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Özdemir M, Dennerlein S. The TOM complex from an evolutionary perspective and the functions of TOMM70. Biol Chem 2024; 0:hsz-2024-0043. [PMID: 39092472 DOI: 10.1515/hsz-2024-0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024]
Abstract
In humans, up to 1,500 mitochondrial precursor proteins are synthesized at cytosolic ribosomes and must be imported into the organelle. This is not only essential for mitochondrial but also for many cytosolic functions. The majority of mitochondrial precursor proteins are imported over the translocase of the outer membrane (TOM). In recent years, high-resolution structure analyses from different organisms shed light on the composition and arrangement of the TOM complex. Although significant similarities have been found, differences were also observed, which have been favored during evolution and could reflect the manifold functions of TOM with cellular signaling and its response to altered metabolic situations. A key component within these regulatory mechanisms is TOMM70, which is involved in protein import, forms contacts to the ER and the nucleus, but is also involved in cellular defense mechanisms during infections.
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Affiliation(s)
- Metin Özdemir
- Institute for Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany
| | - Sven Dennerlein
- Institute for Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany
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2
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Dotson T, Price B, Witrick B, Davis S, Kemper E, Whanger S, Hodder S, Hendricks B. Factors Associated With Surveillance Testing in Individuals With COVID-19 Symptoms During the Last Leg of the Pandemic: Multivariable Regression Analysis. JMIR Public Health Surveill 2024; 10:e52762. [PMID: 39030676 PMCID: PMC11270129 DOI: 10.2196/52762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 07/21/2024] Open
Abstract
Background Rural underserved areas facing health disparities have unequal access to health resources. By the third and fourth waves of SARS-CoV-2 infections in the United States, COVID-19 testing had reduced, with more reliance on home testing, and those seeking testing were mostly symptomatic. Objective This study identifies factors associated with COVID-19 testing among individuals who were symptomatic versus asymptomatic seen at a Rapid Acceleration of Diagnostics for Underserved Populations phase 2 (RADx-UP2) testing site in West Virginia. Methods Demographic, clinical, and behavioral factors were collected via survey from tested individuals. Logistic regression was used to identify factors associated with the presence of individuals who were symptomatic seen at testing sites. Global tests for spatial autocorrelation were conducted to examine clustering in the proportion of symptomatic to total individuals tested by zip code. Bivariate maps were created to display geographic distributions between higher proportions of tested individuals who were symptomatic and social determinants of health. Results Among predictors, the presence of a physical (adjusted odds ratio [aOR] 1.85, 95% CI 1.3-2.65) or mental (aOR 1.53, 95% CI 0.96-2.48) comorbid condition, challenges related to a place to stay/live (aOR 307.13, 95% CI 1.46-10,6372), no community socioeconomic distress (aOR 0.99, 95% CI 0.98-1.00), no challenges in getting needed medicine (aOR 0.01, 95% CI 0.00-0.82) or transportation (aOR 0.23, 95% CI 0.05-0.64), an interaction between community socioeconomic distress and not getting needed medicine (aOR 1.06, 95% CI 1.00-1.13), and having no community socioeconomic distress while not facing challenges related to a place to stay/live (aOR 0.93, 95% CI 0.87-0.99) were statistically associated with an individual being symptomatic at the first test visit. Conclusions This study addresses critical limitations to the current COVID-19 testing literature, which almost exclusively uses population-level disease screening data to inform public health responses.
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Affiliation(s)
- Timothy Dotson
- West Virginia Clinical and Translational Sciences Institute, Morgantown, WV, United States
| | - Brad Price
- West Virginia Clinical and Translational Sciences Institute, Morgantown, WV, United States
- Department of Management Information Systems, West Virginia University, Morgantown, WV, United States
| | - Brian Witrick
- West Virginia Clinical and Translational Sciences Institute, Morgantown, WV, United States
- Department of Public Health Sciences, College of Behavioral, Social, and Health Sciences, Clemson University, Clemson, SC, United States
| | - Sherri Davis
- West Virginia Clinical and Translational Sciences Institute, Morgantown, WV, United States
| | - Emily Kemper
- West Virginia Clinical and Translational Sciences Institute, Morgantown, WV, United States
| | - Stacey Whanger
- American Diabetes Association, Arlington, VA, United States
| | - Sally Hodder
- West Virginia Clinical and Translational Sciences Institute, Morgantown, WV, United States
- School of Medicine, West Virginia University, Morgantown, WV, United States
| | - Brian Hendricks
- West Virginia Clinical and Translational Sciences Institute, Morgantown, WV, United States
- Center for Rural and Community Health, West Virginia School of Osteopathic Medicine, Lewisburg, WV, United States
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3
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Yin X, Pu Y, Yuan S, Pache L, Churas C, Weston S, Riva L, Simons LM, Cisneros WJ, Clausen T, De Jesus PD, Kim HN, Fuentes D, Whitelock J, Esko J, Lord M, Mena I, García-Sastre A, Hultquist JF, Frieman MB, Ideker T, Pratt D, Martin-Sancho L, Chanda SK. Global siRNA Screen Reveals Critical Human Host Factors of SARS-CoV-2 Multicycle Replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602835. [PMID: 39026801 PMCID: PMC11257544 DOI: 10.1101/2024.07.10.602835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Defining the subset of cellular factors governing SARS-CoV-2 replication can provide critical insights into viral pathogenesis and identify targets for host-directed antiviral therapies. While a number of genetic screens have previously reported SARS-CoV-2 host dependency factors, these approaches relied on utilizing pooled genome-scale CRISPR libraries, which are biased towards the discovery of host proteins impacting early stages of viral replication. To identify host factors involved throughout the SARS-CoV-2 infectious cycle, we conducted an arrayed genome-scale siRNA screen. Resulting data were integrated with published datasets to reveal pathways supported by orthogonal datasets, including transcriptional regulation, epigenetic modifications, and MAPK signalling. The identified proviral host factors were mapped into the SARS-CoV-2 infectious cycle, including 27 proteins that were determined to impact assembly and release. Additionally, a subset of proteins were tested across other coronaviruses revealing 17 potential pan-coronavirus targets. Further studies illuminated a role for the heparan sulfate proteoglycan perlecan in SARS-CoV-2 viral entry, and found that inhibition of the non-canonical NF-kB pathway through targeting of BIRC2 restricts SARS-CoV-2 replication both in vitro and in vivo. These studies provide critical insight into the landscape of virus-host interactions driving SARS-CoV-2 replication as well as valuable targets for host-directed antivirals.
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Affiliation(s)
- Xin Yin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuan Pu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, USA
| | - Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Lars Pache
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Christopher Churas
- Department of Medicine, University of California San Diego, La Jolla, USA
| | - Stuart Weston
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Laura Riva
- Calibr-Skaggs at Scripps Research Institute, La Jolla, USA
| | - Lacy M. Simons
- Division of Infectious Diseases, Departments of Medicine and Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - William J. Cisneros
- Division of Infectious Diseases, Departments of Medicine and Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Thomas Clausen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, USA
| | - Paul D. De Jesus
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, USA
| | - Ha Na Kim
- Molecular Surface Interaction Laboratory, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Daniel Fuentes
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, USA
| | - John Whitelock
- Molecular Surface Interaction Laboratory, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Jeffrey Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, USA
| | - Megan Lord
- Molecular Surface Interaction Laboratory, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Ignacio Mena
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, USA; The Tisch Institute, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA; The Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Departments of Medicine and Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Matthew B. Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, USA
| | - Dexter Pratt
- Department of Medicine, University of California San Diego, La Jolla, USA
| | - Laura Martin-Sancho
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Sumit K Chanda
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, USA
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4
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Tsujino S, Deguchi S, Nomai T, Padilla-Blanco M, Plianchaisuk A, Wang L, Begum MM, Uriu K, Mizuma K, Nao N, Kojima I, Tsubo T, Li J, Matsumura Y, Nagao M, Oda Y, Tsuda M, Anraku Y, Kita S, Yajima H, Sasaki-Tabata K, Guo Z, Hinay AA, Yoshimatsu K, Yamamoto Y, Nagamoto T, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Nasser H, Jonathan M, Putri O, Kim Y, Chen L, Suzuki R, Tamura T, Maenaka K, Irie T, Matsuno K, Tanaka S, Ito J, Ikeda T, Takayama K, Zahradnik J, Hashiguchi T, Fukuhara T, Sato K. Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant. Microbiol Immunol 2024. [PMID: 38961765 DOI: 10.1111/1348-0421.13165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/05/2024]
Abstract
In middle to late 2023, a sublineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. We performed multiscale investigations, including phylogenetic analysis, epidemic dynamics modeling, infection experiments using pseudoviruses, clinical isolates, and recombinant viruses in cell cultures and experimental animals, and the use of human sera and antiviral compounds, to reveal the virological features of the newly emerging EG.5.1 variant. Our phylogenetic analysis and epidemic dynamics modeling suggested that two hallmark substitutions of EG.5.1, S:F456L and ORF9b:I5T are critical to its increased viral fitness. Experimental investigations on the growth kinetics, sensitivity to clinically available antivirals, fusogenicity, and pathogenicity of EG.5.1 suggested that the virological features of EG.5.1 are comparable to those of XBB.1.5. However, cryo-electron microscopy revealed structural differences between the spike proteins of EG.5.1 and XBB.1.5. We further assessed the impact of ORF9b:I5T on viral features, but it was almost negligible in our experimental setup. Our multiscale investigations provide knowledge for understanding the evolutionary traits of newly emerging pathogenic viruses, including EG.5.1, in the human population.
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Affiliation(s)
- Shuhei Tsujino
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Tomo Nomai
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Miguel Padilla-Blanco
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
- Departamento de Farmacia, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU (UCH-CEU), CEU Universities, Valencia, Spain
| | - Arnon Plianchaisuk
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keita Mizuma
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Isshu Kojima
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Tomoya Tsubo
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Jingshu Li
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Yuki Anraku
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Shunsuke Kita
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hisano Yajima
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kaori Sasaki-Tabata
- Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Ziyi Guo
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Alfredo A Hinay
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | | | | | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Michael Jonathan
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Olivia Putri
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | - Yoonjin Kim
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Life Sciences, Faculty of Natural Science, Imperial College London, London, UK
| | - Luo Chen
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan
- Division of Pathogen Structure, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Takashi Irie
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Keita Matsuno
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Jiri Zahradnik
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
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5
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Dadonaite B, Brown J, McMahon TE, Farrell AG, Figgins MD, Asarnow D, Stewart C, Lee J, Logue J, Bedford T, Murrell B, Chu HY, Veesler D, Bloom JD. Spike deep mutational scanning helps predict success of SARS-CoV-2 clades. Nature 2024; 631:617-626. [PMID: 38961298 PMCID: PMC11254757 DOI: 10.1038/s41586-024-07636-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/31/2024] [Indexed: 07/05/2024]
Abstract
SARS-CoV-2 variants acquire mutations in the spike protein that promote immune evasion1 and affect other properties that contribute to viral fitness, such as ACE2 receptor binding and cell entry2,3. Knowledge of how mutations affect these spike phenotypes can provide insight into the current and potential future evolution of the virus. Here we use pseudovirus deep mutational scanning4 to measure how more than 9,000 mutations across the full XBB.1.5 and BA.2 spikes affect ACE2 binding, cell entry or escape from human sera. We find that mutations outside the receptor-binding domain (RBD) have meaningfully affected ACE2 binding during SARS-CoV-2 evolution. We also measure how mutations to the XBB.1.5 spike affect neutralization by serum from individuals who recently had SARS-CoV-2 infections. The strongest serum escape mutations are in the RBD at sites 357, 420, 440, 456 and 473; however, the antigenic effects of these mutations vary across individuals. We also identify strong escape mutations outside the RBD; however, many of them decrease ACE2 binding, suggesting they act by modulating RBD conformation. Notably, the growth rates of human SARS-CoV-2 clades can be explained in substantial part by the measured effects of mutations on spike phenotypes, suggesting our data could enable better prediction of viral evolution.
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Affiliation(s)
- Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Teagan E McMahon
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ariana G Farrell
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Marlin D Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jenni Logue
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Helen Y Chu
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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6
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Bai H, Zhang X, Gong T, Ma J, Zhang P, Cai Z, Ren D, Zhang C. A systematic mutation analysis of 13 major SARS-CoV-2 variants. Virus Res 2024; 345:199392. [PMID: 38729218 PMCID: PMC11112362 DOI: 10.1016/j.virusres.2024.199392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 04/22/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
SARS-CoV-2 evolves constantly with various novel mutations. Due to their enhanced infectivity, transmissibility and immune evasion, a comprehensive understanding of the association between these mutations and the respective functional changes is crucial. However, previous mutation studies of major SARS-CoV-2 variants remain limited. Here, we performed systematic analyses of full-length amino acids mutation, phylogenetic features, protein physicochemical properties, molecular dynamics and immune escape as well as pseudotype virus infection assays among thirteen major SARS-CoV-2 variants. We found that Omicron exhibited the most abundant and complex mutation sites, higher indices of hydrophobicity and flexibility than other variants. The results of molecular dynamics simulation suggest that Omicron has the highest number of hydrogen bonds and strongest binding free energy between the S protein and ACE2 receptor. Furthermore, we revealed 10 immune escape sites in 13 major variants, some of them were reported previously, but four of which (i.e. 339/373/477/496) are first reported to be specific to Omicron, whereas 462 is specific to Epslion. The infectivity of these variants was confirmed by the pseudotype virus infection assays. Our findings may help us understand the functional consequences of the mutations within various variants and the underlying mechanisms of the immune escapes conferred by the S proteins.
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Affiliation(s)
- Han Bai
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China
| | - Xuan Zhang
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Tian Gong
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Junpeng Ma
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Peng Zhang
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Zeqiong Cai
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China
| | - Doudou Ren
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China
| | - Chengsheng Zhang
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China; Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China.
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7
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Zhou Y, Chen Z, Liu S, Liu S, Liao Y, Du A, Dong Z, Zhang Y, Chen X, Tao S, Wu X, Razzaq A, Xu G, Tan DA, Li S, Deng Y, Peng J, Dai S, Deng X, Zhang X, Jiang T, Zhang Z, Cheng G, Zhao J, Xia Z. A Cullin 5-based complex serves as an essential modulator of ORF9b stability in SARS-CoV-2 replication. Signal Transduct Target Ther 2024; 9:159. [PMID: 38937432 PMCID: PMC11211426 DOI: 10.1038/s41392-024-01874-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 04/12/2024] [Accepted: 05/15/2024] [Indexed: 06/29/2024] Open
Abstract
The ORF9b protein, derived from the nucleocapsid's open-reading frame in both SARS-CoV and SARS-CoV-2, serves as an accessory protein crucial for viral immune evasion by inhibiting the innate immune response. Despite its significance, the precise regulatory mechanisms underlying its function remain elusive. In the present study, we unveil that the ORF9b protein of SARS-CoV-2, including emerging mutant strains like Delta and Omicron, can undergo ubiquitination at the K67 site and subsequent degradation via the proteasome pathway, despite certain mutations present among these strains. Moreover, our investigation further uncovers the pivotal role of the translocase of the outer mitochondrial membrane 70 (TOM70) as a substrate receptor, bridging ORF9b with heat shock protein 90 alpha (HSP90α) and Cullin 5 (CUL5) to form a complex. Within this complex, CUL5 triggers the ubiquitination and degradation of ORF9b, acting as a host antiviral factor, while HSP90α functions to stabilize it. Notably, treatment with HSP90 inhibitors such as GA or 17-AAG accelerates the degradation of ORF9b, leading to a pronounced inhibition of SARS-CoV-2 replication. Single-cell sequencing data revealed an up-regulation of HSP90α in lung epithelial cells from COVID-19 patients, suggesting a potential mechanism by which SARS-CoV-2 may exploit HSP90α to evade the host immunity. Our study identifies the CUL5-TOM70-HSP90α complex as a critical regulator of ORF9b protein stability, shedding light on the intricate host-virus immune response dynamics and offering promising avenues for drug development against SARS-CoV-2 in clinical settings.
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Affiliation(s)
- Yuzheng Zhou
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, China
| | - Zongpeng Chen
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Sijie Liu
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Sixu Liu
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Yujie Liao
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Ashuai Du
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Zijun Dong
- Department of Basic Medicine, School of Medicine, Hunan Normal University, 410081, Changsha, China
| | - Yongxing Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Xuan Chen
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Siyi Tao
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Xin Wu
- Department of spine surgery, The Third Xiangya Hospital, Central South University, 410013, Changsha, China
| | - Aroona Razzaq
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Gang Xu
- School of Basic Medical Sciences, Anhui Medical University, 230032, Hefei, China
| | - De-An Tan
- Hunan Key Laboratory of Neurorestoratology, 921 Hospital of Joint Logistics Support Force People's Liberation Army of China (The Second Affiliated Hospital of Hunan Normal University), 410003, Changsha, Hunan, China
| | - Shanni Li
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Youwen Deng
- Department of spine surgery, The Third Xiangya Hospital, Central South University, 410013, Changsha, China
| | - Jian Peng
- Department of Geriatric Surgery, Xiangya Hospital, Central South University, 410008, Changsha, China
| | - Shuyan Dai
- Xiangya School of Pharmaceutical Sciences, Central South University, 410013, Changsha, China
| | - Xu Deng
- Xiangya School of Pharmaceutical Sciences, Central South University, 410013, Changsha, China
| | - Xianwen Zhang
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | | | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, China
| | - Gong Cheng
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, 518132, Shenzhen, China
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Jincun Zhao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, China
- Guangzhou Laboratory, 510005, Guangzhou, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, China
| | - Zanxian Xia
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, Hunan Key Laboratory of Medical Genetics & Center for Medical Genetics, School of Life Sciences, Central South University, 410008, Changsha, China.
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8
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Waman VP, Ashford P, Lam SD, Sen N, Abbasian M, Woodridge L, Goldtzvik Y, Bordin N, Wu J, Sillitoe I, Orengo CA. Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics. Sci Rep 2024; 14:14208. [PMID: 38902252 PMCID: PMC11190248 DOI: 10.1038/s41598-024-61541-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/07/2024] [Indexed: 06/22/2024] Open
Abstract
The COVID-19 disease is an ongoing global health concern. Although vaccination provides some protection, people are still susceptible to re-infection. Ostensibly, certain populations or clinical groups may be more vulnerable. Factors causing these differences are unclear and whilst socioeconomic and cultural differences are likely to be important, human genetic factors could influence susceptibility. Experimental studies indicate SARS-CoV-2 uses innate immune suppression as a strategy to speed-up entry and replication into the host cell. Therefore, it is necessary to understand the impact of variants in immunity-associated human proteins on susceptibility to COVID-19. In this work, we analysed missense coding variants in several SARS-CoV-2 proteins and their human protein interactors that could enhance binding affinity to SARS-CoV-2. We curated a dataset of 19 SARS-CoV-2: human protein 3D-complexes, from the experimentally determined structures in the Protein Data Bank and models built using AlphaFold2-multimer, and analysed the impact of missense variants occurring in the protein-protein interface region. We analysed 468 missense variants from human proteins and 212 variants from SARS-CoV-2 proteins and computationally predicted their impacts on binding affinities for the human viral protein complexes. We predicted a total of 26 affinity-enhancing variants from 13 human proteins implicated in increased binding affinity to SARS-CoV-2. These include key-immunity associated genes (TOMM70, ISG15, IFIH1, IFIT2, RPS3, PALS1, NUP98, AXL, ARF6, TRIMM, TRIM25) as well as important spike receptors (KREMEN1, AXL and ACE2). We report both common (e.g., Y13N in IFIH1) and rare variants in these proteins and discuss their likely structural and functional impact, using information on known and predicted functional sites. Potential mechanisms associated with immune suppression implicated by these variants are discussed. Occurrence of certain predicted affinity-enhancing variants should be monitored as they could lead to increased susceptibility and reduced immune response to SARS-CoV-2 infection in individuals/populations carrying them. Our analyses aid in understanding the potential impact of genetic variation in immunity-associated proteins on COVID-19 susceptibility and help guide drug-repurposing strategies.
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Affiliation(s)
- Vaishali P Waman
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Paul Ashford
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Su Datt Lam
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Neeladri Sen
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Mahnaz Abbasian
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Laurel Woodridge
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Yonathan Goldtzvik
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Nicola Bordin
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Jiaxin Wu
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Christine A Orengo
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
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9
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Yang X, Zhu J, Wang Q, Tang B, Shen Y, Wang B, Ji L, Liu H, Wuchty S, Zhang Z, Dong Y, Liang Z. Comparative analysis of dynamic transcriptomes reveals specific COVID-19 features and pathogenesis of immunocompromised populations. mSystems 2024; 9:e0138523. [PMID: 38752789 PMCID: PMC11237560 DOI: 10.1128/msystems.01385-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/10/2024] [Indexed: 06/19/2024] Open
Abstract
A dysfunction of human host genes and proteins in coronavirus infectious disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key factor impacting clinical symptoms and outcomes. Yet, a detailed understanding of human host immune responses is still incomplete. Here, we applied RNA sequencing to 94 samples of COVID-19 patients with and without hematological tumors as well as COVID-19 uninfected non-tumor individuals to obtain a comprehensive transcriptome landscape of both hematological tumor patients and non-tumor individuals. In our analysis, we further accounted for the human-SARS-CoV-2 protein interactome, human protein interactome, and human protein complex subnetworks to understand the mechanisms of SARS-CoV-2 infection and host immune responses. Our data sets enabled us to identify important SARS-CoV-2 (non-)targeted differentially expressed genes and complexes post-SARS-CoV-2 infection in both hematological tumor and non-tumor individuals. We found several unique differentially expressed genes, complexes, and functions/pathways such as blood coagulation (APOE, SERPINE1, SERPINE2, and TFPI), lipoprotein particle remodeling (APOC2, APOE, and CETP), and pro-B cell differentiation (IGHM, VPREB1, and IGLL1) during COVID-19 infection in patients with hematological tumors. In particular, APOE, a gene that is associated with both blood coagulation and lipoprotein particle remodeling, is not only upregulated in hematological tumor patients post-SARS-CoV-2 infection but also significantly expressed in acute dead patients with hematological tumors, providing clues for the design of future therapeutic strategies specifically targeting COVID-19 in patients with hematological tumors. Our data provide a rich resource for understanding the specific pathogenesis of COVID-19 in immunocompromised patients, such as those with hematological malignancies, and developing effective therapeutics for COVID-19. IMPORTANCE A majority of previous studies focused on the characterization of coronavirus infectious disease 2019 (COVID-19) disease severity in people with normal immunity, while the characterization of COVID-19 in immunocompromised populations is still limited. Our study profiles changes in the transcriptome landscape post-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in hematological tumor patients and non-tumor individuals. Furthermore, our integrative and comparative systems biology analysis of the interactome, complexome, and transcriptome provides new insights into the tumor-specific pathogenesis of COVID-19. Our findings confirm that SARS-CoV-2 potentially tends to target more non-functional host proteins to indirectly affect host immune responses in hematological tumor patients. The identified unique genes, complexes, functions/pathways, and expression patterns post-SARS-CoV-2 infection in patients with hematological tumors increase our understanding of how SARS-CoV-2 manipulates the host molecular mechanism. Our observed differential genes/complexes and clinical indicators of normal/long infection and deceased COVID-19 patients provide clues for understanding the mechanism of COVID-19 progression in hematological tumors. Finally, our study provides an important data resource that supports the increasing value of the application of publicly accessible data sets to public health.
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Affiliation(s)
- Xiaodi Yang
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Jialin Zhu
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Qingyun Wang
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Bo Tang
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Ye Shen
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Bingjie Wang
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Li Ji
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Huihui Liu
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Miami, Florida, USA
- Department of Biology, University of Miami, Miami, Florida, USA
- Institute of Data Science and Computation, University of Miami, Miami, Florida, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Ziding Zhang
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yujun Dong
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Zeyin Liang
- Department of Hematology, Peking University First Hospital, Beijing, China
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10
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Yu M, Li J, Gao W, Li Z, Zhang W. Multiple E3 ligases act as antiviral factors against SARS-CoV-2 via inducing the ubiquitination and degradation of ORF9b. J Virol 2024; 98:e0162423. [PMID: 38709105 PMCID: PMC11237466 DOI: 10.1128/jvi.01624-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 04/07/2024] [Indexed: 05/07/2024] Open
Abstract
Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) open reading frame 9b (ORF9b) antagonizes the antiviral type I and III interferon (IFN) responses and is ubiquitinated and degraded via the ubiquitin-proteasome pathway. However, E3 ubiquitin ligases that mediate the polyubiquitination and degradation of ORF9b remain unknown. In this study, we identified 14 E3 ligases that specifically bind to SARS-CoV-2 ORF9b. Specifically, three E3 ligases, HECT, UBA, and WWE domain-containing E3 ubiquitin protein ligase 1 (HUWE1), ubiquitin protein ligase E3 component n-recognin 4 (UBR4), and UBR5, induced K48-linked polyubiquitination and degradation of ORF9b, thereby attenuating ORF9b-mediated inhibition of the IFN response and SARS-CoV-2 replication. Moreover, each E3 ligase performed this function independent of the other two E3 ligases. Therefore, the three E3 ligases identified in this study as anti-SARS-CoV-2 host factors provide novel molecular insight into the virus-host interaction.IMPORTANCEUbiquitination is an important post-translational modification that regulates multiple biological processes, including viral replication. Identification of E3 ubiquitin ligases that target viral proteins for degradation can provide novel targets for antagonizing viral infections. Here, we identified multiple E3 ligases, including HECT, UBA, and WWE domain-containing E3 ubiquitin protein ligase 1 (HUWE1), ubiquitin protein ligase E3 component n-recognin 4 (UBR4), and UBR5, that ubiquitinated and induced the degradation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) open reading frame 9b (ORF9b), an interferon (IFN) antagonist, thereby enhancing IFN production and attenuating SARS-CoV-2 replication. Our study provides new possibilities for drug development targeting the interaction between E3 ligases and ORF9b.
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Affiliation(s)
- Miao Yu
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China
- Department of Geriatrics and Special medical treatment, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Jie Li
- Department of Geriatrics and Special medical treatment, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wenying Gao
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhaolong Li
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wenyan Zhang
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
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11
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Saunders N, Monel B, Cayet N, Archetti L, Moreno H, Jeanne A, Marguier A, Buchrieser J, Wai T, Schwartz O, Fréchin M. Dynamic label-free analysis of SARS-CoV-2 infection reveals virus-induced subcellular remodeling. Nat Commun 2024; 15:4996. [PMID: 38862527 PMCID: PMC11166935 DOI: 10.1038/s41467-024-49260-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 05/30/2024] [Indexed: 06/13/2024] Open
Abstract
Assessing the impact of SARS-CoV-2 on organelle dynamics allows a better understanding of the mechanisms of viral replication. We combine label-free holotomographic microscopy with Artificial Intelligence to visualize and quantify the subcellular changes triggered by SARS-CoV-2 infection. We study the dynamics of shape, position and dry mass of nucleoli, nuclei, lipid droplets and mitochondria within hundreds of single cells from early infection to syncytia formation and death. SARS-CoV-2 infection enlarges nucleoli, perturbs lipid droplets, changes mitochondrial shape and dry mass, and separates lipid droplets from mitochondria. We then used Bayesian network modeling on organelle dry mass states to define organelle cross-regulation networks and report modifications of organelle cross-regulation that are triggered by infection and syncytia formation. Our work highlights the subcellular remodeling induced by SARS-CoV-2 infection and provides an Artificial Intelligence-enhanced, label-free methodology to study in real-time the dynamics of cell populations and their content.
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Affiliation(s)
- Nell Saunders
- Virus & Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 3569, Paris, France
| | - Blandine Monel
- Virus & Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 3569, Paris, France
| | - Nadège Cayet
- Institut Pasteur, Université Paris Cité, Ultrastructural Bioimaging Unit, 75015, Paris, France
| | - Lorenzo Archetti
- Deep Quantitative Biology Department, Nanolive SA, Tolochenaz, Switzerland
| | - Hugo Moreno
- Deep Quantitative Biology Department, Nanolive SA, Tolochenaz, Switzerland
| | - Alexandre Jeanne
- Deep Quantitative Biology Department, Nanolive SA, Tolochenaz, Switzerland
| | - Agathe Marguier
- Deep Quantitative Biology Department, Nanolive SA, Tolochenaz, Switzerland
| | - Julian Buchrieser
- Virus & Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 3569, Paris, France
| | - Timothy Wai
- Mitochondrial Biology Group, Institut Pasteur, Université Paris Cité, CNRS, UMR 3691, Paris, France
| | - Olivier Schwartz
- Virus & Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 3569, Paris, France.
- Vaccine Research Institute, Creteil, France.
| | - Mathieu Fréchin
- Deep Quantitative Biology Department, Nanolive SA, Tolochenaz, Switzerland.
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12
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Carvajal JJ, García-Castillo V, Cuellar SV, Campillay-Véliz CP, Salazar-Ardiles C, Avellaneda AM, Muñoz CA, Retamal-Díaz A, Bueno SM, González PA, Kalergis AM, Lay MK. New insights into the pathogenesis of SARS-CoV-2 during and after the COVID-19 pandemic. Front Immunol 2024; 15:1363572. [PMID: 38911850 PMCID: PMC11190347 DOI: 10.3389/fimmu.2024.1363572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 04/24/2024] [Indexed: 06/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the respiratory distress condition known as COVID-19. This disease broadly affects several physiological systems, including the gastrointestinal, renal, and central nervous (CNS) systems, significantly influencing the patient's overall quality of life. Additionally, numerous risk factors have been suggested, including gender, body weight, age, metabolic status, renal health, preexisting cardiomyopathies, and inflammatory conditions. Despite advances in understanding the genome and pathophysiological ramifications of COVID-19, its precise origins remain elusive. SARS-CoV-2 interacts with a receptor-binding domain within angiotensin-converting enzyme 2 (ACE2). This receptor is expressed in various organs of different species, including humans, with different abundance. Although COVID-19 has multiorgan manifestations, the main pathologies occur in the lung, including pulmonary fibrosis, respiratory failure, pulmonary embolism, and secondary bacterial pneumonia. In the post-COVID-19 period, different sequelae may occur, which may have various causes, including the direct action of the virus, alteration of the immune response, and metabolic alterations during infection, among others. Recognizing the serious adverse health effects associated with COVID-19, it becomes imperative to comprehensively elucidate and discuss the existing evidence surrounding this viral infection, including those related to the pathophysiological effects of the disease and the subsequent consequences. This review aims to contribute to a comprehensive understanding of the impact of COVID-19 and its long-term effects on human health.
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Affiliation(s)
- Jonatan J. Carvajal
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Valeria García-Castillo
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Shelsy V. Cuellar
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | | | - Camila Salazar-Ardiles
- Center for Research in Physiology and Altitude Medicine (FIMEDALT), Biomedical Department, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Andrea M. Avellaneda
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Department of Basic Sciences, Faculty of Sciences, Universidad Santo Tomás, Antofagasta, Chile
| | - Christian A. Muñoz
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Angello Retamal-Díaz
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Susan M. Bueno
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo A. González
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Margarita K. Lay
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
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13
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Maiti AK. Progressive Evolutionary Dynamics of Gene-Specific ω Led to the Emergence of Novel SARS-CoV-2 Strains Having Super-Infectivity and Virulence with Vaccine Neutralization. Int J Mol Sci 2024; 25:6306. [PMID: 38928018 PMCID: PMC11204377 DOI: 10.3390/ijms25126306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/21/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
An estimation of the proportion of nonsynonymous to synonymous mutation (dn/ds, ω) of the SARS-CoV-2 genome would indicate the evolutionary dynamics necessary to evolve into novel strains with increased infection, virulence, and vaccine neutralization. A temporal estimation of ω of the whole genome, and all twenty-nine SARS-CoV-2 genes of major virulent strains of alpha, delta and omicron demonstrates that the SARS-CoV-2 genome originally emerged (ω ~ 0.04) with a strong purifying selection (ω < 1) and reached (ω ~ 0.85) in omicron towards diversifying selection (ω > 1). A marked increase in the ω occurred in the spike gene from alpha (ω = 0.2) to omicron (ω = 1.97). The ω of the replication machinery genes including RDRP, NSP3, NSP4, NSP7, NSP8, NSP10, NSP13, NSP14, and ORF9 are markedly increased, indicating that these genes/proteins are yet to be evolutionary stabilized and are contributing to the evolution of novel virulent strains. The delta-specific maximum increase in ω in the immunomodulatory genes of NSP8, NSP10, NSP16, ORF4, ORF5, ORF6, ORF7A, and ORF8 compared to alpha or omicron indicates delta-specific vulnerabilities for severe COVID-19 related hospitalization and death. The maximum values of ω are observed for spike (S), NSP4, ORF8 and NSP15, which indicates that the gene-specific temporal estimation of ω identifies specific genes for its super-infectivity and virulency that could be targeted for drug development.
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Affiliation(s)
- Amit K Maiti
- Department of Genetics and Genomics, Mydnavar, 28475 Greenfield Rd, Southfield, MI 48076, USA
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14
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Caobi A, Saeed M. Upping the ante: enhanced expression of interferon-antagonizing ORF6 and ORF9b proteins by SARS-CoV-2 variants of concern. Curr Opin Microbiol 2024; 79:102454. [PMID: 38518551 PMCID: PMC11162932 DOI: 10.1016/j.mib.2024.102454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/24/2024]
Abstract
SARS-CoV-2 exhibits a remarkable capability to subvert the host antiviral innate immune system. This adeptness is orchestrated by viral proteins, which initially attempt to obstruct the activation of the antiviral immune program and then act as a fail-safe mechanism to mitigate the downstream effects of the activated immune response. This dual strategy leads to delayed expression and enfeebled action of type-I and -III interferons at the infection site, enabling the virus to replicate extensively in the lungs and subsequently disseminate to other organs. Throughout the course of the COVID-19 pandemic, SARS-CoV-2 has undergone evolution, giving rise to several variants of concern, some with exceedingly higher transmission and virulence. These improved features have been linked, at least in part, to the heightened expression or activity of specific viral proteins involved in circumventing host defense mechanisms. In this review, we aim to provide a concise summary of two SARS-CoV-2 proteins, ORF6 and ORF9b, which provided selective advantage to certain variants, affecting their biology and pathogenesis.
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Affiliation(s)
- Allen Caobi
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Mohsan Saeed
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA.
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15
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Hoenigsperger H, Sivarajan R, Sparrer KM. Differences and similarities between innate immune evasion strategies of human coronaviruses. Curr Opin Microbiol 2024; 79:102466. [PMID: 38555743 DOI: 10.1016/j.mib.2024.102466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/20/2024] [Accepted: 03/12/2024] [Indexed: 04/02/2024]
Abstract
So far, seven coronaviruses have emerged in humans. Four recurring endemic coronaviruses cause mild respiratory symptoms. Infections with epidemic Middle East respiratory syndrome-related coronavirus or severe acute respiratory syndrome coronavirus (SARS-CoV)-1 are associated with high mortality rates. SARS-CoV-2 is the causative agent of the coronavirus disease 2019 pandemic. To establish an infection, coronaviruses evade restriction by human innate immune defenses, such as the interferon system, autophagy and the inflammasome. Here, we review similar and distinct innate immune manipulation strategies employed by the seven human coronaviruses. We further discuss the impact on pathogenesis, zoonotic emergence and adaptation. Understanding the nature of the interplay between endemic/epidemic/pandemic coronaviruses and host defenses may help to better assess the pandemic potential of emerging coronaviruses.
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Affiliation(s)
- Helene Hoenigsperger
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Rinu Sivarajan
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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16
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Li Y, Tan X, Deng J, Liu X, Liu Q, Zhang Z, Huang X, Shen C, Xu K, Zhou L, Chen Y. An optimized high-throughput SARS-CoV-2 dual reporter trans-complementation system for antiviral screening in vitro and in vivo. Virol Sin 2024; 39:447-458. [PMID: 38548102 PMCID: PMC11280264 DOI: 10.1016/j.virs.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/21/2024] [Indexed: 04/25/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still epidemic around the world. The manipulation of SARS-CoV-2 is restricted to biosafety level 3 laboratories (BSL-3). In this study, we developed a SARS-CoV-2 ΔN-GFP-HiBiT replicon delivery particles (RDPs) encoding a dual reporter gene, GFP-HiBiT, capable of producing both GFP signal and luciferase activities. Through optimal selection of the reporter gene, GFP-HiBiT demonstrated superior stability and convenience for antiviral evaluation. Additionally, we established a RDP infection mouse model by delivering the N gene into K18-hACE2 KI mouse through lentivirus. This mouse model supports RDP replication and can be utilized for in vivo antiviral evaluations. In summary, the RDP system serves as a valuable tool for efficient antiviral screening and studying the gene function of SARS-CoV-2. Importantly, this system can be manipulated in BSL-2 laboratories, decreasing the threshold of experimental requirements.
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Affiliation(s)
- Yingjian Li
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Xue Tan
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Jikai Deng
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Xuemei Liu
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Qianyun Liu
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Zhen Zhang
- Institute for Vaccine Research at Animal Bio-safety Level Ⅲ Laboratory, Wuhan University School of Medicine, Wuhan, 430071, China
| | - Xiaoya Huang
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Chao Shen
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Ke Xu
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Li Zhou
- Institute for Vaccine Research at Animal Bio-safety Level Ⅲ Laboratory, Wuhan University School of Medicine, Wuhan, 430071, China
| | - Yu Chen
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China.
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17
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Xue S, Han Y, Wu F, Wang Q. Mutations in the SARS-CoV-2 spike receptor binding domain and their delicate balance between ACE2 affinity and antibody evasion. Protein Cell 2024; 15:403-418. [PMID: 38442025 PMCID: PMC11131022 DOI: 10.1093/procel/pwae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Intensive selection pressure constrains the evolutionary trajectory of SARS-CoV-2 genomes and results in various novel variants with distinct mutation profiles. Point mutations, particularly those within the receptor binding domain (RBD) of SARS-CoV-2 spike (S) protein, lead to the functional alteration in both receptor engagement and monoclonal antibody (mAb) recognition. Here, we review the data of the RBD point mutations possessed by major SARS-CoV-2 variants and discuss their individual effects on ACE2 affinity and immune evasion. Many single amino acid substitutions within RBD epitopes crucial for the antibody evasion capacity may conversely weaken ACE2 binding affinity. However, this weakened effect could be largely compensated by specific epistatic mutations, such as N501Y, thus maintaining the overall ACE2 affinity for the spike protein of all major variants. The predominant direction of SARS-CoV-2 evolution lies neither in promoting ACE2 affinity nor evading mAb neutralization but in maintaining a delicate balance between these two dimensions. Together, this review interprets how RBD mutations efficiently resist antibody neutralization and meanwhile how the affinity between ACE2 and spike protein is maintained, emphasizing the significance of comprehensive assessment of spike mutations.
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Affiliation(s)
- Song Xue
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yuru Han
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Fan Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
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18
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Otter CJ, Renner DM, Fausto A, Tan LH, Cohen NA, Weiss SR. Interferon signaling in the nasal epithelium distinguishes among lethal and common cold coronaviruses and mediates viral clearance. Proc Natl Acad Sci U S A 2024; 121:e2402540121. [PMID: 38758698 PMCID: PMC11127059 DOI: 10.1073/pnas.2402540121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/27/2024] [Indexed: 05/19/2024] Open
Abstract
All respiratory viruses establish primary infections in the nasal epithelium, where efficient innate immune induction may prevent dissemination to the lower airway and thus minimize pathogenesis. Human coronaviruses (HCoVs) cause a range of pathologies, but the host and viral determinants of disease during common cold versus lethal HCoV infections are poorly understood. We model the initial site of infection using primary nasal epithelial cells cultured at an air-liquid interface (ALI). HCoV-229E, HCoV-NL63, and human rhinovirus-16 are common cold-associated viruses that exhibit unique features in this model: early induction of antiviral interferon (IFN) signaling, IFN-mediated viral clearance, and preferential replication at nasal airway temperature (33 °C) which confers muted host IFN responses. In contrast, lethal SARS-CoV-2 and MERS-CoV encode antagonist proteins that prevent IFN-mediated clearance in nasal cultures. Our study identifies features shared among common cold-associated viruses, highlighting nasal innate immune responses as predictive of infection outcomes and nasally directed IFNs as potential therapeutics.
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Affiliation(s)
- Clayton J. Otter
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - David M. Renner
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Alejandra Fausto
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Li Hui Tan
- Department of Otorhinolaryngology-Head and Neck Surgery, Division of Rhinology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Noam A. Cohen
- Department of Otorhinolaryngology-Head and Neck Surgery, Division of Rhinology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Surgery, Corporal Michael J. Crescenz Department of Veterans Affairs Medical Center, Philadelphia, PA19104
- Monell Chemical Senses Center, Philadelphia, PA19104
| | - Susan R. Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
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19
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Solstad AD, Denz PJ, Kenney AD, Mahfooz NS, Speaks S, Gong Q, Robinson RT, Long ME, Forero A, Yount JS, Hemann EA. IFN-λ uniquely promotes CD8 T cell immunity against SARS-CoV-2 relative to type I IFN. JCI Insight 2024; 9:e171830. [PMID: 38973611 DOI: 10.1172/jci.insight.171830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 05/15/2024] [Indexed: 07/09/2024] Open
Abstract
Optimization of protective immune responses against SARS-CoV-2 remains an urgent worldwide priority. In this regard, type III IFN (IFN-λ) restricts SARS-CoV-2 infection in vitro, and treatment with IFN-λ limits infection, inflammation, and pathogenesis in murine models. Furthermore, IFN-λ has been developed for clinical use to limit COVID-19 severity. However, whether endogenous IFN-λ signaling has an effect on SARS-CoV-2 antiviral immunity and long-term immune protection in vivo is unknown. In this study, we identified a requirement for IFN-λ signaling in promoting viral clearance and protective immune programming in SARS-CoV-2 infection of mice. Expression of both IFN and IFN-stimulated gene (ISG) in the lungs were minimally affected by the absence of IFN-λ signaling and correlated with transient increases in viral titers. We found that IFN-λ supported the generation of protective CD8 T cell responses against SARS-CoV-2 by facilitating accumulation of CD103+ DC in lung draining lymph nodes (dLN). IFN-λ signaling specifically in DCs promoted the upregulation of costimulatory molecules and the proliferation of CD8 T cells. Intriguingly, antigen-specific CD8 T cell immunity to SARS-CoV-2 was independent of type I IFN signaling, revealing a nonredundant function of IFN-λ. Overall, these studies demonstrate a critical role for IFN-λ in protective innate and adaptive immunity upon infection with SARS-CoV-2 and suggest that IFN-λ serves as an immune adjuvant to support CD8 T cell immunity.
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Affiliation(s)
- Abigail D Solstad
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Parker J Denz
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Adam D Kenney
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Najmus S Mahfooz
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Samuel Speaks
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Qiaoke Gong
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Richard T Robinson
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Matthew E Long
- Dorothy M. Davis Heart and Lung Research Institute and
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Adriana Forero
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Dorothy M. Davis Heart and Lung Research Institute and
| | - Jacob S Yount
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Emily A Hemann
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Dorothy M. Davis Heart and Lung Research Institute and
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20
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Kong X, Wang Q, Wang X, Yang K, Nie S, Li Y, Lao W, Yu X, Zhang Y, Li Z, Liu Y, Ning J, Wang Y, Bi C, Wu C, Zhai A. LINC01002 functions as a ceRNA to regulate FRMD8 by sponging miR-4324 for the development of COVID-19. Virol J 2024; 21:109. [PMID: 38734674 PMCID: PMC11088083 DOI: 10.1186/s12985-024-02382-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 05/03/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Syndrome coronavirus-2 (SARS-CoV-2) has developed various strategies to evade the antiviral impact of type I IFN. Non-structural proteins and auxiliary proteins have been extensively researched on their role in immune escape. Nevertheless, the detailed mechanisms of structural protein-induced immune evasion have not been well elucidated. METHODS Human alveolar basal epithelial carcinoma cell line (A549) was stimulated with polyinosinic-polycytidylic acid (PIC) and independently transfected with four structural proteins expression plasmids, including nucleocapsid (N), spike (S), membrane (M) and envelope (E) proteins. By RT-qPCR and ELISA, the structural protein with the most pronounced inhibitory effects on IFN-β induction was screened. RNA-sequencing (RNA-Seq) and two differential analysis strategies were used to obtain differentially expressed genes associated with N protein inhibition of IFN-β induction. Based on DIANA-LncBase and StarBase databases, the interactive competitive endogenous RNA (ceRNA) network for N protein-associated genes was constructed. By combining single-cell sequencing data (GSE158055), lncRNA-miRNA-mRNA axis was further determined. Finally, RT-qPCR was utilized to illustrate the regulatory functions among components of the ceRNA axis. RESULTS SARS-CoV-2 N protein inhibited IFN-β induction in human alveolar epithelial cells most significantly compared with other structural proteins. RNA-Seq data analysis revealed genes related to N protein inhibiting IFNs induction. The obtained 858 differentially expressed genes formed the reliable ceRNA network. The function of LINC01002-miR-4324-FRMD8 axis in the IFN-dominated immune evasion was further demonstrated through integrating single-cell sequencing data. Moreover, we validated that N protein could reverse the effect of PIC on LINC01002, FRMD8 and miR-4324 expression, and subsequently on IFN-β expression level. And LINC01002 could regulate the production of FRMD8 by inhibiting miR-4324. CONCLUSION SARS-CoV-2 N protein suppressed the induction of IFN-β by regulating LINC01002 which was as a ceRNA, sponging miR-4324 and participating in the regulation of FRMD8 mRNA. Our discovery provides new insights into early intervention therapy and drug development on SARS-CoV-2 infection.
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Affiliation(s)
- Xinyi Kong
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Qinjin Wang
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Xumeng Wang
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Kaming Yang
- Department of Endocrinology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Shuping Nie
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Yuetong Li
- Department of Endocrinology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Wanwen Lao
- Department of Endocrinology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Xin Yu
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Yanping Zhang
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Zhenlin Li
- Department of Endocrinology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Yang Liu
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Jie Ning
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Yan Wang
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China.
| | - Changlong Bi
- Department of Endocrinology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China.
| | - Chao Wu
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China.
| | - Aixia Zhai
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China.
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21
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Liu JX, Zhang X, Huang YQ, Hao GF, Yang GF. Multi-level bioinformatics resources support drug target discovery of protein-protein interactions. Drug Discov Today 2024; 29:103979. [PMID: 38608830 DOI: 10.1016/j.drudis.2024.103979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/14/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024]
Abstract
Drug discovery often begins with a new target. Protein-protein interactions (PPIs) are crucial to multitudinous cellular processes and offer a promising avenue for drug-target discovery. PPIs are characterized by multi-level complexity: at the protein level, interaction networks can be used to identify potential targets, whereas at the residue level, the details of the interactions of individual PPIs can be used to examine a target's druggability. Much great progress has been made in target discovery through multi-level PPI-related computational approaches, but these resources have not been fully discussed. Here, we systematically survey bioinformatics tools for identifying and assessing potential drug targets, examining their characteristics, limitations and applications. This work will aid the integration of the broader protein-to-network context with the analysis of detailed binding mechanisms to support the discovery of drug targets.
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Affiliation(s)
- Jia-Xin Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China
| | - Xiao Zhang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, PR China
| | - Yuan-Qin Huang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, PR China
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China; State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, PR China.
| | - Guang-Fu Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China.
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22
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Bhat AA, Gupta G, Goyal A, Thapa R, Almalki WH, Kazmi I, Alzarea SI, Kukreti N, Sekar M, Meenakshi DU, Singh SK, MacLoughlin R, Dua K. Unwinding circular RNA's role in inflammatory pulmonary diseases. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:2567-2588. [PMID: 37917370 DOI: 10.1007/s00210-023-02809-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023]
Abstract
Circular RNAs (circRNAs) have emerged as pivotal regulators of gene expression and cellular processes in various physiological and pathological conditions. In recent years, there has been a growing interest in investigating the role of circRNAs in inflammatory lung diseases, owing to their potential to modulate inflammation-associated pathways and contribute to disease pathogenesis. Inflammatory lung diseases, like asthma, chronic obstructive pulmonary disease (COPD), and COVID-19, pose significant global health challenges. The dysregulation of inflammatory responses demonstrates a pivotal function in advancing these diseases. CircRNAs have been identified as important players in regulating inflammation by functioning as miRNA sponges, engaging with RNA-binding proteins, and participating in intricate ceRNA networks. These interactions enable circRNAs to regulate the manifestation of key inflammatory genes and signaling pathways. Furthermore, emerging evidence suggests that specific circRNAs are differentially expressed in response to inflammatory stimuli and exhibit distinct patterns in various lung diseases. Their involvement in immune cell activation, cytokine production, and tissue remodeling processes underscores their possible capabilities as therapeutic targets and diagnostic biomarkers. Harnessing the knowledge of circRNA-mediated regulation in inflammatory lung diseases could lead to the development of innovative strategies for disease management and intervention. This review summarizes the current understanding of the role of circRNAs in inflammatory lung diseases, focusing on their regulatory mechanisms and functional implications.
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Affiliation(s)
- Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, 602105, India.
| | - Ahsas Goyal
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, 281406, India
| | - Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72388, Al-Jouf, Saudi Arabia
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun, 248007, India
| | - Mahendran Sekar
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | | | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Ronan MacLoughlin
- Research and Development, Aerogen Limited, IDA Business Park, Galway, Connacht, H91 HE94, Ireland
- School of Pharmacy & Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Leinster, D02 YN77, Ireland
- School of Pharmacy & Pharmaceutical Sciences, Trinity College, Dublin, Leinster, D02 PN40, Ireland
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, 2007, Australia.
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23
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Makio T, Zhang K, Love N, Mast FD, Liu X, Elaish M, Hobman T, Aitchison JD, Fontoura BMA, Wozniak RW. SARS-CoV-2 Orf6 is positioned in the nuclear pore complex by Rae1 to inhibit nucleocytoplasmic transport. Mol Biol Cell 2024; 35:ar62. [PMID: 38507240 PMCID: PMC11151100 DOI: 10.1091/mbc.e23-10-0386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/07/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) accessory protein Orf6 works as an interferon antagonist, in part, by inhibiting the nuclear import activated p-STAT1, an activator of interferon-stimulated genes, and the export of the poly(A) RNA. Insight into the transport regulatory function of Orf6 has come from the observation that Orf6 binds to the nuclear pore complex (NPC) components: Rae1 and Nup98. To gain further insight into the mechanism of Orf6-mediated transport inhibition, we examined the role of Rae1 and Nup98. We show that Rae1 alone is not necessary to support p-STAT1 import or nuclear export of poly(A) RNA. Moreover, the loss of Rae1 suppresses the transport inhibitory activity of Orf6. We propose that the Rae1/Nup98 complex strategically positions Orf6 within the NPC where it alters FG-Nup interactions and their ability to support nuclear transport. In addition, we show that Rae1 is required for normal viral protein production during SARS-CoV-2 infection presumably through its role in supporting Orf6 function.
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Affiliation(s)
- Tadashi Makio
- Department of Cell Biology and Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Ke Zhang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75235
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nicole Love
- Department of Cell Biology and Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Fred D. Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98101
| | - Xue Liu
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mohamed Elaish
- Department of Cell Biology and Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Tom Hobman
- Department of Cell Biology and Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - John D. Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98101
- Department of Pediatrics, University of Washington, Seattle, WA 98195
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Beatriz M. A. Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75235
| | - Richard W. Wozniak
- Department of Cell Biology and Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada T6G 2H7
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24
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Livieratos A, Gogos C, Akinosoglou K. Impact of Prior COVID-19 Immunization and/or Prior Infection on Immune Responses and Clinical Outcomes. Viruses 2024; 16:685. [PMID: 38793566 PMCID: PMC11125779 DOI: 10.3390/v16050685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Cellular and humoral immunity exhibit dynamic adaptation to the mutating SARS-CoV-2 virus. It is noteworthy that immune responses differ significantly, influenced by whether a patient has received vaccination or whether there is co-occurrence of naturally acquired and vaccine-induced immunity, known as hybrid immunity. The different immune reactions, conditional on vaccination status and the viral variant involved, bear implications for inflammatory responses, patient outcomes, pathogen transmission rates, and lingering post-COVID conditions. Considering these developments, we have performed a review of recently published literature, aiming to disentangle the intricate relationships among immunological profiles, transmission, the long-term health effects post-COVID infection poses, and the resultant clinical manifestations. This investigation is directed toward understanding the variability in the longevity and potency of cellular and humoral immune responses elicited by immunization and hybrid infection.
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Affiliation(s)
| | - Charalambos Gogos
- Department of Medicine, University of Patras, 26504 Rio, Greece; (C.G.); (K.A.)
| | - Karolina Akinosoglou
- Department of Medicine, University of Patras, 26504 Rio, Greece; (C.G.); (K.A.)
- Department of Internal Medicine and Infectious Diseases, University General Hospital of Patras, 26504 Rio, Greece
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25
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Gori Savellini G, Anichini G, Manetti F, Trivisani CI, Cusi MG. Deletion of 82-85 N-Terminal Residues in SARS-CoV-2 Nsp1 Restricts Virus Replication. Viruses 2024; 16:689. [PMID: 38793572 PMCID: PMC11125901 DOI: 10.3390/v16050689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Non-structural protein 1 (Nsp1) represents one of the most crucial SARS-CoV-2 virulence factors by inhibiting the translation of host mRNAs and promoting their degradation. We selected naturally occurring virus lineages with specific Nsp1 deletions located at both the N- and C-terminus of the protein. Our data provide new insights into how Nsp1 coordinates these functions on host and viral mRNA recognition. Residues 82-85 in the N-terminal part of Nsp1 likely play a role in docking the 40S mRNA entry channel, preserving the inhibition of host gene expression without affecting cellular mRNA decay. Furthermore, this domain prevents viral mRNAs containing the 5'-leader sequence to escape translational repression. These findings support the presence of distinct domains within the Nsp1 protein that differentially modulate mRNA recognition, translation and turnover. These insights have implications for the development of drugs targeting viral proteins and provides new evidences of how specific mutations in SARS-CoV-2 Nsp1 could attenuate the virus.
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Affiliation(s)
| | - Gabriele Anichini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
| | - Fabrizio Manetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy (C.I.T.)
| | | | - Maria Grazia Cusi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
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26
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Le Pen J, Rice CM. The antiviral state of the cell: lessons from SARS-CoV-2. Curr Opin Immunol 2024; 87:102426. [PMID: 38795501 PMCID: PMC11260430 DOI: 10.1016/j.coi.2024.102426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 02/20/2024] [Accepted: 05/06/2024] [Indexed: 05/28/2024]
Abstract
In this review, we provide an overview of the intricate host-virus interactions that have emerged from the study of SARS-CoV-2 infection. We focus on the antiviral mechanisms of interferon-stimulated genes (ISGs) and their modulation of viral entry, replication, and release. We explore the role of a selection ISGs, including BST2, CD74, CH25H, DAXX, IFI6, IFITM1-3, LY6E, NCOA7, PLSCR1, OAS1, RTP4, and ZC3HAV1/ZAP, in restricting SARS-CoV-2 infection and discuss the virus's countermeasures. By synthesizing the latest research on SARS-CoV-2 and host antiviral responses, this review aims to provide a deeper understanding of the antiviral state of the cell under SARS-CoV-2 and other viral infections, offering insights for the development of novel antiviral strategies and therapeutics.
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Affiliation(s)
- Jérémie Le Pen
- The Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.
| | - Charles M Rice
- The Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
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27
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Senevirathne TH, Wekking D, Swain JWR, Solinas C, De Silva P. COVID-19: From emerging variants to vaccination. Cytokine Growth Factor Rev 2024; 76:127-141. [PMID: 38135574 DOI: 10.1016/j.cytogfr.2023.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023]
Abstract
The vigorous spread of SARS-CoV-2 resulted in the rapid infection of millions of people worldwide and devastation of not only public healthcare, but also social, educational, and economic infrastructures. The evolution of SARS-CoV-2 over time is due to the mutations that occurred in the genome during each replication. These mutated forms of SARS-CoV-2, otherwise known as variants, were categorized as variants of interest (VOI) or variants of concern (VOC) based on the increased risk of transmissibility, disease severity, immune escape, decreased effectiveness of current social measures, and available vaccines and therapeutics. The swift development of COVID-19 vaccines has been a great success for biomedical research, and billions of vaccine doses, including boosters, have been administered worldwide. BNT162b2 vaccine (Pfizer-BioNTech), mRNA-1273 (Moderna), ChAdOx1 nCoV-19 (AstraZeneca), and Janssen (Johnson & Johnson) are the four major COVID-19 vaccines that received early regulatory authorization based on their efficacy. However, some SARS-CoV-2 variants resulted in higher resistance to available vaccines or treatments. It has been four years since the first reported infection of SARS-CoV-2, yet the Omicron variant and its subvariants are still infecting people worldwide. Despite this, COVID-19 vaccines are still expected to be effective at preventing severe disease, hospitalization, and death from COVID. In this review, we provide a comprehensive overview of the COVID-19 pandemic focused on evolution of VOC and vaccination strategies against them.
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Affiliation(s)
- Thilini H Senevirathne
- Faculty of Science, Katholieke Universiteit Leuven, Kasteelpark Arenberg, Leuven, Belgium
| | - Demi Wekking
- Amsterdam UMC, Location Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Cinzia Solinas
- Medical Oncology, AOU Cagliari, P.O. Duilio Casula, Monserrato (CA), Italy.
| | - Pushpamali De Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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28
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Monteiro MES, Lechuga GC, Napoleão-Pêgo P, Carvalho JPRS, Gomes LR, Morel CM, Provance DW, De-Simone SG. Humoral Immune Response to SARS-CoV-2 Spike Protein Receptor-Binding Motif Linear Epitopes. Vaccines (Basel) 2024; 12:342. [PMID: 38675725 PMCID: PMC11055068 DOI: 10.3390/vaccines12040342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/05/2024] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
The worldwide spread of SARS-CoV-2 has led to a significant economic and social burden on a global scale. Even though the pandemic has concluded, apprehension remains regarding the emergence of highly transmissible variants capable of evading immunity induced by either vaccination or prior infection. The success of viral penetration is due to the specific amino acid residues of the receptor-binding motif (RBM) involved in viral attachment. This region interacts with the cellular receptor ACE2, triggering a neutralizing antibody (nAb) response. In this study, we evaluated serum immunogenicity from individuals who received either a single dose or a combination of different vaccines against the original SARS-CoV-2 strain and a mutated linear RBM. Despite a modest antibody response to wild-type SARS-CoV-2 RBM, the Omicron variants exhibit four mutations in the RBM (S477N, T478K, E484A, and F486V) that result in even lower antibody titers. The primary immune responses observed were directed toward IgA and IgG. While nAbs typically target the RBD, our investigation has unveiled reduced seroreactivity within the RBD's crucial subregion, the RBM. This deficiency may have implications for the generation of protective nAbs. An evaluation of S1WT and S2WT RBM peptides binding to nAbs using microscale thermophoresis revealed a higher affinity (35 nM) for the S2WT sequence (GSTPCNGVEGFNCYF), which includes the FNCY patch. Our findings suggest that the linear RBM of SARS-CoV-2 is not an immunodominant region in vaccinated individuals. Comprehending the intricate dynamics of the humoral response, its interplay with viral evolution, and host genetics is crucial for formulating effective vaccination strategies, targeting not only SARS-CoV-2 but also anticipating potential future coronaviruses.
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Affiliation(s)
- Maria E. S. Monteiro
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Program of Post-Graduation on Parasitic Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - Guilherme C. Lechuga
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - Paloma Napoleão-Pêgo
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - João P. R. S. Carvalho
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Program of Post-Graduation on Science and Biotechnology, Department of Molecular and Cellular Biology, Biology Institute, Federal Fluminense University, Niterói 22040-036, RJ, Brazil
| | - Larissa R. Gomes
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
| | - Carlos M. Morel
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
| | - David W. Provance
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
| | - Salvatore G. De-Simone
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.S.M.); (G.C.L.); (P.N.-P.); (J.P.R.S.C.); (L.R.G.); (C.M.M.); (D.W.P.)
- Program of Post-Graduation on Parasitic Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, RJ, Brazil
- Program of Post-Graduation on Science and Biotechnology, Department of Molecular and Cellular Biology, Biology Institute, Federal Fluminense University, Niterói 22040-036, RJ, Brazil
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29
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Townsley H, Gahir J, Russell TW, Greenwood D, Carr EJ, Dyke M, Adams L, Miah M, Clayton B, Smith C, Miranda M, Mears HV, Bailey C, Black JRM, Fowler AS, Crawford M, Wilkinson K, Hutchinson M, Harvey R, O’Reilly N, Kelly G, Goldstone R, Beale R, Papineni P, Corrah T, Gilson R, Caidan S, Nicod J, Gamblin S, Kassiotis G, Libri V, Williams B, Gandhi S, Kucharski AJ, Swanton C, Bauer DLV, Wall EC. COVID-19 in non-hospitalised adults caused by either SARS-CoV-2 sub-variants Omicron BA.1, BA.2, BA.4/5 or Delta associates with similar illness duration, symptom severity and viral kinetics, irrespective of vaccination history. PLoS One 2024; 19:e0294897. [PMID: 38512960 PMCID: PMC10956747 DOI: 10.1371/journal.pone.0294897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/11/2023] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND SARS-CoV-2 variant Omicron rapidly evolved over 2022, causing three waves of infection due to sub-variants BA.1, BA.2 and BA.4/5. We sought to characterise symptoms and viral loads over the course of COVID-19 infection with these sub-variants in otherwise-healthy, vaccinated, non-hospitalised adults, and compared data to infections with the preceding Delta variant of concern (VOC). METHODS In a prospective, observational cohort study, healthy vaccinated UK adults who reported a positive polymerase chain reaction (PCR) or lateral flow test, self-swabbed on alternate weekdays until day 10. We compared participant-reported symptoms and viral load trajectories between infections caused by VOCs Delta and Omicron (sub-variants BA.1, BA.2 or BA.4/5), and tested for relationships between vaccine dose, symptoms and PCR cycle threshold (Ct) as a proxy for viral load using Chi-squared (χ2) and Wilcoxon tests. RESULTS 563 infection episodes were reported among 491 participants. Across infection episodes, there was little variation in symptom burden (4 [IQR 3-5] symptoms) and duration (8 [IQR 6-11] days). Whilst symptom profiles differed among infections caused by Delta compared to Omicron sub-variants, symptom profiles were similar between Omicron sub-variants. Anosmia was reported more frequently in Delta infections after 2 doses compared with Omicron sub-variant infections after 3 doses, for example: 42% (25/60) of participants with Delta infection compared to 9% (6/67) with Omicron BA.4/5 (χ2 P < 0.001; OR 7.3 [95% CI 2.7-19.4]). Fever was less common with Delta (20/60 participants; 33%) than Omicron BA.4/5 (39/67; 58%; χ2 P = 0.008; OR 0.4 [CI 0.2-0.7]). Amongst infections with an Omicron sub-variants, symptoms of coryza, fatigue, cough and myalgia predominated. Viral load trajectories and peaks did not differ between Delta, and Omicron, irrespective of symptom severity (including asymptomatic participants), VOC or vaccination status. PCR Ct values were negatively associated with time since vaccination in participants infected with BA.1 (β = -0.05 (CI -0.10-0.01); P = 0.031); however, this trend was not observed in BA.2 or BA.4/5 infections. CONCLUSION Our study emphasises both the changing symptom profile of COVID-19 infections in the Omicron era, and ongoing transmission risk of Omicron sub-variants in vaccinated adults. TRIAL REGISTRATION NCT04750356.
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Affiliation(s)
- Hermaleigh Townsley
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Joshua Gahir
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Timothy W. Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | | | - Matala Dyke
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Lorin Adams
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Murad Miah
- The Francis Crick Institute, London, United Kingdom
| | | | - Callie Smith
- The Francis Crick Institute, London, United Kingdom
| | | | | | - Chris Bailey
- The Francis Crick Institute, London, United Kingdom
| | - James R. M. Black
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | | | | | | | | | - Ruth Harvey
- The Francis Crick Institute, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | | | - Gavin Kelly
- The Francis Crick Institute, London, United Kingdom
| | | | - Rupert Beale
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | | | - Tumena Corrah
- London Northwest University Healthcare NHS Trust, London, United Kingdom
| | - Richard Gilson
- Camden and North West London NHS Community Trust, London, United Kingdom
| | - Simon Caidan
- The Francis Crick Institute, London, United Kingdom
| | - Jerome Nicod
- The Francis Crick Institute, London, United Kingdom
| | | | - George Kassiotis
- The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, St Mary’s Hospital, Imperial College London, London, United Kingdom
| | - Vincenzo Libri
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Sonia Gandhi
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Adam J. Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Charles Swanton
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - David L. V. Bauer
- The Francis Crick Institute, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | - Emma C. Wall
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
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30
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Karim F, Riou C, Bernstein M, Jule Z, Lustig G, van Graan S, Keeton RS, Upton JL, Ganga Y, Khan K, Reedoy K, Mazibuko M, Govender K, Thambu K, Ngcobo N, Venter E, Makhado Z, Hanekom W, von Gottberg A, Hoque M, Karim QA, Abdool Karim SS, Manickchund N, Magula N, Gosnell BI, Lessells RJ, Moore PL, Burgers WA, de Oliveira T, Moosa MYS, Sigal A. Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation. Nat Commun 2024; 15:2360. [PMID: 38491050 PMCID: PMC10943233 DOI: 10.1038/s41467-024-46673-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/27/2024] [Indexed: 03/18/2024] Open
Abstract
SARS-CoV-2 clearance requires adaptive immunity but the contribution of neutralizing antibodies and T cells in different immune states is unclear. Here we ask which adaptive immune responses associate with clearance of long-term SARS-CoV-2 infection in HIV-mediated immunosuppression after suppressive antiretroviral therapy (ART) initiation. We assembled a cohort of SARS-CoV-2 infected people in South Africa (n = 994) including participants with advanced HIV disease characterized by immunosuppression due to T cell depletion. Fifty-four percent of participants with advanced HIV disease had prolonged SARS-CoV-2 infection (>1 month). In the five vaccinated participants with advanced HIV disease tested, SARS-CoV-2 clearance associates with emergence of neutralizing antibodies but not SARS-CoV-2 specific CD8 T cells, while CD4 T cell responses were not determined due to low cell numbers. Further, complete HIV suppression is not required for clearance, although it is necessary for an effective vaccine response. Persistent SARS-CoV-2 infection led to SARS-CoV-2 evolution, including virus with extensive neutralization escape in a Delta variant infected participant. The results provide evidence that neutralizing antibodies are required for SARS-CoV-2 clearance in HIV-mediated immunosuppression recovery, and that suppressive ART is necessary to curtail evolution of co-infecting pathogens to reduce individual health consequences as well as public health risk linked with generation of escape mutants.
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Affiliation(s)
- Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | | | - Zesuliwe Jule
- Africa Health Research Institute, Durban, South Africa
| | - Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Strauss van Graan
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Roanne S Keeton
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | | | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, Durban, South Africa
| | | | | | | | | | - Elizabeth Venter
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Zanele Makhado
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Willem Hanekom
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Monjurul Hoque
- KwaDabeka Community Health Centre, KwaDabeka, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nithendra Manickchund
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nombulelo Magula
- Department of Internal Medicine, Nelson R. Mandela School of Medicine, University of Kwa-Zulu Natal, Durban, South Africa
| | - Bernadett I Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J Lessells
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Penny L Moore
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Tulio de Oliveira
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.
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Álvarez-Herrera M, Sevilla J, Ruiz-Rodriguez P, Vergara A, Vila J, Cano-Jiménez P, González-Candelas F, Comas I, Coscollá M. VIPERA: Viral Intra-Patient Evolution Reporting and Analysis. Virus Evol 2024; 10:veae018. [PMID: 38510921 PMCID: PMC10953798 DOI: 10.1093/ve/veae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/02/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Viral mutations within patients nurture the adaptive potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during chronic infections, which are a potential source of variants of concern. However, there is no integrated framework for the evolutionary analysis of intra-patient SARS-CoV-2 serial samples. Herein, we describe Viral Intra-Patient Evolution Reporting and Analysis (VIPERA), a new software that integrates the evaluation of the intra-patient ancestry of SARS-CoV-2 sequences with the analysis of evolutionary trajectories of serial sequences from the same viral infection. We have validated it using positive and negative control datasets and have successfully applied it to a new case, which revealed population dynamics and evidence of adaptive evolution. VIPERA is available under a free software license at https://github.com/PathoGenOmics-Lab/VIPERA.
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Affiliation(s)
- Miguel Álvarez-Herrera
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Jordi Sevilla
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Paula Ruiz-Rodriguez
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Andrea Vergara
- Department of Clinical Microbiology, CDB, Hospital Clínic of Barcelona; University of Barcelona; ISGlobal, C. de Villarroel, 170, Barcelona 08007, Spain
- CIBER of Infectious Diseases (CIBERINFEC), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Jordi Vila
- Department of Clinical Microbiology, CDB, Hospital Clínic of Barcelona; University of Barcelona; ISGlobal, C. de Villarroel, 170, Barcelona 08007, Spain
- CIBER of Infectious Diseases (CIBERINFEC), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Pablo Cano-Jiménez
- Institute of Biomedicine of Valencia (IBV-CSIC), C/ Jaime Roig, 11, Valencia 46010, Spain
| | - Fernando González-Candelas
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Iñaki Comas
- Institute of Biomedicine of Valencia (IBV-CSIC), C/ Jaime Roig, 11, Valencia 46010, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Mireia Coscollá
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
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32
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Kaneko T, Ezra S, Abdo R, Voss C, Zhong S, Liu X, Hovey O, Slessarev M, Van Nynatten LR, Ye M, Fraser DD, Li SSC. Kinome and phosphoproteome reprogramming underlies the aberrant immune responses in critically ill COVID-19 patients. Clin Proteomics 2024; 21:13. [PMID: 38389037 PMCID: PMC10882830 DOI: 10.1186/s12014-024-09457-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
SARS-CoV-2 infection triggers extensive host immune reactions, leading to severe diseases in certain individuals. However, the molecular basis underlying the excessive yet non-productive immune responses in severe COVID-19 remains incompletely understood. In this study, we conducted a comprehensive analysis of the peripheral blood mononuclear cell (PBMC) proteome and phosphoproteome in sepsis patients positive or negative for SARS-CoV-2 infection, as well as healthy subjects, using quantitative mass spectrometry. Our findings demonstrate dynamic changes in the COVID-19 PBMC proteome and phosphoproteome during disease progression, with distinctive protein or phosphoprotein signatures capable of distinguishing longitudinal disease states. Furthermore, SARS-CoV-2 infection induces a global reprogramming of the kinome and phosphoproteome, resulting in defective adaptive immune response mediated by the B and T lymphocytes, compromised innate immune responses involving the SIGLEC and SLAM family of immunoreceptors, and excessive cytokine-JAK-STAT signaling. In addition to uncovering host proteome and phosphoproteome aberrations caused by SARS-CoV-2, our work recapitulates several reported therapeutic targets for COVID-19 and identified numerous new candidates, including the kinases PKG1, CK2, ROCK1/2, GRK2, SYK, JAK2/3, TYK2, DNA-PK, PKCδ, and the cytokine IL-12.
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Affiliation(s)
- Tomonori Kaneko
- Departments of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Sally Ezra
- Departments of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Rober Abdo
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Courtney Voss
- Departments of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Shanshan Zhong
- Departments of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Xuguang Liu
- Departments of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Owen Hovey
- Departments of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Marat Slessarev
- Departments of Medicine and Pediatrics, Western University, London, Canada
| | | | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Douglas D Fraser
- Departments of Medicine and Pediatrics, Western University, London, Canada
- Lawson Health Research Institute, 750 Base Line Rd E, London, ON, N6C 2R5, Canada
| | - Shawn Shun-Cheng Li
- Departments of Biochemistry, Western University, London, ON, N6A 5C1, Canada.
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33
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Korosec CS, Wahl LM, Heffernan JM. Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections? Virus Evol 2024; 10:veae006. [PMID: 38425472 PMCID: PMC10904108 DOI: 10.1093/ve/veae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/20/2023] [Accepted: 01/12/2024] [Indexed: 03/02/2024] Open
Abstract
Despite a relatively low mutation rate, the large number of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has allowed for substantial genetic change, leading to a multitude of emerging variants. Using a recently determined mutation rate (per site replication), as well as within-host parameter estimates for symptomatic SARS-CoV-2 infection, we apply a stochastic transmission-bottleneck model to describe the survival probability of de novo SARS-CoV-2 mutations as a function of bottleneck size and selection coefficient. For narrow bottlenecks, we find that mutations affecting per-target-cell attachment rate (with phenotypes associated with fusogenicity and ACE2 binding) have similar transmission probabilities to mutations affecting viral load clearance (with phenotypes associated with humoral evasion). We further find that mutations affecting the eclipse rate (with phenotypes associated with reorganization of cellular metabolic processes and synthesis of viral budding precursor material) are highly favoured relative to all other traits examined. We find that mutations leading to reduced removal rates of infected cells (with phenotypes associated with innate immune evasion) have limited transmission advantage relative to mutations leading to humoral evasion. Predicted transmission probabilities, however, for mutations affecting innate immune evasion are more consistent with the range of clinically estimated household transmission probabilities for de novo mutations. This result suggests that although mutations affecting humoral evasion are more easily transmitted when they occur, mutations affecting innate immune evasion may occur more readily. We examine our predictions in the context of a number of previously characterized mutations in circulating strains of SARS-CoV-2. Our work offers both a null model for SARS-CoV-2 mutation rates and predicts which aspects of viral life history are most likely to successfully evolve, despite low mutation rates and repeated transmission bottlenecks.
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Affiliation(s)
- Chapin S Korosec
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
- Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
| | - Lindi M Wahl
- Applied Mathematics, Western University, 1151 Richmond St, London, ON N6A 5B7, Canada
| | - Jane M Heffernan
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
- Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
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34
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Qin Q, Jiang X, Huo L, Qian J, Yu H, Zhu H, Du W, Cao Y, Zhang X, Huang Q. Computational design and engineering of self-assembling multivalent microproteins with therapeutic potential against SARS-CoV-2. J Nanobiotechnology 2024; 22:58. [PMID: 38341574 PMCID: PMC10858482 DOI: 10.1186/s12951-024-02329-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Multivalent drugs targeting homo-oligomeric viral surface proteins, such as the SARS-CoV-2 trimeric spike (S) protein, have the potential to elicit more potent and broad-spectrum therapeutic responses than monovalent drugs by synergistically engaging multiple binding sites on viral targets. However, rational design and engineering of nanoscale multivalent protein drugs are still lacking. Here, we developed a computational approach to engineer self-assembling trivalent microproteins that simultaneously bind to the three receptor binding domains (RBDs) of the S protein. This approach involves four steps: structure-guided linker design, molecular simulation evaluation of self-assembly, experimental validation of self-assembly state, and functional testing. Using this approach, we first designed trivalent constructs of the microprotein miniACE2 (MP) with different trimerization scaffolds and linkers, and found that one of the constructs (MP-5ff) showed high trimerization efficiency, good conformational homogeneity, and strong antiviral neutralizing activity. With its trimerization unit (5ff), we then engineered a trivalent nanobody (Tr67) that exhibited potent and broad neutralizing activity against the dominant Omicron variants, including XBB.1 and XBB.1.5. Cryo-EM complex structure confirmed that Tr67 stably binds to all three RBDs of the Omicron S protein in a synergistic form, locking them in the "3-RBD-up" conformation that could block human receptor (ACE2) binding and potentially facilitate immune clearance. Therefore, our approach provides an effective strategy for engineering potent protein drugs against SARS-CoV-2 and other deadly coronaviruses.
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Affiliation(s)
- Qin Qin
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xinyi Jiang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Liyun Huo
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jiaqiang Qian
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | | | - Haixia Zhu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Wenhao Du
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yuhui Cao
- ACROBiosystems Inc, Beijing, 100176, China
| | - Xing Zhang
- ACROBiosystems Inc, Beijing, 100176, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, 201203, China.
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35
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Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser MC, Zhou Y, McKetney J, Guiley KZ, Chan U, Kaye JA, Chadha N, Cakir M, Gordon M, Khare P, Drake S, Drury V, Burke DF, Gonzalez S, Alkhairy S, Thomas R, Lam S, Morris M, Bader E, Seyler M, Baum T, Krasnoff R, Wang S, Pham P, Arbalaez J, Pratt D, Chag S, Mahmood N, Rolland T, Bourgeron T, Finkbeiner S, Swaney DL, Bandyopadhay S, Ideker T, Beltrao P, Willsey HR, Obernier K, Nowakowski TJ, Hüttenhain R, State MW, Willsey AJ, Krogan NJ. A foundational atlas of autism protein interactions reveals molecular convergence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.03.569805. [PMID: 38076945 PMCID: PMC10705567 DOI: 10.1101/2023.12.03.569805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Translating high-confidence (hc) autism spectrum disorder (ASD) genes into viable treatment targets remains elusive. We constructed a foundational protein-protein interaction (PPI) network in HEK293T cells involving 100 hcASD risk genes, revealing over 1,800 PPIs (87% novel). Interactors, expressed in the human brain and enriched for ASD but not schizophrenia genetic risk, converged on protein complexes involved in neurogenesis, tubulin biology, transcriptional regulation, and chromatin modification. A PPI map of 54 patient-derived missense variants identified differential physical interactions, and we leveraged AlphaFold-Multimer predictions to prioritize direct PPIs and specific variants for interrogation in Xenopus tropicalis and human forebrain organoids. A mutation in the transcription factor FOXP1 led to reconfiguration of DNA binding sites and altered development of deep cortical layer neurons in forebrain organoids. This work offers new insights into molecular mechanisms underlying ASD and describes a powerful platform to develop and test therapeutic strategies for many genetically-defined conditions.
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36
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den Brave F, Pfanner N, Becker T. Mitochondrial entry gate as regulatory hub. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119529. [PMID: 37951505 DOI: 10.1016/j.bbamcr.2023.119529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 11/14/2023]
Abstract
Mitochondria import 1000-1300 different precursor proteins from the cytosol. The main mitochondrial entry gate is formed by the translocase of the outer membrane (TOM complex). Molecular coupling and modification of TOM subunits control and modulate protein import in response to cellular signaling. The TOM complex functions as regulatory hub to integrate mitochondrial protein biogenesis and quality control into the cellular proteostasis network.
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Affiliation(s)
- Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany.
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37
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Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Cell Mol Immunol 2024; 21:171-183. [PMID: 37985854 PMCID: PMC10805730 DOI: 10.1038/s41423-023-01104-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
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Affiliation(s)
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kata Csiba
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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38
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Ciubotariu II, Wilkes RP, Kattoor JJ, Christian EN, Carpi G, Kitchen A. Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population. Microb Genom 2024; 10:001194. [PMID: 38334271 PMCID: PMC10926704 DOI: 10.1099/mgen.0.001194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the coronavirus disease 2019 (COVID-19) pandemic extends into its fourth year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in higher education settings and will inform public health policy during pandemics. In this study, we generated 793 whole-genome sequences collected over an entire academic year in a university population in Indiana, USA. We clearly captured the rapidity with which Delta variant was wholly replaced by Omicron variant across the West Lafayette campus over the length of two academic semesters in a community with high vaccination rates. This mirrored the emergence of Omicron throughout the state of Indiana and the USA. Further, phylogenetic analyses demonstrated that there was a more diverse set of potential geographic origins for Omicron viruses introduction into campus when compared to Delta. Lastly, statistics indicated that there was a more significant role for international and out-of-state migration in the establishment of Omicron variants at Purdue. This surveillance workflow, coupled with viral genomic sequencing and phylogeographic analyses, provided critical insights into SARS-CoV-2 transmission dynamics and variant arrival.
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Affiliation(s)
- Ilinca I. Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Rebecca P. Wilkes
- Department of Comparative Pathobiology, Animal Disease Diagnostic Laboratory, Purdue University College of Veterinary Medicine, West Lafayette, Indiana 47907, USA
| | - Jobin J. Kattoor
- Department of Comparative Pathobiology, Animal Disease Diagnostic Laboratory, Purdue University College of Veterinary Medicine, West Lafayette, Indiana 47907, USA
| | - Erin N. Christian
- Department of Comparative Pathobiology, Animal Disease Diagnostic Laboratory, Purdue University College of Veterinary Medicine, West Lafayette, Indiana 47907, USA
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, Indiana 47907, USA
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, Iowa, USA
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39
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Reuschl AK, Thorne LG, Whelan MVX, Ragazzini R, Furnon W, Cowton VM, De Lorenzo G, Mesner D, Turner JLE, Dowgier G, Bogoda N, Bonfanti P, Palmarini M, Patel AH, Jolly C, Towers GJ. Evolution of enhanced innate immune suppression by SARS-CoV-2 Omicron subvariants. Nat Microbiol 2024; 9:451-463. [PMID: 38228858 PMCID: PMC10847042 DOI: 10.1038/s41564-023-01588-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/13/2023] [Indexed: 01/18/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) human adaptation resulted in distinct lineages with enhanced transmissibility called variants of concern (VOCs). Omicron is the first VOC to evolve distinct globally dominant subvariants. Here we compared their replication in human cell lines and primary airway cultures and measured host responses to infection. We discovered that subvariants BA.4 and BA.5 have improved their suppression of innate immunity when compared with earlier subvariants BA.1 and BA.2. Similarly, more recent subvariants (BA.2.75 and XBB lineages) also triggered reduced innate immune activation. This correlated with increased expression of viral innate antagonists Orf6 and nucleocapsid, reminiscent of VOCs Alpha to Delta. Increased Orf6 levels suppressed host innate responses to infection by decreasing IRF3 and STAT1 signalling measured by transcription factor phosphorylation and nuclear translocation. Our data suggest that convergent evolution of enhanced innate immune antagonist expression is a common pathway of human adaptation and link Omicron subvariant dominance to improved innate immune evasion.
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Affiliation(s)
| | - Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
- Department of Infectious Diseases, St Mary's Medical School, Imperial College London, London, UK
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, London, UK
| | - Roberta Ragazzini
- Division of Infection and Immunity, University College London, London, UK
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Vanessa M Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Dejan Mesner
- Division of Infection and Immunity, University College London, London, UK
| | - Jane L E Turner
- Division of Infection and Immunity, University College London, London, UK
| | - Giulia Dowgier
- Division of Infection and Immunity, University College London, London, UK
- COVID Surveillance Unit, The Francis Crick Institute, London, UK
| | - Nathasha Bogoda
- Division of Infection and Immunity, University College London, London, UK
| | - Paola Bonfanti
- Division of Infection and Immunity, University College London, London, UK
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | | | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - 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.
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Ghildiyal T, Rai N, Mishra Rawat J, Singh M, Anand J, Pant G, Kumar G, Shidiki A. Challenges in Emerging Vaccines and Future Promising Candidates against SARS-CoV-2 Variants. J Immunol Res 2024; 2024:9125398. [PMID: 38304142 PMCID: PMC10834093 DOI: 10.1155/2024/9125398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/10/2023] [Accepted: 12/18/2023] [Indexed: 02/03/2024] Open
Abstract
Since the COVID-19 outbreak, the severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) virus has evolved into variants with varied infectivity. Vaccines developed against COVID-19 infection have boosted immunity, but there is still uncertainty on how long the immunity from natural infection or vaccination will last. The present study attempts to outline the present level of information about the contagiousness and spread of SARS-CoV-2 variants of interest and variants of concern (VOCs). The keywords like COVID-19 vaccine types, VOCs, universal vaccines, bivalent, and other relevant terms were searched in NCBI, Science Direct, and WHO databases to review the published literature. The review provides an integrative discussion on the current state of knowledge on the type of vaccines developed against SARS-CoV-2, the safety and efficacy of COVID-19 vaccines concerning the VOCs, and prospects of novel universal, chimeric, and bivalent mRNA vaccines efficacy to fend off existing variants and other emerging coronaviruses. Genomic variation can be quite significant, as seen by the notable differences in impact, transmission rate, morbidity, and death during several human coronavirus outbreaks. Therefore, understanding the amount and characteristics of coronavirus genetic diversity in historical and contemporary strains can help researchers get an edge over upcoming variants.
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Affiliation(s)
- Tanmay Ghildiyal
- Department of Microbial Biotechnology, Panjab University, Chandigarh, India
| | - Nishant Rai
- Department of Biotechnology, Graphic Era Deemed to be University, Dehradun, India
| | - Janhvi Mishra Rawat
- Department of Biotechnology, Graphic Era Deemed to be University, Dehradun, India
| | - Maargavi Singh
- Department of Instrumentation and Control Engineering, Manipal Institute of Technology, Manipal, Karnataka, India
| | - Jigisha Anand
- Department of Biotechnology, Graphic Era Deemed to be University, Dehradun, India
| | - Gaurav Pant
- Department of Microbiology, Graphic Era Deemed to be University, Dehradun, India
| | - Gaurav Kumar
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
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Funk LM, Poschmann G, Rabe von Pappenheim F, Chari A, Stegmann KM, Dickmanns A, Wensien M, Eulig N, Paknia E, Heyne G, Penka E, Pearson AR, Berndt C, Fritz T, Bazzi S, Uranga J, Mata RA, Dobbelstein M, Hilgenfeld R, Curth U, Tittmann K. Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design. Nat Commun 2024; 15:411. [PMID: 38195625 PMCID: PMC10776599 DOI: 10.1038/s41467-023-44621-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 12/21/2023] [Indexed: 01/11/2024] Open
Abstract
Besides vaccines, the development of antiviral drugs targeting SARS-CoV-2 is critical for preventing future COVID outbreaks. The SARS-CoV-2 main protease (Mpro), a cysteine protease with essential functions in viral replication, has been validated as an effective drug target. Here, we show that Mpro is subject to redox regulation in vitro and reversibly switches between the enzymatically active dimer and the functionally dormant monomer through redox modifications of cysteine residues. These include a disulfide-dithiol switch between the catalytic cysteine C145 and cysteine C117, and generation of an allosteric cysteine-lysine-cysteine SONOS bridge that is required for structural stability under oxidative stress conditions, such as those exerted by the innate immune system. We identify homo- and heterobifunctional reagents that mimic the redox switching and inhibit Mpro activity. The discovered redox switches are conserved in main proteases from other coronaviruses, e.g. MERS-CoV and SARS-CoV, indicating their potential as common druggable sites.
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Affiliation(s)
- Lisa-Marie Funk
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Fabian Rabe von Pappenheim
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Ashwin Chari
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Kim M Stegmann
- Institute of Molecular Oncology, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Antje Dickmanns
- Institute of Molecular Oncology, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Marie Wensien
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Nora Eulig
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Elham Paknia
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Gabi Heyne
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Elke Penka
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Arwen R Pearson
- Institute for Nanostructure and Solid-State Physics, Hamburg Centre for Ultrafast Imaging, Hamburg University, HARBOR, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Carsten Berndt
- Department of Neurology, Medical Faculty, Heinrich-Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Tobias Fritz
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Sophia Bazzi
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Jon Uranga
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Ricardo A Mata
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Rolf Hilgenfeld
- Institute for Biochemistry, Lübeck University, Ratzeburger Allee 160, 23562, Lübeck, Germany
- German Center for Infection Research, Hamburg - Lübeck-Borstel-Riems Site, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany.
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany.
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Ravkov EV, Williams ESCP, Elgort M, Barker AP, Planelles V, Spivak AM, Delgado JC, Lin L, Hanley TM. Reduced monocyte proportions and responsiveness in convalescent COVID-19 patients. Front Immunol 2024; 14:1329026. [PMID: 38250080 PMCID: PMC10797708 DOI: 10.3389/fimmu.2023.1329026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/06/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction The clinical manifestations of acute severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection and coronavirus disease 2019 (COVID-19) suggest a dysregulation of the host immune response that leads to inflammation, thrombosis, and organ dysfunction. It is less clear whether these dysregulated processes persist during the convalescent phase of disease or during long COVID. We sought to examine the effects of SARS-CoV-2 infection on the proportions of classical, intermediate, and nonclassical monocytes, their activation status, and their functional properties in convalescent COVID-19 patients. Methods Peripheral blood mononuclear cells (PBMCs) from convalescent COVID-19 patients and uninfected controls were analyzed by multiparameter flow cytometry to determine relative percentages of total monocytes and monocyte subsets. The expression of activation markers and proinflammatory cytokines in response to LPS treatment were measured by flow cytometry and ELISA, respectively. Results We found that the percentage of total monocytes was decreased in convalescent COVID-19 patients compared to uninfected controls. This was due to decreased intermediate and non-classical monocytes. Classical monocytes from convalescent COVID-19 patients demonstrated a decrease in activation markers, such as CD56, in response to stimulation with bacterial lipopolysaccharide (LPS). In addition, classical monocytes from convalescent COVID-19 patients showed decreased expression of CD142 (tissue factor), which can initiate the extrinsic coagulation cascade, in response to LPS stimulation. Finally, we found that monocytes from convalescent COVID-19 patients produced less TNF-α and IL-6 in response to LPS stimulation, than those from uninfected controls. Conclusion SARS-CoV-2 infection exhibits a clear effect on the relative proportions of monocyte subsets, the activation status of classical monocytes, and proinflammatory cytokine production that persists during the convalescent phase of disease.
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Affiliation(s)
- Eugene V. Ravkov
- ARUP Laboratories Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
| | - Elizabeth S. C. P. Williams
- Department of Internal Medicine, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, UT, United States
| | - Marc Elgort
- ARUP Laboratories Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
| | - Adam P. Barker
- ARUP Laboratories Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
- Department of Pathology, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, UT, United States
| | - Vicente Planelles
- Department of Pathology, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, UT, United States
| | - Adam M. Spivak
- Department of Internal Medicine, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, UT, United States
| | - Julio C. Delgado
- ARUP Laboratories Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
- Department of Pathology, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, UT, United States
| | - Leo Lin
- ARUP Laboratories Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
- Department of Pathology, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, UT, United States
| | - Timothy M. Hanley
- ARUP Laboratories Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
- Department of Pathology, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, UT, United States
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Li W, Li G, Sun Y, Zhang L, Cui X, Jia Y, Zhao T. Prediction of SARS-CoV-2 Infection Phosphorylation Sites and Associations of these Modifications with Lung Cancer Development. Curr Gene Ther 2024; 24:239-248. [PMID: 37957848 DOI: 10.2174/0115665232268074231026111634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 11/15/2023]
Abstract
INTRODUCTION Since the emergence of SARS-CoV-2 viruses, multiple mutant strains have been identified. Infection with SARS-CoV-2 virus leads to alterations in host cell phosphorylation signal, which systematically modulates the immune response. METHODS Identification and analysis of SARS-CoV-2 virus infection phosphorylation sites enable insight into the mechanisms of viral infection and effects on host cells, providing important fundamental data for the study and development of potent drugs for the treatment of immune inflammatory diseases. In this paper, we have analyzed the SARS-CoV-2 virus-infected phosphorylation region and developed a transformer-based deep learning-assisted identification method for the specific identification of phosphorylation sites in SARS-CoV-2 virus-infected host cells. RESULTS Furthermore, through association analysis with lung cancer, we found that SARS-CoV-2 infection may affect the regulatory role of the immune system, leading to an abnormal increase or decrease in the immune inflammatory response, which may be associated with the development and progression of cancer. CONCLUSION We anticipate that this study will provide an important reference for SARS-CoV-2 virus evolution as well as immune-related studies and provide a reliable complementary screening tool for anti-SARS-CoV-2 virus drug and vaccine design.
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Affiliation(s)
- Wei Li
- Institute of Bioinformatics, Harbin Institute of Technology, Harbin, China
| | - Gen Li
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yuzhi Sun
- Institute for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Liyuan Zhang
- Institute for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Xinran Cui
- Institute for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yuran Jia
- Institute for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Tianyi Zhao
- School of Medicine and Health, Harbin Institute of Technology, Harbin, China
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Ponce-Cusi R, Bravo L, Paez KJ, Pinto JA, Pilco-Ferreto N. Host-Pathogen Interaction: Biology and Public Health. Methods Mol Biol 2024; 2751:3-18. [PMID: 38265706 DOI: 10.1007/978-1-0716-3617-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Interactions between host and pathogenic microorganisms are common in nature and have a significant impact on host health, often leading to several types of infections. These interactions have evolved as a result of the ongoing battle between the host's defense mechanisms and the pathogens' invasion strategies. In this chapter, we will explore the evolution of host-pathogen interactions, explore their molecular mechanisms, examine the different stages of interaction, and discuss the development of pharmacological treatments. Understanding these interactions is crucial for improving public health, as it enables us to develop effective strategies to prevent and control infectious diseases. By gaining insights into the intricate dynamics between pathogens and their hosts, we can work towards reducing the burden of such diseases on society.
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Affiliation(s)
- Richard Ponce-Cusi
- Escuela Profesional de Medicina, Facultad de Ciencias de la Salud, Universidad Nacional de Moquegua, Moquegua, Peru.
| | - Leny Bravo
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | - Kevin J Paez
- Escuela Profesional de Medicina Humana - Filial Ica, Universidad Privada San Juan Bautista, Ica, Peru
| | - Joseph A Pinto
- Escuela Profesional de Medicina Humana - Filial Ica, Universidad Privada San Juan Bautista, Ica, Peru
| | - Nesstor Pilco-Ferreto
- Unidad de Posgrado. Facultad de Medicina, Universidad Nacional de San Agustín de Arequipa, Arequipa, Peru
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Garcia I, Lee Y, Brynildsrud O, Eldholm V, Magnus P, Blomfeldt A, Leegaard TM, Müller F, Dudman S, Caugant DA. Tracing the adaptive evolution of SARS-CoV-2 during vaccine roll-out in Norway. Virus Evol 2024; 10:vead081. [PMID: 38205440 PMCID: PMC10776306 DOI: 10.1093/ve/vead081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Vaccination against SARS-CoV-2 has greatly mitigated the impact of the COVID-19 pandemic. However, concerns have been raised about the degree to which vaccination might drive the emergence and selection of immune escape mutations that will hamper the efficacy of the vaccines. In this study, we investigate whether vaccination impacted the micro-scale adaptive evolution of SARS-CoV-2 in the Oslo region of Norway, during the first nine months of 2021, a period in which the population went from near-zero to almost 90 per cent vaccine coverage in the population over 50 years old. Weekly aggregated data stratified by age on vaccine uptake and number of SARS-CoV-2 cases in the area were obtained from the National Immunization Registry and the Norwegian Surveillance System for Communicable Diseases, respectively. A total of 6,438 virus sequences (7.5 per cent of the registered cases) along with metadata were available. We used a causal-driven approach to investigate the relationship between vaccination progress and changes in the frequency of 362 mutations present in at least ten samples, conditioned on the emergence of new lineages, time, and population vaccination coverage. After validating our approach, we identified 21 positive and 12 negative connections between vaccination progress and mutation prevalence, and most of them were outside the Spike protein. We observed a tendency for the mutations that we identified as positively connected with vaccination to decrease as the vaccinated population increased. After modelling the fitness of different competing mutations in a population, we found that our observations could be explained by a clonal interference phenomenon in which high fitness mutations would be outcompeted by the emergence or introduction of other high-fitness mutations.
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Affiliation(s)
| | - Yunsung Lee
- Centre for Fertility and Health, Norwegian Institute of Public Health, 0213 Oslo, Norway
| | - Ola Brynildsrud
- Division for Infection Control, Norwegian Institute of Public Health, 0213 Oslo, Norway
| | - Vegard Eldholm
- Division for Infection Control, Norwegian Institute of Public Health, 0213 Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, 0213 Oslo, Norway
| | - Anita Blomfeldt
- Department of Microbiology and Infection Control, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Truls M Leegaard
- Department of Microbiology and Infection Control, Akershus University Hospital, 1478 Lørenskog, Norway
- Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
| | - Fredrik Müller
- Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
- Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Susanne Dudman
- Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
- Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Dominique A Caugant
- Division for Infection Control, Norwegian Institute of Public Health, 0213 Oslo, Norway
- Department of Community Medicine and Global Health, Faculty of Medicine, University of Oslo, Blindern, 0316 Oslo, Norway
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Foxman EF. Double-take: SARS-CoV-2 has evolved to evade human innate immunity, twice. Trends Immunol 2024; 45:1-3. [PMID: 38143224 DOI: 10.1016/j.it.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 12/26/2023]
Abstract
Sequential replacement of the dominant SARS-CoV-2 virus by new variants has been a striking feature of the COVID-19 pandemic. In two recent articles, Bouhaddou et al. and Kehrer et al. demonstrate that, like the original virus, the SARS-CoV-2 omicron strain has progressively evolved to evade host innate immune defenses.
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Affiliation(s)
- Ellen F Foxman
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA.
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Lamb KD, Luka MM, Saathoff M, Orton RJ, Phan MVT, Cotten M, Yuan K, Robertson DL. Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. PLoS Comput Biol 2024; 20:e1011795. [PMID: 38271457 PMCID: PMC10868779 DOI: 10.1371/journal.pcbi.1011795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 02/15/2024] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
The COVID-19 pandemic has been characterised by sequential variant-specific waves shaped by viral, individual human and population factors. SARS-CoV-2 variants are defined by their unique combinations of mutations and there has been a clear adaptation to more efficient human infection since the emergence of this new human coronavirus in late 2019. Here, we use machine learning models to identify shared signatures, i.e., common underlying mutational processes and link these to the subset of mutations that define the variants of concern (VOCs). First, we examined the global SARS-CoV-2 genomes and associated metadata to determine how viral properties and public health measures have influenced the magnitude of waves, as measured by the number of infection cases, in different geographic locations using regression models. This analysis showed that, as expected, both public health measures and virus properties were associated with the waves of regional SARS-CoV-2 reported infection numbers and this impact varies geographically. We attribute this to intrinsic differences such as vaccine coverage, testing and sequencing capacity and the effectiveness of government stringency. To assess underlying evolutionary change, we used non-negative matrix factorisation and observed three distinct mutational signatures, unique in their substitution patterns and exposures from the SARS-CoV-2 genomes. Signatures 1, 2 and 3 were biased to C→T, T→C/A→G and G→T point mutations. We hypothesise assignments of these mutational signatures to the host antiviral molecules APOBEC, ADAR and ROS respectively. We observe a shift amidst the pandemic in relative mutational signature activity from predominantly Signature 1 changes to an increasingly high proportion of changes consistent with Signature 2. This could represent changes in how the virus and the host immune response interact and indicates how SARS-CoV-2 may continue to generate variation in the future. Linkage of the detected mutational signatures to the VOC-defining amino acids substitutions indicates the majority of SARS-CoV-2's evolutionary capacity is likely to be associated with the action of host antiviral molecules rather than virus replication errors.
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Affiliation(s)
- Kieran D. Lamb
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
- School of Computing Science, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Martha M. Luka
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
- School of Computing Science, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Megan Saathoff
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
| | - Richard J. Orton
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
| | - My V. T. Phan
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- College of Health Solutions, Arizona State University, Phoenix, Arizona, United States of America
| | - Matthew Cotten
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- College of Health Solutions, Arizona State University, Phoenix, Arizona, United States of America
- Complex Adaptive Systems Initiative, Arizona State University, Scottsdale, Arizona, United States of America
| | - Ke Yuan
- School of Computing Science, University of Glasgow, Glasgow, Scotland, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- Cancer Research UK Scotland Institute, Glasgow, Scotland, United Kingdom
| | - David L. Robertson
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
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Lee JD, Menasche BL, Mavrikaki M, Uyemura MM, Hong SM, Kozlova N, Wei J, Alfajaro MM, Filler RB, Müller A, Saxena T, Posey RR, Cheung P, Muranen T, Heng YJ, Paulo JA, Wilen CB, Slack FJ. Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53. Cell Rep 2023; 42:113478. [PMID: 37991919 PMCID: PMC10785701 DOI: 10.1016/j.celrep.2023.113478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/13/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) remains a significant public health threat due to the ability of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and Middle East respiratory syndrome (MERS)-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here, we use our recently developed integrative DNA And Protein Tagging methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. SARS-CoV-2 infection induces TP53 stabilization on chromatin, which contributes to its host cytopathic effect. We mapped this TP53 stabilization to the SARS-CoV-2 spike and its propensity to form syncytia, a consequence of cell-cell fusion. Differences in SARS-CoV-2 spike variant-induced syncytia formation modify chromatin accessibility, cellular senescence, and inflammatory cytokine release via TP53. Our findings suggest that differences in syncytia formation alter senescence-associated inflammation, which varies among SARS-CoV-2 variants.
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Affiliation(s)
- Jonathan D Lee
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA.
| | - Bridget L Menasche
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Maria Mavrikaki
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Madison M Uyemura
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Su Min Hong
- Department of Genetics, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Nina Kozlova
- Department of Genetics, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mia M Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Arne Müller
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Tanvi Saxena
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan R Posey
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Priscilla Cheung
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Taru Muranen
- Department of Genetics, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Yujing J Heng
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Frank J Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Department of Genetics, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
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49
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Otter CJ, Renner DM, Fausto A, Tan LH, Cohen NA, Weiss SR. Interferon signaling in the nasal epithelium distinguishes among lethal and common cold respiratory viruses and is critical for viral clearance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.571720. [PMID: 38187597 PMCID: PMC10769301 DOI: 10.1101/2023.12.18.571720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
All respiratory viruses establish primary infections in the nasal epithelium, where efficient innate immune induction may prevent dissemination to the lower airway and thus minimize pathogenesis. Human coronaviruses (HCoVs) cause a range of pathologies, but the host and viral determinants of disease during common cold versus lethal HCoV infections are poorly understood. We model the initial site of infection using primary nasal epithelial cells cultured at air-liquid interface (ALI). HCoV-229E, HCoV-NL63 and human rhinovirus-16 are common cold-associated viruses that exhibit unique features in this model: early induction of antiviral interferon (IFN) signaling, IFN-mediated viral clearance, and preferential replication at nasal airway temperature (33°C) which confers muted host IFN responses. In contrast, lethal SARS-CoV-2 and MERS-CoV encode antagonist proteins that prevent IFN-mediated clearance in nasal cultures. Our study identifies features shared among common cold-associated viruses, highlighting nasal innate immune responses as predictive of infection outcomes and nasally-directed IFNs as potential therapeutics.
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Affiliation(s)
- Clayton J. Otter
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David M. Renner
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alejandra Fausto
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Li Hui Tan
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Noam A. Cohen
- Department of Otorhinolaryngology-Head and Neck Surgery, Division of Rhinology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Monell Chemical Senses Center, Philadelphia, PA, USA
| | - Susan R. Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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50
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Wong LYR, Odle A, Luhmann E, Wu DC, Wang Y, Teo QW, Ptak C, Sariol A, Lowery S, Mack M, Meyerholz DK, Wu NC, Radoshevich L, Perlman S. Contrasting roles of MERS-CoV and SARS-CoV-2 internal proteins in pathogenesis in mice. mBio 2023; 14:e0247623. [PMID: 37882568 PMCID: PMC10746224 DOI: 10.1128/mbio.02476-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE The function of betacoronavirus internal protein has been relatively understudied. The earliest report on the internal protein of mouse hepatitis virus suggested that the internal protein is a structural protein without significant functions in virus replication and virulence. However, the internal proteins of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle-East respiratory syndrome coronavirus, and SARS-CoV-2 have been shown to evade immune responses. Despite the reported functions of the internal protein in these highly pathogenic human coronaviruses, its role in mediating pathogenesis in experimentally infected animals has not been characterized. Our data indicated that despite the similar genomic location and expression strategy of these internal proteins, their effects on virulence are vastly different and virus specific, highlighting the complexity between host-virus interaction and disease outcome.
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Affiliation(s)
- Lok-Yin Roy Wong
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Abby Odle
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Emma Luhmann
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Douglas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Qi Wen Teo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Celeste Ptak
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Alan Sariol
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Shea Lowery
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Matthias Mack
- Department of Internal Medicine, University Hospital Regensburg, Regensburg, Germany
| | | | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Lilliana Radoshevich
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Stanley Perlman
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
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