [PMID: 36907305 PMCID: PMC9998285 DOI: 10.1016/j.ijbiomac.2023.123979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/12/2023]
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shaken the global health system. Various nanotechnology-based strategies for vaccine development have played pivotal roles in fighting against SARS-CoV-2. Among them, the safe and effective protein-based nanoparticle (NP) platforms display a highly repetitive array of foreign antigens on their surface, which is urgent for improving the immunogenicity of vaccines. These platforms greatly improved antigen uptake by antigen presenting cells (APCs), lymph node trafficking, and B cell activation, due to the optimal size, multivalence, and versatility of NPs. In this review, we summarize the advances of protein-based NP platforms, strategies of antigen attachment, and the current progress of clinical and preclinical trials in the development of SARS-CoV-2 vaccines based on protein-based NP platforms. Importantly, the lessons learnt and design approaches developed for these NP platforms against SARS-CoV-2 also provide insights into the development of protein-based NP strategies for preventing other epidemic diseases.
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Affiliation(s)
- Dongliang Wang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; College of Biology, Hunan University, Changsha 410082, China
| | - Youqing Yuan
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Bin Liu
- College of Biology, Hunan University, Changsha 410082, China
| | - Neal D Epstein
- Cell and Developmental Biology Center, NHLBI, NIH, Bethesda, MD 20892, USA
| | - Yi Yang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China.
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Wei J, Patil A, Collings CK, Alfajaro MM, Liang Y, Cai WL, Strine MS, Filler RB, DeWeirdt PC, Hanna RE, Menasche BL, Ökten A, Peña-Hernández MA, Klein J, McNamara A, Rosales R, McGovern BL, Luis Rodriguez M, García-Sastre A, White KM, Qin Y, Doench JG, Yan Q, Iwasaki A, Zwaka TP, Qi J, Kadoch C, Wilen CB. Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection. Nat Genet 2023; 55:471-483. [PMID: 36894709 PMCID: PMC10011139 DOI: 10.1038/s41588-023-01307-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/23/2023] [Indexed: 03/11/2023]
Abstract
Identification of host determinants of coronavirus infection informs mechanisms of viral pathogenesis and can provide new drug targets. Here we demonstrate that mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) chromatin remodeling complexes, specifically canonical BRG1/BRM-associated factor (cBAF) complexes, promote severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and represent host-directed therapeutic targets. The catalytic activity of SMARCA4 is required for mSWI/SNF-driven chromatin accessibility at the ACE2 locus, ACE2 expression and virus susceptibility. The transcription factors HNF1A/B interact with and recruit mSWI/SNF complexes to ACE2 enhancers, which contain high HNF1A motif density. Notably, small-molecule mSWI/SNF ATPase inhibitors or degraders abrogate angiotensin-converting enzyme 2 (ACE2) expression and confer resistance to SARS-CoV-2 variants and a remdesivir-resistant virus in three cell lines and three primary human cell types, including airway epithelial cells, by up to 5 logs. These data highlight the role of mSWI/SNF complex activities in conferring SARS-CoV-2 susceptibility and identify a potential class of broad-acting antivirals to combat emerging coronaviruses and drug-resistant variants.
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Affiliation(s)
- Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ajinkya Patil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Clayton K Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yu Liang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Wesley L Cai
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Madison S Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Peter C DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruth E Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bridget L Menasche
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Arya Ökten
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mario A Peña-Hernández
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jon Klein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Andrew McNamara
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Briana L McGovern
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Luis Rodriguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yiren Qin
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Thomas P Zwaka
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
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A SARS-CoV-2-Related Virus from Malayan Pangolin Causes Lung Infection without Severe Disease in Human ACE2-Transgenic Mice. J Virol 2023; 97:e0171922. [PMID: 36688655 PMCID: PMC9972989 DOI: 10.1128/jvi.01719-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the most severe emerging infectious disease in the current century. The discovery of SARS-CoV-2-related coronaviruses (SARSr-CoV-2) in bats and pangolins in South Asian countries indicates that SARS-CoV-2 likely originated from wildlife. To date, two SARSr-CoV-2 strains have been isolated from pangolins seized in Guangxi and Guangdong by the customs agency of China, respectively. However, it remains unclear whether these viruses cause disease in animal models and whether they pose a transmission risk to humans. In this study, we investigated the biological features of a SARSr-CoV-2 strain isolated from a smuggled Malayan pangolin (Manis javanica) captured by the Guangxi customs agency, termed MpCoV-GX, in terms of receptor usage, cell tropism, and pathogenicity in wild-type BALB/c mice, human angiotensin-converting enzyme 2 (ACE2)-transgenic mice, and human ACE2 knock-in mice. We found that MpCoV-GX can utilize ACE2 from humans, pangolins, civets, bats, pigs, and mice for cell entry and infect cell lines derived from humans, monkeys, bats, minks, and pigs. The virus could infect three mouse models but showed limited pathogenicity, with mild peribronchial and perivascular inflammatory cell infiltration observed in lungs. Our results suggest that this SARSr-CoV-2 virus from pangolins has the potential for interspecies infection, but its pathogenicity is mild in mice. Future surveillance among these wildlife hosts of SARSr-CoV-2 is needed to monitor variants that may have higher pathogenicity and higher spillover risk. IMPORTANCE SARS-CoV-2, which likely spilled over from wildlife, is the third highly pathogenic human coronavirus. Being highly transmissible, it is perpetuating a pandemic and continuously posing a severe threat to global public health. Several SARS-CoV-2-related coronaviruses (SARSr-CoV-2) in bats and pangolins have been identified since the SARS-CoV-2 outbreak. It is therefore important to assess their potential of crossing species barriers for better understanding of their risk of future emergence. In this work, we investigated the biological features and pathogenicity of a SARSr-CoV-2 strain isolated from a smuggled Malayan pangolin, named MpCoV-GX. We found that MpCoV-GX can utilize ACE2 from 7 species for cell entry and infect cell lines derived from a variety of mammalian species. MpCoV-GX can infect mice expressing human ACE2 without causing severe disease. These findings suggest the potential of cross-species transmission of MpCoV-GX, and highlight the need of further surveillance of SARSr-CoV-2 in pangolins and other potential animal hosts.
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45
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Honrubia JM, Gutierrez-Álvarez J, Sanz-Bravo A, González-Miranda E, Muñoz-Santos D, Castaño-Rodriguez C, Wang L, Villarejo-Torres M, Ripoll-Gómez J, Esteban A, Fernandez-Delgado R, Sánchez-Cordón PJ, Oliveros JC, Perlman S, McCray PB, Sola I, Enjuanes L. SARS-CoV-2-Mediated Lung Edema and Replication Are Diminished by Cystic Fibrosis Transmembrane Conductance Regulator Modulators. mBio 2023; 14:e0313622. [PMID: 36625656 PMCID: PMC9973274 DOI: 10.1128/mbio.03136-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/01/2022] [Indexed: 01/11/2023] Open
Abstract
Coronaviruses (CoVs) of genera α, β, γ, and δ encode proteins that have a PDZ-binding motif (PBM) consisting of the last four residues of the envelope (E) protein (PBM core). PBMs may bind over 400 cellular proteins containing PDZ domains (an acronym formed by the combination of the first letter of the names of the three first proteins where this domain was identified), making them relevant for the control of cell function. Three highly pathogenic human CoVs have been identified to date: severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2. The PBMs of the three CoVs were virulence factors. SARS-CoV mutants in which the E protein PBM core was replaced by the E protein PBM core from virulent or attenuated CoVs were constructed. These mutants showed a gradient of virulence, depending on whether the alternative PBM core introduced was derived from a virulent or an attenuated CoV. Gene expression patterns in the lungs of mice infected with SARS-CoVs encoding each of the different PBMs were analyzed by RNA sequencing of infected lung tissues. E protein PBM of SARS-CoV and SARS-CoV-2 dysregulated gene expression related to ion transport and cell homeostasis. Decreased expression of cystic fibrosis transmembrane conductance regulator (CFTR) mRNA, essential for alveolar edema resolution, was shown. Reduced CFTR mRNA levels were associated with edema accumulation in the alveoli of mice infected with SARS-CoV and SARS-CoV-2. Compounds that increased CFTR expression and activity, significantly reduced SARS-CoV-2 growth in cultured cells and protected against mouse infection, suggesting that E protein virulence is mediated by a decreased CFTR expression. IMPORTANCE Three highly pathogenic human CoVs have been identified: SARS-CoV, MERS-CoV, and SARS-CoV-2. The E protein PBMs of these three CoVs were virulence factors. Gene expression patterns associated with the different PBM motifs in the lungs of infected mice were analyzed by deep sequencing. E protein PBM motif of SARS-CoV and SARS-CoV-2 dysregulated the expression of genes related to ion transport and cell homeostasis. A decrease in the mRNA expression of the cystic fibrosis transmembrane conductance regulator (CFTR), which is essential for edema resolution, was observed. The reduction of CFTR mRNA levels was associated with edema accumulation in the lungs of mice infected with SARS-CoV-2. Compounds that increased the expression and activity of CFTR drastically reduced the production of SARS-CoV-2 and protected against its infection in a mice model. These results allowed the identification of cellular targets for the selection of antivirals.
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Affiliation(s)
- Jose M. Honrubia
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Javier Gutierrez-Álvarez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Alejandro Sanz-Bravo
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Ezequiel González-Miranda
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Diego Muñoz-Santos
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Carlos Castaño-Rodriguez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Li Wang
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Marta Villarejo-Torres
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Jorge Ripoll-Gómez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Ana Esteban
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Raul Fernandez-Delgado
- Department of Infectious Diseases and Global Health, Animal Health Research Center (CISA), National Institute of Research, Agricultural and Food Technology (INIA-CSIC), Valdeolmos, Madrid, Spain
| | - Pedro José Sánchez-Cordón
- Veterinary Pathology Department, Animal Health Research Center (CISA), National Institute of Research, Agricultural and Food Technology (INIA-CSIC), Valdeolmos, Madrid, Spain
| | - Juan Carlos Oliveros
- Bioinformatics for Genomics and Proteomics Unit, CNB-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Stanley Perlman
- Department of Microbiology, University of Iowa, Iowa City, USA
- Stead Family Department of Pediatrics, The University of Iowa, Iowa City, Iowa, USA
- Interdisciplinary Program in Immunology, University of Iowa, Iowa City, USA
| | - Paul B. McCray
- Stead Family Department of Pediatrics, The University of Iowa, Iowa City, Iowa, USA
- Pappajohn Biomedical Institute, The University of Iowa, Iowa City, Iowa, USA
- Center for Gene Therapy, The University of Iowa, Iowa City, Iowa, USA
| | - Isabel Sola
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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Strategy To Assess Zoonotic Potential Reveals Low Risk Posed by SARS-Related Coronaviruses from Bat and Pangolin. mBio 2023; 14:e0328522. [PMID: 36786573 PMCID: PMC10127581 DOI: 10.1128/mbio.03285-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
In the last 2 decades, pathogens originating in animals may have triggered three coronavirus pandemics, including the coronavirus disease 2019 pandemic. Thus, evaluation of the spillover risk of animal severe acute respiratory syndrome (SARS)-related coronavirus (SARSr-CoV) is important in the context of future disease preparedness. However, there is no analytical framework to assess the spillover risk of SARSr-CoVs, which cannot be determined by sequence analysis alone. Here, we established an integrity framework to evaluate the spillover risk of an animal SARSr-CoV by testing how viruses break through key human immune barriers, including viral cell tropism, replication dynamics, interferon signaling, inflammation, and adaptive immune barriers, using human ex vivo lung tissues, human airway and nasal organoids, and human lung cells. Using this framework, we showed that the two pre-emergent animal SARSr-CoVs, bat BtCoV-WIV1 and pangolin PCoV-GX, shared similar cell tropism but exhibited less replicative fitness in the human nasal cavity or airway than did SARS-CoV-2. Furthermore, these viruses triggered fewer proinflammatory responses and less cell death, yet showed interferon antagonist activity and the ability to partially escape adaptive immune barriers to SARS-CoV-2. Collectively, these animal viruses did not fully adapt to spread or cause severe diseases, thus causing successful zoonoses in humans. We believe that this experimental framework provides a path to identifying animal coronaviruses with the potential to cause future zoonoses. IMPORTANCE Evaluation of the zoonotic risk of animal SARSr-CoVs is important for future disease preparedness. However, there are misconceptions regarding the risk of animal viruses. For example, an animal SARSr-CoV could readily infect humans. Alternately, human receptor usage may result in spillover risk. Here, we established an analytical framework to assess the zoonotic risk of SARSr-CoV by testing a series of virus-host interaction profiles. Our data showed that the pre-emergent bat BtCoV-WIV1 and pangolin PCoV-GX were less adapted to humans than SARS-CoV-2 was, suggesting that it may be extremely rare for animal SARSr-CoVs to break all bottlenecks and cause successful zoonoses.
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Shark nanobodies with potent SARS-CoV-2 neutralizing activity and broad sarbecovirus reactivity. Nat Commun 2023; 14:580. [PMID: 36737435 PMCID: PMC9896449 DOI: 10.1038/s41467-023-36106-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/13/2023] [Indexed: 02/05/2023] Open
Abstract
Despite rapid and ongoing vaccine and therapeutic development, SARS-CoV-2 continues to evolve and evade, presenting a need for next-generation diverse therapeutic modalities. Here we show that nurse sharks immunized with SARS-CoV-2 recombinant receptor binding domain (RBD), RBD-ferritin (RFN), or spike protein ferritin nanoparticle (SpFN) immunogens elicit a set of new antigen receptor antibody (IgNAR) molecules that target two non-overlapping conserved epitopes on the spike RBD. Representative shark antibody variable NAR-Fc chimeras (ShAbs) targeting either of the two epitopes mediate cell-effector functions, with high affinity to all SARS-CoV-2 viral variants of concern, including the divergent Omicron strains. The ShAbs potently cross-neutralize SARS-CoV-2 WA-1, Alpha, Beta, Delta, Omicron BA.1 and BA.5, and SARS-CoV-1 pseudoviruses, and confer protection against SARS-CoV-2 challenge in the K18-hACE2 transgenic mouse model. Structural definition of the RBD-ShAb01-ShAb02 complex enabled design and production of multi-specific nanobodies with enhanced neutralization capacity, and picomolar affinity to divergent sarbecovirus clade 1a, 1b and 2 RBD molecules. These shark nanobodies represent potent immunotherapeutics both for current use, and future sarbecovirus pandemic preparation.
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Snouwaert JN, Jania LA, Nguyen T, Martinez DR, Schäfer A, Catanzaro NJ, Gully KL, Baric RS, Heise M, Ferris MT, Anderson E, Pressey K, Dillard JA, Taft-Benz S, Baxter VK, Ting JPY, Koller BH. Human ACE2 expression, a major tropism determinant for SARS-CoV-2, is regulated by upstream and intragenic elements. PLoS Pathog 2023; 19:e1011168. [PMID: 36812267 PMCID: PMC9987828 DOI: 10.1371/journal.ppat.1011168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 03/06/2023] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2), part of the renin-angiotensin system (RAS), serves as an entry point for SARS-CoV-2, leading to viral proliferation in permissive cell types. Using mouse lines in which the Ace2 locus has been humanized by syntenic replacement, we show that regulation of basal and interferon induced ACE2 expression, relative expression levels of different ACE2 transcripts, and sexual dimorphism in ACE2 expression are unique to each species, differ between tissues, and are determined by both intragenic and upstream promoter elements. Our results indicate that the higher levels of expression of ACE2 observed in the lungs of mice relative to humans may reflect the fact that the mouse promoter drives expression of ACE2 in populous airway club cells while the human promoter drives expression in alveolar type 2 (AT2) cells. In contrast to transgenic mice in which human ACE2 is expressed in ciliated cells under the control of the human FOXJ1 promoter, mice expressing ACE2 in club cells under the control of the endogenous Ace2 promoter show a robust immune response after infection with SARS-CoV-2, leading to rapid clearance of the virus. This supports a model in which differential expression of ACE2 determines which cell types in the lung are infected, and this in turn modulates the host response and outcome of COVID-19.
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Affiliation(s)
- John N. Snouwaert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Leigh A. Jania
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Trang Nguyen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - David R. Martinez
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Alexandra Schäfer
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Nicholas J. Catanzaro
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kendra L. Gully
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ralph S. Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Mark Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Elizabeth Anderson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Katia Pressey
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jacob A. Dillard
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sharon Taft-Benz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Victoria K. Baxter
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jenny P-Y Ting
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Center for Translational Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Beverly H. Koller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
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Feng Y, Yuan M, Powers JM, Hu M, Munt JE, Arunachalam PS, Leist SR, Bellusci L, Adams LE, Sundaramurthy S, Shirreff LM, Mallory ML, Scooby TD, Moreno A, O’Hagan DT, Kleanthous H, Villinger FJ, Veesler D, King NP, Suthar MS, Khurana S, Baric RS, Wilson IA, Pulendran B. Extremely potent pan-sarbecovirus neutralizing antibodies generated by immunization of macaques with an AS03-adjuvanted monovalent subunit vaccine against SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524784. [PMID: 36711543 PMCID: PMC9882348 DOI: 10.1101/2023.01.19.524784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The rapid emergence of SARS-CoV-2 variants that evade immunity to vaccination has placed a global health imperative on the development of therapeutic countermeasures that provide broad protection against SARS-CoV-2 and related sarbecoviruses. Here, we identified extremely potent pan-sarbecovirus antibodies from non-human primates vaccinated with an AS03 adjuvanted subunit vaccine against SARS-CoV-2 that recognize conserved epitopes in the receptor binding domain (RBD) with femtomolar affinities. Longitudinal analysis revealed progressive accumulation of somatic mutation in the immunoglobulin genes of antigen-specific memory B cells for at least one year following primary vaccination. 514 monoclonal antibodies (mAbs) were generated from antigen-specific memory B cells. Antibodies isolated at 5 to 12 months following vaccination displayed greater potency and breadth, relative to those identified at 1.4 months. Notably, 15 out of 338 (∼4.4%) antibodies isolated at 1.4∼6 months after the primary vaccination showed extraordinary neutralization potency against SARS-CoV-2 omicron BA.1, despite the absence of BA.1 neutralization in serum. Two of them, 25F9 and 20A7, neutralized authentic clade Ia sarbecoviruses (SARS-CoV, WIV-1, SHC014) and clade Ib sarbecoviruses (SARS-CoV-2 D614G, SARS-CoV-2 BA.1, Pangolin-GD) with half-maximal inhibition concentrations of (0.85 ng/ml, 3 ng/ml, 6 ng/ml, 6 ng/ml, 42 ng/ml, 6 ng/ml) and (13 ng/ml, 2 ng/ml, 18 ng/ml, 9 ng/ml, 6 ng/ml, 345 ng/ml), respectively. Furthermore, 20A7 and 27A12 showed potent neutralization against all SARS-CoV-2 variants of concern and multiple Omicron sublineages, including BA.1, BA.2, BA.3, BA.4/5, BQ.1, BQ.1.1 and XBB variants. X-ray crystallography studies revealed the molecular basis of broad and potent neutralization through targeting conserved RBD sites. In vivo prophylactic protection of 25F9, 20A7 and 27A12 was confirmed in aged Balb/c mice. Notably, administration of 25F9 provided complete protection against SARS-CoV-2, SARS-CoV-2 BA.1, SARS-CoV, and SHC014 challenge, underscoring that these mAbs are promising pan-sarbecovirus therapeutic antibodies. One Sentence Summary Extremely potent pan-sarbecovirus neutralizing antibodies.
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50
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Zhou J, Liu Z, Zhang G, Xu W, Xing L, Lu L, Wang Q, Jiang S. Development of variant-proof severe acute respiratory syndrome coronavirus 2, pan-sarbecovirus, and pan-β-coronavirus vaccines. J Med Virol 2023; 95:e28172. [PMID: 36161303 PMCID: PMC9538210 DOI: 10.1002/jmv.28172] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 01/11/2023]
Abstract
The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with high transmission rates and striking immune evasion have posed a serious challenge to the application of current first-generation SARS-CoV-2 vaccines. Other sarbecoviruses, such as SARS-CoV and SARS-related coronaviruses (SARSr-CoVs), have the potential to cause outbreaks in the future. These facts call for the development of variant-proof SARS-CoV-2, pan-sarbecovirus or pan-β-CoV vaccines. Several novel vaccine platforms have been used to develop vaccines with broad-spectrum neutralizing antibody responses and protective immunity to combat the current SARS-CoV-2 and its variants, other sarbecoviruses, as well as other β-CoVs, in the future. In this review, we discussed the major target antigens and protective efficacy of current SARS-CoV-2 vaccines and summarized recent advances in broad-spectrum vaccines against sarbecoviruses and β-CoVs.
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Affiliation(s)
- Jie Zhou
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Zezhong Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
- Department of Pharmacology, School of PharmacyFudan UniversityShanghaiChina
| | - Guangxu Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Lixiao Xing
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Qian Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
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