1
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Miyakawa K, Machida M, Kawasaki T, Kakizaki M, Kimura Y, Sugiyama M, Hasegawa H, Umezawa A, Akutsu H, Ryo A. Replication Efficiency of SARS-CoV-2 Omicron Subvariants BA.2.75, BA.5, and XBB.1 in Human Mini-Gut Organoids. Cell Mol Gastroenterol Hepatol 2024; 17:1066-1068. [PMID: 38494057 PMCID: PMC11127620 DOI: 10.1016/j.jcmgh.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/19/2024]
Affiliation(s)
- Kei Miyakawa
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, Tokyo, Japan; Department of Microbiology, Yokohama City University School of Medicine, Kanagawa, Japan.
| | - Masakazu Machida
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoyuki Kawasaki
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Masatoshi Kakizaki
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Masaya Sugiyama
- Department of Viral Pathogenesis and Controls, National Center for Global Health and Medicine, Chiba, Japan
| | - Hideki Hasegawa
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan.
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Kanagawa, Japan; Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan.
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2
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Takeda M. Cleavage-Activation of Respiratory Viruses - Half a Century of History from Sendai Virus to SARS-CoV-2. Jpn J Infect Dis 2024; 77:1-6. [PMID: 38030267 DOI: 10.7883/yoken.jjid.2023.353] [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] [Indexed: 12/01/2023]
Abstract
Many viruses require the cleavage-activation of membrane fusion proteins by host proteases in the course of infection. This knowledge is based on historical studies of Sendai virus in the 1970s. From the 1970s to the 1990s, avian influenza virus and Newcastle disease virus were studied, showing a clear link between virulence and the cleavage-activation of viral membrane fusion proteins (hemagglutinin and fusion proteins) by host proteases. In these viruses, cleavage of viral membrane fusion proteins by furin is the basis for their high virulence. Subsequently, from the 2000s to the 2010s, the importance of TMPRSS2 in activating the membrane fusion proteins of various respiratory viruses, including seasonal influenza viruses, was demonstrated. In late 2019, severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) emerged and caused a pandemic. The virus continues to mutate, producing variants that have caused global pandemics. The spike protein of SARS-CoV-2 is characterized by two cleavage sites, each of which is cleaved by furin and TMPRSS2 to achieve membrane fusion. SARS-CoV-2 variants exhibit altered sensitivity to these proteases. Thus, studying the cleavage-activation of membrane fusion proteins by host proteases is critical for understanding the ongoing pandemic and developing countermeasures against it.
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Affiliation(s)
- Makoto Takeda
- Department of Microbiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Japan
- Pandemic Preparedness, Infection and Advanced Research Center, The University of Tokyo, Japan
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3
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Wang E, Yang QJ, Xu XX, Zou QC, Long Y, Ma G, Deng ZH, Zhao JB, Li MH, Zeng J. Differential pathogenic and molecular features in neurological infection of SARS-CoV-2 Omicron BA.5.2 and BA.2.75 and Delta. J Med Virol 2024; 96:e29357. [PMID: 38235532 DOI: 10.1002/jmv.29357] [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: 07/31/2023] [Revised: 11/07/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024]
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a global threat, exacerbated by the emergence of viral variants. Two variants of SARS-CoV-2, Omicron BA.2.75 and BA.5, led to global infection peaks between May 2022 and May 2023, yet their precise characteristics in pathogenesis are not well understood. In this study, we compared these two Omicron sublineages with the previously dominant Delta variant using a human angiotensin-converting enzyme 2 knock-in mouse model. As expected, Delta exhibited higher viral replication in the lung and brain than both Omicron sublineages which induced less severe lung damage and immune activation. In contrast, the Omicron variants especially BA.5.2 showed a propensity for cellular proliferation and developmental pathways. Both Delta and BA.5.2 variants, but not BA.2.75, led to decreased pulmonary lymphocytes, indicating differential adaptive immune response. Neuroinvasiveness was shared with all strains, accompanied by vascular abnormalities, synaptic injury, and loss of astrocytes. However, Immunostaining assays and transcriptomic analysis showed that BA.5.2 displayed stronger immune suppression and neurodegeneration, while BA.2.75 exhibited more similar characteristics to Delta in the cortex. Such differentially infectious features could be partially attributed to the weakened interaction between Omicron Spike protein and host proteomes decoded via co-immunoprecipitation followed by mass spectrometry in neuronal cells. Our present study supports attenuated replication and pathogenicity of Omicron variants but also highlights their newly infectious characteristics in the lung and brain, especially with BA.5.2 demonstrating enhanced immune evasion and neural damage that could exacerbate neurological sequelae.
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Affiliation(s)
- Erlin Wang
- Songjiang Research Institute, Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qiao-Jiang Yang
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiang-Xiong Xu
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qing-Cui Zou
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yanghaopeng Long
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Guanqin Ma
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhong-Hua Deng
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jie-Bin Zhao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ming-Hua Li
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jianxiong Zeng
- Songjiang Research Institute, Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, China
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4
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Uraki R, Kiso M, Iwatsuki-Horimoto K, Yamayoshi S, Ito M, Chiba S, Sakai-Tagawa Y, Imai M, Kashima Y, Koga M, Fuwa N, Okumura N, Hojo M, Iwamoto N, Kato H, Nakajima H, Ohmagari N, Yotsuyanagi H, Suzuki Y, Kawaoka Y. Characterization of a SARS-CoV-2 EG.5.1 clinical isolate in vitro and in vivo. Cell Rep 2023; 42:113580. [PMID: 38103202 DOI: 10.1016/j.celrep.2023.113580] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/24/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
EG.5.1 is a subvariant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron XBB variant that is rapidly increasing in prevalence worldwide. However, the pathogenicity, transmissibility, and immune evasion properties of isolates of EG.5.1 are largely unknown. Here, we show that there are no obvious differences in growth ability and pathogenicity between EG.5.1 and XBB.1.5 in hamsters. We also demonstrate that, like XBB.1.5, EG.5.1 is transmitted more efficiently between hamsters compared to its predecessor, BA.2. In contrast, unlike XBB.1.5, we detect EG.5.1 in the lungs of four of six exposed hamsters, suggesting that the virus properties of EG.5.1 are different from those of XBB.1.5. Finally, we find that the neutralizing activity of plasma from convalescent individuals against EG.5.1 was slightly, but significantly, lower than that against XBB.1.5 or XBB.1.9.2. Our data suggest that the different virus properties after transmission and the altered antigenicity of EG.5.1 may be driving its increasing prevalence over XBB.1.5 in humans.
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Affiliation(s)
- Ryuta Uraki
- Division of Virology, 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
| | - Maki Kiso
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | | | - Seiya Yamayoshi
- Division of Virology, 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
| | - Mutsumi Ito
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Shiho Chiba
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yuko Sakai-Tagawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Masaki Imai
- Division of Virology, 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
| | - Yukie Kashima
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
| | - Michiko Koga
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Noriko Fuwa
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo 162-8655, Japan
| | - Nobumasa Okumura
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo 162-8655, Japan
| | - Masayuki Hojo
- Department of Respiratory Medicine, National Center for Global Health and Medicine Hospital, Tokyo 162-8655, Japan
| | - Noriko Iwamoto
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo 162-8655, Japan
| | - Hideaki Kato
- Department of Hematology and Clinical Immunology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan; Infection Prevention and Control Department, Yokohama City University Hospital, Kanagawa 236-0004, Japan
| | - Hideaki Nakajima
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Kanagawa 236-0004, Japan
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo 162-8655, Japan
| | - Hiroshi Yotsuyanagi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, 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; Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), The University of Tokyo, Tokyo 108-8639, Japan.
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5
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Lee B, Ko JH, Kim YC, Baek JY, Park YS, Song KH, Kim ES, Lee KH, Song YG, Ahn JY, Choi JY, Choi WS, Bae S, Kim SH, Jeong HW, Lee YJ, Kim HJ, Choi JY, Kim B, Kim SW, Kwon KT, Peck KR, Kang ES. Clinical utility of quantitative immunoassays and surrogate virus neutralization tests for predicting neutralizing activity against the SARS-CoV-2 Omicron BA.1 and BA.5 variants. J Med Virol 2023; 95:e29329. [PMID: 38140877 DOI: 10.1002/jmv.29329] [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: 08/16/2023] [Revised: 11/13/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023]
Abstract
Developing new antibody assays for emerging SARS-CoV-2 variants is challenging. SARS-CoV-2 surrogate virus neutralization tests (sVNT) targeting Omicron BA.1 and BA.5 have been devised, but their performance needs to be validated in comparison with quantitative immunoassays. First, using 1749 PRNT-positive sera, we noticed that log-transformed optical density (OD) ratio of wild-type (WT) sVNT exhibited better titer-correlation with plaque reduction neutralization test (PRNT) than % inhibition value. Second, we tried 798 dilutional titration tests with 103 sera, but nonlinear correlation between OD ratio and antibody concentration limited titration of sVNT. Third, the titer-correlations of two sVNT kits for BA.1 and two quantitative immunoassays for WT were evaluated with BA.1 and BA.5 PRNT. All tested kits exhibited a linear correlation with PRNT titers, but the sVNT kits exhibited high false-negative rates (cPass-BA.1 kit, 45.4% for BA.1 and 44.2% for BA.5; STANDARD F-BA.1 kit, 1.9% for BA.1 and 2.2% for BA.5), while quantitative immunoassays showed 100% sensitivity. Linear mixed-effects model suggested superior titer-correlation with PRNT for quantitative immunoassays compared to sVNT kits. Taken together, the use of quantitative immunoassays for WT, rather than rapid development of new kits, would be practical for predicting neutralizing activities against emerging new variants.
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Affiliation(s)
- Beomki Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Jae-Hoon Ko
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Yong Chan Kim
- Division of Infectious Diseases, Department of Internal Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin, South Korea
| | - Jin Yang Baek
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
- Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, South Korea
| | - Yoon Soo Park
- Division of Infectious Diseases, Department of Internal Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin, South Korea
| | - Kyoung-Ho Song
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Eu Suk Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Kyoung Hwa Lee
- Division of Infectious Diseases, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Young Goo Song
- Division of Infectious Diseases, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Jin Young Ahn
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Jun Yong Choi
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Won Suk Choi
- Division of Infectious Diseases, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, South Korea
| | - Seongman Bae
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Hye Won Jeong
- Department of Internal Medicine, Chungbuk National University College of Medicine, Cheongju, South Korea
| | - Young Jae Lee
- Division of Vaccine Clinical Research, Center for Vaccine Research, National Institute of Infectious Diseases, Korea National Institute of Health, Cheongju, South Korea
| | - Hye-Jin Kim
- Division of Vaccine Clinical Research, Center for Vaccine Research, National Institute of Infectious Diseases, Korea National Institute of Health, Cheongju, South Korea
| | - Ju-Yeon Choi
- Division of Vaccine Clinical Research, Center for Vaccine Research, National Institute of Infectious Diseases, Korea National Institute of Health, Cheongju, South Korea
| | - Byoungguk Kim
- Division of Vaccine Clinical Research, Center for Vaccine Research, National Institute of Infectious Diseases, Korea National Institute of Health, Cheongju, South Korea
| | - Shin-Woo Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Ki Tae Kwon
- Division of Infectious Diseases, Department of Internal Medicine, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Eun-Suk Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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6
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Condor Capcha JM, Kamiar A, Robleto E, Saad AG, Cui T, Wong A, Villano J, Zhong W, Pekosz A, Medina E, Cai R, Sha W, Ranek MJ, Webster KA, Schally AV, Jackson RM, Shehadeh LA. Growth hormone-releasing hormone receptor antagonist MIA-602 attenuates cardiopulmonary injury induced by BSL-2 rVSV-SARS-CoV-2 in hACE2 mice. Proc Natl Acad Sci U S A 2023; 120:e2308342120. [PMID: 37983492 PMCID: PMC10691341 DOI: 10.1073/pnas.2308342120] [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: 05/25/2023] [Accepted: 09/07/2023] [Indexed: 11/22/2023] Open
Abstract
COVID-19 pneumonia causes acute lung injury and acute respiratory distress syndrome (ALI/ARDS) characterized by early pulmonary endothelial and epithelial injuries with altered pulmonary diffusing capacity and obstructive or restrictive physiology. Growth hormone-releasing hormone receptor (GHRH-R) is expressed in the lung and heart. GHRH-R antagonist, MIA-602, has been reported to modulate immune responses to bleomycin lung injury and inflammation in granulomatous sarcoidosis. We hypothesized that MIA-602 would attenuate rVSV-SARS-CoV-2-induced pulmonary dysfunction and heart injury in a BSL-2 mouse model. Male and female K18-hACE2tg mice were inoculated with SARS-CoV-2/USA-WA1/2020, BSL-2-compliant recombinant VSV-eGFP-SARS-CoV-2-Spike (rVSV-SARS-CoV-2), or PBS, and lung viral load, weight loss, histopathology, and gene expression were compared. K18-hACE2tg mice infected with rVSV-SARS-CoV-2 were treated daily with subcutaneous MIA-602 or vehicle and conscious, unrestrained plethysmography performed on days 0, 3, and 5 (n = 7 to 8). Five days after infection mice were killed, and blood and tissues collected for histopathology and protein/gene expression. Both native SARS-CoV-2 and rVSV-SARS-CoV-2 presented similar patterns of weight loss, infectivity (~60%), and histopathologic changes. Daily treatment with MIA-602 conferred weight recovery, reduced lung perivascular inflammation/pneumonia, and decreased lung/heart ICAM-1 expression compared to vehicle. MIA-602 rescued altered respiratory rate, increased expiratory parameters (Te, PEF, EEP), and normalized airflow parameters (Penh and Rpef) compared to vehicle, consistent with decreased airway inflammation. RNASeq followed by protein analysis revealed heightened levels of inflammation and end-stage necroptosis markers, including ZBP1 and pMLKL induced by rVSV-SARS-CoV-2, that were normalized by MIA-602 treatment, consistent with an anti-inflammatory and pro-survival mechanism of action in this preclinical model of COVID-19 pneumonia.
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Affiliation(s)
- Jose M. Condor Capcha
- Department of Medicine, Division of Cardiology, University of Miami Leonard M. Miller School of Medicine, Miami, FL33136
- Interdisciplinary Stem Cell Institute, University of Miami Leonard M. Miller School of Medicine, Miami, FL33136
| | - Ali Kamiar
- Department of Medicine, Division of Cardiology, University of Miami Leonard M. Miller School of Medicine, Miami, FL33136
- Interdisciplinary Stem Cell Institute, University of Miami Leonard M. Miller School of Medicine, Miami, FL33136
| | - Emely Robleto
- Department of Medicine, Division of Cardiology, University of Miami Leonard M. Miller School of Medicine, Miami, FL33136
- Interdisciplinary Stem Cell Institute, University of Miami Leonard M. Miller School of Medicine, Miami, FL33136
| | - Ali G. Saad
- Department of Pathology, University of Miami Leonard M. Miller School of Medicine, Miami, FL33136
| | - Tengjiao Cui
- Research Service, Miami Veterans Affairs Health System (VAHS), Miami, FL33125
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Miami Miller School of Medicine, Miami, FL33101
| | - Amanda Wong
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University, Baltimore, MD21205
| | - Jason Villano
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University, Baltimore, MD21205
| | - William Zhong
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD21205
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD21205
| | - Edgar Medina
- Qualityminds Gesellschaft mit beschränkter Haftung (GmbH), Munchen, Munich81549, Germany
| | - Renzhi Cai
- Interdisciplinary Stem Cell Institute, University of Miami Leonard M. Miller School of Medicine, Miami, FL33136
- Research Service, Miami Veterans Affairs Health System (VAHS), Miami, FL33125
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Miami Miller School of Medicine, Miami, FL33101
| | - Wei Sha
- Research Service, Miami Veterans Affairs Health System (VAHS), Miami, FL33125
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Miami Miller School of Medicine, Miami, FL33101
| | - Mark J. Ranek
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD21205
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD21205
| | - Keith A. Webster
- Integene International Holdings, Miami, FL33179
- Baylor College of Medicine, Houston, TX77030
| | - Andrew V. Schally
- Interdisciplinary Stem Cell Institute, University of Miami Leonard M. Miller School of Medicine, Miami, FL33136
- Research Service, Miami Veterans Affairs Health System (VAHS), Miami, FL33125
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Miami Miller School of Medicine, Miami, FL33101
| | - Robert M. Jackson
- Research Service, Miami Veterans Affairs Health System (VAHS), Miami, FL33125
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Miami Miller School of Medicine, Miami, FL33101
| | - Lina A. Shehadeh
- Department of Medicine, Division of Cardiology, University of Miami Leonard M. Miller School of Medicine, Miami, FL33136
- Interdisciplinary Stem Cell Institute, University of Miami Leonard M. Miller School of Medicine, Miami, FL33136
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7
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Meehan GR, Herder V, Allan J, Huang X, Kerr K, Mendonca DC, Ilia G, Wright DW, Nomikou K, Gu Q, Molina Arias S, Hansmann F, Hardas A, Attipa C, De Lorenzo G, Cowton V, Upfold N, Palmalux N, Brown JC, Barclay WS, Filipe ADS, Furnon W, Patel AH, Palmarini M. Phenotyping the virulence of SARS-CoV-2 variants in hamsters by digital pathology and machine learning. PLoS Pathog 2023; 19:e1011589. [PMID: 37934791 PMCID: PMC10656012 DOI: 10.1371/journal.ppat.1011589] [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: 07/31/2023] [Revised: 11/17/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to evolve throughout the coronavirus disease-19 (COVID-19) pandemic, giving rise to multiple variants of concern (VOCs) with different biological properties. As the pandemic progresses, it will be essential to test in near real time the potential of any new emerging variant to cause severe disease. BA.1 (Omicron) was shown to be attenuated compared to the previous VOCs like Delta, but it is possible that newly emerging variants may regain a virulent phenotype. Hamsters have been proven to be an exceedingly good model for SARS-CoV-2 pathogenesis. Here, we aimed to develop robust quantitative pipelines to assess the virulence of SARS-CoV-2 variants in hamsters. We used various approaches including RNAseq, RNA in situ hybridization, immunohistochemistry, and digital pathology, including software assisted whole section imaging and downstream automatic analyses enhanced by machine learning, to develop methods to assess and quantify virus-induced pulmonary lesions in an unbiased manner. Initially, we used Delta and Omicron to develop our experimental pipelines. We then assessed the virulence of recent Omicron sub-lineages including BA.5, XBB, BQ.1.18, BA.2, BA.2.75 and EG.5.1. We show that in experimentally infected hamsters, accurate quantification of alveolar epithelial hyperplasia and macrophage infiltrates represent robust markers for assessing the extent of virus-induced pulmonary pathology, and hence virus virulence. In addition, using these pipelines, we could reveal how some Omicron sub-lineages (e.g., BA.2.75 and EG.5.1) have regained virulence compared to the original BA.1. Finally, to maximise the utility of the digital pathology pipelines reported in our study, we developed an online repository containing representative whole organ histopathology sections that can be visualised at variable magnifications (https://covid-atlas.cvr.gla.ac.uk). Overall, this pipeline can provide unbiased and invaluable data for rapidly assessing newly emerging variants and their potential to cause severe disease.
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Affiliation(s)
- Gavin R. Meehan
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Vanessa Herder
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Jay Allan
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Xinyi Huang
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Karen Kerr
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Diogo Correa Mendonca
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Georgios Ilia
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Derek W. Wright
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Sergi Molina Arias
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Florian Hansmann
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Germany
| | - Alexandros Hardas
- Department of Pathobiology & Population Sciences, The Royal Veterinary College, North Mymms, United Kingdom
| | - Charalampos Attipa
- The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, United Kingdom
| | | | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Nicole Upfold
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Jonathan C. Brown
- Department of Infectious Disease, Imperial College London, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, United Kingdom
| | | | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
- CVR-CRUSH, MRC-University of Glasgow Centre for Virus Research, United Kingdom
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8
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Mohandas S, Shete A, Kumar A, Wakchaure K, Rai V, Mote C, Dighe H, Sarkale P, Gawande P, Yemul J, Suryawanshi A, Joshi Y, Yadav PD. Comparative pathogenicity of BA.2.12, BA.5.2 and XBB.1 with the Delta variant in Syrian hamsters. Front Microbiol 2023; 14:1183763. [PMID: 37426033 PMCID: PMC10325568 DOI: 10.3389/fmicb.2023.1183763] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/02/2023] [Indexed: 07/11/2023] Open
Abstract
Omicron variant is evolving into numerous sub variants with time and the information on the characteristics of these newly evolving variants are scant. Here we performed a pathogenicity evaluation of Omicron sub variants BA.2.12, BA.5.2 and XBB.1 against the Delta variant in 6-8-week-old Syrian hamster model. Body weight change, viral load in respiratory organs by real time RT-PCR/titration, cytokine mRNA quantification and histopathological evaluation of the lungs were performed. The intranasal infection of the BA.2.12, BA.5.2 and XBB.1 variants in hamster model resulted in body weight loss/reduced weight gain, inflammatory cytokine response and interstitial pneumonia with lesser severity compared to the Delta variant infection. Among the variants studied, BA.2.12 and XBB.1 showed lesser viral shedding through the upper respiratory tract, whereas the BA.5.2 showed comparable viral RNA shedding as that of the Delta variant. The study shows that the Omicron BA.2 sub variants may show difference in disease severity and transmissibility amongst each other whereas the overall disease severity of the Omicron sub variants studied were less compared to the Delta variant. The evolving Omicron sub variants and recombinants should be monitored for their properties.
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Affiliation(s)
- Sreelekshmy Mohandas
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Anita Shete
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Abhimanyu Kumar
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Kundan Wakchaure
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Vishal Rai
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Chandrasekhar Mote
- Department of Veterinary Pathology, Krantisinh Nana Patil College of Veterinary Science, Shirwal, Maharashtra, India
| | - Hitesh Dighe
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Prasad Sarkale
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Pranita Gawande
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Jyoti Yemul
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Annasaheb Suryawanshi
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Yash Joshi
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Pragya D. Yadav
- Maximum Containment Facility, ICMR-National Institute of Virology, Pune, Maharashtra, India
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