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Zheng T, Shen B, Bai Y, Li E, Zhang X, Hu Y, Gao T, Dong Q, Zhu L, Jin R, Shi H, Liu H, Gao Y, Liu X, Cao C. The PKA-CREB1 axis regulates coronavirus proliferation by viral helicase nsp13 association. J Virol 2024; 98:e0156523. [PMID: 38445884 PMCID: PMC11019953 DOI: 10.1128/jvi.01565-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/09/2024] [Indexed: 03/07/2024] Open
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a worldwide threat in the past 3 years. Although it has been widely and intensively investigated, the mechanism underlying the coronavirus-host interaction requires further elucidation, which may contribute to the development of new antiviral strategies. Here, we demonstrated that the host cAMP-responsive element-binding protein (CREB1) interacts with the non-structural protein 13 (nsp13) of SARS-CoV-2, a conserved helicase for coronavirus replication, both in cells and in lung tissues subjected to SARS-CoV-2 infection. The ATPase and helicase activity of viral nsp13 were shown to be potentiated by CREB1 association, as well as by Protein kinase A (PKA)-mediated CREB1 activation. SARS-CoV-2 replication is significantly suppressed by PKA Cα, cAMP-activated protein kinase catalytic subunit alpha (PRKACA), and CREB1 knockdown or inhibition. Consistently, the CREB1 inhibitor 666-15 has shown significant antiviral effects against both the WIV04 strain and the Omicron strain of the SARS-CoV-2. Our findings indicate that the PKA-CREB1 signaling axis may serve as a novel therapeutic target against coronavirus infection. IMPORTANCE In this study, we provide solid evidence that host transcription factor cAMP-responsive element-binding protein (CREB1) interacts directly with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) helicase non-structural protein 13 (nsp13) and potentiate its ATPase and helicase activity. And by live SARS-CoV-2 virus infection, the inhibition of CREB1 dramatically impairs SARS-CoV-2 replication in vivo. Notably, the IC50 of CREB1 inhibitor 666-15 is comparable to that of remdesivir. These results may extend to all highly pathogenic coronaviruses due to the conserved nsp13 sequences in the virus.
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Affiliation(s)
- Tong Zheng
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Beilei Shen
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yu Bai
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China
| | - Entao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Xun Zhang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China
| | - Yong Hu
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Ting Gao
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Qincai Dong
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Lin Zhu
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Rui Jin
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Hui Shi
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Hainan Liu
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Yuwei Gao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xuan Liu
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Cheng Cao
- Genetic Engineering Research Laboratory, Beijing Institute of Biotechnology, Beijing, China
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2
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Li J, Gui Q, Liang FX, Sall J, Zhang Q, Duan Y, Dhabaria A, Askenazi M, Ueberheide B, Stapleford KA, Pagano M. The REEP5/TRAM1 complex binds SARS-CoV-2 NSP3 and promotes virus replication. J Virol 2023; 97:e0050723. [PMID: 37768083 PMCID: PMC10617467 DOI: 10.1128/jvi.00507-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Generation of virus-host protein-protein interactions (PPIs) maps may provide clues to uncover SARS-CoV-2-hijacked cellular processes. However, these PPIs maps were created by expressing each viral protein singularly, which does not reflect the life situation in which certain viral proteins synergistically interact with host proteins. Our results reveal the host-viral protein-protein interactome of SARS-CoV-2 NSP3, NSP4, and NSP6 expressed individually or in combination. Furthermore, REEP5/TRAM1 complex interacts with NSP3 at ROs and promotes viral replication. The significance of our research is identifying virus-host interactions that may be targeted for therapeutic intervention.
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Affiliation(s)
- Jie Li
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Qi Gui
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Feng-Xia Liang
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
| | - Joseph Sall
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
| | - Qingyue Zhang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Yatong Duan
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- William A. Shine Great Neck South High School, Lake Success, New York, USA
| | - Avantika Dhabaria
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
| | - Manor Askenazi
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Biomedical Hosting LLC, Arlington, Massachusetts, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, New York, USA
| | - Kenneth A. Stapleford
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, New York, USA
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3
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Zhao Y, Sui L, Wu P, Li L, Liu L, Ma B, Wang W, Chi H, Wang ZD, Wei Z, Hou Z, Zhang K, Niu J, Jin N, Li C, Zhao J, Wang G, Liu Q. EGR1 functions as a new host restriction factor for SARS-CoV-2 to inhibit virus replication through the E3 ubiquitin ligase MARCH8. J Virol 2023; 97:e0102823. [PMID: 37772822 PMCID: PMC10653994 DOI: 10.1128/jvi.01028-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/13/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE Emerging vaccine-breakthrough severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants highlight an urgent need for novel antiviral therapies. Understanding the pathogenesis of coronaviruses is critical for developing antiviral drugs. Here, we demonstrate that the SARS-CoV-2 N protein suppresses interferon (IFN) responses by reducing early growth response gene-1 (EGR1) expression. The overexpression of EGR1 inhibits SARS-CoV-2 replication by promoting IFN-regulated antiviral protein expression, which interacts with and degrades SARS-CoV-2 N protein via the E3 ubiquitin ligase MARCH8 and the cargo receptor NDP52. The MARCH8 mutants without ubiquitin ligase activity are no longer able to degrade SARS-CoV-2 N proteins, indicating that MARCH8 degrades SARS-CoV-2 N proteins dependent on its ubiquitin ligase activity. This study found a novel immune evasion mechanism of SARS-CoV-2 utilized by the N protein, which is helpful for understanding the pathogenesis of SARS-CoV-2 and guiding the design of new prevention strategies against the emerging coronaviruses.
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Affiliation(s)
- Yinghua Zhao
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Liyan Sui
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Ping Wu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Letian Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Li Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Baohua Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Wenfang Wang
- Department of Pathogenbiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, China
| | - Hongmiao Chi
- Department of Pathogenbiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, China
| | - Ze-Dong Wang
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Zhengkai Wei
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Zhijun Hou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Kaiyu Zhang
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Junqi Niu
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Ningyi Jin
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Chang Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jixue Zhao
- Department of Pediatric Surgery, The First Hospital of Jilin University, Changchun, China
| | - Guoqing Wang
- Department of Pathogenbiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, China
| | - Quan Liu
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- School of Life Sciences and Engineering, Foshan University, Foshan, China
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
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4
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Duan Y, Zhou H, Liu X, Iketani S, Lin M, Zhang X, Bian Q, Wang H, Sun H, Hong SJ, Culbertson B, Mohri H, Luck MI, Zhu Y, Liu X, Lu Y, Yang X, Yang K, Sabo Y, Chavez A, Goff SP, Rao Z, Ho DD, Yang H. Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature 2023; 622:376-382. [PMID: 37696289 DOI: 10.1038/s41586-023-06609-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 09/05/2023] [Indexed: 09/13/2023]
Abstract
Nirmatrelvir is a specific antiviral drug that targets the main protease (Mpro) of SARS-CoV-2 and has been approved to treat COVID-191,2. As an RNA virus characterized by high mutation rates, whether SARS-CoV-2 will develop resistance to nirmatrelvir is a question of concern. Our previous studies have shown that several mutational pathways confer resistance to nirmatrelvir, but some result in a loss of viral replicative fitness, which is then compensated for by additional alterations3. The molecular mechanisms for this observed resistance are unknown. Here we combined biochemical and structural methods to demonstrate that alterations at the substrate-binding pocket of Mpro can allow SARS-CoV-2 to develop resistance to nirmatrelvir in two distinct ways. Comprehensive studies of the structures of 14 Mpro mutants in complex with drugs or substrate revealed that alterations at the S1 and S4 subsites substantially decreased the level of inhibitor binding, whereas alterations at the S2 and S4' subsites unexpectedly increased protease activity. Both mechanisms contributed to nirmatrelvir resistance, with the latter compensating for the loss in enzymatic activity of the former, which in turn accounted for the restoration of viral replicative fitness, as observed previously3. Such a profile was also observed for ensitrelvir, another clinically relevant Mpro inhibitor. These results shed light on the mechanisms by which SARS-CoV-2 evolves to develop resistance to the current generation of protease inhibitors and provide the basis for the design of next-generation Mpro inhibitors.
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Affiliation(s)
- Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Hao Zhou
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Xiang Liu
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Mengmeng Lin
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Xiaoyu Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
- Lingang Laboratory, Shanghai, China
| | - Qucheng Bian
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Haofeng Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Haoran Sun
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Seo Jung Hong
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Bruce Culbertson
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Medical Scientist Training Program, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Hiroshi Mohri
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Maria I Luck
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yan Zhu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Xiaoce Liu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Yuchi Lu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
- Lingang Laboratory, Shanghai, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Kailin Yang
- Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Yosef Sabo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stephen P Goff
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
- Innovation Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
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5
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Zhang Y, Zhang L, Wu J, Yu Y, Liu S, Li T, Li Q, Ding R, Wang H, Nie J, Cui Z, Wang Y, Huang W, Wang Y. A second functional furin site in the SARS-CoV-2 spike protein. Emerg Microbes Infect 2022; 11:182-194. [PMID: 34856891 PMCID: PMC8741242 DOI: 10.1080/22221751.2021.2014284] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The ubiquitously-expressed proteolytic enzyme furin is closely related to the pathogenesis of SARS-CoV-2 and therefore represents a key target for antiviral therapy. Based on bioinformatic analysis and pseudovirus tests, we discovered a second functional furin site located in the spike protein. Furin still increased the infectivity of mutated SARS-CoV-2 pseudovirus in 293T-ACE2 cells when the canonical polybasic cleavage site (682-686) was deleted. However, K814A mutation eliminated the enhancing effect of furin on virus infection. Furin inhibitor prevented infection by 682-686-deleted SARS-CoV-2 in 293T-ACE2-furin cells, but not the K814A mutant. K814A mutation did not affect the activity of TMPRSS2 and cathepsin L but did impact the cleavage of S2 into S2' and cell-cell fusion. Additionally, we showed that this functional furin site exists in RaTG13 from bat and PCoV-GD/GX from pangolin. Therefore, we discovered a new functional furin site that is pivotal in promoting SARS-CoV-2 infection.
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Affiliation(s)
- Yue Zhang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
- National Vaccine & Serum Institute, Beijing, People's Republic of China
| | - Li Zhang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Jiajing Wu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Yuanling Yu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Shuo Liu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Tao Li
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Qianqian Li
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Ruxia Ding
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Haixin Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Jianhui Nie
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Zhimin Cui
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Yulin Wang
- National Vaccine & Serum Institute, Beijing, People's Republic of China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
- Lead Contact
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6
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McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, Ji X, Raghwani J, Jackson B, Colquhoun R, O'Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R, Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, Kraemer MUG. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature 2022; 610:154-160. [PMID: 35952712 PMCID: PMC9534748 DOI: 10.1038/s41586-022-05200-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 08/05/2022] [Indexed: 02/01/2023]
Abstract
The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide1,2. The emergence of the Delta variant in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 SARS-CoV-2 genomes from England together with 93,649 genomes from the rest of the world to reconstruct the emergence of Delta and quantify its introduction to and regional dissemination across England in the context of changing travel and social restrictions. Using analysis of human movement, contact tracing and virus genomic data, we find that the geographic focus of the expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced more than 1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers reduced onward transmission from importations; however, the transmission chains that later dominated the Delta wave in England were seeded before travel restrictions were introduced. Increasing inter-regional travel within England drove the nationwide dissemination of Delta, with some cities receiving more than 2,000 observable lineage introductions from elsewhere. Subsequently, increased levels of local population mixing-and not the number of importations-were associated with the faster relative spread of Delta. The invasion dynamics of Delta depended on spatial heterogeneity in contact patterns, and our findings will inform optimal spatial interventions to reduce the transmission of current and future variants of concern, such as Omicron (Pango lineage B.1.1.529).
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Affiliation(s)
- John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Sumali Bajaj
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Ben C Lambert
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
| | - Rhys Inward
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Erik Volz
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | | | - Neo Wu
- Google, Mountain View, CA, USA
| | | | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | | | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- UK Health Security Agency, London, UK
| | | | | | | | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | - Isaac I Bogoch
- Divisions of Internal Medicine and Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Kamran Khan
- BlueDot, Toronto, Ontario, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Ontario, Canada
| | - Louis du Plessis
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Thomas Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK
- Quadram Institute, Norwich, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Marc A Suchard
- Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK.
- Pandemic Sciences Institute, University of Oxford, Oxford, UK.
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK.
- Pandemic Sciences Institute, University of Oxford, Oxford, UK.
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7
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MacLachlan R, Vahedi F, Imani SM, Ashkar AA, Didar TF, Soleymani L. Pathogen-Repellent Plastic Warp with Built-In Hierarchical Structuring Prevents the Contamination of Surfaces with Coronaviruses. ACS Appl Mater Interfaces 2022; 14:11068-11077. [PMID: 35225604 PMCID: PMC8903211 DOI: 10.1021/acsami.1c21476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Amidst the COVID-19 pandemic, it is evident that viral spread is mediated through several different transmission pathways. Reduction of these transmission pathways is urgently needed to control the spread of viruses between infected and susceptible individuals. Herein, we report the use of pathogen-repellent plastic wraps (RepelWrap) with engineered surface structures at multiple length scales (nanoscale to microscale) as a means of reducing the indirect contact transmission of viruses through fomites. To quantify viral repellency, we developed a touch-based viral quantification assay to mimic the interaction of a contaminated human touch with a surface through the modification of traditional viral quantification methods (viral plaque and TCID50 assays). These studies demonstrate that RepelWrap reduced contamination with an enveloped DNA virus as well as the human coronavirus 229E (HuCoV-229E) by more than 4 log 10 (>99.99%) compared to a standard commercially available polyethylene plastic wrap. In addition, RepelWrap maintained its repellent properties after repeated 300 touches and did not show an accumulation in viral titer after multiple contacts with contaminated surfaces, while increases were seen on other commonly used surfaces. These findings show the potential use of repellent surfaces in reducing viral contamination on surfaces, which could, in turn, reduce the surface-based spread and transmission.
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Affiliation(s)
- Roderick MacLachlan
- Department
of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
| | - Fatemeh Vahedi
- Department
of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
| | - Sara M. Imani
- School
of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
| | - Ali A. Ashkar
- Department
of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
- McMaster
Immunology Research Center, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
| | - Tohid F. Didar
- School
of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
- Department
of Mechanical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4L7, Canada
- Michael G.
DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | - Leyla Soleymani
- Department
of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
- School
of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
- Michael G.
DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
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8
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Bates TA, McBride SK, Leier HC, Guzman G, Lyski ZL, Schoen D, Winders B, Lee JY, Lee DX, Messer WB, Curlin ME, Tafesse FG. Vaccination before or after SARS-CoV-2 infection leads to robust humoral response and antibodies that effectively neutralize variants. Sci Immunol 2022; 7:eabn8014. [PMID: 35076258 PMCID: PMC8939472 DOI: 10.1126/sciimmunol.abn8014] [Citation(s) in RCA: 175] [Impact Index Per Article: 87.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/19/2022] [Indexed: 12/18/2022]
Abstract
Current coronavirus disease 2019 (COVID-19) vaccines effectively reduce overall morbidity and mortality and are vitally important to controlling the pandemic. Individuals who previously recovered from COVID-19 have enhanced immune responses after vaccination (hybrid immunity) compared with their naïve-vaccinated peers; however, the effects of post-vaccination breakthrough infections on humoral immune response remain to be determined. Here, we measure neutralizing antibody responses from 104 vaccinated individuals, including those with breakthrough infections, hybrid immunity, and no infection history. We find that human immune sera after breakthrough infection and vaccination after natural infection broadly neutralize SARS-CoV-2 (severe acute respiratory coronavirus 2) variants to a similar degree. Although age negatively correlates with antibody response after vaccination alone, no correlation with age was found in breakthrough or hybrid immune groups. Together, our data suggest that the additional antigen exposure from natural infection substantially boosts the quantity, quality, and breadth of humoral immune response regardless of whether it occurs before or after vaccination.
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Affiliation(s)
- Timothy A. Bates
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
| | - Savannah K. McBride
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
| | - Hans C. Leier
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
| | - Gaelen Guzman
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
| | - Zoe L. Lyski
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
| | - Devin Schoen
- Division of Infectious Diseases, Oregon Health & Science University; Portland, OR 97239, United States
| | - Bradie Winders
- Division of Infectious Diseases, Oregon Health & Science University; Portland, OR 97239, United States
| | - Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - David Xthona Lee
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
| | - William B. Messer
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
- Division of Infectious Diseases, Oregon Health & Science University; Portland, OR 97239, United States
- OHSU-PSU School of Public Health, Oregon Health & Science University; Portland, OR 97239, United States
| | - Marcel E. Curlin
- Division of Infectious Diseases, Oregon Health & Science University; Portland, OR 97239, United States
| | - Fikadu G. Tafesse
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University; Portland, OR 97239, United States
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9
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Dulovic A, Kessel B, Harries M, Becker M, Ortmann J, Griesbaum J, Jüngling J, Junker D, Hernandez P, Gornyk D, Glöckner S, Melhorn V, Castell S, Heise JK, Kemmling Y, Tonn T, Frank K, Illig T, Klopp N, Warikoo N, Rath A, Suckel C, Marzian AU, Grupe N, Kaiser PD, Traenkle B, Rothbauer U, Kerrinnes T, Krause G, Lange B, Schneiderhan-Marra N, Strengert M. Comparative Magnitude and Persistence of Humoral SARS-CoV-2 Vaccination Responses in the Adult Population in Germany. Front Immunol 2022; 13:828053. [PMID: 35251012 PMCID: PMC8888837 DOI: 10.3389/fimmu.2022.828053] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/17/2022] [Indexed: 12/01/2022] Open
Abstract
Recent increases in SARS-CoV-2 infections have led to questions about duration and quality of vaccine-induced immune protection. While numerous studies have been published on immune responses triggered by vaccination, these often focus on studying the impact of one or two immunisation schemes within subpopulations such as immunocompromised individuals or healthcare workers. To provide information on the duration and quality of vaccine-induced immune responses against SARS-CoV-2, we analyzed antibody titres against various SARS-CoV-2 antigens and ACE2 binding inhibition against SARS-CoV-2 wild-type and variants of concern in samples from a large German population-based seroprevalence study (MuSPAD) who had received all currently available immunisation schemes. We found that homologous mRNA-based or heterologous prime-boost vaccination produced significantly higher antibody responses than vector-based homologous vaccination. Ad26.CoV2S.2 performance was particularly concerning with reduced titres and 91.7% of samples classified as non-responsive for ACE2 binding inhibition, suggesting that recipients require a booster mRNA vaccination. While mRNA vaccination induced a higher ratio of RBD- and S1-targeting antibodies, vector-based vaccines resulted in an increased proportion of S2-targeting antibodies. Given the role of RBD- and S1-specific antibodies in neutralizing SARS-CoV-2, their relative over-representation after mRNA vaccination may explain why these vaccines have increased efficacy compared to vector-based formulations. Previously infected individuals had a robust immune response once vaccinated, regardless of which vaccine they received, which could aid future dose allocation should shortages arise for certain manufacturers. Overall, both titres and ACE2 binding inhibition peaked approximately 28 days post-second vaccination and then decreased.
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Affiliation(s)
- Alex Dulovic
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Barbora Kessel
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Manuela Harries
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Matthias Becker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Julia Ortmann
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Johanna Griesbaum
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Jennifer Jüngling
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Daniel Junker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Pilar Hernandez
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Daniela Gornyk
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stephan Glöckner
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Vanessa Melhorn
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefanie Castell
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jana-Kristin Heise
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Yvonne Kemmling
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Torsten Tonn
- German Red Cross Blood Donation Service North East, Dresden, Germany
| | - Kerstin Frank
- German Red Cross Blood Donation Service North East, Dresden, Germany
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Norman Klopp
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Neha Warikoo
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Angelika Rath
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Christina Suckel
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Anne Ulrike Marzian
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Nicole Grupe
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Philipp D. Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
- Pharmaceutical Biotechnology, Department of Pharmacy and Biochemistry, University of Tübingen, Tübingen, Germany
| | - Tobias Kerrinnes
- Department of RNA-Biology of Bacterial Infections, Helmholtz Institute for RNA-Based Infection Research, Würzburg, Germany
| | - Gérard Krause
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Berit Lange
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | | | - Monika Strengert
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
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10
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Bamford CGG, Broadbent L, Aranday-Cortes E, McCabe M, McKenna J, Courtney DG, Touzelet O, Ali A, Roberts G, Lopez Campos G, Simpson D, McCaughey C, Fairley D, Mills K, Power UF. Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Viruses 2022; 14:325. [PMID: 35215919 PMCID: PMC8877208 DOI: 10.3390/v14020325] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 can efficiently infect both children and adults, albeit with morbidity and mortality positively associated with increasing host age and presence of co-morbidities. SARS-CoV-2 continues to adapt to the human population, resulting in several variants of concern (VOC) with novel properties, such as Alpha and Delta. However, factors driving SARS-CoV-2 fitness and evolution in paediatric cohorts remain poorly explored. Here, we provide evidence that both viral and host factors co-operate to shape SARS-CoV-2 genotypic and phenotypic change in primary airway cell cultures derived from children. Through viral whole-genome sequencing, we explored changes in genetic diversity over time of two pre-VOC clinical isolates of SARS-CoV-2 during passage in paediatric well-differentiated primary nasal epithelial cell (WD-PNEC) cultures and in parallel, in unmodified Vero-derived cell lines. We identified a consistent, rich genetic diversity arising in vitro, variants of which could rapidly rise to near fixation within two passages. Within isolates, SARS-CoV-2 evolution was dependent on host cells, with paediatric WD-PNECs showing a reduced diversity compared to Vero (E6) cells. However, mutations were not shared between strains. Furthermore, comparison of both Vero-grown isolates on WD-PNECs disclosed marked growth attenuation mapping to the loss of the polybasic cleavage site (PBCS) in Spike, while the strain with mutations in Nsp12 (T293I), Spike (P812R) and a truncation of Orf7a remained viable in WD-PNECs. Altogether, our work demonstrates that pre-VOC SARS-CoV-2 efficiently infects paediatric respiratory epithelial cells, and its evolution is restrained compared to Vero (E6) cells, similar to the case of adult cells. We highlight the significant genetic plasticity of SARS-CoV-2 while uncovering an influential role for collaboration between viral and host cell factors in shaping viral evolution and ultimately fitness in human respiratory epithelium.
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Affiliation(s)
- Connor G. G. Bamford
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (L.B.); (M.M.); (D.G.C.); (O.T.); (A.A.); (G.R.); (G.L.C.); (D.S.)
| | - Lindsay Broadbent
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (L.B.); (M.M.); (D.G.C.); (O.T.); (A.A.); (G.R.); (G.L.C.); (D.S.)
| | - Elihu Aranday-Cortes
- Medical Research Council-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK;
| | - Mary McCabe
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (L.B.); (M.M.); (D.G.C.); (O.T.); (A.A.); (G.R.); (G.L.C.); (D.S.)
| | - James McKenna
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast BT12 6BA, UK; (J.M.); (C.M.); (D.F.)
| | - David G. Courtney
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (L.B.); (M.M.); (D.G.C.); (O.T.); (A.A.); (G.R.); (G.L.C.); (D.S.)
| | - Olivier Touzelet
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (L.B.); (M.M.); (D.G.C.); (O.T.); (A.A.); (G.R.); (G.L.C.); (D.S.)
| | - Ahlam Ali
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (L.B.); (M.M.); (D.G.C.); (O.T.); (A.A.); (G.R.); (G.L.C.); (D.S.)
- Patrick G. Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK;
| | - Grace Roberts
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (L.B.); (M.M.); (D.G.C.); (O.T.); (A.A.); (G.R.); (G.L.C.); (D.S.)
| | - Guillermo Lopez Campos
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (L.B.); (M.M.); (D.G.C.); (O.T.); (A.A.); (G.R.); (G.L.C.); (D.S.)
| | - David Simpson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (L.B.); (M.M.); (D.G.C.); (O.T.); (A.A.); (G.R.); (G.L.C.); (D.S.)
| | - Conall McCaughey
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast BT12 6BA, UK; (J.M.); (C.M.); (D.F.)
| | - Derek Fairley
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast BT12 6BA, UK; (J.M.); (C.M.); (D.F.)
| | - Ken Mills
- Patrick G. Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK;
| | - Ultan F. Power
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (L.B.); (M.M.); (D.G.C.); (O.T.); (A.A.); (G.R.); (G.L.C.); (D.S.)
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11
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Yoshida M, Worlock KB, Huang N, Lindeboom RGH, Butler CR, Kumasaka N, Dominguez Conde C, Mamanova L, Bolt L, Richardson L, Polanski K, Madissoon E, Barnes JL, Allen-Hyttinen J, Kilich E, Jones BC, de Wilton A, Wilbrey-Clark A, Sungnak W, Pett JP, Weller J, Prigmore E, Yung H, Mehta P, Saleh A, Saigal A, Chu V, Cohen JM, Cane C, Iordanidou A, Shibuya S, Reuschl AK, Herczeg IT, Argento AC, Wunderink RG, Smith SB, Poor TA, Gao CA, Dematte JE, Reynolds G, Haniffa M, Bowyer GS, Coates M, Clatworthy MR, Calero-Nieto FJ, Göttgens B, O'Callaghan C, Sebire NJ, Jolly C, De Coppi P, Smith CM, Misharin AV, Janes SM, Teichmann SA, Nikolić MZ, Meyer KB. Local and systemic responses to SARS-CoV-2 infection in children and adults. Nature 2022; 602:321-327. [PMID: 34937051 PMCID: PMC8828466 DOI: 10.1038/s41586-021-04345-x] [Citation(s) in RCA: 147] [Impact Index Per Article: 73.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 12/14/2021] [Indexed: 02/03/2023]
Abstract
It is not fully understood why COVID-19 is typically milder in children1-3. Here, to examine the differences between children and adults in their response to SARS-CoV-2 infection, we analysed paediatric and adult patients with COVID-19 as well as healthy control individuals (total n = 93) using single-cell multi-omic profiling of matched nasal, tracheal, bronchial and blood samples. In the airways of healthy paediatric individuals, we observed cells that were already in an interferon-activated state, which after SARS-CoV-2 infection was further induced especially in airway immune cells. We postulate that higher paediatric innate interferon responses restrict viral replication and disease progression. The systemic response in children was characterized by increases in naive lymphocytes and a depletion of natural killer cells, whereas, in adults, cytotoxic T cells and interferon-stimulated subpopulations were significantly increased. We provide evidence that dendritic cells initiate interferon signalling in early infection, and identify epithelial cell states associated with COVID-19 and age. Our matching nasal and blood data show a strong interferon response in the airways with the induction of systemic interferon-stimulated populations, which were substantially reduced in paediatric patients. Together, we provide several mechanisms that explain the milder clinical syndrome observed in children.
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Affiliation(s)
- Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
- Division of Respiratory Diseases, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Ni Huang
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Colin R Butler
- NIHR Great Ormond Street BRC and UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | | | | | | | - Liam Bolt
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Elo Madissoon
- Wellcome Sanger Institute, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Josephine L Barnes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Eliz Kilich
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Brendan C Jones
- NIHR Great Ormond Street BRC and UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Angus de Wilton
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | | | | | | | | | - Henry Yung
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Puja Mehta
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Aarash Saleh
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Anita Saigal
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Vivian Chu
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Jonathan M Cohen
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Clare Cane
- Royal Free Hospital NHS Foundation Trust, London, UK
| | | | - Soichi Shibuya
- NIHR Great Ormond Street BRC and UCL Institute of Child Health, London, UK
| | - Ann-Kathrin Reuschl
- UCL Division of Infection and Immunity, University College London, London, UK
| | - Iván T Herczeg
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - A Christine Argento
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sean B Smith
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Taylor A Poor
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Catherine A Gao
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jane E Dematte
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Gary Reynolds
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Matthew Coates
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Berthold Göttgens
- Wellcome, MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Christopher O'Callaghan
- NIHR Great Ormond Street BRC and UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Neil J Sebire
- NIHR Great Ormond Street BRC and UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Clare Jolly
- UCL Division of Infection and Immunity, University College London, London, UK
| | - Paolo De Coppi
- NIHR Great Ormond Street BRC and UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Claire M Smith
- NIHR Great Ormond Street BRC and UCL Institute of Child Health, London, UK
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sam M Janes
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK.
- University College London Hospitals NHS Foundation Trust, London, UK.
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Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, Bischof ML, Obernier K, Braberg H, Soucheray M, Richards A, Chen KH, Harjai B, Memon D, Hiatt J, Rosales R, McGovern BL, Jahun A, Fabius JM, White K, Goodfellow IG, Takeuchi Y, Bonfanti P, Shokat K, Jura N, Verba K, Noursadeghi M, Beltrao P, Kellis M, Swaney DL, García-Sastre A, Jolly C, Towers GJ, Krogan NJ. Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature 2022; 602:487-495. [PMID: 34942634 PMCID: PMC8850198 DOI: 10.1038/s41586-021-04352-y] [Citation(s) in RCA: 175] [Impact Index Per Article: 87.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/14/2021] [Indexed: 11/09/2022]
Abstract
The emergence of SARS-CoV-2 variants of concern suggests viral adaptation to enhance human-to-human transmission1,2. Although much effort has focused on the characterization of changes in the spike protein in variants of concern, mutations outside of spike are likely to contribute to adaptation. Here, using unbiased abundance proteomics, phosphoproteomics, RNA sequencing and viral replication assays, we show that isolates of the Alpha (B.1.1.7) variant3 suppress innate immune responses in airway epithelial cells more effectively than first-wave isolates. We found that the Alpha variant has markedly increased subgenomic RNA and protein levels of the nucleocapsid protein (N), Orf9b and Orf6-all known innate immune antagonists. Expression of Orf9b alone suppressed the innate immune response through interaction with TOM70, a mitochondrial protein that is required for activation of the RNA-sensing adaptor MAVS. Moreover, the activity of Orf9b and its association with TOM70 was regulated by phosphorylation. We propose that more effective innate immune suppression, through enhanced expression of specific viral antagonist proteins, increases the likelihood of successful transmission of the Alpha variant, and may increase in vivo replication and duration of infection4. The importance of mutations outside the spike coding region in the adaptation of SARS-CoV-2 to humans is underscored by the observation that similar mutations exist in the N and Orf9b regulatory regions of the Delta and Omicron variants.
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Affiliation(s)
- Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
| | - Mehdi Bouhaddou
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | | | - Lorena Zuliani-Alvarez
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Ben Polacco
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Adrian Pelin
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jyoti Batra
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, London, UK
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Andrea Fossati
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Roberta Ragazzini
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manisha Ummadi
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Ajda Rojc
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jane Turner
- Division of Infection and Immunity, University College London, London, UK
| | - Marie L Bischof
- Division of Infection and Immunity, University College London, London, UK
| | - Kirsten Obernier
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Hannes Braberg
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Soucheray
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alicia Richards
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kuei-Ho Chen
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bhavya Harjai
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Joseph Hiatt
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and 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 and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aminu Jahun
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Jacqueline M Fabius
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kris White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Yasu Takeuchi
- Division of Infection and Immunity, University College London, London, UK
| | - Paola Bonfanti
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Kevan Shokat
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Natalia Jura
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Division of Advanced Therapies, National Institute for Biological Standards and Control, South Mimms, UK
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Klim Verba
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Pedro Beltrao
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Danielle L Swaney
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, 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
| | - Clare Jolly
- Division of Infection and Immunity, University College London, London, UK.
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK.
| | - Nevan J Krogan
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- J. David Gladstone Institutes, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
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13
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Yan W, Zheng Y, Zeng X, He B, Cheng W. Structural biology of SARS-CoV-2: open the door for novel therapies. Signal Transduct Target Ther 2022; 7:26. [PMID: 35087058 PMCID: PMC8793099 DOI: 10.1038/s41392-022-00884-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/08/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent of the pandemic disease COVID-19, which is so far without efficacious treatment. The discovery of therapy reagents for treating COVID-19 are urgently needed, and the structures of the potential drug-target proteins in the viral life cycle are particularly important. SARS-CoV-2, a member of the Orthocoronavirinae subfamily containing the largest RNA genome, encodes 29 proteins including nonstructural, structural and accessory proteins which are involved in viral adsorption, entry and uncoating, nucleic acid replication and transcription, assembly and release, etc. These proteins individually act as a partner of the replication machinery or involved in forming the complexes with host cellular factors to participate in the essential physiological activities. This review summarizes the representative structures and typically potential therapy agents that target SARS-CoV-2 or some critical proteins for viral pathogenesis, providing insights into the mechanisms underlying viral infection, prevention of infection, and treatment. Indeed, these studies open the door for COVID therapies, leading to ways to prevent and treat COVID-19, especially, treatment of the disease caused by the viral variants are imperative.
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Affiliation(s)
- Weizhu Yan
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Yanhui Zheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Xiaotao Zeng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Bin He
- Department of Emergency Medicine, West China Hospital of Sichuan University, 610041, Chengdu, China.
- The First People's Hospital of Longquanyi District Chengdu, 610100, Chengdu, China.
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China.
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14
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Lavilla Olleros C, Ausín García C, Bendala Estrada AD, Muñoz A, Wikman Jogersen PE, Fernández Cruz A, Giner Galvañ V, Vargas JA, Seguí Ripoll JM, Rubio-Rivas M, Miranda Godoy R, Mérida Rodrigo L, Fonseca Aizpuru E, Arnalich Fernández F, Artero A, Loureiro Amigo J, García García GM, Corral Gudino L, Jiménez Torres J, Casas-Rojo JM, Millán Núñez-Cortés J. Use of glucocorticoids megadoses in SARS-CoV-2 infection in a spanish registry: SEMI-COVID-19. PLoS One 2022; 17:e0261711. [PMID: 35061713 PMCID: PMC8782507 DOI: 10.1371/journal.pone.0261711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 12/07/2021] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE To describe the impact of different doses of corticosteroids on the evolution of patients with COVID-19 pneumonia, based on the potential benefit of the non-genomic mechanism of these drugs at higher doses. METHODS Observational study using data collected from the SEMI-COVID-19 Registry. We evaluated the epidemiological, radiological and analytical scenario between patients treated with megadoses therapy of corticosteroids vs low-dose of corticosteroids and the development of complications. The primary endpoint was all-cause in-hospital mortality according to use of corticosteroids megadoses. RESULTS Of a total of 14,921 patients, corticosteroids were used in 5,262 (35.3%). Of them, 2,216 (46%) specifically received megadoses. Age was a factor that differed between those who received megadoses therapy versus those who did not in a significant manner (69 years [IQR 59-79] vs 73 years [IQR 61-83]; p < .001). Radiological and analytical findings showed a higher use of megadoses therapy among patients with an interstitial infiltrate and elevated inflammatory markers associated with COVID-19. In the univariate study it appears that steroid use is associated with increased mortality (OR 2.07 95% CI 1.91-2.24 p < .001) and megadose use with increased survival (OR 0.84 95% CI 0.75-0.96, p 0.011), but when adjusting for possible confounding factors, it is observed that the use of megadoses is also associated with higher mortality (OR 1.54, 95% CI 1.32-1.80; p < .001). There is no difference between megadoses and low-dose (p .298). Although, there are differences in the use of megadoses versus low-dose in terms of complications, mainly infectious, with fewer pneumonias and sepsis in the megadoses group (OR 0.82 95% CI 0.71-0.95; p < .001 and OR 0.80 95% CI 0.65-0.97; p < .001) respectively. CONCLUSION There is no difference in mortality with megadoses versus low-dose, but there is a lower incidence of infectious complications with glucocorticoid megadoses.
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Affiliation(s)
| | - Cristina Ausín García
- General Internal Medicine Department, Hospital Universitario Gregorio Marañón, Madrid, Spain
| | | | - Ana Muñoz
- General Internal Medicine Department, Infanta Cristina Hospital: Hospital Universitario Infanta 2 Cristina, Parla-Madrid, Spain
| | - Philip Erick Wikman Jogersen
- General Internal Medicine Department, Hospital Universitario San Juan de Alicante, San Juan de Alicante-Alicante, Spain
| | - Ana Fernández Cruz
- General Internal Medicine Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Vicente Giner Galvañ
- General Internal Medicine Department, Hospital Universitario San Juan de Alicante, San Juan de Alicante-Alicante, Spain
| | - Juan Antonio Vargas
- General Internal Medicine Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - José Miguel Seguí Ripoll
- General Internal Medicine Department, Hospital Universitario San Juan de Alicante, San Juan de Alicante-Alicante, Spain
| | - Manuel Rubio-Rivas
- General Internal Medicine Department, H. Univ. de Bellvitge, L’Hospitalet de Llobregat, Barcelona, Spain
| | - Rodrigo Miranda Godoy
- General Internal Medicine Department, 12th of October University Hospital: Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | - Eva Fonseca Aizpuru
- General Internal Medicine Department, Hospital de Cabueñes: Hospital de Cabuenes, Gijón, Spain
| | | | - Arturo Artero
- General Internal Medicine Department, Hospital Universitario Dr Peset: Hospital Universitario Doctor Peset, Valencia, Spain
| | - Jose Loureiro Amigo
- General Internal Medicine Department, Hospital de Sant Joan Despí Moisès Broggi: Hospital de Sant Joan Despi Moises Broggi, Barcelona, Spain
| | - Gema María García García
- General Internal Medicine Department, University Hospital Complex Badajoz: Complejo Hospitalario Universitario de Badajoz, Badajoz, Spain
| | | | - Jose Jiménez Torres
- General Internal Medicine Department, Hospital Reina Sofía: Hospital Reina Sofia, Córdoba, Madrid, Spain
| | - José-Manuel Casas-Rojo
- General Internal Medicine Department, Infanta Cristina Hospital: Hospital Universitario Infanta Cristina, Parla-Madrid, Spain
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15
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Liu QH, Zhang J, Peng C, Litvinova M, Huang S, Poletti P, Trentini F, Guzzetta G, Marziano V, Zhou T, Viboud C, Bento AI, Lv J, Vespignani A, Merler S, Yu H, Ajelli M. Model-based evaluation of alternative reactive class closure strategies against COVID-19. Nat Commun 2022; 13:322. [PMID: 35031600 PMCID: PMC8760266 DOI: 10.1038/s41467-021-27939-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 12/17/2021] [Indexed: 01/10/2023] Open
Abstract
There are contrasting results concerning the effect of reactive school closure on SARS-CoV-2 transmission. To shed light on this controversy, we developed a data-driven computational model of SARS-CoV-2 transmission. We found that by reactively closing classes based on syndromic surveillance, SARS-CoV-2 infections are reduced by no more than 17.3% (95%CI: 8.0-26.8%), due to the low probability of timely identification of infections in the young population. We thus investigated an alternative triggering mechanism based on repeated screening of students using antigen tests. Depending on the contribution of schools to transmission, this strategy can greatly reduce COVID-19 burden even when school contribution to transmission and immunity in the population is low. Moving forward, the adoption of antigen-based screenings in schools could be instrumental to limit COVID-19 burden while vaccines continue to be rolled out.
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Affiliation(s)
- Quan-Hui Liu
- College of Computer Science, Sichuan University, Chengdu, China
| | - Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Cheng Peng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Maria Litvinova
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Shudong Huang
- College of Computer Science, Sichuan University, Chengdu, China
| | - Piero Poletti
- Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy
| | - Filippo Trentini
- Dondena Centre for Research on Social Dynamics and Public Policy, Bocconi University, Milan, Italy
| | - Giorgio Guzzetta
- Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy
| | | | - Tao Zhou
- Big Data Research Center, University of Electronic Science and Technology of China, Chengdu, China
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Ana I Bento
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Jiancheng Lv
- College of Computer Science, Sichuan University, Chengdu, China
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Stefano Merler
- Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.
| | - Marco Ajelli
- Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA.
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16
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Sarma U, Ghosh B. Country-specific optimization strategy for testing through contact tracing can help maintain a low reproduction number ([Formula: see text]) during unlock. Sci Rep 2022; 12:212. [PMID: 34996937 PMCID: PMC8742011 DOI: 10.1038/s41598-021-03846-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 12/02/2021] [Indexed: 12/14/2022] Open
Abstract
In response to the COVID19 pandemic, many countries have implemented lockdowns in multiple phases to ensure social distancing and quarantining of the infected subjects. Subsequent unlocks to reopen the economies started next waves of infection and imposed an extra burden on quarantine to keep the reproduction number ([Formula: see text]) < 1. However, most countries could not effectively contain the infection spread, suggesting identification of the potential sources weakening the effect of lockdowns could help design better informed lockdown-unlock cycles in the future. Here, through building quantitative epidemic models and analyzing the metadata of 50 countries from across the continents we first found that the estimated value of [Formula: see text], adjusted w.r.t the distribution of medical facilities and virus clades correlates strongly with the testing rates in a country. Since the testing capacity of a country is limited by its medical resources, we investigated if a cost-benefit trade-off can be designed connecting testing rate and extent of unlocking. We present a strategy to optimize this trade-off in a country specific manner by providing a quantitative estimate of testing and quarantine rates required to allow different extents of unlocks while aiming to maintain [Formula: see text]. We further show that a small fraction of superspreaders can dramatically increase the number of infected individuals even during strict lockdowns by strengthening the positive feedback loop driving infection spread. Harnessing the benefit of optimized country-specific testing rates would critically require minimizing the movement of these superspreaders via strict social distancing norms, such that the positive feedback driven switch-like exponential spread phase of infection can be avoided/delayed.
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Affiliation(s)
- Uddipan Sarma
- Vantage Research, Sivasamy St, CIT Colony, Mylapore, Chennai, Tamil Nadu 600004 India
| | - Bhaswar Ghosh
- Center for Computational Natural Sciences, International Institute of Information Technology, Hyderabad, 500032 India
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17
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Swadling L, Diniz MO, Schmidt NM, Amin OE, Chandran A, Shaw E, Pade C, Gibbons JM, Le Bert N, Tan AT, Jeffery-Smith A, Tan CCS, Tham CYL, Kucykowicz S, Aidoo-Micah G, Rosenheim J, Davies J, Johnson M, Jensen MP, Joy G, McCoy LE, Valdes AM, Chain BM, Goldblatt D, Altmann DM, Boyton RJ, Manisty C, Treibel TA, Moon JC, van Dorp L, Balloux F, McKnight Á, Noursadeghi M, Bertoletti A, Maini MK. Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2. Nature 2022; 601:110-117. [PMID: 34758478 PMCID: PMC8732273 DOI: 10.1038/s41586-021-04186-8] [Citation(s) in RCA: 229] [Impact Index Per Article: 114.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/27/2021] [Indexed: 12/15/2022]
Abstract
Individuals with potential exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) do not necessarily develop PCR or antibody positivity, suggesting that some individuals may clear subclinical infection before seroconversion. T cells can contribute to the rapid clearance of SARS-CoV-2 and other coronavirus infections1-3. Here we hypothesize that pre-existing memory T cell responses, with cross-protective potential against SARS-CoV-2 (refs. 4-11), would expand in vivo to support rapid viral control, aborting infection. We measured SARS-CoV-2-reactive T cells, including those against the early transcribed replication-transcription complex (RTC)12,13, in intensively monitored healthcare workers (HCWs) who tested repeatedly negative according to PCR, antibody binding and neutralization assays (seronegative HCWs (SN-HCWs)). SN-HCWs had stronger, more multispecific memory T cells compared with a cohort of unexposed individuals from before the pandemic (prepandemic cohort), and these cells were more frequently directed against the RTC than the structural-protein-dominated responses observed after detectable infection (matched concurrent cohort). SN-HCWs with the strongest RTC-specific T cells had an increase in IFI27, a robust early innate signature of SARS-CoV-2 (ref. 14), suggesting abortive infection. RNA polymerase within RTC was the largest region of high sequence conservation across human seasonal coronaviruses (HCoV) and SARS-CoV-2 clades. RNA polymerase was preferentially targeted (among the regions tested) by T cells from prepandemic cohorts and SN-HCWs. RTC-epitope-specific T cells that cross-recognized HCoV variants were identified in SN-HCWs. Enriched pre-existing RNA-polymerase-specific T cells expanded in vivo to preferentially accumulate in the memory response after putative abortive compared to overt SARS-CoV-2 infection. Our data highlight RTC-specific T cells as targets for vaccines against endemic and emerging Coronaviridae.
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Affiliation(s)
- Leo Swadling
- Division of Infection and Immunity, University College London, London, UK.
| | - Mariana O Diniz
- Division of Infection and Immunity, University College London, London, UK
| | - Nathalie M Schmidt
- Division of Infection and Immunity, University College London, London, UK
| | - Oliver E Amin
- Division of Infection and Immunity, University College London, London, UK
| | - Aneesh Chandran
- Division of Infection and Immunity, University College London, London, UK
| | - Emily Shaw
- Division of Infection and Immunity, University College London, London, UK
| | - Corinna Pade
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Joseph M Gibbons
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Nina Le Bert
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore, Singapore
| | - Anthony T Tan
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore, Singapore
| | - Anna Jeffery-Smith
- Division of Infection and Immunity, University College London, London, UK
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, London, UK
| | - Christine Y L Tham
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore, Singapore
| | | | | | - Joshua Rosenheim
- Division of Infection and Immunity, University College London, London, UK
| | - Jessica Davies
- Division of Infection and Immunity, University College London, London, UK
| | - Marina Johnson
- Great Ormond Street Institute of Child Health NIHR Biomedical Research Centre, University College London, London, UK
| | - Melanie P Jensen
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
- Department of Cellular Pathology, Northwest London Pathology, Imperial College London NHS Trust, London, UK
| | - George Joy
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
- Institute of Cardiovascular Science, University College London, London, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Ana M Valdes
- Academic Rheumatology, Clinical Sciences, Nottingham City Hospital, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Benjamin M Chain
- Division of Infection and Immunity, University College London, London, UK
| | - David Goldblatt
- Great Ormond Street Institute of Child Health NIHR Biomedical Research Centre, University College London, London, UK
| | - Daniel M Altmann
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Rosemary J Boyton
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Lung Division, Royal Brompton & Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Charlotte Manisty
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
- Institute of Cardiovascular Science, University College London, London, UK
| | - Thomas A Treibel
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
- Institute of Cardiovascular Science, University College London, London, UK
| | - James C Moon
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
- Institute of Cardiovascular Science, University College London, London, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | | | - Áine McKnight
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Antonio Bertoletti
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore, Singapore
- Singapore Immunology Network, A*STAR, Singapore, Singapore
| | - Mala K Maini
- Division of Infection and Immunity, University College London, London, UK.
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18
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Abdelnabi R, Foo CS, Zhang X, Lemmens V, Maes P, Slechten B, Raymenants J, André E, Weynand B, Dallmeier K, Neyts J. The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. Antiviral Res 2022; 198:105253. [PMID: 35066015 PMCID: PMC8776349 DOI: 10.1016/j.antiviral.2022.105253] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 02/05/2023]
Abstract
The emergence of SARS-CoV-2 variants of concern (VoCs) has exacerbated the COVID-19 pandemic. End of November 2021, a new SARS-CoV-2 variant namely the omicron (B.1.1.529) emerged. Since this omicron variant is heavily mutated in the spike protein, WHO classified this variant as the 5th variant of concern (VoC). We previously demonstrated that the ancestral strain and the other SARS-CoV-2 VoCs replicate efficiently in and cause a COVID19-like pathology in Syrian hamsters. We here wanted to explore the infectivity of the omicron variant in comparison to the ancestral D614G strain in the hamster model. Strikingly, in hamsters that had been infected with the omicron variant, a 3 log10 lower viral RNA load was detected in the lungs as compared to animals infected with D614G and no infectious virus was detectable in this organ. Moreover, histopathological examination of the lungs from omicron-infected hamsters revealed no signs of peri-bronchial inflammation or bronchopneumonia. End of Nov 2021, WHO classified the omicron variant as a variant of concern. The omicron SARS-CoV-2 variant does not replicate in Syrian hamsters lungs. There are no signs of COVID19-like pathology in lungs of omicron-infected hamsters.
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Affiliation(s)
- Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
| | - Caroline S Foo
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
| | - Xin Zhang
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
| | - Viktor Lemmens
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium; Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Department of Microbiology, Immunology and Transplantation, 3000, Leuven, Belgium; Zoonotic Infectious Diseases Unit, Leuven, Belgium
| | - Bram Slechten
- Department of Laboratory Medicine, UZ Leuven Hospital, 3000, Leuven, Belgium
| | - Joren Raymenants
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium
| | - Emmanuel André
- Department of Laboratory Medicine, UZ Leuven Hospital, 3000, Leuven, Belgium; Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium
| | - Birgit Weynand
- KU Leuven Department of Imaging and Pathology, Translational Cell and Tissue Research, Division of Translational Cell and Tissue Research, B-3000, Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium; Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium; Global Virus Network, GVN, Leuven, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium; Molecular Vaccinology and Vaccine Discovery, Leuven, Belgium; Global Virus Network, GVN, Leuven, Belgium.
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19
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Mediouni S, Mou H, Otsuka Y, Jablonski JA, Adcock RS, Batra L, Chung DH, Rood C, de Vera IMS, Rahaim R, Ullah S, Yu X, Getmanenko YA, Kennedy NM, Wang C, Nguyen TT, Hull M, Chen E, Bannister TD, Baillargeon P, Scampavia L, Farzan M, Valente ST, Spicer TP. Identification of potent small molecule inhibitors of SARS-CoV-2 entry. SLAS Discov 2022; 27:8-19. [PMID: 35058179 PMCID: PMC8577999 DOI: 10.1016/j.slasd.2021.10.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 responsible for COVID-19 remains a persistent threat to mankind, especially for the immunocompromised and elderly for which the vaccine may have limited effectiveness. Entry of SARS-CoV-2 requires a high affinity interaction of the viral spike protein with the cellular receptor angiotensin-converting enzyme 2. Novel mutations on the spike protein correlate with the high transmissibility of new variants of SARS-CoV-2, highlighting the need for small molecule inhibitors of virus entry into target cells. We report the identification of such inhibitors through a robust high-throughput screen testing 15,000 small molecules from unique libraries. Several leads were validated in a suite of mechanistic assays, including whole cell SARS-CoV-2 infectivity assays. The main lead compound, calpeptin, was further characterized using SARS-CoV-1 and the novel SARS-CoV-2 variant entry assays, SARS-CoV-2 protease assays and molecular docking. This study reveals calpeptin as a potent and specific inhibitor of SARS-CoV-2 and some variants.
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Affiliation(s)
- Sonia Mediouni
- Scripps Research, Department of Immunology and Microbiology, Scripps Research, Jupiter, FL 33458, USA
| | - Huihui Mou
- Scripps Research, Department of Immunology and Microbiology, Scripps Research, Jupiter, FL 33458, USA
| | - Yuka Otsuka
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Joseph Anthony Jablonski
- Scripps Research, Department of Immunology and Microbiology, Scripps Research, Jupiter, FL 33458, USA
| | - Robert Scott Adcock
- Center for Predictive Medicine, Department of Microbiology Immunology, School of Medicine, University of Louisville, KY 40202, USA
| | - Lalit Batra
- Center for Predictive Medicine, Department of Microbiology Immunology, School of Medicine, University of Louisville, KY 40202, USA
| | - Dong-Hoon Chung
- Center for Predictive Medicine, Department of Microbiology Immunology, School of Medicine, University of Louisville, KY 40202, USA
| | - Christopher Rood
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Ian Mitchelle S de Vera
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Ronald Rahaim
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Sultan Ullah
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Xuerong Yu
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Yulia A Getmanenko
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Nicole M Kennedy
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Chao Wang
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Tu-Trinh Nguyen
- CALIBR, Scripps Research, 11119N Torrey Pines Rd, La Jolla, CA 9203, USA
| | - Mitchell Hull
- CALIBR, Scripps Research, 11119N Torrey Pines Rd, La Jolla, CA 9203, USA
| | - Emily Chen
- CALIBR, Scripps Research, 11119N Torrey Pines Rd, La Jolla, CA 9203, USA
| | - Thomas D Bannister
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Pierre Baillargeon
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Louis Scampavia
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Michael Farzan
- Scripps Research, Department of Immunology and Microbiology, Scripps Research, Jupiter, FL 33458, USA
| | - Susana T Valente
- Scripps Research, Department of Immunology and Microbiology, Scripps Research, Jupiter, FL 33458, USA
| | - Timothy P Spicer
- Scripps Research, Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.
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20
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Madden PJ, Arif MS, Becker ME, McRaven MD, Carias AM, Lorenzo-Redondo R, Xiao S, Midkiff CC, Blair RV, Potter EL, Martin-Sancho L, Dodson A, Martinelli E, Todd JPM, Villinger FJ, Chanda SK, Aye PP, Roy CJ, Roederer M, Lewis MG, Veazey RS, Hope TJ. Development of an In Vivo Probe to Track SARS-CoV-2 Infection in Rhesus Macaques. Front Immunol 2021; 12:810047. [PMID: 35003140 PMCID: PMC8739270 DOI: 10.3389/fimmu.2021.810047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/10/2021] [Indexed: 01/02/2023] Open
Abstract
Infection with the novel coronavirus, SARS-CoV-2, results in pneumonia and other respiratory symptoms as well as pathologies at diverse anatomical sites. An outstanding question is whether these diverse pathologies are due to replication of the virus in these anatomical compartments and how and when the virus reaches those sites. To answer these outstanding questions and study the spatiotemporal dynamics of SARS-CoV-2 infection a method for tracking viral spread in vivo is needed. We developed a novel, fluorescently labeled, antibody-based in vivo probe system using the anti-spike monoclonal antibody CR3022 and demonstrated that it could successfully identify sites of SARS-CoV-2 infection in a rhesus macaque model of COVID-19. Our results showed that the fluorescent signal from our antibody-based probe could differentiate whole lungs of macaques infected for 9 days from those infected for 2 or 3 days. Additionally, the probe signal corroborated the frequency and density of infected cells in individual tissue blocks from infected macaques. These results provide proof of concept for the use of in vivo antibody-based probes to study SARS-CoV-2 infection dynamics in rhesus macaques.
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Affiliation(s)
- Patrick J. Madden
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Muhammad S. Arif
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Mark E. Becker
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Michael D. McRaven
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Ann M. Carias
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL, United States
| | - Sixia Xiao
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Cecily C. Midkiff
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, United States
| | - Robert V. Blair
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, United States
| | - Elizabeth Lake Potter
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Laura Martin-Sancho
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | | | - Elena Martinelli
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - John-Paul M. Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Francois J. Villinger
- New Iberia Research Center, University of Louisiana-Lafayette, New Iberia, LA, United States
| | - Sumit K. Chanda
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Pyone Pyone Aye
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, United States
| | - Chad J. Roy
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA, United States
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | | | - Ronald S. Veazey
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, United States
| | - Thomas J. Hope
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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21
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Baczenas JJ, Andersen H, Rashid S, Yarmosh D, Puthuveetil N, Parker M, Bradford R, Florence C, Stemple KJ, Lewis MG, O’Connor SL. Propagation of SARS-CoV-2 in Calu-3 Cells to Eliminate Mutations in the Furin Cleavage Site of Spike. Viruses 2021; 13:v13122434. [PMID: 34960703 PMCID: PMC8704555 DOI: 10.3390/v13122434] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 01/13/2023] Open
Abstract
SARS-CoV-2 pathogenesis, vaccine, and therapeutic studies rely on the use of animals challenged with highly pathogenic virus stocks produced in cell cultures. Ideally, these virus stocks should be genetically and functionally similar to the original clinical isolate, retaining wild-type properties to be reliably used in animal model studies. It is well-established that SARS-CoV-2 isolates serially passaged on Vero cell lines accumulate mutations and deletions in the furin cleavage site; however, these can be eliminated when passaged on Calu-3 lung epithelial cell lines, as presented in this study. As numerous stocks of SARS-CoV-2 variants of concern are being grown in cell cultures with the intent for use in animal models, it is essential that propagation methods generate virus stocks that are pathogenic in vivo. Here, we found that the propagation of a B.1.351 SARS-CoV-2 stock on Calu-3 cells eliminated viruses that previously accumulated mutations in the furin cleavage site. Notably, there were alternative variants that accumulated at the same nucleotide positions in virus populations grown on Calu-3 cells at multiple independent facilities. When a Calu-3-derived B.1.351 virus stock was used to infect hamsters, the virus remained pathogenic and the Calu-3-specific variants persisted in the population. These results suggest that Calu-3-derived virus stocks are pathogenic but care should still be taken to evaluate virus stocks for newly arising mutations during propagation.
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Affiliation(s)
| | - Hanne Andersen
- BIOQUAL, Inc., Rockville, MD 20852, USA; (H.A.); (M.G.L.)
| | - Sujatha Rashid
- American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, USA; (S.R.); (D.Y.); (N.P.); (M.P.); (R.B.)
- The Biodefense and Emerging Infections Research Resources Repository (BEI Resources), 10801 University Boulevard, Manassas, VA 20110, USA
| | - David Yarmosh
- American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, USA; (S.R.); (D.Y.); (N.P.); (M.P.); (R.B.)
- The Biodefense and Emerging Infections Research Resources Repository (BEI Resources), 10801 University Boulevard, Manassas, VA 20110, USA
| | - Nikhita Puthuveetil
- American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, USA; (S.R.); (D.Y.); (N.P.); (M.P.); (R.B.)
- The Biodefense and Emerging Infections Research Resources Repository (BEI Resources), 10801 University Boulevard, Manassas, VA 20110, USA
| | - Michael Parker
- American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, USA; (S.R.); (D.Y.); (N.P.); (M.P.); (R.B.)
- The Biodefense and Emerging Infections Research Resources Repository (BEI Resources), 10801 University Boulevard, Manassas, VA 20110, USA
| | - Rebecca Bradford
- American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, USA; (S.R.); (D.Y.); (N.P.); (M.P.); (R.B.)
- The Biodefense and Emerging Infections Research Resources Repository (BEI Resources), 10801 University Boulevard, Manassas, VA 20110, USA
| | - Clint Florence
- Office of Biodefense, Research Resources and Translational Research, Division of Microbiology and Infectious Diseases, NIAID, NIH, Bethesda, MD 20892, USA; (C.F.); (K.J.S.)
| | - Kimberly J. Stemple
- Office of Biodefense, Research Resources and Translational Research, Division of Microbiology and Infectious Diseases, NIAID, NIH, Bethesda, MD 20892, USA; (C.F.); (K.J.S.)
| | - Mark G. Lewis
- BIOQUAL, Inc., Rockville, MD 20852, USA; (H.A.); (M.G.L.)
| | - Shelby L. O’Connor
- Wisconsin National Primate Center, UW-Madison, Madison, WI 53711, USA;
- Department of Pathology and Laboratory Medicine, UW-Madison, Madison, WI 53705, USA
- Correspondence: ; Tel.: +1-608-890-0843
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22
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Neira V, Brito B, Agüero B, Berrios F, Valdés V, Gutierrez A, Ariyama N, Espinoza P, Retamal P, Holmes EC, Gonzalez-Reiche AS, Khan Z, van de Guchte A, Dutta J, Miorin L, Kehrer T, Galarce N, Almonacid LI, Levican J, van Bakel H, García-Sastre A, Medina RA. A household case evidences shorter shedding of SARS-CoV-2 in naturally infected cats compared to their human owners. Emerg Microbes Infect 2021; 10:376-383. [PMID: 33317424 PMCID: PMC7939552 DOI: 10.1080/22221751.2020.1863132] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been detected in domestic and wild cats. However, little is known about natural viral infections of domestic cats, although their importance for modelling disease spread, informing strategies for managing positive human-animal relationships and disease prevention. Here, we describe the SARS-CoV-2 infection in a household of two human adults and sibling cats (one male and two females) using real-time RT-PCR, an ELISA test, viral sequencing, and virus isolation. On May 5th, 2020, the cat-owners tested positive for SARS-CoV-2. Two days later, the male cat showed mild respiratory symptoms and tested positive. Four days after the male cat, the two female cats became positive, asymptomatically. Also, one human and one cat showed antibodies against SARS-CoV-2. All cats excreted detectable SARS-CoV-2 RNA for a shorter duration than humans and viral sequences analysis confirmed human-to-cat transmission. We could not determine if cat-to-cat transmission also occurred.
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Affiliation(s)
- Víctor Neira
- Facultad de Ciencias Veterinarias y Pecuarias, Departamento de Medicina Preventiva, Universidad de Chile, Santiago, Chile
| | - Bárbara Brito
- The three institute – University of Technology Sydney, Sydney, Australia
| | - Belén Agüero
- Facultad de Ciencias Veterinarias y Pecuarias, Departamento de Medicina Preventiva, Universidad de Chile, Santiago, Chile
| | - Felipe Berrios
- Facultad de Ciencias Veterinarias y Pecuarias, Departamento de Medicina Preventiva, Universidad de Chile, Santiago, Chile
| | - Valentina Valdés
- Facultad de Ciencias Veterinarias y Pecuarias, Departamento de Medicina Preventiva, Universidad de Chile, Santiago, Chile
| | - Alberto Gutierrez
- Facultad de Ciencias Veterinarias y Pecuarias, Departamento de Medicina Preventiva, Universidad de Chile, Santiago, Chile
| | - Naomi Ariyama
- Facultad de Ciencias Veterinarias y Pecuarias, Departamento de Medicina Preventiva, Universidad de Chile, Santiago, Chile
| | - Patricio Espinoza
- Facultad de Ciencias Veterinarias y Pecuarias, Departamento de Medicina Preventiva, Universidad de Chile, Santiago, Chile
| | - Patricio Retamal
- Facultad de Ciencias Veterinarias y Pecuarias, Departamento de Medicina Preventiva, Universidad de Chile, Santiago, Chile
| | - Edward C. Holmes
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Ana S. Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zenab Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jayeeta Dutta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicolás Galarce
- Facultad de Ciencias Veterinarias y Pecuarias, Departamento de Medicina Preventiva, Universidad de Chile, Santiago, Chile
| | - Leonardo I. Almonacid
- Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jorge Levican
- Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, 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 and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rafael A. Medina
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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23
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Chepurnov AA, Kazachinskaya EI, Kazachkova EA, Sharshov KA, Kononova YV, Shelemba AA, Alekseev AY, Gulyeva MA, Voevoda MI, Shestopalov AM. Development of a Purified Viral Preparation for Studies of COVID-19 (SARS-CoV-2) Biology. Bull Exp Biol Med 2021; 172:49-52. [PMID: 34787781 PMCID: PMC8596366 DOI: 10.1007/s10517-021-05329-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Indexed: 11/25/2022]
Abstract
Different methods for producing bulk quantities of concentrated and purified SARS-CoV-2 for the use as antigens and for the research into COVID-19 biology were tested.
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Affiliation(s)
- A A Chepurnov
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia.
| | - E I Kazachinskaya
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - E A Kazachkova
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - K A Sharshov
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Yu V Kononova
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - A A Shelemba
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - A Yu Alekseev
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - M A Gulyeva
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - M I Voevoda
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - A M Shestopalov
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
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24
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Trout LJ, Weisman A, Miller JS, Kramer C, Keshavjee S, Kleinman AM, Kulkarni S, Baldwin T, Tobey ML, Buffey T, Harris NS. Siamit: A Novel Academic-Tribal Health Partnership in Northwest Alaska. Acad Med 2021; 96:1560-1563. [PMID: 34261866 DOI: 10.1097/acm.0000000000004239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
PROBLEM American Indians and Alaska Natives hold a state-conferred right to health, yet significant health and health care disparities persist. Academic medical centers are resource-rich institutions committed to public service, yet few are engaged in responsive, equitable, and lasting tribal health partnerships to address these challenges. APPROACH Maniilaq Association, a rural and remote tribal health organization in Northwest Alaska, partnered with Massachusetts General Hospital and Harvard Medical School to address health care needs through physician staffing, training, and quality improvement initiatives. This partnership, called Siamit, falls under tribal governance, focuses on supporting community health leaders, addresses challenges shaped by extreme geographic remoteness, and advances the mission of academic medicine in the context of tribal health priorities. OUTCOMES Throughout the 2019-2020 academic year, Siamit augmented local physician staffing, mentored health professions trainees, provided continuing medical education courses, implemented quality improvement initiatives, and provided clinical care and operational support during the COVID-19 pandemic. Siamit began with a small budget and limited human resources, demonstrating that relatively small investments in academic-tribal health partnerships can support meaningful and positive outcomes. NEXT STEPS During the 2020-2021 academic year, the authors plan to expand Siamit's efforts with a broader social medicine curriculum, additional attending staff, more frequent trainee rotations, an increasingly robust mentorship network for Indigenous health professions trainees, and further study of the impact of these efforts. Such partnerships may be replicable in other settings and represent a significant opportunity to advance community health priorities, strengthen tribal health systems, support the next generation of Indigenous health leaders, and carry out the academic medicine mission of teaching, research, and service.
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Affiliation(s)
- Lucas J Trout
- L.J. Trout is managing partner, Siamit, Sayaqagvik director, Maniilaq Social Medicine, and lecturer on global health and social medicine, Harvard Medical School, Kotzebue, Alaska; ORCID: https://orcid.org/0000-0002-5074-6092
| | - Ashley Weisman
- A. Weisman is emergency medicine faculty, Siamit, and assistant professor of emergency medicine, Department of Surgery, University of Vermont Medical Center, Burlington, Vermont
| | - James S Miller
- J.S. Miller is internal medicine faculty, Siamit, and a fellow in global medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Corina Kramer
- C. Kramer is social medicine faculty and community director, Della Keats Fellowship in Indigenous Health Equity, Siamit, and lead Qargi facilitator, Maniilaq Social Medicine, Kotzebue, Alaska
| | - Salmaan Keshavjee
- S. Keshavjee is faculty advisor, Siamit, director, Harvard Medical School Center for Global Health Delivery, and professor of global health and social medicine, Harvard Medical School, Boston, Massachusetts
| | - Arthur M Kleinman
- A.M. Kleinman is faculty advisor, Siamit, Esther and Sidney Rabb Professor of Anthropology, Harvard University, professor of medical anthropology in global health and social medicine, and professor of psychiatry, Harvard Medical School, Boston, Massachusetts
| | - Suchitra Kulkarni
- S. Kulkarni is senior program coordinator, Siamit and Harvard Medical School Center for Global Health Delivery, Boston, Massachusetts
| | - Teressa Baldwin
- T. Baldwin is Sayaqagvik youth counselor, Maniilaq Social Medicine, and a Della Keats Fellow in Indigenous Health Equity, Siamit, Kotzebue, Alaska
| | - Matthew L Tobey
- M.L. Tobey is rural medicine faculty, Siamit, and rural health leadership fellowship director, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Timothy Buffey
- T. Buffey is medical director, Department of Medicine, Maniilaq Health Services, Kotzebue, Alaska
| | - N Stuart Harris
- N.S. Harris is emergency medicine faculty, Siamit, associate professor of emergency medicine, Harvard Medical School, and chief, Division of Wilderness Medicine, Massachusetts General Hospital, Boston, Massachusetts
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25
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Mlcochova P, Kemp SA, Dhar MS, Papa G, Meng B, Ferreira IATM, Datir R, Collier DA, Albecka A, Singh S, Pandey R, Brown J, Zhou J, Goonawardane N, Mishra S, Whittaker C, Mellan T, Marwal R, Datta M, Sengupta S, Ponnusamy K, Radhakrishnan VS, Abdullahi A, Charles O, Chattopadhyay P, Devi P, Caputo D, Peacock T, Wattal C, Goel N, Satwik A, Vaishya R, Agarwal M, Mavousian A, Lee JH, Bassi J, Silacci-Fegni C, Saliba C, Pinto D, Irie T, Yoshida I, Hamilton WL, Sato K, Bhatt S, Flaxman S, James LC, Corti D, Piccoli L, Barclay WS, Rakshit P, Agrawal A, Gupta RK. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 2021; 599:114-119. [PMID: 34488225 DOI: 10.1101/2021.05.08.443253] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/23/2021] [Indexed: 05/23/2023]
Abstract
The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)1. In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era.
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Affiliation(s)
- Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- University College London, London, UK
| | | | - Guido Papa
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Dami A Collier
- Department of Medicine, University of Cambridge, Cambridge, UK
- University College London, London, UK
| | - Anna Albecka
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Sujeet Singh
- National Centre for Disease Control, Delhi, India
| | - Rajesh Pandey
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Jonathan Brown
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Jie Zhou
- Department of Infectious Diseases, Imperial College London, London, UK
| | | | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Thomas Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | | | | | - Adam Abdullahi
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Priti Devi
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Tom Peacock
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | - Joo Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Takashi Irie
- Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Isao Yoshida
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Kei Sato
- Division of Systems Virology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
| | - Samir Bhatt
- National Centre for Disease Control, Delhi, India
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Leo C James
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Wendy S Barclay
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | | | - Anurag Agrawal
- CSIR Institute of Genomics and Integrative Biology, Delhi, India.
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Africa Health Research Institute, Durban, South Africa.
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26
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Mlcochova P, Kemp SA, Dhar MS, Papa G, Meng B, Ferreira IATM, Datir R, Collier DA, Albecka A, Singh S, Pandey R, Brown J, Zhou J, Goonawardane N, Mishra S, Whittaker C, Mellan T, Marwal R, Datta M, Sengupta S, Ponnusamy K, Radhakrishnan VS, Abdullahi A, Charles O, Chattopadhyay P, Devi P, Caputo D, Peacock T, Wattal C, Goel N, Satwik A, Vaishya R, Agarwal M, Mavousian A, Lee JH, Bassi J, Silacci-Fegni C, Saliba C, Pinto D, Irie T, Yoshida I, Hamilton WL, Sato K, Bhatt S, Flaxman S, James LC, Corti D, Piccoli L, Barclay WS, Rakshit P, Agrawal A, Gupta RK. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 2021; 599:114-119. [PMID: 34488225 PMCID: PMC8566220 DOI: 10.1038/s41586-021-03944-y] [Citation(s) in RCA: 815] [Impact Index Per Article: 271.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/23/2021] [Indexed: 12/26/2022]
Abstract
The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)1. In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era.
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Affiliation(s)
- Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- University College London, London, UK
| | | | - Guido Papa
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Dami A Collier
- Department of Medicine, University of Cambridge, Cambridge, UK
- University College London, London, UK
| | - Anna Albecka
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Sujeet Singh
- National Centre for Disease Control, Delhi, India
| | - Rajesh Pandey
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Jonathan Brown
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Jie Zhou
- Department of Infectious Diseases, Imperial College London, London, UK
| | | | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Thomas Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | | | | | - Adam Abdullahi
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Priti Devi
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Tom Peacock
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | - Joo Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Takashi Irie
- Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Isao Yoshida
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Kei Sato
- Division of Systems Virology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
| | - Samir Bhatt
- National Centre for Disease Control, Delhi, India
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Leo C James
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Wendy S Barclay
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | | | - Anurag Agrawal
- CSIR Institute of Genomics and Integrative Biology, Delhi, India.
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Africa Health Research Institute, Durban, South Africa.
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27
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Al-Jaf SMA, Niranji SS, Ali HN, Mohammed OA. Association of Apolipoprotein e polymorphism with SARS-CoV-2 infection. Infect Genet Evol 2021; 95:105043. [PMID: 34419671 PMCID: PMC8375275 DOI: 10.1016/j.meegid.2021.105043] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 12/12/2022]
Abstract
Coronavirus 2019 (COVID-19) is a viral disease caused by severe acute respiratory syndrome coronavirus-2 (SARS CoV-2). The disease resulted in global morbidity and mortality that led to considering as pandemic. The human body response to COVID-19 infection was massively different from being asymptomatic to developing severe symptoms. Host genetic factors are thought to be one of the reasons for these disparities in body responses. Few studies have suggested that Apolipoprotein Epsilon (Apo E) is a candidate gene for playing roles in the development of the disease symptoms. This work aims to find an association between different Apo E genotypes and alleles to COVID-19 infection comparing a general population and a group of COVID-19 patients. For the first time, the results found that Apo E4 is associated with COVID-19 disease in a Kurdish population of Iraq. Further study is required to reveal this association in different ethnic backgrounds all over the world.
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Affiliation(s)
- Sirwan M A Al-Jaf
- Department of Biology, College of Education, University of Garmian, Kurdistan region, Iraq; Coronavirus Research and Identification Lab., University of Garmian, Kurdistan region, Iraq.
| | - Sherko S Niranji
- Department of Biology, College of Education, University of Garmian, Kurdistan region, Iraq; Coronavirus Research and Identification Lab., University of Garmian, Kurdistan region, Iraq.
| | - Hussein N Ali
- College of Medicine, University of Garmian, Kurdistan region, Iraq
| | - Omed A Mohammed
- College of Medicine, University of Garmian, Kurdistan region, Iraq
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28
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Rowland R, Brandariz-Nuñez A. Analysis of the Role of N-Linked Glycosylation in Cell Surface Expression, Function, and Binding Properties of SARS-CoV-2 Receptor ACE2. Microbiol Spectr 2021; 9:e0119921. [PMID: 34494876 PMCID: PMC8557876 DOI: 10.1128/spectrum.01199-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/13/2021] [Indexed: 12/28/2022] Open
Abstract
Human angiotensin I-converting enzyme 2 (hACE2) is a type I transmembrane glycoprotein that serves as the major cell entry receptor for SARS-CoV and SARS-CoV-2. The viral spike (S) protein is required for the attachment to ACE2 and subsequent virus-host cell membrane fusion. Previous work has demonstrated the presence of N-linked glycans in ACE2. N-glycosylation is implicated in many biological activities, including protein folding, protein activity, and cell surface expression of biomolecules. However, the contribution of N-glycosylation to ACE2 function is poorly understood. Here, we examined the role of N-glycosylation in the activity and localization of two species with different susceptibility to SARS-CoV-2 infection, porcine ACE2 (pACE2) and hACE2. The elimination of N-glycosylation by tunicamycin (TM) treatment, or mutagenesis, showed that N-glycosylation is critical for the proper cell surface expression of ACE2 but not for its carboxiprotease activity. Furthermore, nonglycosylable ACE2 was localized predominantly in the endoplasmic reticulum (ER) and not at the cell surface. Our data also revealed that binding of SARS-CoV or SARS-CoV-2 S protein to porcine or human ACE2 was not affected by deglycosylation of ACE2 or S proteins, suggesting that N-glycosylation does not play a role in the interaction between SARS coronaviruses and the ACE2 receptor. Impairment of hACE2 N-glycosylation decreased cell-to-cell fusion mediated by SARS-CoV S protein but not that mediated by SARS-CoV-2 S protein. Finally, we found that hACE2 N-glycosylation is required for an efficient viral entry of SARS-CoV/SARS-CoV-2 S pseudotyped viruses, which may be the result of low cell surface expression of the deglycosylated ACE2 receptor. IMPORTANCE Understanding the role of glycosylation in the virus-receptor interaction is important for developing approaches that disrupt infection. In this study, we showed that deglycosylation of both ACE2 and S had a minimal effect on the spike-ACE2 interaction. In addition, we found that the removal of N-glycans of ACE2 impaired its ability to support an efficient transduction of SARS-CoV and SARS-CoV-2 S pseudotyped viruses. Our data suggest that the role of deglycosylation of ACE2 on reducing infection is likely due to a reduced expression of the viral receptor on the cell surface. These findings offer insight into the glycan structure and function of ACE2 and potentially suggest that future antiviral therapies against coronaviruses and other coronavirus-related illnesses involving inhibition of ACE2 recruitment to the cell membrane could be developed.
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Affiliation(s)
- Raymond Rowland
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alberto Brandariz-Nuñez
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Tolksdorf B, Nie C, Niemeyer D, Röhrs V, Berg J, Lauster D, Adler JM, Haag R, Trimpert J, Kaufer B, Drosten C, Kurreck J. Inhibition of SARS-CoV-2 Replication by a Small Interfering RNA Targeting the Leader Sequence. Viruses 2021; 13:v13102030. [PMID: 34696460 PMCID: PMC8539227 DOI: 10.3390/v13102030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 12/16/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected almost 200 million people worldwide and led to approximately 4 million deaths as of August 2021. Despite successful vaccine development, treatment options are limited. A promising strategy to specifically target viral infections is to suppress viral replication through RNA interference (RNAi). Hence, we designed eight small interfering RNAs (siRNAs) targeting the highly conserved 5′-untranslated region (5′-UTR) of SARS-CoV-2. The most promising candidate identified in initial reporter assays, termed siCoV6, targets the leader sequence of the virus, which is present in the genomic as well as in all subgenomic RNAs. In assays with infectious SARS-CoV-2, it reduced replication by two orders of magnitude and prevented the development of a cytopathic effect. Moreover, it retained its activity against the SARS-CoV-2 alpha variant and has perfect homology against all sequences of the delta variant that were analyzed by bioinformatic means. Interestingly, the siRNA was even highly active in virus replication assays with the SARS-CoV-1 family member. This work thus identified a very potent siRNA with a broad activity against various SARS-CoV viruses that represents a promising candidate for the development of new treatment options.
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Affiliation(s)
- Beatrice Tolksdorf
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
| | - Chuanxiong Nie
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; (C.N.); (D.L.); (R.H.)
| | - Daniela Niemeyer
- German Centre for Infection Research (DZIF), Charitéplatz 1, 10117 Berlin, Germany; (D.N.); (C.D.)
- Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Viola Röhrs
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
| | - Johanna Berg
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
| | - Daniel Lauster
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; (C.N.); (D.L.); (R.H.)
| | - Julia M. Adler
- Department of Veterinary Medicine, Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.M.A.); (J.T.); (B.K.)
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; (C.N.); (D.L.); (R.H.)
| | - Jakob Trimpert
- Department of Veterinary Medicine, Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.M.A.); (J.T.); (B.K.)
| | - Benedikt Kaufer
- Department of Veterinary Medicine, Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.M.A.); (J.T.); (B.K.)
| | - Christian Drosten
- German Centre for Infection Research (DZIF), Charitéplatz 1, 10117 Berlin, Germany; (D.N.); (C.D.)
- Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Jens Kurreck
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
- Correspondence: ; Tel.:+ 49-30-314-27581
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Affiliation(s)
- Ásgeir Haraldsson
- Children’s Hospital Iceland, Landspitali University Hospital, Iceland, University of Iceland, Faculty of Medicine, Reykjavík, Iceland
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Lim YS, Nguyen LP, Lee GH, Lee SG, Lyoo KS, Kim B, Hwang SB. Asunaprevir, a Potent Hepatitis C Virus Protease Inhibitor, Blocks SARS-CoV-2 Propagation. Mol Cells 2021; 44:688-695. [PMID: 34518443 PMCID: PMC8490202 DOI: 10.14348/molcells.2021.0076] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/27/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has become a global health concern. Various SARS-CoV-2 vaccines have been developed and are being used for vaccination worldwide. However, no therapeutic agents against coronavirus disease 2019 (COVID-19) have been developed so far; therefore, new therapeutic agents are urgently needed. In the present study, we evaluated several hepatitis C virus direct-acting antivirals as potential candidates for drug repurposing against COVID-19. Theses include asunaprevir (a protease inhibitor), daclatasvir (an NS5A inhibitor), and sofosbuvir (an RNA polymerase inhibitor). We found that asunaprevir, but not sofosbuvir and daclatasvir, markedly inhibited SARS-CoV-2-induced cytopathic effects in Vero E6 cells. Both RNA and protein levels of SARS-CoV-2 were significantly decreased by treatment with asunaprevir. Moreover, asunaprevir profoundly decreased virion release from SARS-CoV-2-infected cells. A pseudoparticle entry assay revealed that asunaprevir blocked SARS-CoV-2 infection at the binding step of the viral life cycle. Furthermore, asunaprevir inhibited SARS-CoV-2 propagation in human lung Calu-3 cells. Collectively, we found that asunaprevir displays broad-spectrum antiviral activity and therefore might be worth developing as a new drug repurposing candidate for COVID-19.
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Affiliation(s)
- Yun-Sook Lim
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Korea
| | - Lap P. Nguyen
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Korea
- Ilsong Institute of Life Science, Hallym University, Seoul 07247, Korea
| | - Gun-Hee Lee
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Korea
| | - Sung-Geun Lee
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Korea
| | - Kwang-Soo Lyoo
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Korea
| | - Bumseok Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan 54531, Korea
| | - Soon B. Hwang
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Korea
- Ilsong Institute of Life Science, Hallym University, Seoul 07247, Korea
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Hirotsu Y, Omata M. SARS-CoV-2 B.1.1.7 lineage rapidly spreads and replaces R.1 lineage in Japan: Serial and stationary observation in a community. Infect Genet Evol 2021; 95:105088. [PMID: 34560289 PMCID: PMC8454025 DOI: 10.1016/j.meegid.2021.105088] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/09/2021] [Accepted: 09/17/2021] [Indexed: 11/18/2022]
Abstract
Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulates in the world and acquires mutations during evolution. To identify the new emergent variants, the surveillance of the variants of concern (VOC) and variants of interest (VOI) is ongoing. This study aimed to determine how the transition of viral lineage occurred by stationary genome analysis in Yamanashi, Japan. Methods We performed the whole genome sequencing using SARS-CoV-2 positive samples collected from February 2020 to the end of June 2021. Viral lineage was defined by the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineages. Results We successfully obtained 325 viral genome sequences and the number of analyzed samples accounted for 15.4% of the total 2109 COVID-19 patients identified in our district. We identified 13 types of viral lineages including R.1, P.1, B.1.1.7 (Alpha) and B.1.617.2 (Delta). These virus lineages had distinct periods of expansion and decline. After the emerging of the R.1 lineage harboring E484K variant (designated VOI in Japan), the prevalent B.1.1.214 lineage were no longer identified. The R.1 lineages were temporarily prevalent afterwards, but the influx of B.1.1.7 lineage (designated VOC) led to a decline in R.1. Currently, B.1.1.7 has become dominant after mid-April 2021. Conclusion We clearly elucidated the transition and replacement of viral lineage by the community-based analysis. The virus completely replaced by more infectious lineages, therefore, it will be necessary to continue to monitor the VOC and VOI.
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Affiliation(s)
- Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
| | - Masao Omata
- Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
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Nie C, Trimpert J, Moon S, Haag R, Gilmore K, Kaufer BB, Seeberger PH. In vitro efficacy of Artemisia extracts against SARS-CoV-2. Virol J 2021; 18:182. [PMID: 34496903 DOI: 10.1101/2021.02.14.431122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/29/2021] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND Traditional medicines based on herbal extracts have been proposed as affordable treatments for patients suffering from coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Teas and drinks containing extracts of Artemisia annua and Artemisia afra have been widely used in Africa in efforts to prevent SARS-CoV-2 infection and fight COVID-19. METHODS The plant extracts and Covid-Organics drink produced in Madagascar were tested for plaque reduction using both feline coronavirus and SARS-CoV-2 in vitro. Their cytotoxicities were also investigated. RESULTS Several extracts as well as Covid-Organics inhibited SARS-CoV-2 and FCoV infection at concentrations that did not affect cell viability. CONCLUSIONS Some plant extracts show inhibitory activity against FCoV and SARS-CoV-2. However, it remains unclear whether peak plasma concentrations in humans can reach levels needed to inhibit viral infection following consumption of teas or Covid-Organics. Clinical studies are required to evaluate the utility of these drinks for COVID-19 prevention or treatment of patients.
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Affiliation(s)
- Chuanxiong Nie
- Institute for Virology, Freie Universität Berlin, Robert von Ostertag-Str. 7-13, 14163, Berlin, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Jakob Trimpert
- Institute for Virology, Freie Universität Berlin, Robert von Ostertag-Str. 7-13, 14163, Berlin, Germany
| | - Sooyeon Moon
- Department for Biomolecular Systems, Max-Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Rainer Haag
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Kerry Gilmore
- Department for Biomolecular Systems, Max-Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
- Department of Chemistry, University of Connecticut, 55 N. Eagleville Rd., Storrs, CT, 06268, USA
| | - Benedikt B Kaufer
- Institute for Virology, Freie Universität Berlin, Robert von Ostertag-Str. 7-13, 14163, Berlin, Germany.
| | - Peter H Seeberger
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
- Department for Biomolecular Systems, Max-Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
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Affiliation(s)
- Rachael Pung
- Ministry of Health, Singapore, London School of Hygiene & Tropical Medicine, London, UK; Centre for the Mathematical Modelling of infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.
| | - Tze Minn Mak
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Adam J Kucharski
- Centre for the Mathematical Modelling of infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Vernon J Lee
- Ministry of Health, Singapore, London School of Hygiene & Tropical Medicine, London, UK; Saw Swee Hock School of Public Health, National University of Singapore, Singapore
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Raiteux J, Eschlimann M, Marangon A, Rogée S, Dadvisard M, Taysse L, Larigauderie G. Inactivation of SARS-CoV-2 by Simulated Sunlight on Contaminated Surfaces. Microbiol Spectr 2021; 9:e0033321. [PMID: 34287031 PMCID: PMC8552605 DOI: 10.1128/spectrum.00333-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 06/30/2021] [Indexed: 12/21/2022] Open
Abstract
We studied the stability of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) under different simulated outdoor conditions by changing the temperature (20°C and 35°C), the illuminance (darkness, 10 klx, and 56 klx), and/or the cleanness of the surfaces at 50% relative humidity (RH). In darkness, the loss of viability of the virus on stainless steel is temperature dependent, but this is hidden by the effect of the sunlight from the first minutes of exposure. The virus shows a sensitivity to sunlight proportional to the illuminance intensity of the sunlight. The presence of interfering substances has a moderate effect on virus viability even with an elevated illuminance. Thus, SARS-CoV-2 is rapidly inactivated by simulated sunlight in the presence or absence of high levels of interfering substances at 20°C or 35°C and 50% relative humidity. IMPORTANCE Clinical matrix contains high levels of interfering substances. This study is the first to reveal that the presence of high levels of interfering substances had little impact on the persistence of SARS-CoV-2 on stainless steel following exposure to simulated sunlight. Thus, SARS-CoV-2 should be rapidly inactivated in outdoor environments in the presence or absence of interfering substances. Our results indicate that transmission of SARS-CoV-2 is unlikely to occur through outdoor surfaces, dependent on illuminance intensity. Moreover, most studies are interested in lineage S of SARS-CoV-2. In our experiments, we studied the stability of L-type strains, which comprise the majority of strains isolated from worldwide patients. Nevertheless, the effect of sunlight seems to be similar regardless of the strain studied, suggesting that the greater spread of certain variants is not correlated with better survival in outdoor conditions.
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Annavajhala MK, Mohri H, Wang P, Nair M, Zucker JE, Sheng Z, Gomez-Simmonds A, Kelley AL, Tagliavia M, Huang Y, Bedford T, Ho DD, Uhlemann AC. Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Nature 2021; 597:703-708. [PMID: 34428777 PMCID: PMC8481122 DOI: 10.1038/s41586-021-03908-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/13/2021] [Indexed: 12/21/2022]
Abstract
SARS-CoV-2 infections have surged across the globe in recent months, concomitant with considerable viral evolution1-3. Extensive mutations in the spike protein may threaten the efficacy of vaccines and therapeutic monoclonal antibodies4. Two signature spike mutations of concern are E484K, which has a crucial role in the loss of neutralizing activity of antibodies, and N501Y, a driver of rapid worldwide transmission of the B.1.1.7 lineage. Here we report the emergence of the variant lineage B.1.526 (also known as the Iota variant5), which contains E484K, and its rise to dominance in New York City in early 2021. This variant is partially or completely resistant to two therapeutic monoclonal antibodies that are in clinical use and is less susceptible to neutralization by plasma from individuals who had recovered from SARS-CoV-2 infection or serum from vaccinated individuals, posing a modest antigenic challenge. The presence of the B.1.526 lineage has now been reported in all 50 states in the United States and in many other countries. B.1.526 rapidly replaced earlier lineages in New York, with an estimated transmission advantage of 35%. These transmission dynamics, together with the relative antibody resistance of its E484K sub-lineage, are likely to have contributed to the sharp rise and rapid spread of B.1.526. Although SARS-CoV-2 B.1.526 initially outpaced B.1.1.7 in the region, its growth subsequently slowed concurrently with the rise of B.1.1.7 and ensuing variants.
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Affiliation(s)
- Medini K Annavajhala
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Hiroshi Mohri
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Manoj Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jason E Zucker
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Angela Gomez-Simmonds
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Anne L Kelley
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Maya Tagliavia
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David D Ho
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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Annavajhala MK, Mohri H, Wang P, Nair M, Zucker JE, Sheng Z, Gomez-Simmonds A, Kelley AL, Tagliavia M, Huang Y, Bedford T, Ho DD, Uhlemann AC. Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Nature 2021. [PMID: 34428777 DOI: 10.1101/2021.02.23.21252259v4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
SARS-CoV-2 infections have surged across the globe in recent months, concomitant with considerable viral evolution1-3. Extensive mutations in the spike protein may threaten the efficacy of vaccines and therapeutic monoclonal antibodies4. Two signature spike mutations of concern are E484K, which has a crucial role in the loss of neutralizing activity of antibodies, and N501Y, a driver of rapid worldwide transmission of the B.1.1.7 lineage. Here we report the emergence of the variant lineage B.1.526 (also known as the Iota variant5), which contains E484K, and its rise to dominance in New York City in early 2021. This variant is partially or completely resistant to two therapeutic monoclonal antibodies that are in clinical use and is less susceptible to neutralization by plasma from individuals who had recovered from SARS-CoV-2 infection or serum from vaccinated individuals, posing a modest antigenic challenge. The presence of the B.1.526 lineage has now been reported in all 50 states in the United States and in many other countries. B.1.526 rapidly replaced earlier lineages in New York, with an estimated transmission advantage of 35%. These transmission dynamics, together with the relative antibody resistance of its E484K sub-lineage, are likely to have contributed to the sharp rise and rapid spread of B.1.526. Although SARS-CoV-2 B.1.526 initially outpaced B.1.1.7 in the region, its growth subsequently slowed concurrently with the rise of B.1.1.7 and ensuing variants.
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Affiliation(s)
- Medini K Annavajhala
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Hiroshi Mohri
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Manoj Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jason E Zucker
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Angela Gomez-Simmonds
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Anne L Kelley
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Maya Tagliavia
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David D Ho
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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Mendes Correa MC, Leal FE, Villas Boas LS, Witkin SS, de Paula A, Tozetto Mendonza TR, Ferreira NE, Curty G, de Carvalho PS, Buss LF, Costa SF, da Cunha Carvalho FM, Kawakami J, Taniwaki NN, Paiao H, da Silva Bizário JC, de Jesus JG, Sabino EC, Romano CM, Grepan RMZ, Sesso A. Prolonged presence of replication-competent SARS-CoV-2 in mildly symptomatic individuals: A report of two cases. J Med Virol 2021; 93:5603-5607. [PMID: 33851749 PMCID: PMC8250959 DOI: 10.1002/jmv.27021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/07/2021] [Accepted: 04/12/2021] [Indexed: 12/17/2022]
Abstract
It has been estimated that individuals with COVID-19 can shed replication-competent virus up to a maximum of 20 days after initiation of symptoms. The majority of studies that addressed this situation involved hospitalized individuals and those with severe disease. Studies to address the possible presence of SARS-CoV-2 during the different phases of COVID-19 disease in mildly infected individuals, and utilization of viral culture techniques to identify replication-competent viruses, have been limited. This report describes two patients with mild forms of the disease who shed replication-competent virus for 24 and 37 days, respectively, after symptom onset.
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Affiliation(s)
- Maria C. Mendes Correa
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de MedicinaUniversidade de São PauloSão PauloSão PauloBrazil
| | - Fabio E. Leal
- Faculdade de MedicinaUniversidade Municipal de Sao Caetano do SulSão Caetano do SulSão PauloBrazil
- Instituto Nacional do Cancer Rio de JaneiroRio de JaneiroRio de JaneiroBrazil
| | - Lucy S. Villas Boas
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
| | - Steven S. Witkin
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
- Weill Cornell MedicineNew YorkNew YorkUSA
| | - Anderson de Paula
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
| | - Tania R. Tozetto Mendonza
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
| | - Noely E. Ferreira
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
| | - Gislaine Curty
- Instituto Nacional do Cancer Rio de JaneiroRio de JaneiroRio de JaneiroBrazil
| | | | - Lewis F. Buss
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de MedicinaUniversidade de São PauloSão PauloSão PauloBrazil
| | - Silvia F. Costa
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de MedicinaUniversidade de São PauloSão PauloSão PauloBrazil
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloSão PauloBrazil
| | - Flavia M. da Cunha Carvalho
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloSão PauloBrazil
| | - Joyce Kawakami
- Instituto do Coracao do Hospital das Clinicas da Faculdade de MedicinaUniversidade de Sao PauloSão PauloSão PauloBrazil
| | | | - Heuder Paiao
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
| | - Joao C. da Silva Bizário
- Faculdade de MedicinaUniversidade Municipal de Sao Caetano do SulSão Caetano do SulSão PauloBrazil
| | - Jaqueline G. de Jesus
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de MedicinaUniversidade de São PauloSão PauloSão PauloBrazil
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloSão PauloBrazil
| | - Ester C. Sabino
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de MedicinaUniversidade de São PauloSão PauloSão PauloBrazil
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloSão PauloBrazil
| | - Camila M. Romano
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
| | - Regina M. Z. Grepan
- Faculdade de MedicinaUniversidade Municipal de Sao Caetano do SulSão Caetano do SulSão PauloBrazil
| | - Antonio Sesso
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloSão PauloBrazil
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Schneider-Schaulies S, Schumacher F, Wigger D, Schöl M, Waghmare T, Schlegel J, Seibel J, Kleuser B. Sphingolipids: Effectors and Achilles Heals in Viral Infections? Cells 2021; 10:cells10092175. [PMID: 34571822 PMCID: PMC8466362 DOI: 10.3390/cells10092175] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/26/2022] Open
Abstract
As viruses are obligatory intracellular parasites, any step during their life cycle strictly depends on successful interaction with their particular host cells. In particular, their interaction with cellular membranes is of crucial importance for most steps in the viral replication cycle. Such interactions are initiated by uptake of viral particles and subsequent trafficking to intracellular compartments to access their replication compartments which provide a spatially confined environment concentrating viral and cellular components, and subsequently, employ cellular membranes for assembly and exit of viral progeny. The ability of viruses to actively modulate lipid composition such as sphingolipids (SLs) is essential for successful completion of the viral life cycle. In addition to their structural and biophysical properties of cellular membranes, some sphingolipid (SL) species are bioactive and as such, take part in cellular signaling processes involved in regulating viral replication. It is especially due to the progress made in tools to study accumulation and dynamics of SLs, which visualize their compartmentalization and identify interaction partners at a cellular level, as well as the availability of genetic knockout systems, that the role of particular SL species in the viral replication process can be analyzed and, most importantly, be explored as targets for therapeutic intervention.
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Affiliation(s)
- Sibylle Schneider-Schaulies
- Institute for Virology and Immunobiology, University of Wuerzburg, 97078 Würzburg, Germany; (S.S.-S.); (M.S.); (T.W.)
| | - Fabian Schumacher
- Institute of Pharmacy, Pharmacology and Toxicology, Freie Universität Berlin, 14195 Berlin, Germany; (F.S.); (D.W.)
| | - Dominik Wigger
- Institute of Pharmacy, Pharmacology and Toxicology, Freie Universität Berlin, 14195 Berlin, Germany; (F.S.); (D.W.)
| | - Marie Schöl
- Institute for Virology and Immunobiology, University of Wuerzburg, 97078 Würzburg, Germany; (S.S.-S.); (M.S.); (T.W.)
| | - Trushnal Waghmare
- Institute for Virology and Immunobiology, University of Wuerzburg, 97078 Würzburg, Germany; (S.S.-S.); (M.S.); (T.W.)
| | - Jan Schlegel
- Department for Biotechnology and Biophysics, University of Wuerzburg, 97074 Würzburg, Germany;
| | - Jürgen Seibel
- Department for Organic Chemistry, University of Wuerzburg, 97074 Würzburg, Germany;
| | - Burkhard Kleuser
- Institute of Pharmacy, Pharmacology and Toxicology, Freie Universität Berlin, 14195 Berlin, Germany; (F.S.); (D.W.)
- Correspondence: ; Tel.: +49-30-8386-9823
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40
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Yu J, Tostanoski LH, Mercado NB, McMahan K, Liu J, Jacob-Dolan C, Chandrashekar A, Atyeo C, Martinez DR, Anioke T, Bondzie EA, Chang A, Gardner S, Giffin VM, Hope DL, Nampanya F, Nkolola J, Patel S, Sanborn O, Sellers D, Wan H, Hayes T, Bauer K, Pessaint L, Valentin D, Flinchbaugh Z, Brown R, Cook A, Bueno-Wilkerson D, Teow E, Andersen H, Lewis MG, Martinot AJ, Baric RS, Alter G, Wegmann F, Zahn R, Schuitemaker H, Barouch DH. Protective efficacy of Ad26.COV2.S against SARS-CoV-2 B.1.351 in macaques. Nature 2021; 596:423-427. [PMID: 34161961 PMCID: PMC8373608 DOI: 10.1038/s41586-021-03732-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023]
Abstract
The emergence of SARS-CoV-2 variants that partially evade neutralizing antibodies poses a threat to the efficacy of current COVID-19 vaccines1,2. The Ad26.COV2.S vaccine expresses a stabilized spike protein from the WA1/2020 strain of SARS-CoV-2, and has recently demonstrated protective efficacy against symptomatic COVID-19 in humans in several geographical regions-including in South Africa, where 95% of sequenced viruses in cases of COVID-19 were the B.1.351 variant3. Here we show that Ad26.COV2.S elicits humoral and cellular immune responses that cross-react with the B.1.351 variant and protects against B.1.351 challenge in rhesus macaques. Ad26.COV2.S induced lower binding and neutralizing antibodies against B.1.351 as compared to WA1/2020, but elicited comparable CD8 and CD4 T cell responses against the WA1/2020, B.1.351, B.1.1.7, P.1 and CAL.20C variants. B.1.351 infection of control rhesus macaques resulted in higher levels of virus replication in bronchoalveolar lavage and nasal swabs than did WA1/2020 infection. Ad26.COV2.S provided robust protection against both WA1/2020 and B.1.351, although we observed higher levels of virus in vaccinated macaques after B.1.351 challenge. These data demonstrate that Ad26.COV2.S provided robust protection against B.1.351 challenge in rhesus macaques. Our findings have important implications for vaccine control of SARS-CoV-2 variants of concern.
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Affiliation(s)
- Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Lisa H Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Noe B Mercado
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Caroline Atyeo
- Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - David R Martinez
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tochi Anioke
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Esther A Bondzie
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Aiquan Chang
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sarah Gardner
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Victoria M Giffin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - David L Hope
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Felix Nampanya
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Joseph Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Shivani Patel
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Owen Sanborn
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Daniel Sellers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Huahua Wan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Tammy Hayes
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Katherine Bauer
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | | | | | | | | | | | | | | | | | | | - Amanda J Martinot
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Ralph S Baric
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Frank Wegmann
- Janssen Vaccines & Prevention, Leiden, The Netherlands
| | - Roland Zahn
- Janssen Vaccines & Prevention, Leiden, The Netherlands
| | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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Constant O, Barthelemy J, Bolloré K, Tuaillon E, Gosselet F, Chable-Bessia C, Merida P, Muriaux D, Van de Perre P, Salinas S, Simonin Y. SARS-CoV-2 Poorly Replicates in Cells of the Human Blood-Brain Barrier Without Associated Deleterious Effects. Front Immunol 2021; 12:697329. [PMID: 34386007 PMCID: PMC8353323 DOI: 10.3389/fimmu.2021.697329] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/05/2021] [Indexed: 12/23/2022] Open
Abstract
Various neurological symptoms have been associated to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection including headache, fever, anosmia, ageusia, but also, encephalitis, Guillain-Barre syndrome and ischemic stroke. Responsible for the current coronavirus disease (COVID-19) pandemic, SARS-CoV-2 may access and affect the central nervous system (CNS) by several pathways such as axonal retrograde transport or through interaction with the blood-brain barrier (BBB) or blood-cerebrospinal fluid (CSF) barrier. Here, we explored the molecular and cellular effects of direct SARS-CoV-2 infection of human BBB cells. We observed low replication of SARS-CoV-2 that was accompanied by very moderate inflammatory response. Using a human in vitro BBB model, we also described low replication levels without strong inflammatory response or modulation of endothelium integrity. Finally, using serum samples from COVID-19 patients, we highlighted strong concentrations of pro-inflammatory factors that did not perturb BBB integrity after short term exposure. Altogether, our results show that the main mechanism of brain access following SARS-CoV-2 infection does not seem to be directed by brain infection through endothelial cells.
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Affiliation(s)
- Orianne Constant
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, Antilles University, Montpellier, France
| | - Jonathan Barthelemy
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, Antilles University, Montpellier, France
| | - Karine Bolloré
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, Antilles University, Montpellier, France
| | - Edouard Tuaillon
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, Antilles University, Montpellier, France
| | - Fabien Gosselet
- Univ. Artois, UR 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Lens, France
| | - Christine Chable-Bessia
- Centre d’Etude des Maladies Infectieuses et de Pharmacologie Anti-Infectieuses, CNRS, Université de Montpellier, Montpellier, France
| | - Peggy Merida
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, Montpellier, France
| | - Delphine Muriaux
- Centre d’Etude des Maladies Infectieuses et de Pharmacologie Anti-Infectieuses, CNRS, Université de Montpellier, Montpellier, France
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, Montpellier, France
| | - Philippe Van de Perre
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, Antilles University, Montpellier, France
- Laboratory of Virology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Sara Salinas
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, Antilles University, Montpellier, France
| | - Yannick Simonin
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, Antilles University, Montpellier, France
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Gardner A, Ghosh S, Dunowska M, Brightwell G. Virucidal Efficacy of Blue LED and Far-UVC Light Disinfection against Feline Infectious Peritonitis Virus as a Model for SARS-CoV-2. Viruses 2021; 13:1436. [PMID: 34452302 PMCID: PMC8402852 DOI: 10.3390/v13081436] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 12/17/2022] Open
Abstract
Transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurs through respiratory droplets passed directly from person to person or indirectly through fomites, such as common use surfaces or objects. The aim of this study was to determine the virucidal efficacy of blue LED (405 nm) and far-UVC (222 nm) light in comparison to standard UVC (254 nm) irradiation for the inactivation of feline infectious peritonitis virus (FIPV) on different matrices as a model for SARS-CoV-2. Wet or dried FIPV on stainless steel, plastic, or paper discs, in the presence or absence of artificial saliva, were exposed to various wavelengths of light for different time periods (1-90 min). Dual activity of blue LED and far-UVC lights were virucidal for most wet and dried FIPV within 4 to 16 min on all matrices. Individual action of blue LED and far-UVC lights were virucidal for wet FIPV but required longer irradiation times (8-90 min) to reach a 4-log reduction. In comparison, LED (265 nm) and germicidal UVC (254 nm) were virucidal on almost all matrices for both wet and dried FIPV within 1 min exposure. UVC was more effective for the disinfection of surfaces as compared to blue LED and far-UVC individually or together. However, dual action of blue LED and far-UVC was virucidal. This combination of lights could be used as a safer alternative to traditional UVC.
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Affiliation(s)
- Amanda Gardner
- AgResearch Ltd., Hopkirk Research Institute, Massey University, Corner University Ave and Library Road, Palmerston North 4442, New Zealand;
| | - Sayani Ghosh
- School of Veterinary Science, Massey University Manawatu (Turitea), Tennent Drive, Palmerston North 4474, New Zealand; (S.G.); (M.D.)
| | - Magdalena Dunowska
- School of Veterinary Science, Massey University Manawatu (Turitea), Tennent Drive, Palmerston North 4474, New Zealand; (S.G.); (M.D.)
| | - Gale Brightwell
- AgResearch Ltd., Hopkirk Research Institute, Massey University, Corner University Ave and Library Road, Palmerston North 4442, New Zealand;
- New Zealand Food Safety Science and Research Centre, Massey University Manawatu (Turitea), Tennent Drive, Palmerston North 4474, New Zealand
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Canal B, Fujisawa R, McClure AW, Deegan TD, Wu M, Ulferts R, Weissmann F, Drury LS, Bertolin AP, Zeng J, Beale R, Howell M, Labib K, Diffley JF. Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of nsp15 endoribonuclease. Biochem J 2021; 478:2465-2479. [PMID: 34198324 PMCID: PMC8286823 DOI: 10.1042/bcj20210199] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 is responsible for COVID-19, a human disease that has caused over 2 million deaths, stretched health systems to near-breaking point and endangered economies of countries and families around the world. Antiviral treatments to combat COVID-19 are currently lacking. Remdesivir, the only antiviral drug approved for the treatment of COVID-19, can affect disease severity, but better treatments are needed. SARS-CoV-2 encodes 16 non-structural proteins (nsp) that possess different enzymatic activities with important roles in viral genome replication, transcription and host immune evasion. One key aspect of host immune evasion is performed by the uridine-directed endoribonuclease activity of nsp15. Here we describe the expression and purification of nsp15 recombinant protein. We have developed biochemical assays to follow its activity, and we have found evidence for allosteric behaviour. We screened a custom chemical library of over 5000 compounds to identify nsp15 endoribonuclease inhibitors, and we identified and validated NSC95397 as an inhibitor of nsp15 endoribonuclease in vitro. Although NSC95397 did not inhibit SARS-CoV-2 growth in VERO E6 cells, further studies will be required to determine the effect of nsp15 inhibition on host immune evasion.
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Affiliation(s)
- Berta Canal
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Ryo Fujisawa
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Allison W. McClure
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Tom D. Deegan
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Mary Wu
- High Throughput Screening, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Florian Weissmann
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Lucy S. Drury
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Agustina P. Bertolin
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Jingkun Zeng
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Rupert Beale
- Cell Biology of Infection Laboratory, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Michael Howell
- High Throughput Screening, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Karim Labib
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - John F.X. Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
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Abstract
The coronavirus pandemic has had a huge impact on public health with over 165 million people infected, 3.4 million deaths and a hugely deleterious effect on most economies. While vaccination effectively protects against the disease it is likely that viruses will evolve that can replicate in hosts immunised with the present vaccines. Thus, there is a great unmet need for effective antivirals that can block the development of serious disease in infected patients. The seven papers published in this issue of the Biochemical Journal address this need by expressing and purifying components required for viral replication, developing biochemical assays for these components and using the assays to screen a library of pre-existing pharmaceuticals for drugs that inhibited the target in vitro and inhibited viral replication in cell culture. The candidate drugs obtained are potential antivirals that may protect against SARS-CoV-2 infection. While not all the antiviral candidates will make it through to the clinic, they will be useful tool compounds and can act as the starting point for further drug discovery programmes.
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Affiliation(s)
- Ronald T. Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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Lim CT, Tan KW, Wu M, Ulferts R, Armstrong LA, Ozono E, Drury LS, Milligan JC, Zeisner TU, Zeng J, Weissmann F, Canal B, Bineva-Todd G, Howell M, O'Reilly N, Beale R, Kulathu Y, Labib K, Diffley JF. Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of Nsp3 papain-like protease. Biochem J 2021; 478:2517-2531. [PMID: 34198325 PMCID: PMC8286840 DOI: 10.1042/bcj20210244] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/05/2021] [Accepted: 06/07/2021] [Indexed: 02/07/2023]
Abstract
The COVID-19 pandemic has emerged as the biggest life-threatening disease of this century. Whilst vaccination should provide a long-term solution, this is pitted against the constant threat of mutations in the virus rendering the current vaccines less effective. Consequently, small molecule antiviral agents would be extremely useful to complement the vaccination program. The causative agent of COVID-19 is a novel coronavirus, SARS-CoV-2, which encodes at least nine enzymatic activities that all have drug targeting potential. The papain-like protease (PLpro) contained in the nsp3 protein generates viral non-structural proteins from a polyprotein precursor, and cleaves ubiquitin and ISG protein conjugates. Here we describe the expression and purification of PLpro. We developed a protease assay that was used to screen a custom compound library from which we identified dihydrotanshinone I and Ro 08-2750 as compounds that inhibit PLpro in protease and isopeptidase assays and also inhibit viral replication in cell culture-based assays.
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Affiliation(s)
- Chew Theng Lim
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Kang Wei Tan
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Mary Wu
- High-Throughput Screening, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Lee A. Armstrong
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Eiko Ozono
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Lucy S. Drury
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Jennifer C. Milligan
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Theresa U. Zeisner
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Jingkun Zeng
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Florian Weissmann
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Berta Canal
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Ganka Bineva-Todd
- Peptide Chemistry STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Michael Howell
- High-Throughput Screening, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Nicola O'Reilly
- Peptide Chemistry STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Yogesh Kulathu
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Karim Labib
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - John F.X. Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
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Morris DH, Yinda KC, Gamble A, Rossine FW, Huang Q, Bushmaker T, Fischer RJ, Matson MJ, Van Doremalen N, Vikesland PJ, Marr LC, Munster VJ, Lloyd-Smith JO. Mechanistic theory predicts the effects of temperature and humidity on inactivation of SARS-CoV-2 and other enveloped viruses. eLife 2021; 10:e65902. [PMID: 33904403 PMCID: PMC8277363 DOI: 10.7554/elife.65902] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/20/2021] [Indexed: 12/14/2022] Open
Abstract
Ambient temperature and humidity strongly affect inactivation rates of enveloped viruses, but a mechanistic, quantitative theory of these effects has been elusive. We measure the stability of SARS-CoV-2 on an inert surface at nine temperature and humidity conditions and develop a mechanistic model to explain and predict how temperature and humidity alter virus inactivation. We find SARS-CoV-2 survives longest at low temperatures and extreme relative humidities (RH); median estimated virus half-life is >24 hr at 10°C and 40% RH, but ∼1.5 hr at 27°C and 65% RH. Our mechanistic model uses fundamental chemistry to explain why inactivation rate increases with increased temperature and shows a U-shaped dependence on RH. The model accurately predicts existing measurements of five different human coronaviruses, suggesting that shared mechanisms may affect stability for many viruses. The results indicate scenarios of high transmission risk, point to mitigation strategies, and advance the mechanistic study of virus transmission.
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Affiliation(s)
- Dylan H Morris
- Department of Ecology and Evolutionary Biology, Princeton UniversityPrincetonUnited States
- Department of Ecology and Evolutionary Biology, University of California, Los AngelesLos AngelesUnited States
| | - Kwe Claude Yinda
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious DiseasesHamiltonUnited States
| | - Amandine Gamble
- Department of Ecology and Evolutionary Biology, University of California, Los AngelesLos AngelesUnited States
| | - Fernando W Rossine
- Department of Ecology and Evolutionary Biology, Princeton UniversityPrincetonUnited States
| | - Qishen Huang
- Department of Civil and Environmental Engineering, Virginia TechBlacksburgUnited States
| | - Trenton Bushmaker
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious DiseasesHamiltonUnited States
| | - Robert J Fischer
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious DiseasesHamiltonUnited States
| | - M Jeremiah Matson
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious DiseasesHamiltonUnited States
- Joan C. Edwards School of Medicine, Marshall UniversityHuntingtonUnited States
| | - Neeltje Van Doremalen
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious DiseasesHamiltonUnited States
| | - Peter J Vikesland
- Department of Civil and Environmental Engineering, Virginia TechBlacksburgUnited States
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia TechBlacksburgUnited States
| | - Vincent J Munster
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious DiseasesHamiltonUnited States
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los AngelesLos AngelesUnited States
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47
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Nelson TL, Fosdick BK, Biela LM, Schoenberg H, Mast S, McGinnis E, Young MC, Lynn L, Fahrner S, Nolt L, Dihle T, Quicke K, Gallichotte EN, Fitzmeyer E, Ebel GD, Pabilonia K, Ehrhart N, VandeWoude S. Association Between COVID-19 Exposure and Self-reported Compliance With Public Health Guidelines Among Essential Employees at an Institution of Higher Education in the US. JAMA Netw Open 2021; 4:e2116543. [PMID: 34287634 PMCID: PMC8295736 DOI: 10.1001/jamanetworkopen.2021.16543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/07/2021] [Indexed: 12/24/2022] Open
Abstract
Importance Detailed analysis of infection rates paired with behavioral and employee-reported risk factors is vital to understanding how transmission of SARS-CoV-2 infection may be exacerbated or mitigated in the workplace. Institutions of higher education are heterogeneous work units that supported continued in-person employment during the COVID-19 pandemic, providing a test site for occupational health evaluation. Objective To evaluate the association between self-reported protective behaviors and prevalence of SARS-CoV-2 infection among essential in-person employees during the first 6 months of the COVID-19 pandemic in the US. Design, Setting, and Participants This cross-sectional study was conducted from July 13 to September 2, 2020, at an institution of higher education in Fort Collins, Colorado. Employees 18 years or older without symptoms of COVID-19 who identified as essential in-person workers during the first 6 months of the pandemic were included. Participants completed a survey, and blood and nasal swab samples were collected to assess active SARS-CoV-2 infection via quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) and past infection by serologic testing. Exposure Self-reported practice of protective behaviors against COVID-19 according to public health guidelines provided to employees. Main Outcomes and Measures Prevalence of current SARS-CoV-2 infection detected by qRT-PCR or previous SARS-CoV-2 infection detected by an IgG SARS-CoV-2 testing platform. The frequency of protective behavior practices and essential workers' concerns regarding contracting COVID-19 and exposing others were measured based on survey responses. Results Among 508 participants (305 [60.0%] women, 451 [88.8%] non-Hispanic White individuals; mean [SD] age, 41.1 [12.5] years), there were no qRT-PCR positive test results, and only 2 participants (0.4%) had seroreactive IgG antibodies. Handwashing and mask wearing were reported frequently both at work (480 [94.7%] and 496 [97.8%] participants, respectively) and outside work (465 [91.5%] and 481 [94.7%] participants, respectively). Social distancing was reported less frequently at work (403 [79.5%]) than outside work (465 [91.5%]) (P < .001). Participants were more highly motivated to avoid exposures because of concern about spreading the infection to others (419 [83.0%]) than for personal protection (319 [63.2%]) (P < .001). Conclusions and Relevance In this cross-sectional study of essential workers at an institution of higher education, when employees reported compliance with public health practices both at and outside work, they were able to operate safely in their work environment during the COVID-19 pandemic.
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Affiliation(s)
- Tracy L. Nelson
- Colorado School of Public Health, Colorado State University, Fort Collins
- Department of Health and Exercise Science, Colorado State University, Fort Collins
| | | | - Laurie M. Biela
- Human Performance Clinical Research Laboratory, Department of Health and Exercise Science, Colorado State University, Fort Collins
| | - Hayden Schoenberg
- Human Performance Clinical Research Laboratory, Department of Health and Exercise Science, Colorado State University, Fort Collins
| | - Sarah Mast
- Human Performance Clinical Research Laboratory, Department of Health and Exercise Science, Colorado State University, Fort Collins
| | - Emma McGinnis
- Human Performance Clinical Research Laboratory, Department of Health and Exercise Science, Colorado State University, Fort Collins
| | - Michael C. Young
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins
| | - Lori Lynn
- Health Network, Colorado State University, Fort Collins
| | - Scott Fahrner
- Human Performance Clinical Research Laboratory, Department of Health and Exercise Science, Colorado State University, Fort Collins
| | - Laura Nolt
- Department of Statistics, Colorado State University, Fort Collins
| | - Tina Dihle
- Health Network, Colorado State University, Fort Collins
| | - Kendra Quicke
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins
| | - Emily N. Gallichotte
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins
| | - Emily Fitzmeyer
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins
| | - Greg D. Ebel
- Arthropod-Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins
| | - Kristy Pabilonia
- Veterinary Diagnostics Laboratories, Colorado State University, Fort Collins
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins
| | - Nicole Ehrhart
- Columbine Health Systems Center for Healthy Aging, Colorado State University, Fort Collins
- Department of Clinical Sciences, Colorado State University, Fort Collins
| | - Sue VandeWoude
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins
- One Health Institute, Colorado State University, Fort Collins
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48
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Kissler SM, Fauver JR, Mack C, Olesen SW, Tai C, Shiue KY, Kalinich CC, Jednak S, Ott IM, Vogels CBF, Wohlgemuth J, Weisberger J, DiFiori J, Anderson DJ, Mancell J, Ho DD, Grubaugh ND, Grad YH. Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies. PLoS Biol 2021; 19:e3001333. [PMID: 34252080 PMCID: PMC8297933 DOI: 10.1371/journal.pbio.3001333] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/22/2021] [Accepted: 06/21/2021] [Indexed: 02/04/2023] Open
Abstract
SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level persistent viral RNA shedding. The dynamics of viral RNA concentration, particularly in the early stages of infection, can inform clinical measures and interventions such as test-based screening. We used prospective longitudinal quantitative reverse transcription PCR testing to measure the viral RNA trajectories for 68 individuals during the resumption of the 2019-2020 National Basketball Association season. For 46 individuals with acute infections, we inferred the peak viral concentration and the duration of the viral proliferation and clearance phases. According to our mathematical model, we found that viral RNA concentrations peaked an average of 3.3 days (95% credible interval [CI] 2.5, 4.2) after first possible detectability at a cycle threshold value of 22.3 (95% CI 20.5, 23.9). The viral clearance phase lasted longer for symptomatic individuals (10.9 days [95% CI 7.9, 14.4]) than for asymptomatic individuals (7.8 days [95% CI 6.1, 9.7]). A second test within 2 days after an initial positive PCR test substantially improves certainty about a patient's infection stage. The effective sensitivity of a test intended to identify infectious individuals declines substantially with test turnaround time. These findings indicate that SARS-CoV-2 viral concentrations peak rapidly regardless of symptoms. Sequential tests can help reveal a patient's progress through infection stages. Frequent, rapid-turnaround testing is needed to effectively screen individuals before they become infectious.
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Affiliation(s)
- Stephen M. Kissler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Christina Mack
- Real World Solutions, IQVIA, Durham, North Carolina, United States of America
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Scott W. Olesen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Caroline Tai
- Real World Solutions, IQVIA, Durham, North Carolina, United States of America
| | - Kristin Y. Shiue
- Real World Solutions, IQVIA, Durham, North Carolina, United States of America
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Sarah Jednak
- Department of Health Management and Policy, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Jay Wohlgemuth
- Quest Diagnostics, San Juan Capistrano, California, United States of America
| | - James Weisberger
- Bioreference Laboratories, Elmwood Park, New Jersey, United States of America
| | - John DiFiori
- Hospital for Special Surgery, New York, New York, United States of America
- National Basketball Association, New York, New York, United States of America
| | - Deverick J. Anderson
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, North Carolina, United States of America
| | - Jimmie Mancell
- Department of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
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49
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Yang AC, Kern F, Losada PM, Agam MR, Maat CA, Schmartz GP, Fehlmann T, Stein JA, Schaum N, Lee DP, Calcuttawala K, Vest RT, Berdnik D, Lu N, Hahn O, Gate D, McNerney MW, Channappa D, Cobos I, Ludwig N, Schulz-Schaeffer WJ, Keller A, Wyss-Coray T. Dysregulation of brain and choroid plexus cell types in severe COVID-19. Nature 2021; 595:565-571. [PMID: 34153974 PMCID: PMC8400927 DOI: 10.1038/s41586-021-03710-0] [Citation(s) in RCA: 340] [Impact Index Per Article: 113.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 06/07/2021] [Indexed: 01/08/2023]
Abstract
Although SARS-CoV-2 primarily targets the respiratory system, patients with and survivors of COVID-19 can suffer neurological symptoms1-3. However, an unbiased understanding of the cellular and molecular processes that are affected in the brains of patients with COVID-19 is missing. Here we profile 65,309 single-nucleus transcriptomes from 30 frontal cortex and choroid plexus samples across 14 control individuals (including 1 patient with terminal influenza) and 8 patients with COVID-19. Although our systematic analysis yields no molecular traces of SARS-CoV-2 in the brain, we observe broad cellular perturbations indicating that barrier cells of the choroid plexus sense and relay peripheral inflammation into the brain and show that peripheral T cells infiltrate the parenchyma. We discover microglia and astrocyte subpopulations associated with COVID-19 that share features with pathological cell states that have previously been reported in human neurodegenerative disease4-6. Synaptic signalling of upper-layer excitatory neurons-which are evolutionarily expanded in humans7 and linked to cognitive function8-is preferentially affected in COVID-19. Across cell types, perturbations associated with COVID-19 overlap with those found in chronic brain disorders and reside in genetic variants associated with cognition, schizophrenia and depression. Our findings and public dataset provide a molecular framework to understand current observations of COVID-19-related neurological disease, and any such disease that may emerge at a later date.
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Affiliation(s)
- Andrew C Yang
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Patricia M Losada
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Maayan R Agam
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Christina A Maat
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Georges P Schmartz
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Julian A Stein
- Institute for Neuropathology, Saarland University Hospital and Medical Faculty of Saarland University, Homburg, Germany
| | - Nicholas Schaum
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Davis P Lee
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Kruti Calcuttawala
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan T Vest
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniela Berdnik
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Nannan Lu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Hahn
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - David Gate
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - M Windy McNerney
- Department of Psychiatry, Stanford University School of Medicine, Stanford, CA, USA
| | - Divya Channappa
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Inma Cobos
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Walter J Schulz-Schaeffer
- Institute for Neuropathology, Saarland University Hospital and Medical Faculty of Saarland University, Homburg, Germany
| | - Andreas Keller
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.
| | - Tony Wyss-Coray
- ChEM-H, Stanford University, Stanford, CA, USA.
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
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50
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Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a novel virus that causes coronavirus disease 2019 (COVID-19). To understand the identity, functional characteristics and therapeutic targets of the virus and the diseases, appropriate infection models that recapitulate the in vivo pathophysiology of the viral infection are necessary. This article reviews the various infection models, including Vero cells, human cell lines, organoids, and animal models, and discusses their advantages and disadvantages. This knowledge will be helpful for establishing an efficient system for defense against emerging infectious diseases.
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Affiliation(s)
- Taewoo Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | | | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- GENOME INSIGHT Inc., Daejeon 34051, Korea
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