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Cortellini A, Tabernero J, Mukherjee U, Salazar R, Sureda A, Maluquer C, Ferrante D, Bower M, Sharkey R, Mirallas O, Plaja A, Cucurull M, Mesia R, Dalla Pria A, Newsom-Davis T, Van Hemelrijck M, Sita-Lumsden A, Apthorp E, Vincenzi B, Di Fazio GR, Tonini G, Pantano F, Bertuzzi A, Rossi S, Brunet J, Lambertini M, Pedrazzoli P, Biello F, D'Avanzo F, Lee AJX, Shawe-Taylor M, Rogers L, Murphy C, Cooper L, Andaleeb R, Khalique S, Bawany S, Ahmed S, Carmona-García MC, Fort-Culillas R, Liñan R, Zoratto F, Rizzo G, Perachino M, Doonga K, Gaidano G, Bruna R, Patriarca A, Martinez-Vila C, Pérez Criado I, Giusti R, Mazzoni F, Antonuzzo L, Santoro A, Parisi A, Queirolo P, Aujayeb A, Rimassa L, Diamantis N, Bertulli R, Fulgenzi CAM, D'Alessio A, Ruiz-Camps I, Saoudi-Gonzalez N, Garcia Illescas D, Medina I, Fox L, Gennari A, Aguilar-Company J, Pinato DJ, Swallow J, Hanbury G, Chung C, Patel M, Dettorre G, Belessiotis K, Saorise D, Jones E, Apthorp E, Moss C, Russell B, Townsend S, Jackson A, Loizidou A, Piccart M, Pommeret F, Colomba-Blameble E, Prat A, Cruz CA, Reyes R, Segui E, Marco-Hernández J, Viladot M, Harbeck N, Wuerstlein R, Henze F, Mahner S, Felip E, Scotti L, Marrari A, Grosso F, Fusco V, Delfanti S, Rossi M, Zambelli A, Tondini C, Chiudinelli L, Franchi M, Libertini M, Provenzano S, Generali D, Grisanti S, Baggi A, Tovazzi V, Ficorella C, Porzio G, Saponara M, Filetti M, Tucci M, Berardi R, Cantini L, Paoloni F, Guida A, Bracarda S, Iglesias M, Sanchez de Torre A, Tagliamento M. SARS-CoV-2 omicron (B.1.1.529)-related COVID-19 sequelae in vaccinated and unvaccinated patients with cancer: results from the OnCovid registry. Lancet Oncol 2023; 24:335-346. [PMID: 36898391 PMCID: PMC9991062 DOI: 10.1016/s1470-2045(23)00056-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 03/09/2023]
Abstract
BACKGROUND COVID-19 sequelae can affect about 15% of patients with cancer who survive the acute phase of SARS-CoV-2 infection and can substantially impair their survival and continuity of oncological care. We aimed to investigate whether previous immunisation affects long-term sequelae in the context of evolving variants of concern of SARS-CoV-2. METHODS OnCovid is an active registry that includes patients aged 18 years or older from 37 institutions across Belgium, France, Germany, Italy, Spain, and the UK with a laboratory-confirmed diagnosis of COVID-19 and a history of solid or haematological malignancy, either active or in remission, followed up from COVID-19 diagnosis until death. We evaluated the prevalence of COVID-19 sequelae in patients who survived COVID-19 and underwent a formal clinical reassessment, categorising infection according to the date of diagnosis as the omicron (B.1.1.529) phase from Dec 15, 2021, to Jan 31, 2022; the alpha (B.1.1.7)-delta (B.1.617.2) phase from Dec 1, 2020, to Dec 14, 2021; and the pre-vaccination phase from Feb 27 to Nov 30, 2020. The prevalence of overall COVID-19 sequelae was compared according to SARS-CoV-2 immunisation status and in relation to post-COVID-19 survival and resumption of systemic anticancer therapy. This study is registered with ClinicalTrials.gov, NCT04393974. FINDINGS At the follow-up update on June 20, 2022, 1909 eligible patients, evaluated after a median of 39 days (IQR 24-68) from COVID-19 diagnosis, were included (964 [50·7%] of 1902 patients with sex data were female and 938 [49·3%] were male). Overall, 317 (16·6%; 95% CI 14·8-18·5) of 1909 patients had at least one sequela from COVID-19 at the first oncological reassessment. The prevalence of COVID-19 sequelae was highest in the pre-vaccination phase (191 [19·1%; 95% CI 16·4-22·0] of 1000 patients). The prevalence was similar in the alpha-delta phase (110 [16·8%; 13·8-20·3] of 653 patients, p=0·24), but significantly lower in the omicron phase (16 [6·2%; 3·5-10·2] of 256 patients, p<0·0001). In the alpha-delta phase, 84 (18·3%; 95% CI 14·6-22·7) of 458 unvaccinated patients and three (9·4%; 1·9-27·3) of 32 unvaccinated patients in the omicron phase had sequelae. Patients who received a booster and those who received two vaccine doses had a significantly lower prevalence of overall COVID-19 sequelae than unvaccinated or partially vaccinated patients (ten [7·4%; 95% CI 3·5-13·5] of 136 boosted patients, 18 [9·8%; 5·8-15·5] of 183 patients who had two vaccine doses vs 277 [18·5%; 16·5-20·9] of 1489 unvaccinated patients, p=0·0001), respiratory sequelae (six [4·4%; 1·6-9·6], 11 [6·0%; 3·0-10·7] vs 148 [9·9%; 8·4-11·6], p=0·030), and prolonged fatigue (three [2·2%; 0·1-6·4], ten [5·4%; 2·6-10·0] vs 115 [7·7%; 6·3-9·3], p=0·037). INTERPRETATION Unvaccinated patients with cancer remain highly vulnerable to COVID-19 sequelae irrespective of viral strain. This study confirms the role of previous SARS-CoV-2 immunisation as an effective measure to protect patients from COVID-19 sequelae, disruption of therapy, and ensuing mortality. FUNDING UK National Institute for Health and Care Research Imperial Biomedical Research Centre and the Cancer Treatment and Research Trust.
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Affiliation(s)
- Alessio Cortellini
- Department of Surgery and Cancer, Imperial College London, London, UK; Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200 - 00128 Roma, Italy.
| | - Josep Tabernero
- Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology, IOB-Quiron, UVic-UCC, Barcelona, Spain
| | - Uma Mukherjee
- Medical Oncology, Barts Health NHS Trust, London, UK
| | - Ramon Salazar
- Catalan Institute of Oncology (ICO), University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), CIBERONC, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Anna Sureda
- Haematology Department, ICO Hospitalet, Hospitalet de Llobregat, IDIBELL, Universitat de Barcelona, Barcelona, Spain
| | - Clara Maluquer
- Haematology Department, ICO Hospitalet, Hospitalet de Llobregat, IDIBELL, Universitat de Barcelona, Barcelona, Spain
| | - Daniela Ferrante
- Unit of Medical Statistics, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Mark Bower
- Department of Oncology and National Centre for HIV Malignancy, Chelsea and Westminster Hospital, London, UK
| | - Rachel Sharkey
- Department of Oncology and National Centre for HIV Malignancy, Chelsea and Westminster Hospital, London, UK
| | - Oriol Mirallas
- Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology, IOB-Quiron, UVic-UCC, Barcelona, Spain
| | - Andrea Plaja
- Medical Oncology Department, B-ARGO Group, IGTP, Catalan Institute of Oncology, Badalona, Spain
| | - Marc Cucurull
- Medical Oncology Department, B-ARGO Group, IGTP, Catalan Institute of Oncology, Badalona, Spain
| | - Ricard Mesia
- Medical Oncology Department, B-ARGO Group, IGTP, Catalan Institute of Oncology, Badalona, Spain
| | - Alessia Dalla Pria
- Department of Oncology and National Centre for HIV Malignancy, Chelsea and Westminster Hospital, London, UK
| | - Thomas Newsom-Davis
- Department of Oncology and National Centre for HIV Malignancy, Chelsea and Westminster Hospital, London, UK
| | - Mieke Van Hemelrijck
- Medical Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK; Translational Oncology and Urology Research, School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | | | | | - Bruno Vincenzi
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200 - 00128 Roma, Italy; Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21 - 00128 Roma, Italy
| | - Giuseppina Rita Di Fazio
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200 - 00128 Roma, Italy; Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21 - 00128 Roma, Italy
| | - Giuseppe Tonini
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200 - 00128 Roma, Italy; Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21 - 00128 Roma, Italy
| | - Francesco Pantano
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200 - 00128 Roma, Italy; Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21 - 00128 Roma, Italy
| | - Alexia Bertuzzi
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Sabrina Rossi
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Joan Brunet
- Department of Medical Oncology, Catalan Institute of Oncology, University Hospital Josep Trueta, Girona, Spain
| | - Matteo Lambertini
- Medical Oncology Department, UO Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova, Italy; Department of Internal Medicine and Medical Specialties, School of Medicine, University of Genova, Genova, Italy
| | - Paolo Pedrazzoli
- Department of Internal Medicine and Medical Therapy, University of Pavia, Pavia, Italy; Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Federica Biello
- Division of Oncology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy; Ospedale Maggiore della Caritá, Novara, Italy
| | - Francesca D'Avanzo
- Division of Oncology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy; Ospedale Maggiore della Caritá, Novara, Italy
| | - Alvin J X Lee
- Cancer Division, University College London Hospitals, London, UK
| | | | - Lucy Rogers
- Cancer Division, University College London Hospitals, London, UK
| | - Cian Murphy
- Cancer Division, University College London Hospitals, London, UK
| | - Lee Cooper
- Cancer Division, University College London Hospitals, London, UK
| | - Ramis Andaleeb
- Cancer Division, University College London Hospitals, London, UK
| | - Saira Khalique
- Cancer Division, University College London Hospitals, London, UK
| | - Samira Bawany
- Cancer Division, University College London Hospitals, London, UK
| | - Sarah Ahmed
- Cancer Division, University College London Hospitals, London, UK
| | - M Carmen Carmona-García
- Department of Medical Oncology, Catalan Institute of Oncology, University Hospital Josep Trueta, Girona, Spain
| | - Roser Fort-Culillas
- Department of Medical Oncology, Catalan Institute of Oncology, University Hospital Josep Trueta, Girona, Spain
| | - Raquel Liñan
- Department of Medical Oncology, Catalan Institute of Oncology, University Hospital Josep Trueta, Girona, Spain
| | | | - Gianpiero Rizzo
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marta Perachino
- Medical Oncology Department, UO Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova, Italy; Department of Internal Medicine and Medical Specialties, School of Medicine, University of Genova, Genova, Italy
| | - Kris Doonga
- Department of Oncology and National Centre for HIV Malignancy, Chelsea and Westminster Hospital, London, UK
| | - Gianluca Gaidano
- Division of Haematology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy; Ospedale Maggiore della Caritá, Novara, Italy
| | - Riccardo Bruna
- Division of Haematology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy; Ospedale Maggiore della Caritá, Novara, Italy
| | - Andrea Patriarca
- Division of Haematology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy; Ospedale Maggiore della Caritá, Novara, Italy
| | | | | | | | | | | | - Armando Santoro
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy; Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Alessandro Parisi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Paola Queirolo
- Melanoma and Sarcoma Medical Treatment Unit, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Avinash Aujayeb
- Respiratory Department, Northumbria Healthcare NHS Foundation Trust, North Shields, UK
| | - Lorenza Rimassa
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy; Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | | | - Rossella Bertulli
- Medical Oncology 2, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Claudia A M Fulgenzi
- Department of Surgery and Cancer, Imperial College London, London, UK; Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21 - 00128 Roma, Italy
| | - Antonio D'Alessio
- Department of Surgery and Cancer, Imperial College London, London, UK; Division of Oncology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Isabel Ruiz-Camps
- Department of Infectious Diseases, Vall d'Hebron University Hospital and Institute of Oncology, Barcelona, Spain
| | - Nadia Saoudi-Gonzalez
- Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology, IOB-Quiron, UVic-UCC, Barcelona, Spain
| | - David Garcia Illescas
- Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology, IOB-Quiron, UVic-UCC, Barcelona, Spain
| | - Irene Medina
- Department of Hematology, Vall d'Hebron University Hospital and Institute of Oncology, Barcelona, Spain
| | - Laura Fox
- Department of Hematology, Vall d'Hebron University Hospital and Institute of Oncology, Barcelona, Spain
| | - Alessandra Gennari
- Division of Oncology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy; Ospedale Maggiore della Caritá, Novara, Italy
| | - Juan Aguilar-Company
- Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology, IOB-Quiron, UVic-UCC, Barcelona, Spain; Department of Infectious Diseases, Vall d'Hebron University Hospital and Institute of Oncology, Barcelona, Spain
| | - David J Pinato
- Department of Surgery and Cancer, Imperial College London, London, UK; Division of Oncology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
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Fontes-Dantas FL, Fernandes GG, Gutman EG, De Lima EV, Antonio LS, Hammerle MB, Mota-Araujo HP, Colodeti LC, Araújo SM, Froz GM, da Silva TN, Duarte LA, Salvio AL, Pires KL, Leon LA, Vasconcelos CCF, Romão L, Savio LEB, Silva JL, da Costa R, Clarke JR, Da Poian AT, Alves-Leon SV, Passos GF, Figueiredo CP. SARS-CoV-2 Spike protein induces TLR4-mediated long-term cognitive dysfunction recapitulating post-COVID-19 syndrome in mice. Cell Rep 2023; 42:112189. [PMID: 36857178 PMCID: PMC9935273 DOI: 10.1016/j.celrep.2023.112189] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/16/2022] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Cognitive dysfunction is often reported in patients with post-coronavirus disease 2019 (COVID-19) syndrome, but its underlying mechanisms are not completely understood. Evidence suggests that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike protein or its fragments are released from cells during infection, reaching different tissues, including the CNS, irrespective of the presence of the viral RNA. Here, we demonstrate that brain infusion of Spike protein in mice has a late impact on cognitive function, recapitulating post-COVID-19 syndrome. We also show that neuroinflammation and hippocampal microgliosis mediate Spike-induced memory dysfunction via complement-dependent engulfment of synapses. Genetic or pharmacological blockage of Toll-like receptor 4 (TLR4) signaling protects animals against synapse elimination and memory dysfunction induced by Spike brain infusion. Accordingly, in a cohort of 86 patients who recovered from mild COVID-19, the genotype GG TLR4-2604G>A (rs10759931) is associated with poor cognitive outcome. These results identify TLR4 as a key target to investigate the long-term cognitive dysfunction after COVID-19 infection in humans and rodents.
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Affiliation(s)
- Fabricia L. Fontes-Dantas
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil,Department of Pharmacology, Institute of Biology, Rio de Janeiro State University, Rio de Janeiro, RJ, Brazil
| | - Gabriel G. Fernandes
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Elisa G. Gutman
- Translational Neuroscience Laboratory (LabNet), Post-Graduate Program in Neurology, Federal University of Rio de Janeiro State, Rio de Janeiro, RJ, Brazil,Clinical Medicine Post-graduation Program, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Emanuelle V. De Lima
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Leticia S. Antonio
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Mariana B. Hammerle
- Clinical Medicine Post-graduation Program, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Hannah P. Mota-Araujo
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lilian C. Colodeti
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Suzana M.B. Araújo
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Gabrielle M. Froz
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Talita N. da Silva
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Larissa A. Duarte
- Translational Neuroscience Laboratory (LabNet), Post-Graduate Program in Neurology, Federal University of Rio de Janeiro State, Rio de Janeiro, RJ, Brazil,Clinical Medicine Post-graduation Program, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Andreza L. Salvio
- Translational Neuroscience Laboratory (LabNet), Post-Graduate Program in Neurology, Federal University of Rio de Janeiro State, Rio de Janeiro, RJ, Brazil
| | - Karina L. Pires
- Neurology Department, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, RJ, Brazil
| | - Luciane A.A. Leon
- Laboratório de Desenvolvimento Tecnológico em Virologia, IOC/FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | | | - Luciana Romão
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Luiz Eduardo B. Savio
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Jerson L. Silva
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Robson da Costa
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Julia R. Clarke
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Andrea T. Da Poian
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil,Corresponding author
| | - Soniza V. Alves-Leon
- Translational Neuroscience Laboratory (LabNet), Post-Graduate Program in Neurology, Federal University of Rio de Janeiro State, Rio de Janeiro, RJ, Brazil,Division of Neurology, Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil,Corresponding author
| | - Giselle F. Passos
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil,Corresponding author
| | - Claudia P. Figueiredo
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil,Corresponding author
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Camara MB, Sobeh AM, Eichhorn CD. Progress in 7SK ribonucleoprotein structural biology. Front Mol Biosci 2023; 10:1154622. [PMID: 37051324 PMCID: PMC10083321 DOI: 10.3389/fmolb.2023.1154622] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
The 7SK ribonucleoprotein (RNP) is a dynamic and multifunctional regulator of RNA Polymerase II (RNAPII) transcription in metazoa. Comprised of the non-coding 7SK RNA, core proteins, and numerous accessory proteins, the most well-known 7SK RNP function is the sequestration and inactivation of the positive transcription elongation factor b (P-TEFb). More recently, 7SK RNP has been shown to regulate RNAPII transcription through P-TEFb-independent pathways. Due to its fundamental role in cellular function, dysregulation has been linked with human diseases including cancers, heart disease, developmental disorders, and viral infection. Significant advances in 7SK RNP structural biology have improved our understanding of 7SK RNP assembly and function. Here, we review progress in understanding the structural basis of 7SK RNA folding, biogenesis, and RNP assembly.
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Affiliation(s)
- Momodou B. Camara
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
| | - Amr M. Sobeh
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
| | - Catherine D. Eichhorn
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
- Nebraska Center for Integrated Biomolecular Communication, Lincoln, NE, United States
- *Correspondence: Catherine D. Eichhorn,
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104
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Liu JF, Peng WJ, Wu Y, Yang YH, Wu SF, Liu DP, Liu JN, Yang JT. Proteomic and phosphoproteomic characteristics of the cortex, hippocampus, thalamus, lung, and kidney in COVID-19-infected female K18-hACE2 mice. EBioMedicine 2023; 90:104518. [PMID: 36933413 PMCID: PMC10017276 DOI: 10.1016/j.ebiom.2023.104518] [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: 10/24/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Neurological damage caused by coronavirus disease 2019 (COVID-19) has attracted increasing attention. Recently, through autopsies of patients with COVID-19, the direct identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in their central nervous system (CNS) has been reported, indicating that SARS-CoV-2 might directly attack the CNS. The need to prevent COVID-19-induced severe injuries and potential sequelae is urgent, requiring the elucidation of large-scale molecular mechanisms in vivo. METHODS In this study, we performed liquid chromatography-mass spectrometry-based proteomic and phosphoproteomic analyses of the cortex, hippocampus, thalamus, lungs, and kidneys of SARS-CoV-2-infected K18-hACE2 female mice. We then performed comprehensive bioinformatic analyses, including differential analyses, functional enrichment, and kinase prediction, to identify key molecules involved in COVID-19. FINDINGS We found that the cortex had higher viral loads than did the lungs, and the kidneys did not have SARS-COV-2. After SARS-CoV-2 infection, RIG-I-associated virus recognition, antigen processing and presentation, and complement and coagulation cascades were activated to different degrees in all five organs, especially the lungs. The infected cortex exhibited disorders of multiple organelles and biological processes, including dysregulated spliceosome, ribosome, peroxisome, proteasome, endosome, and mitochondrial oxidative respiratory chain. The hippocampus and thalamus had fewer disorders than did the cortex; however, hyperphosphorylation of Mapt/Tau, which may contribute to neurodegenerative diseases, such as Alzheimer's disease, was found in all three brain regions. Moreover, SARS-CoV-2-induced elevation of human angiotensin-converting enzyme 2 (hACE2) was observed in the lungs and kidneys, but not in the three brain regions. Although the virus was not detected, the kidneys expressed high levels of hACE2 and exhibited obvious functional dysregulation after infection. This indicates that SARS-CoV-2 can cause tissue infections or damage via complicated routes. Thus, the treatment of COVID-19 requires a multipronged approach. INTERPRETATION This study provides observations and in vivo datasets for COVID-19-associated proteomic and phosphoproteomic alterations in multiple organs, especially cerebral tissues, of K18-hACE2 mice. In mature drug databases, the differentially expressed proteins and predicted kinases in this study can be used as baits to identify candidate therapeutic drugs for COVID-19. This study can serve as a solid resource for the scientific community. The data in this manuscript will serve as a starting point for future research on COVID-19-associated encephalopathy. FUNDING This study was supported by grants from the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences, the National Natural Science Foundation of China, and the Natural Science Foundation of Beijing.
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Affiliation(s)
- Jiang-Feng Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Wan-Jun Peng
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, CAMS and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
| | - Yue Wu
- School of Statistics and Data Science, Nankai University, Tianjin 300071, China
| | - Ye-Hong Yang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Song-Feng Wu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - De-Pei Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China.
| | - Jiang-Ning Liu
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, CAMS and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China.
| | - Jun-Tao Yang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China.
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Hysenaj L, Little S, Kulhanek K, Magnen M, Bahl K, Gbenedio OM, Prinz M, Rodriguez L, Andersen C, Rao AA, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Mick E, Khalid MM, Taha TY, Kumar R, Li JZ, Ding VW, Matsumoto S, Maishan M, Sreekumar B, Simoneau C, Nazarenko I, Tomlinson MG, Khan K, von Gottberg A, Sigal A, Looney MR, Fragiadakis GK, Jablons DM, Langelier CR, Matthay M, Krummel M, Erle DJ, Combes AJ, Sil A, Ott M, Kratz JR, Roose JP. SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants. Stem Cell Reports 2023; 18:636-653. [PMID: 36827975 PMCID: PMC9948283 DOI: 10.1016/j.stemcr.2023.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/25/2023] Open
Abstract
Ancestral SARS coronavirus-2 (SARS-CoV-2) and variants of concern (VOC) caused a global pandemic with a spectrum of disease severity. The mechanistic explaining variations related to airway epithelium are relatively understudied. Here, we biobanked airway organoids (AO) by preserving stem cell function. We optimized viral infection with H1N1/PR8 and comprehensively characterized epithelial responses to SARS-CoV-2 infection in phenotypically stable AO from 20 different subjects. We discovered Tetraspanin-8 (TSPAN8) as a facilitator of SARS-CoV-2 infection. TSPAN8 facilitates SARS-CoV-2 infection rates independently of ACE2-Spike interaction. In head-to-head comparisons with Ancestral SARS-CoV-2, Delta and Omicron VOC displayed lower overall infection rates of AO but triggered changes in epithelial response. All variants shared highest tropism for ciliated and goblet cells. TSPAN8-blocking antibodies diminish SARS-CoV-2 infection and may spur novel avenues for COVID-19 therapy.
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Affiliation(s)
- Lisiena Hysenaj
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Samantha Little
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Kayla Kulhanek
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Melia Magnen
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kriti Bahl
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Oghenekevwe M Gbenedio
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Morgan Prinz
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Lauren Rodriguez
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher Andersen
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
| | - Arjun Arkal Rao
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alan Shen
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Leonard C Lupin-Jimenez
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
| | - Luke R Bonser
- Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nina K Serwas
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eran Mick
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Mir M Khalid
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Taha Y Taha
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Renuka Kumar
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jack Z Li
- Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Vivianne W Ding
- Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Shotaro Matsumoto
- Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mazharul Maishan
- Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bharath Sreekumar
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Camille Simoneau
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Irina Nazarenko
- Institute for Infection Prevention and Hospital Epidemiology, University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; German Cancer Consortium, Partner Site Freiburg and German Cancer Research Center, Heidelberg, Germany
| | - Michael G Tomlinson
- School of Biosciences, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, Midlands, UK
| | - Khajida Khan
- Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, 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; Max Planck Institute for Infection Biology, Berlin, Germany; Centre for the AIDS Program of Research, Durban, South Africa
| | - Mark R Looney
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA
| | - Gabriela K Fragiadakis
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David M Jablons
- Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charles R Langelier
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Michael Matthay
- Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew Krummel
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David J Erle
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA
| | - Alexis J Combes
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute COVID-19 Research Group, University of California, San Francisco, San Francisco, CA, USA
| | - Johannes R Kratz
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
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106
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Seasonal trends in COVID-19 cases, hospitalizations, and mortality in the United States and Europe. Sci Rep 2023; 13:3886. [PMID: 36890264 PMCID: PMC9994397 DOI: 10.1038/s41598-023-31057-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 03/06/2023] [Indexed: 03/10/2023] Open
Abstract
Determining whether SARS-CoV-2 exhibits seasonality like other respiratory viruses is critical for public health planning. We evaluated whether COVID-19 rates follow a seasonal pattern using time series models. We used time series decomposition to extract the annual seasonal component of COVID-19 case, hospitalization, and mortality rates from March 2020 through December 2022 for the United States and Europe. Models were adjusted for a country-specific stringency index to account for confounding by various interventions. Despite year-round disease activity, we identified seasonal spikes in COVID-19 from approximately November through April for all outcomes and in all countries. Our results support employing annual preventative measures against SARS-CoV-2, such as administering seasonal booster vaccines in a similar timeframe as those in place for influenza. Whether certain high-risk individuals may need more than one COVID-19 vaccine booster dose each year will depend on factors like vaccine durability against severe illness and levels of year-round disease activity.
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107
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Abstract
SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has been associated with substantial global morbidity and mortality. Despite a tropism that is largely confined to the airways, COVID-19 is associated with multiorgan dysfunction and long-term cognitive pathologies. A major driver of this biology stems from the combined effects of virus-mediated interference with the host antiviral defences in infected cells and the sensing of pathogen-associated material by bystander cells. Such a dynamic results in delayed induction of type I and III interferons (IFN-I and IFN-III) at the site of infection, but systemic IFN-I and IFN-III priming in distal organs and barrier epithelial surfaces, respectively. In this Review, we examine the relationship between SARS-CoV-2 biology and the cellular response to infection, detailing how antagonism and dysregulation of host innate immune defences contribute to disease severity of COVID-19.
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Affiliation(s)
- Judith M Minkoff
- Department of Microbiology, New York University Langone Health, New York, NY, USA
| | - Benjamin tenOever
- Department of Microbiology, New York University Langone Health, New York, NY, USA.
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108
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Beahm DR, Deng Y, DeAngelo TM, Sarpeshkar R. Drug Cocktail Formulation via Circuit Design. IEEE TRANSACTIONS ON MOLECULAR, BIOLOGICAL, AND MULTI-SCALE COMMUNICATIONS 2023; 9:28-48. [PMID: 37397625 PMCID: PMC10312325 DOI: 10.1109/tmbmc.2023.3246928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Electronic circuits intuitively visualize and quantitatively simulate biological systems with nonlinear differential equations that exhibit complicated dynamics. Drug cocktail therapies are a powerful tool against diseases that exhibit such dynamics. We show that just six key states, which are represented in a feedback circuit, enable drug-cocktail formulation: 1) healthy cell number; 2) infected cell number; 3) extracellular pathogen number; 4) intracellular pathogenic molecule number; 5) innate immune system strength; and 6) adaptive immune system strength. To enable drug cocktail formulation, the model represents the effects of the drugs in the circuit. For example, a nonlinear feedback circuit model fits measured clinical data, represents cytokine storm and adaptive autoimmune behavior, and accounts for age, sex, and variant effects for SARS-CoV-2 with few free parameters. The latter circuit model provided three quantitative insights on the optimal timing and dosage of drug components in a cocktail: 1) antipathogenic drugs should be given early in the infection, but immunosuppressant timing involves a tradeoff between controlling pathogen load and mitigating inflammation; 2) both within and across-class combinations of drugs have synergistic effects; 3) if they are administered sufficiently early in the infection, anti-pathogenic drugs are more effective at mitigating autoimmune behavior than immunosuppressant drugs.
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Affiliation(s)
| | - Yijie Deng
- Thayer School or Engineering, Dartmouth College, Hanover, NH 03755 USA
| | - Thomas M DeAngelo
- Thayer School or Engineering, Dartmouth College, Hanover, NH 03755 USA
| | - Rahul Sarpeshkar
- Departments of Engineering, Physics, Microbiology & Immunobiology, and Molecular & Systems Biology, Dartmouth College, Hanover, NH 03755 USA
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109
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Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes J, Peacock SJ, Barclay WS, de Silva TI, Towers GJ, Robertson DL. SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat Rev Microbiol 2023; 21:162-177. [PMID: 36653446 PMCID: PMC9847462 DOI: 10.1038/s41579-022-00841-7] [Citation(s) in RCA: 225] [Impact Index Per Article: 225.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 01/19/2023]
Abstract
In late 2020, after circulating for almost a year in the human population, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited a major step change in its adaptation to humans. These highly mutated forms of SARS-CoV-2 had enhanced rates of transmission relative to previous variants and were termed 'variants of concern' (VOCs). Designated Alpha, Beta, Gamma, Delta and Omicron, the VOCs emerged independently from one another, and in turn each rapidly became dominant, regionally or globally, outcompeting previous variants. The success of each VOC relative to the previously dominant variant was enabled by altered intrinsic functional properties of the virus and, to various degrees, changes to virus antigenicity conferring the ability to evade a primed immune response. The increased virus fitness associated with VOCs is the result of a complex interplay of virus biology in the context of changing human immunity due to both vaccination and prior infection. In this Review, we summarize the literature on the relative transmissibility and antigenicity of SARS-CoV-2 variants, the role of mutations at the furin spike cleavage site and of non-spike proteins, the potential importance of recombination to virus success, and SARS-CoV-2 evolution in the context of T cells, innate immunity and population immunity. SARS-CoV-2 shows a complicated relationship among virus antigenicity, transmission and virulence, which has unpredictable implications for the future trajectory and disease burden of COVID-19.
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Affiliation(s)
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Wendy S Barclay
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
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110
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Porter LM, Guo W, Crozier TWM, Greenwood EJD, Ortmann B, Kottmann D, Nathan JA, Mahadeva R, Lehner PJ, McCaughan F. Cigarette smoke preferentially induces full length ACE2 expression in differentiated primary human airway cultures but does not alter the efficiency of cellular SARS-CoV-2 infection. Heliyon 2023; 9:e14383. [PMID: 36938474 PMCID: PMC10005841 DOI: 10.1016/j.heliyon.2023.e14383] [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: 08/26/2022] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/12/2023] Open
Abstract
Cigarette smoking has many serious negative health consequences. The relationship between smoking and SARS-CoV-2 infection is controversial, specifically whether smokers are at increased risk of infection. We investigated the impact of cigarette smoke on ACE2 isoform expression and SARS-CoV-2 infection in differentiated primary human bronchial epithelial cells at the air-liquid-interface (ALI). We assessed the expression of ACE2 in response to CSE and therapeutics reported to modulate ACE2. We exposed ALI cultures to cigarette smoke extract (CSE) and then infected them with SARS-CoV-2. We measured cellular infection using flow cytometry and whole-transwell immunofluorescence. We found that CSE increased expression of full-length ACE2 (flACE2) but did not alter the expression of a Type I-interferon sensitive truncated isoform (dACE2) that lacks the capacity to bind SARS-CoV-2. CSE did not have a significant impact on key mediators of the innate immune response. Importantly, we show that, despite the increase in flACE2, CSE did not alter airway cell infection after CSE exposure. We found that nicotine does not significantly alter flACE2 expression but that NRF2 agonists do lead to an increase in flACE2 expression. This increase was not associated with an increase in SARS-CoV-2 infection. Our results are consistent with the epidemiological data suggesting that current smokers do not have an excess of SARS-CoV-2 infection. but that those with chronic respiratory or cardiovascular disease are more vulnerable to severe COVID-19. They suggest that, in differentiated conducting airway cells, flACE2 expression levels may not limit airway SARS-CoV-2 infection.
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Affiliation(s)
- Linsey M. Porter
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, CB2 OQQ, UK
| | - Wenrui Guo
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, CB2 OQQ, UK
| | - Thomas WM. Crozier
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Edward JD. Greenwood
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Brian Ortmann
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Daniel Kottmann
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, CB2 OQQ, UK
| | - James A. Nathan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Ravindra Mahadeva
- Cambridge University Hospitals NHS Foundation Trust, University of Cambridge, Addenbrookes Hospital, Cambridge, CB2 OQQ, UK
| | - Paul J. Lehner
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Frank McCaughan
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, CB2 OQQ, UK
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111
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Intragenomic rearrangements involving 5'-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses. Virol J 2023; 20:36. [PMID: 36829234 PMCID: PMC9957694 DOI: 10.1186/s12985-023-01998-0] [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: 05/08/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Variation of the betacoronavirus SARS-CoV-2 has been the bane of COVID-19 control. Documented variation includes point mutations, deletions, insertions, and recombination among closely or distantly related coronaviruses. Here, we describe yet another aspect of genome variation by beta- and alphacoronaviruses that was first documented in an infectious isolate of the betacoronavirus SARS-CoV-2, obtained from 3 patients in Hong Kong that had a 5'-untranslated region segment at the end of the ORF6 gene that in its new location translated into an ORF6 protein with a predicted modified carboxyl terminus. While comparing the amino acid sequences of translated ORF8 genes in the GenBank database, we found a subsegment of the same 5'-UTR-derived amino acid sequence modifying the distal end of ORF8 of an isolate from the United States and decided to carry out a systematic search. METHODS Using the nucleotide and in the case of SARS-CoV-2 also the translated amino acid sequence in three reading frames of the genomic termini of coronaviruses as query sequences, we searched for 5'-UTR sequences in regions other than the 5'-UTR in SARS-CoV-2 and reference strains of alpha-, beta-, gamma-, and delta-coronaviruses. RESULTS We here report numerous genomic insertions of 5'-untranslated region sequences into coding regions of SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses, but not delta- or gammacoronaviruses. To our knowledge this is the first systematic description of such insertions. In many cases, these insertions would change viral protein sequences and further foster genomic flexibility and viral adaptability through insertion of transcription regulatory sequences in novel positions within the genome. Among human Embecorivus betacoronaviruses, for instance, from 65% to all of the surveyed sequences in publicly available databases contain inserted 5'-UTR sequences. CONCLUSION The intragenomic rearrangements involving 5'-untranslated region sequences described here, which in several cases affect highly conserved genes with a low propensity for recombination, may underlie the generation of variants homotypic with those of concern or interest and with potentially differing pathogenic profiles. Intragenomic rearrangements thus add to our appreciation of how variants of SARS-CoV-2 and other beta- and alphacoronaviruses may arise.
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112
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Rosain J, Neehus AL, Manry J, Yang R, Le Pen J, Daher W, Liu Z, Chan YH, Tahuil N, Türel Ö, Bourgey M, Ogishi M, Doisne JM, Izquierdo HM, Shirasaki T, Le Voyer T, Guérin A, Bastard P, Moncada-Velez M, Han JE, Khan T, Rapaport F, Hong SH, Cheung A, Haake K, Mindt BC, Perez L, Philippot Q, Lee D, Zhang P, Rinchai D, Al Ali F, Ata MMA, Rahman M, Peel JN, Heissel S, Molina H, Kendir-Demirkol Y, Bailey R, Zhao S, Bohlen J, Mancini M, Seeleuthner Y, Roelens M, Lorenzo L, Soudée C, Paz MEJ, Gonzalez ML, Jeljeli M, Soulier J, Romana S, L’Honneur AS, Materna M, Martínez-Barricarte R, Pochon M, Oleaga-Quintas C, Michev A, Migaud M, Lévy R, Alyanakian MA, Rozenberg F, Croft CA, Vogt G, Emile JF, Kremer L, Ma CS, Fritz JH, Lemon SM, Spaan AN, Manel N, Abel L, MacDonald MR, Boisson-Dupuis S, Marr N, Tangye SG, Di Santo JP, Zhang Q, Zhang SY, Rice CM, Béziat V, Lachmann N, Langlais D, Casanova JL, Gros P, Bustamante J. Human IRF1 governs macrophagic IFN-γ immunity to mycobacteria. Cell 2023; 186:621-645.e33. [PMID: 36736301 PMCID: PMC9907019 DOI: 10.1016/j.cell.2022.12.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 02/05/2023]
Abstract
Inborn errors of human IFN-γ-dependent macrophagic immunity underlie mycobacterial diseases, whereas inborn errors of IFN-α/β-dependent intrinsic immunity underlie viral diseases. Both types of IFNs induce the transcription factor IRF1. We describe unrelated children with inherited complete IRF1 deficiency and early-onset, multiple, life-threatening diseases caused by weakly virulent mycobacteria and related intramacrophagic pathogens. These children have no history of severe viral disease, despite exposure to many viruses, including SARS-CoV-2, which is life-threatening in individuals with impaired IFN-α/β immunity. In leukocytes or fibroblasts stimulated in vitro, IRF1-dependent responses to IFN-γ are, both quantitatively and qualitatively, much stronger than those to IFN-α/β. Moreover, IRF1-deficient mononuclear phagocytes do not control mycobacteria and related pathogens normally when stimulated with IFN-γ. By contrast, IFN-α/β-dependent intrinsic immunity to nine viruses, including SARS-CoV-2, is almost normal in IRF1-deficient fibroblasts. Human IRF1 is essential for IFN-γ-dependent macrophagic immunity to mycobacteria, but largely redundant for IFN-α/β-dependent antiviral immunity.
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Affiliation(s)
- Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France; Paris Cité University, Imagine Institute, 75015 Paris, France.
| | - Anna-Lena Neehus
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,Institute of Experimental Hematology, REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Jeremy Manry
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Rui Yang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Jérémie Le Pen
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Wassim Daher
- Infectious Disease Research Institute of Montpellier (IRIM), Montpellier University, 34000 Montpellier, France,Inserm, IRIM, 34293 Montpellier, France
| | - Zhiyong Liu
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Yi-Hao Chan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Natalia Tahuil
- Department of Immunology, Del Niño Jesus Hospital, T4000 San Miguel de Tucuman, Tucuman, Argentina
| | - Özden Türel
- Department of Pediatric Infectious Disease, Bezmialem Vakif University Faculty of Medicine, 34093 İstanbul, Turkey
| | - Mathieu Bourgey
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada,Canadian Centre for Computation Genomics, Montreal, QC H3A 0G1, Canada
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Jean-Marc Doisne
- Innate Immunity Unit, Institut Pasteur, 75015 Paris, France,Inserm U1223, 75015 Paris, France
| | | | - Takayoshi Shirasaki
- Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292, USA
| | - Tom Le Voyer
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Antoine Guérin
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of NSW, Sydney, NSW 2052, Australia
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA,Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
| | - Marcela Moncada-Velez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Ji Eun Han
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Taushif Khan
- Department of Immunology, Sidra Medicine, Doha, Qatar
| | - Franck Rapaport
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Seon-Hui Hong
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Andrew Cheung
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Kathrin Haake
- Institute of Experimental Hematology, REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Barbara C. Mindt
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G1, Canada,McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3A 0G1, Canada,FOCiS Centre of Excellence in Translational Immunology, McGill University, Montreal, QC H3A 0G1, Canada
| | - Laura Perez
- Department of Immunology and Rheumatology, “J. P. Garrahan” National Hospital of Pediatrics, C1245 CABA, Buenos Aires, Argentina
| | - Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Danyel Lee
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Fatima Al Ali
- Department of Immunology, Sidra Medicine, Doha, Qatar
| | | | | | - Jessica N. Peel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Yasemin Kendir-Demirkol
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA,Umraniye Education and Research Hospital, Department of Pediatric Genetics, 34764 İstanbul, Turkey
| | - Rasheed Bailey
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Shuxiang Zhao
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Jonathan Bohlen
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Mathieu Mancini
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada,Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G1, Canada,McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3A 0G1, Canada
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Marie Roelens
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France,Paris Cité University, 75006 Paris, France
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Camille Soudée
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - María Elvira Josefina Paz
- Department of Pediatric Pathology, Del Niño Jesus Hospital, T4000 San Miguel de Tucuman, Tucuman, Argentina
| | - Maria Laura Gonzalez
- Central Laboratory, Del Niño Jesus Hospital, T4000 San Miguel de Tucuman, Tucuman, Argentina
| | - Mohamed Jeljeli
- Cochin University Hospital, Biological Immunology Unit, AP-HP, 75014 Paris, France
| | - Jean Soulier
- Inserm/CNRS U944/7212, Paris Cité University, 75006 Paris, France,Hematology Laboratory, Saint-Louis Hospital, AP-HP, 75010 Paris, France,,National Reference Center for Bone Marrow Failures, Saint-Louis and Robert Debré Hospitals, 75010 Paris, France
| | - Serge Romana
- Rare Disease Genomic Medicine Department, Paris Cité University, Necker Hospital for Sick Children, 75015 Paris, France
| | | | - Marie Materna
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Rubén Martínez-Barricarte
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Department of Pathology, Microbiology, and Immunology, Vanderbilt Center for Immunobiology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mathieu Pochon
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Carmen Oleaga-Quintas
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Alexandre Michev
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Romain Lévy
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
| | | | - Flore Rozenberg
- Department of Virology, Paris Cité University, Cochin Hospital, 75014 Paris, France
| | - Carys A. Croft
- Innate Immunity Unit, Institut Pasteur, 75015 Paris, France,Inserm U1223, 75015 Paris, France,Paris Cité University, 75006 Paris, France
| | - Guillaume Vogt
- Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes, Lille University, Lille Pasteur Institute, Lille University Hospital, 59000 Lille, France,Neglected Human Genetics Laboratory, Paris Cité University, 75006 Paris, France
| | - Jean-François Emile
- Pathology Department, Ambroise-Paré Hospital, AP-HP, 92100 Boulogne-Billancourt, France
| | - Laurent Kremer
- Infectious Disease Research Institute of Montpellier (IRIM), Montpellier University, 34000 Montpellier, France,Inserm, IRIM, 34293 Montpellier, France
| | - Cindy S. Ma
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of NSW, Sydney, NSW 2052, Australia
| | - Jörg H. Fritz
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G1, Canada,McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3A 0G1, Canada,FOCiS Centre of Excellence in Translational Immunology, McGill University, Montreal, QC H3A 0G1, Canada,Department of Physiology, McGill University, Montreal, QC H3A 0G1, Canada
| | - Stanley M. Lemon
- Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292, USA
| | - András N. Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584CX Utrecht, The Netherlands
| | - Nicolas Manel
- Institut Curie, PSL Research University, Inserm U932, 75005 Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Margaret R. MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Stéphanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Nico Marr
- Department of Immunology, Sidra Medicine, Doha, Qatar,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Stuart G. Tangye
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of NSW, Sydney, NSW 2052, Australia
| | - James P. Di Santo
- Innate Immunity Unit, Institut Pasteur, 75015 Paris, France,Inserm U1223, 75015 Paris, France
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Nico Lachmann
- Institute of Experimental Hematology, REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany,Department of Pediatric Pulmonology, Allergology and Neonatology and Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover Medical School, 30625 Hannover, Germany, EU,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - David Langlais
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada,Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G1, Canada,Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France; Paris Cité University, Imagine Institute, 75015 Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA; Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France; Howard Hughes Medical Institute, New York, NY 10065, USA.
| | - Philippe Gros
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada,Department of Biochemistry, McGill University, Montreal, QC H3A 0G1, Canada
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France; Paris Cité University, Imagine Institute, 75015 Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA; Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France.
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113
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Albarnaz JD, Weekes MP. Proteomic analysis of antiviral innate immunity. Curr Opin Virol 2023; 58:101291. [PMID: 36529073 DOI: 10.1016/j.coviro.2022.101291] [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: 07/28/2022] [Revised: 10/03/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022]
Abstract
The capacity of host cells to detect and restrict an infecting virus rests on an array of cell-autonomous antiviral effectors and innate immune receptors that can trigger inflammatory processes at tissue and organismal levels. Dynamic changes in protein abundance, subcellular localisation, post-translational modifications and interactions with other biomolecules govern these processes. Proteomics is therefore an ideal experimental tool to discover novel mechanisms of host antiviral immunity. Additional information can be gleaned both about host and virus by systematic analysis of viral immune evasion strategies. In this review, we summarise recent advances in proteomic technologies and their application to antiviral innate immunity.
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Affiliation(s)
- Jonas D Albarnaz
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, CB2 0XY Cambridge, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, CB2 0XY Cambridge, UK.
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114
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Liu X, Zheng F, Tian L, Li T, Zhang Z, Ren Z, Chen X, Chen W, Li K, Sheng J. Lidocaine inhibits influenza a virus replication by up-regulating IFNα4 via TBK1-IRF7 and JNK-AP1 signaling pathways. Int Immunopharmacol 2023; 115:109706. [PMID: 36638664 DOI: 10.1016/j.intimp.2023.109706] [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: 10/04/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 01/13/2023]
Abstract
Influenza A viruses (IAV), significant respiratory pathogenic agents, cause seasonal epidemics and global pandemics in intra- and interannual cycles. Despite effective therapies targeting viral proteins, the continuous generation of drug-resistant IAV strains is challenging. Therefore, exploring novel host-specific antiviral treatment strategies is urgently needed. Here, we found that lidocaine, widely used for local anesthesia and sedation, significantly inhibited H1N1(PR8) replication in macrophages. Interestingly, its antiviral effect did not depend on the inhibition of voltage-gated sodium channels (VGSC), the main target of lidocaine for anesthesia. Lidocaine significantly upregulated early IFN-I, interferon α4 (IFNα4) mRNA, and protein levels, but not those of early IFNβ in mouse RAW 264.7 cell line and human THP-1 derived macrophages. Knocking out IFNα4 by CRISPR-Cas9 partly reversed lidocaine's inhibition of PR8 replication in macrophages. Mechanistically, lidocaine upregulated IFNα4 by activating TANK-binding kinase 1 (TBK1)-IRF7 and JNK-AP1 signaling pathways. These findings indicate that lidocaine has an incredible antiviral potential by enhancing IFN-I signaling in macrophages. In conclusion, our results indicate the potential auxiliary role of lidocaine for anti-influenza A virus therapy and even for anti-SARS-CoV-2 virus therapy, especially in the absence of a specific medicine.
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Affiliation(s)
- Xueer Liu
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, Guangdong, China
| | - Fengqing Zheng
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, Guangdong, China
| | - Lu Tian
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, Guangdong, China
| | - Tian Li
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, Guangdong, China
| | - Zelin Zhang
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, Guangdong, China
| | - Zhihui Ren
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, Guangdong, China
| | - Xiaoxuan Chen
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, Guangdong, China
| | - Weiqiang Chen
- Department of Neurosurgery, First Affiliated Hospital of Shantou University Medical College, 57 Changping Road, Shantou 515041, Guangdong, China.
| | - Kangsheng Li
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, Guangdong, China.
| | - Jiangtao Sheng
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, Guangdong, China.
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115
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Abstract
SARS-CoV-2 spike requires proteolytic processing for viral entry. A polybasic furin-cleavage site (FCS) in spike, and evolution toward an optimized FCS by dominant variants of concern (VOCs), are linked to enhanced infectivity and transmission. Here we show interferon-inducible restriction factors Guanylate-binding proteins (GBP) 2 and 5 interfere with furin-mediated spike cleavage and inhibit the infectivity of early-lineage isolates Wuhan-Hu-1 and VIC. By contrast, VOCs Alpha and Delta escape restriction by GBP2/5 that we map to the spike substitution D614G present in these VOCs. Despite inhibition of spike cleavage, these viruses remained sensitive to plasma membrane IFITM1, but not endosomal IFITM2 and 3, consistent with a preference for TMPRSS2-dependent plasma membrane entry. Strikingly, we find that Omicron is unique among VOCs, being sensitive to restriction factors GBP2/5, and also IFITM1, 2, and 3. Using chimeric spike mutants, we map the Omicron phenotype and show that the S1 domain determines Omicron's sensitivity to GBP2/5, whereas the S2' domain determines its sensitivity to endosomal IFITM2/3 and preferential use of TMPRSS2-independent entry. We propose that evolution of SARS-CoV-2 for the D614G substitution has allowed for escape from GBP restriction factors, but the selective pressures on Omicron for spike changes that mediate antibody escape, and altered tropism, have come at the expense of increased sensitivity to innate immune restriction factors that target virus entry.
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116
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Sun H, Chan JFW, Yuan S. Cellular Sensors and Viral Countermeasures: A Molecular Arms Race between Host and SARS-CoV-2. Viruses 2023; 15:352. [PMID: 36851564 PMCID: PMC9962416 DOI: 10.3390/v15020352] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19) pandemic that has caused disastrous effects on the society and human health globally. SARS-CoV-2 is a sarbecovirus in the Coronaviridae family with a positive-sense single-stranded RNA genome. It mainly replicates in the cytoplasm and viral components including RNAs and proteins can be sensed by pattern recognition receptors including toll-like receptors (TLRs), RIG-I-like receptors (RLRs), and NOD-like receptors (NLRs) that regulate the host innate and adaptive immune responses. On the other hand, the SARS-CoV-2 genome encodes multiple proteins that can antagonize the host immune response to facilitate viral replication. In this review, we discuss the current knowledge on host sensors and viral countermeasures against host innate immune response to provide insights on virus-host interactions and novel approaches to modulate host inflammation and antiviral responses.
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Affiliation(s)
- Haoran Sun
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518009, China
| | - Jasper Fuk-Woo Chan
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518009, China
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
| | - Shuofeng Yuan
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518009, China
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
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117
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Tang C, Coelho AR, Rebelo M, Kiely-Collins H, Carvalho T, Bernardes GJL. A Selective SARS-CoV-2 Host-Directed Antiviral Targeting Stress Response to Reactive Oxygen Species. ACS CENTRAL SCIENCE 2023; 9:109-121. [PMID: 36712488 PMCID: PMC9881195 DOI: 10.1021/acscentsci.2c01243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Indexed: 06/18/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) catalyzed the development of vaccines and antivirals. Clinically approved drugs against SARS-CoV-2 target the virus directly, which makes them susceptible to viral mutations, which in turn can attenuate their antiviral activity. Here we report a host-directed antiviral (HDA), piperlongumine (PL), which exhibits robust antiviral activity as a result of selective induction of reactive oxygen species in infected cells by GSTP1 inhibition. Using a transgenic K18-hACE2 mouse model, we benchmarked PL against plitidepsin, a HDA undergoing phase III clinical trials. We observed that intranasal administration of PL is superior in delaying disease progression and reducing lung inflammation. Importantly, we showed that PL is effective against several variants of concern (VOCs), making it an ideal pan-variant antiviral. PL may display a critical role as an intranasal treatment or prophylaxis against a range of viruses, expanding the arsenal of tools to fight future outbreaks.
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Affiliation(s)
- Cong Tang
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Ana R. Coelho
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Maria Rebelo
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Hannah Kiely-Collins
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Tânia Carvalho
- Champalimaud
Foundation, Avenida de Brasília, 1400-038, Lisboa, Portugal
| | - Gonçalo J. L. Bernardes
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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118
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Towards precision medicine: Omics approach for COVID-19. BIOSAFETY AND HEALTH 2023; 5:78-88. [PMID: 36687209 PMCID: PMC9846903 DOI: 10.1016/j.bsheal.2023.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic had a devastating impact on human society. Beginning with genome surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the development of omics technologies brought a clearer understanding of the complex SARS-CoV-2 and COVID-19. Here, we reviewed how omics, including genomics, proteomics, single-cell multi-omics, and clinical phenomics, play roles in answering biological and clinical questions about COVID-19. Large-scale sequencing and advanced analysis methods facilitate COVID-19 discovery from virus evolution and severity risk prediction to potential treatment identification. Omics would indicate precise and globalized prevention and medicine for the COVID-19 pandemic under the utilization of big data capability and phenotypes refinement. Furthermore, decoding the evolution rule of SARS-CoV-2 by deep learning models is promising to forecast new variants and achieve more precise data to predict future pandemics and prevent them on time.
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119
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Bendall EE, Callear AP, Getz A, Goforth K, Edwards D, Monto AS, Martin ET, Lauring AS. Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants. Nat Commun 2023; 14:272. [PMID: 36650162 PMCID: PMC9844183 DOI: 10.1038/s41467-023-36001-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Transmission bottlenecks limit the spread of novel mutations and reduce the efficiency of selection along a transmission chain. While increased force of infection, receptor binding, or immune evasion may influence bottleneck size, the relationship between transmissibility and the transmission bottleneck is unclear. Here we compare the transmission bottleneck of non-VOC SARS-CoV-2 lineages to those of Alpha, Delta, and Omicron. We sequenced viruses from 168 individuals in 65 households. Most virus populations had 0-1 single nucleotide variants (iSNV). From 64 transmission pairs with detectable iSNV, we identify a per clade bottleneck of 1 (95% CI 1-1) for Alpha, Delta, and Omicron and 2 (95% CI 2-2) for non-VOC. These tight bottlenecks reflect the low diversity at the time of transmission, which may be more pronounced in rapidly transmissible variants. Tight bottlenecks will limit the development of highly mutated VOC in transmission chains, adding to the evidence that selection over prolonged infections may drive their evolution.
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Affiliation(s)
- Emily E Bendall
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Amy P Callear
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Amy Getz
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Kendra Goforth
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Drew Edwards
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Arnold S Monto
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Emily T Martin
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Adam S Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA. .,Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
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Cheng N, Liu M, Li W, Sun B, Liu D, Wang G, Shi J, Li L. Protein post-translational modification in SARS-CoV-2 and host interaction. Front Immunol 2023; 13:1068449. [PMID: 36713387 PMCID: PMC9880545 DOI: 10.3389/fimmu.2022.1068449] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/27/2022] [Indexed: 01/14/2023] Open
Abstract
SARS-CoV-2 can cause lung diseases, such as pneumonia and acute respiratory distress syndrome, and multi-system dysfunction. Post-translational modifications (PTMs) related to SARS-CoV-2 are conservative and pathogenic, and the common PTMs are glycosylation, phosphorylation, and acylation. The glycosylation of SARS-CoV-2 mainly occurs on spike (S) protein, which mediates the entry of the virus into cells through interaction with angiotensin-converting enzyme 2. SARS-CoV-2 utilizes glycans to cover its epitopes and evade the immune response through glycosylation of S protein. Phosphorylation of SARS-CoV-2 nucleocapsid (N) protein improves its selective binding to viral RNA and promotes viral replication and transcription, thereby increasing the load of the virus in the host. Succinylated N and membrane(M) proteins of SARS-CoV-2 synergistically affect virus particle assembly. N protein regulates its affinity for other proteins and the viral genome through acetylation. The acetylated envelope (E) protein of SARS-CoV-2 interacts with bromodomain-containing protein 2/4 to influence the host immune response. Both palmitoylation and myristoylation sites on S protein can affect the virus infectivity. Papain-like protease is a domain of NSP3 that dysregulates host inflammation by deubiquitination and impinges host IFN-I antiviral immune responses by deISGylation. Ubiquitination of ORF7a inhibits host IFN-α signaling by blocking STAT2 phosphorylation. The methylation of N protein can inhibit the formation of host stress granules and promote the binding of N protein to viral RNA, thereby promoting the production of virus particles. NSP3 macrodomain can reverse the ADP-ribosylation of host proteins, and inhibit the cascade immune response with IFN as the core, thereby promoting the intracellular replication of SARS-CoV-2. On the whole, PTMs have fundamental roles in virus entry, replication, particle assembly, and host immune response. Mutations in various SARS-CoV-2 variants, which lead to changes in PTMs at corresponding sites, cause different biological effects. In this paper, we mainly reviewed the effects of PTMs on SARS-CoV-2 and host cells, whose application is to inform the strategies for inhibiting viral infection and facilitating antiviral treatment and vaccine development for COVID-19.
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Affiliation(s)
- Nana Cheng
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China
| | - Mingzhu Liu
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
| | - Wanting Li
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
| | - BingYue Sun
- First Affiliated Hospital of Jilin University, Changchun, China
| | - Dandan Liu
- First Affiliated Hospital of Jilin University, Changchun, China
| | - Guoqing Wang
- Department of Pathogenobiology, The Key Laboratory of Zoonosis Research, Chinese Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Jingwei Shi
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
| | - Lisha Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China
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121
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Shan SO. Role of Hsp70 in Post-Translational Protein Targeting: Tail-Anchored Membrane Proteins and Beyond. Int J Mol Sci 2023; 24:1170. [PMID: 36674686 PMCID: PMC9866221 DOI: 10.3390/ijms24021170] [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: 11/29/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The Hsp70 family of molecular chaperones acts as a central 'hub' in the cell that interacts with numerous newly synthesized proteins to assist in their biogenesis. Apart from its central and well-established role in facilitating protein folding, Hsp70s also act as key decision points in the cellular chaperone network that direct client proteins to distinct biogenesis and quality control pathways. In this paper, we review accumulating data that illustrate a new branch in the Hsp70 network: the post-translational targeting of nascent membrane and organellar proteins to diverse cellular organelles. Work in multiple pathways suggests that Hsp70, via its ability to interact with components of protein targeting and translocation machineries, can initiate elaborate substrate relays in a sophisticated cascade of chaperones, cochaperones, and receptor proteins, and thus provide a mechanism to safeguard and deliver nascent membrane proteins to the correct cellular membrane. We discuss the mechanistic principles gleaned from better-studied Hsp70-dependent targeting pathways and outline the observations and outstanding questions in less well-studied systems.
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Affiliation(s)
- Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Jin X, Sun X, Chai Y, Bai Y, Li Y, Hao T, Qi J, Song H, Wong CCL, Gao GF. Structural characterization of SARS-CoV-2 dimeric ORF9b reveals potential fold-switching trigger mechanism. SCIENCE CHINA. LIFE SCIENCES 2023; 66:152-164. [PMID: 36184694 PMCID: PMC9527070 DOI: 10.1007/s11427-022-2168-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/20/2022] [Indexed: 11/06/2022]
Abstract
The constant emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants indicates the evolution and adaptation of the virus. Enhanced innate immune evasion through increased expression of viral antagonist proteins, including ORF9b, contributes to the improved transmission of the Alpha variant; hence, more attention should be paid to these viral proteins. ORF9b is an accessory protein that suppresses innate immunity via a monomer conformation by binding to Tom70. Here, we solved the dimeric structure of SARS-CoV-2 ORF9b with a long hydrophobic tunnel containing a lipid molecule that is crucial for the dimeric conformation and determined the specific lipid ligands as monoglycerides by conducting a liquid chromatography with tandem mass spectrometry analysis, suggesting an important role in the viral life cycle. Notably, a long intertwined loop accessible for host factor binding was observed in the structure. Eight phosphorylated residues in ORF9b were identified, and residues S50 and S53 were found to contribute to the stabilization of dimeric ORF9b. Additionally, we proposed a model of multifunctional ORF9b with a distinct conformation, suggesting that ORF9b is a fold-switching protein, while both lipids and phosphorylation contribute to the switching. Specifically, the ORF9b monomer interacts with Tom70 to suppress the innate immune response, whereas the ORF9b dimer binds to the membrane involving mature virion assembly. Our results provide a better understanding of the multiple functions of ORF9b.
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Affiliation(s)
- Xiyue Jin
- grid.59053.3a0000000121679639School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027 China ,grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xue Sun
- grid.11135.370000 0001 2256 9319Peking University First Hospital, Peking University, Beijing, 100034 China ,grid.11135.370000 0001 2256 9319Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, 100191 China
| | - Yan Chai
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yu Bai
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ying Li
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Tianjiao Hao
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jianxun Qi
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Hao Song
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Catherine C. L. Wong
- grid.11135.370000 0001 2256 9319Peking University First Hospital, Peking University, Beijing, 100034 China ,grid.11135.370000 0001 2256 9319Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, 100191 China ,grid.11135.370000 0001 2256 9319Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China ,grid.11135.370000 0001 2256 9319School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, 100191 China
| | - George F. Gao
- grid.59053.3a0000000121679639School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027 China ,grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
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Meseguer S, Rubio MP, Lainez B, Pérez-Benavente B, Pérez-Moraga R, Romera-Giner S, García-García F, Martinez-Macias O, Cremades A, Iborra FJ, Candelas-Rivera O, Almazan F, Esplugues E. SARS-CoV-2-encoded small RNAs are able to repress the host expression of SERINC5 to facilitate viral replication. Front Microbiol 2023; 14:1066493. [PMID: 36876111 PMCID: PMC9978209 DOI: 10.3389/fmicb.2023.1066493] [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: 10/10/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023] Open
Abstract
Serine incorporator protein 5 (SERINC5) is a key innate immunity factor that operates in the cell to restrict the infectivity of certain viruses. Different viruses have developed strategies to antagonize SERINC5 function but, how SERINC5 is controlled during viral infection is poorly understood. Here, we report that SERINC5 levels are reduced in COVID-19 patients during the infection by SARS-CoV-2 and, since no viral protein capable of repressing the expression of SERINC5 has been identified, we hypothesized that SARS-CoV-2 non-coding small viral RNAs (svRNAs) could be responsible for this repression. Two newly identified svRNAs with predicted binding sites in the 3'-untranslated region (3'-UTR) of the SERINC5 gene were characterized and we found that the expression of both svRNAs during the infection was not dependent on the miRNA pathway proteins Dicer and Argonaute-2. By using svRNAs mimic oligonucleotides, we demonstrated that both viral svRNAs can bind the 3'UTR of SERINC5 mRNA, reducing SERINC5 expression in vitro. Moreover, we found that an anti-svRNA treatment to Vero E6 cells before SARS-CoV-2 infection recovered the levels of SERINC5 and reduced the levels of N and S viral proteins. Finally, we showed that SERINC5 positively controls the levels of Mitochondrial Antiviral Signalling (MAVS) protein in Vero E6. These results highlight the therapeutic potential of targeting svRNAs based on their action on key proteins of the innate immune response during SARS-CoV-2 viral infection.
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Affiliation(s)
- Salvador Meseguer
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Mari-Paz Rubio
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Begoña Lainez
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Beatriz Pérez-Benavente
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Raúl Pérez-Moraga
- Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Sergio Romera-Giner
- Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Francisco García-García
- Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | | | | | - Francisco J Iborra
- Biological Noise and Cell Plasticity Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Associated Unit to Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain
| | - Oscar Candelas-Rivera
- Molecular and Cellular Biology Department, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Fernando Almazan
- Molecular and Cellular Biology Department, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Enric Esplugues
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, United States
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124
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Väisänen E, Jiang M, Laine L, Waris M, Julkunen I, Österlund P. Infectious viruses from transfected SARS-CoV-2 genomic RNA. Front Bioeng Biotechnol 2023; 11:1129111. [PMID: 37064222 PMCID: PMC10098207 DOI: 10.3389/fbioe.2023.1129111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/22/2023] [Indexed: 04/18/2023] Open
Abstract
SARS-CoV-2 emerged at the end of 2019, and like other novel pathogens causing severe symptoms, WHO recommended heightened biosafety measures for laboratories working with the virus. The positive-stranded genomic RNA of coronaviruses has been known to be infectious since the 1970s, and overall, all experiments with the possibility of SARS-CoV-2 propagation are carried out in higher containment level laboratories. However, as SARS-CoV-2 RNA has been routinely handled in BSL-2 laboratories, the question of the true nature of RNA infectiousness has risen along with discussion of appropriate biosafety measures. Here, we studied the ability of native SARS-CoV-2 genomic RNA to produce infectious viruses when transfected into permissive cells and discussed the biosafety control measures related to these assays. In transfection assays large quantities of genomic vRNA of SARS-CoV-2 was required for a successful production of infectious viruses. However, the quantity of vRNA alone was not the only factor, and especially when the transfected RNA was derived from infected cells, even small amounts of genomic vRNA was enough for an infection. Virus replication was found to start rapidly after transfection, and infectious viruses were detected in the cell culture media at 24 h post-transfection. In addition, silica membrane-based kits were shown to be as good as traditional TRI-reagent based methods in extracting high-quality, 30 kb-long genomic vRNA. Taken together, our data indicates that all transfection experiments with samples containing genomic SARS-CoV-2 RNA should be categorized as a propagative work and the work should be conducted only in a higher containment BSL-3 laboratory.
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Affiliation(s)
- Elina Väisänen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
- *Correspondence: Elina Väisänen,
| | - Miao Jiang
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Larissa Laine
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Matti Waris
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Ilkka Julkunen
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Pamela Österlund
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
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125
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Pinto SM, Subbannayya Y, Kim H, Hagen L, Górna MW, Nieminen AI, Bjørås M, Espevik T, Kainov D, Kandasamy RK. Multi-OMICs landscape of SARS-CoV-2-induced host responses in human lung epithelial cells. iScience 2022; 26:105895. [PMID: 36590899 PMCID: PMC9794516 DOI: 10.1016/j.isci.2022.105895] [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: 09/09/2022] [Revised: 12/03/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
COVID-19 pandemic continues to remain a global health concern owing to the emergence of newer variants. Several multi-Omics studies have produced extensive evidence on host-pathogen interactions and potential therapeutic targets. Nonetheless, an increased understanding of host signaling networks regulated by post-translational modifications and their ensuing effect on the cellular dynamics is critical to expanding the current knowledge on SARS-CoV-2 infections. Through an unbiased transcriptomics, proteomics, acetylomics, phosphoproteomics, and exometabolome analysis of a lung-derived human cell line, we show that SARS-CoV-2 Norway/Trondheim-S15 strain induces time-dependent alterations in the induction of type I IFN response, activation of DNA damage response, dysregulated Hippo signaling, among others. We identified interplay of phosphorylation and acetylation dynamics on host proteins and its effect on the altered release of metabolites, especially organic acids and ketone bodies. Together, our findings serve as a resource of potential targets that can aid in designing novel host-directed therapeutic strategies.
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Affiliation(s)
- Sneha M. Pinto
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway,Corresponding author
| | - Yashwanth Subbannayya
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Hera Kim
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway,Proteomics and Modomics Experimental Core, PROMEC, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Maria W. Górna
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Anni I. Nieminen
- Institute for Molecular Medicine Finland, University of Helsinki, 00014Helsinki, Finland
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Terje Espevik
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Denis Kainov
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Richard K. Kandasamy
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway,Department of Laboratory Medicine and Pathology, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA,Corresponding author
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126
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Warger J, Gaudieri S. On the Evolutionary Trajectory of SARS-CoV-2: Host Immunity as a Driver of Adaptation in RNA Viruses. Viruses 2022; 15:70. [PMID: 36680110 PMCID: PMC9866609 DOI: 10.3390/v15010070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
Host immunity can exert a complex array of selective pressures on a pathogen, which can drive highly mutable RNA viruses towards viral escape. The plasticity of a virus depends on its rate of mutation, as well as the balance of fitness cost and benefit of mutations, including viral adaptations to the host's immune response. Since its emergence, SARS-CoV-2 has diversified into genetically distinct variants, which are characterised often by clusters of mutations that bolster its capacity to escape human innate and adaptive immunity. Such viral escape is well documented in the context of other pandemic RNA viruses such as the human immunodeficiency virus (HIV) and influenza virus. This review describes the selection pressures the host's antiviral immunity exerts on SARS-CoV-2 and other RNA viruses, resulting in divergence of viral strains into more adapted forms. As RNA viruses obscure themselves from host immunity, they uncover weak points in their own armoury that can inform more comprehensive, long-lasting, and potentially cross-protective vaccine coverage.
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Affiliation(s)
- Jacob Warger
- School of Medicine and Pharmacology, University of Western Australia, Crawley, WA 6009, Australia
| | - Silvana Gaudieri
- School of Human Sciences, University of Western Australia, Crawley, WA 6009, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Mandurah, WA 6150, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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127
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Moriyama M, Lucas C, Monteiro VS, Iwasaki A. SARS-CoV-2 Omicron subvariants evolved to promote further escape from MHC-I recognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.05.04.490614. [PMID: 35547852 PMCID: PMC9094094 DOI: 10.1101/2022.05.04.490614] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
SARS-CoV-2 variants of concern (VOCs) possess mutations that confer resistance to neutralizing antibodies within the Spike protein and are associated with breakthrough infection and reinfection. By contrast, less is known about the escape from CD8+ T cell-mediated immunity by VOC. Here, we demonstrated that all SARS-CoV-2 VOCs possess the ability to suppress MHC I expression. We identified several viral genes that contribute to the suppression of MHC I expression. Notably, MHC-I upregulation was strongly inhibited after SARS-CoV-2 infection in vivo. While earlier VOCs possess similar capacity as the ancestral strain to suppress MHC I, Omicron subvariants exhibit a greater ability to suppress surface MHC-I expressions. Collectively, our data suggest that, in addition to escape from neutralizing antibodies, the success of Omicron subvariants to cause breakthrough infection and reinfection may in part be due to its optimized evasion from T cell recognition.
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128
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Kwon HJ, Kosikova M, Tang W, Ortega-Rodriguez U, Radvak P, Xiang R, Mercer KE, Muskhelishvili L, Davis K, Ward JM, Kosik I, Holly J, Kang I, Yewdell JW, Plant EP, Chen WH, Shriver MC, Barnes RS, Pasetti MF, Zhou B, Wentworth DE, Xie H. Enhanced virulence and waning vaccine-elicited antibodies account for breakthrough infections caused by SARS-CoV-2 delta and beyond. iScience 2022; 25:105507. [PMID: 36373096 PMCID: PMC9635945 DOI: 10.1016/j.isci.2022.105507] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/05/2022] [Accepted: 11/01/2022] [Indexed: 11/08/2022] Open
Abstract
Here we interrogate the factors responsible for SARS-CoV-2 breakthrough infections in a K18-hACE2 transgenic mouse model. We show that Delta and the closely related Kappa variant cause viral pneumonia and severe lung lesions in K18-hACE2 mice. Human COVID-19 mRNA post-vaccination sera after the 2nd dose are significantly less efficient in neutralizing Delta/Kappa than early 614G virus in vitro and in vivo. By 5 months post-vaccination, ≥50% of donors lack detectable neutralizing antibodies against Delta and Kappa and all mice receiving 5-month post-vaccination sera die after the lethal challenges. Although a 3rd vaccine dose can boost antibody neutralization against Delta in vitro and in vivo, the mean log neutralization titers against the latest Omicron subvariants are 1/3-1/2 of those against the original 614D virus. Our results suggest that enhanced virulence, greater immune evasion, and waning of vaccine-elicited protection account for SARS-CoV-2 variants caused breakthrough infections.
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Affiliation(s)
- Hyung-Joon Kwon
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Martina Kosikova
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Weichun Tang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Uriel Ortega-Rodriguez
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Peter Radvak
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Ruoxuan Xiang
- Division of Biostatistics, Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Kelly E. Mercer
- Biomarkers and Alternative Models Branch, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, AR, USA
| | | | - Kelly Davis
- Toxicologic Pathology Associates, Jefferson, AR, USA
| | | | - Ivan Kosik
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jaroslav Holly
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Insung Kang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Jonathan W. Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ewan P. Plant
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
| | - Wilbur H. Chen
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mallory C. Shriver
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robin S. Barnes
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Marcela F. Pasetti
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bin Zhou
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - David E. Wentworth
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Hang Xie
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA
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Wu Z, Berlemann LA, Bader V, Sehr DA, Dawin E, Covallero A, Meschede J, Angersbach L, Showkat C, Michaelis JB, Münch C, Rieger B, Namgaladze D, Herrera MG, Fiesel FC, Springer W, Mendes M, Stepien J, Barkovits K, Marcus K, Sickmann A, Dittmar G, Busch KB, Riedel D, Brini M, Tatzelt J, Cali T, Winklhofer KF. LUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF-κB to the nucleus. EMBO J 2022; 41:e112006. [PMID: 36398858 PMCID: PMC9753471 DOI: 10.15252/embj.2022112006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
Mitochondria are increasingly recognized as cellular hubs to orchestrate signaling pathways that regulate metabolism, redox homeostasis, and cell fate decisions. Recent research revealed a role of mitochondria also in innate immune signaling; however, the mechanisms of how mitochondria affect signal transduction are poorly understood. Here, we show that the NF-κB pathway activated by TNF employs mitochondria as a platform for signal amplification and shuttling of activated NF-κB to the nucleus. TNF treatment induces the recruitment of HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), and its substrate NEMO to the outer mitochondrial membrane, where M1- and K63-linked ubiquitin chains are generated. NF-κB is locally activated and transported to the nucleus by mitochondria, leading to an increase in mitochondria-nucleus contact sites in a HOIP-dependent manner. Notably, TNF-induced stabilization of the mitochondrial kinase PINK1 furthermore contributes to signal amplification by antagonizing the M1-ubiquitin-specific deubiquitinase OTULIN. Overall, our study reveals a role for mitochondria in amplifying TNF-mediated NF-κB activation, both serving as a signaling platform, as well as a transport mode for activated NF-κB to the nuclear.
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Affiliation(s)
- Zhixiao Wu
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Lena A Berlemann
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Dominik A Sehr
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Eva Dawin
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- Leibniz‐Institut für Analytische Wissenschaften—ISAS—e.VDortmundGermany
| | | | - Jens Meschede
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Lena Angersbach
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Cathrin Showkat
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Jonas B Michaelis
- Faculty of Medicine, Institute of Biochemistry IIGoethe University FrankfurtFrankfurt am MainGermany
| | - Christian Münch
- Faculty of Medicine, Institute of Biochemistry IIGoethe University FrankfurtFrankfurt am MainGermany
| | - Bettina Rieger
- Institute for Integrative Cell Biology and Physiology, Faculty of BiologyUniversity of MünsterMünsterGermany
| | - Dmitry Namgaladze
- Institute of Biochemistry I, Faculty of MedicineGoethe‐University FrankfurtFrankfurtGermany
| | - Maria Georgina Herrera
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Fabienne C Fiesel
- Department of NeuroscienceMayo ClinicJacksonvilleFLUSA
- Neuroscience PhD ProgramMayo Clinic Graduate School of Biomedical SciencesJacksonvilleFLUSA
| | - Wolfdieter Springer
- Department of NeuroscienceMayo ClinicJacksonvilleFLUSA
- Neuroscience PhD ProgramMayo Clinic Graduate School of Biomedical SciencesJacksonvilleFLUSA
| | - Marta Mendes
- Proteomics of Cellular Signaling, Department of Infection and ImmunityLuxembourg Institute of HealthStrassenLuxembourg
| | - Jennifer Stepien
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Katalin Barkovits
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Katrin Marcus
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Albert Sickmann
- Leibniz‐Institut für Analytische Wissenschaften—ISAS—e.VDortmundGermany
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Department of Infection and ImmunityLuxembourg Institute of HealthStrassenLuxembourg
- Department of Life Sciences and MedicineUniversity of LuxembourgBelvauxLuxembourg
| | - Karin B Busch
- Institute for Integrative Cell Biology and Physiology, Faculty of BiologyUniversity of MünsterMünsterGermany
| | - Dietmar Riedel
- Laboratory for Electron MicroscopyMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Marisa Brini
- Department of BiologyUniversity of PaduaPaduaItaly
- Centro Studi per la Neurodegenerazione (CESNE)University of PadovaPaduaItaly
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- RESOLV Cluster of ExcellenceRuhr University BochumBochumGermany
| | - Tito Cali
- Department of Biomedical SciencesUniversity of PaduaPaduaItaly
- Centro Studi per la Neurodegenerazione (CESNE)University of PadovaPaduaItaly
- Padua Neuroscience Center (PNC)University of PaduaPaduaItaly
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- RESOLV Cluster of ExcellenceRuhr University BochumBochumGermany
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Lista MJ, Winstone H, Wilson HD, Dyer A, Pickering S, Galao RP, De Lorenzo G, Cowton VM, Furnon W, Suarez N, Orton R, Palmarini M, Patel AH, Snell L, Nebbia G, Swanson C, Neil SJD. The P681H Mutation in the Spike Glycoprotein of the Alpha Variant of SARS-CoV-2 Escapes IFITM Restriction and Is Necessary for Type I Interferon Resistance. J Virol 2022; 96:e0125022. [PMID: 36350154 PMCID: PMC9749455 DOI: 10.1128/jvi.01250-22] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022] Open
Abstract
The appearance of new dominant variants of concern (VOC) of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) threatens the global response to the coronavirus disease 2019 (COVID-19) pandemic. Of these, the alpha variant (also known as B.1.1.7), which appeared initially in the United Kingdom, became the dominant variant in much of Europe and North America in the first half of 2021. The spike (S) glycoprotein of alpha acquired seven mutations and two deletions compared to the ancestral virus, including the P681H mutation adjacent to the polybasic cleavage site, which has been suggested to enhance S cleavage. Here, we show that the alpha spike protein confers a level of resistance to beta interferon (IFN-β) in human lung epithelial cells. This correlates with resistance to an entry restriction mediated by interferon-induced transmembrane protein 2 (IFITM2) and a pronounced infection enhancement by IFITM3. Furthermore, the P681H mutation is essential for resistance to IFN-β and context-dependent resistance to IFITMs in the alpha S. P681H reduces dependence on endosomal cathepsins, consistent with enhanced cell surface entry. However, reversion of H681 does not reduce cleaved spike incorporation into particles, indicating that it exerts its effect on entry and IFN-β downstream of furin cleavage. Overall, we suggest that, in addition to adaptive immune escape, mutations associated with VOC may well also confer a replication and/or transmission advantage through adaptation to resist innate immune mechanisms. IMPORTANCE Accumulating evidence suggests that variants of concern (VOC) of SARS-CoV-2 evolve to evade the human immune response, with much interest focused on mutations in the spike protein that escape from antibodies. However, resistance to the innate immune response is essential for efficient viral replication and transmission. Here, we show that the alpha (B.1.1.7) VOC of SARS-CoV-2 is substantially more resistant to type I interferons than the parental Wuhan-like virus. This correlates with resistance to the antiviral protein IFITM2 and enhancement by its paralogue IFITM3. The key determinant of this is a proline-to-histidine change at position 681 in S adjacent to the furin cleavage site, which in the context of the alpha spike modulates cell entry pathways of SARS-CoV-2. Reversion of the mutation is sufficient to restore interferon and IFITM2 sensitivity, highlighting the dynamic nature of the SARS CoV-2 as it adapts to both innate and adaptive immunity in the humans.
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Affiliation(s)
- Maria Jose Lista
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Helena Winstone
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Harry D. Wilson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Adam Dyer
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Suzanne Pickering
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Rui Pedro Galao
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Vanessa M. Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nicolas Suarez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Luke Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Chad Swanson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
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Parigger L, Krassnigg A, Schopper T, Singh A, Tappler K, Köchl K, Hetmann M, Gruber K, Steinkellner G, Gruber CC. Recent changes in the mutational dynamics of the SARS-CoV-2 main protease substantiate the danger of emerging resistance to antiviral drugs. Front Med (Lausanne) 2022; 9:1061142. [PMID: 36590977 PMCID: PMC9794616 DOI: 10.3389/fmed.2022.1061142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Introduction The current coronavirus pandemic is being combated worldwide by nontherapeutic measures and massive vaccination programs. Nevertheless, therapeutic options such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main-protease (Mpro) inhibitors are essential due to the ongoing evolution toward escape from natural or induced immunity. While antiviral strategies are vulnerable to the effects of viral mutation, the relatively conserved Mpro makes an attractive drug target: Nirmatrelvir, an antiviral targeting its active site, has been authorized for conditional or emergency use in several countries since December 2021, and a number of other inhibitors are under clinical evaluation. We analyzed recent SARS-CoV-2 genomic data, since early detection of potential resistances supports a timely counteraction in drug development and deployment, and discovered accelerated mutational dynamics of Mpro since early December 2021. Methods We performed a comparative analysis of 10.5 million SARS-CoV-2 genome sequences available by June 2022 at GISAID to the NCBI reference genome sequence NC_045512.2. Amino-acid exchanges within high-quality regions in 69,878 unique Mpro sequences were identified and time- and in-depth sequence analyses including a structural representation of mutational dynamics were performed using in-house software. Results The analysis showed a significant recent event of mutational dynamics in Mpro. We report a remarkable increase in mutational variability in an eight-residue long consecutive region (R188-G195) near the active site since December 2021. Discussion The increased mutational variability in close proximity to an antiviral-drug binding site as described herein may suggest the onset of the development of antiviral resistance. This emerging diversity urgently needs to be further monitored and considered in ongoing drug development and lead optimization.
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Affiliation(s)
- Lena Parigger
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | | | - Amit Singh
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Katharina Tappler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Michael Hetmann
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Karl Gruber
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Georg Steinkellner
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Christian C. Gruber
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
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132
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Laxminarayana D. Molecular insights into onset of autoimmunity in SARS-CoV-2 infected patients. RHEUMATOLOGY & AUTOIMMUNITY 2022; 2:198-202. [PMID: 36714799 PMCID: PMC9874720 DOI: 10.1002/rai2.12056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/01/2022] [Accepted: 09/03/2022] [Indexed: 11/06/2022]
Abstract
Some of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected patients are facing long-term devastating effects like induction of autoimmune diseases. Here, I discuss molecular mechanisms and risk factors involved in the induction of autoimmune diseases after SARS-CoV-2 infections. Transcript editing genes were upregulated during SARS-CoV-2 infections, which might have edited host gene transcripts and paved the way for autoantigens generation and presented as nonself to generate autoantibodies followed by auto immunogenicity after SARS-CoV-2 infections. Therefore, some SARS-CoV-2 patients acquire autoimmunity. The transient and/or innocuous autoimmune response in some SARS-CoV-2 infected patients may be due to a lack of repeated production of autoantibodies to host autoantigens and/or viral antigens, which are needed to boost autoimmune response. In the future, SARS-CoV-2 mediated autoimmune disease onset will be a challenging task. Therefore, possible preventive measures and strategies to minimize and/or preclude such SARS-CoV-2 mediated autoimmune diseases have been presented in this commentary.
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Kehrer T, Cupic A, Ye C, Yildiz S, Bouhhadou M, Crossland NA, Barrall E, Cohen P, Tseng A, Çağatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena N, Aslam S, Saqi A, Marin A, Rutkowska M, Ummadi MR, Pisanelli G, Richardson RB, Veit EC, Fabius JM, Soucheray M, Polacco BJ, Evans MJ, Swaney DL, Gonzalez-Reiche AS, Sordillo EM, van Bakel H, Simon V, Zuliani-Alvarez L, Fontoura BMA, Rosenberg BR, Krogan NJ, Martinez-Sobrido L, García-Sastre A, Miorin L. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.18.512708. [PMID: 36299428 PMCID: PMC9603824 DOI: 10.1101/2022.10.18.512708] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We and others have previously shown that the SARS-CoV-2 accessory protein ORF6 is a powerful antagonist of the interferon (IFN) signaling pathway by directly interacting with Nup98-Rae1 at the nuclear pore complex (NPC) and disrupting bidirectional nucleo-cytoplasmic trafficking. In this study, we further assessed the role of ORF6 during infection using recombinant SARS-CoV-2 viruses carrying either a deletion or a well characterized M58R loss-of-function mutation in ORF6. We show that ORF6 plays a key role in the antagonism of IFN signaling and in viral pathogenesis by interfering with karyopherin(importin)-mediated nuclear import during SARS-CoV-2 infection both in vitro , and in the Syrian golden hamster model in vivo . In addition, we found that ORF6-Nup98 interaction also contributes to inhibition of cellular mRNA export during SARS-CoV-2 infection. As a result, ORF6 expression significantly remodels the host cell proteome upon infection. Importantly, we also unravel a previously unrecognized function of ORF6 in the modulation of viral protein expression, which is independent of its function at the nuclear pore. Lastly, we characterized the ORF6 D61L mutation that recently emerged in Omicron BA.2 and BA.4 and demonstrated that it is able to disrupt ORF6 protein functions at the NPC and to impair SARS-CoV-2 innate immune evasion strategies. Importantly, the now more abundant Omicron BA.5 lacks this loss-of-function polymorphism in ORF6. Altogether, our findings not only further highlight the key role of ORF6 in the antagonism of the antiviral innate immune response, but also emphasize the importance of studying the role of non-spike mutations to better understand the mechanisms governing differential pathogenicity and immune evasion strategies of SARS-CoV-2 and its evolving variants. ONE SENTENCE SUMMARY SARS-CoV-2 ORF6 subverts bidirectional nucleo-cytoplasmic trafficking to inhibit host gene expression and contribute to viral pathogenesis.
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Subgenomic RNAs and Their Encoded Proteins Contribute to the Rapid Duplication of SARS-CoV-2 and COVID-19 Progression. Biomolecules 2022; 12:biom12111680. [DOI: 10.3390/biom12111680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/30/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently widespread throughout the world, accompanied by a rising number of people infected and breakthrough infection of variants, which make the virus highly transmissible and replicable. A comprehensive understanding of the molecular virological events and induced immunological features during SARS-CoV-2 replication can provide reliable targets for vaccine and drug development. Among the potential targets, subgenomic RNAs and their encoded proteins involved in the life cycle of SARS-CoV-2 are extremely important in viral duplication and pathogenesis. Subgenomic RNAs employ a range of coping strategies to evade immune surveillance from replication to translation, which allows RNAs to synthesize quickly, encode structural proteins efficiently and complete the entire process of virus replication and assembly successfully. This review focuses on the characteristics and functions of SARS-CoV-2 subgenomic RNAs and their encoded proteins and explores in depth the role of subgenomic RNAs in the replication and infection of host cells to provide important clues to the mechanism of COVID-19 pathogenesis.
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Ravi V, Swaminathan A, Yadav S, Arya H, Pandey R. SARS-CoV-2 Variants of Concern and Variations within Their Genome Architecture: Does Nucleotide Distribution and Mutation Rate Alter the Functionality and Evolution of the Virus? Viruses 2022; 14:v14112499. [PMID: 36423107 PMCID: PMC9694950 DOI: 10.3390/v14112499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/02/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 virus pathogenicity and transmissibility are correlated with the mutations acquired over time, giving rise to variants of concern (VOCs). Mutations can significantly influence the genetic make-up of the virus. Herein, we analyzed the SARS-CoV-2 genomes and sub-genomic nucleotide composition in relation to the mutation rate. Nucleotide percentage distributions of 1397 in-house-sequenced SARS-CoV-2 genomes were enumerated, and comparative analyses (i) within the VOCs and of (ii) recovered and mortality patients were performed. Fisher's test was carried out to highlight the significant mutations, followed by RNA secondary structure prediction and protein modeling for their functional impacts. Subsequently, a uniform dinucleotide composition of AT and GC was found across study cohorts. Notably, the N gene was observed to have a high GC percentage coupled with a relatively higher mutation rate. Functional analysis demonstrated the N gene mutations, C29144T and G29332T, to induce structural changes at the RNA level. Protein secondary structure prediction with N gene missense mutations revealed a differential composition of alpha helices, beta sheets, and coils, whereas the tertiary structure displayed no significant changes. Additionally, the N gene CTD region displayed no mutations. The analysis highlighted the importance of N protein in viral evolution with CTD as a possible target for antiviral drugs.
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Affiliation(s)
- Varsha Ravi
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Aparna Swaminathan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Sunita Yadav
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Hemant Arya
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, Division of Immunology and Infectious Disease Biology, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Correspondence: or ; Tel.: +91-9811029551
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Abstract
Of the 13 known independent zoonoses of simian immunodeficiency viruses to humans, only one, leading to human immunodeficiency virus (HIV) type 1(M) has become pandemic, causing over 80 million human infections. To understand the specific features associated with pandemic human-to-human HIV spread, we compared replication of HIV-1(M) with non-pandemic HIV-(O) and HIV-2 strains in myeloid cell models. We found that non-pandemic HIV lineages replicate less well than HIV-1(M) owing to activation of cGAS and TRIM5-mediated antiviral responses. We applied phylogenetic and X-ray crystallography structural analyses to identify differences between pandemic and non-pandemic HIV capsids. We found that genetic reversal of two specific amino acid adaptations in HIV-1(M) enables activation of TRIM5, cGAS and innate immune responses. We propose a model in which the parental lineage of pandemic HIV-1(M) evolved a capsid that prevents cGAS and TRIM5 triggering, thereby allowing silent replication in myeloid cells. We hypothesize that this capsid adaptation promotes human-to-human spread through avoidance of innate immune response activation.
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137
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Niemeyer D, Stenzel S, Veith T, Schroeder S, Friedmann K, Weege F, Trimpert J, Heinze J, Richter A, Jansen J, Emanuel J, Kazmierski J, Pott F, Jeworowski LM, Olmer R, Jaboreck MC, Tenner B, Papies J, Walper F, Schmidt ML, Heinemann N, Möncke-Buchner E, Baumgardt M, Hoffmann K, Widera M, Thao TTN, Balázs A, Schulze J, Mache C, Jones TC, Morkel M, Ciesek S, Hanitsch LG, Mall MA, Hocke AC, Thiel V, Osterrieder K, Wolff T, Martin U, Corman VM, Müller MA, Goffinet C, Drosten C. SARS-CoV-2 variant Alpha has a spike-dependent replication advantage over the ancestral B.1 strain in human cells with low ACE2 expression. PLoS Biol 2022; 20:e3001871. [PMID: 36383605 PMCID: PMC9710838 DOI: 10.1371/journal.pbio.3001871] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/30/2022] [Accepted: 10/06/2022] [Indexed: 11/17/2022] Open
Abstract
Epidemiological data demonstrate that Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) Alpha and Delta are more transmissible, infectious, and pathogenic than previous variants. Phenotypic properties of VOC remain understudied. Here, we provide an extensive functional study of VOC Alpha replication and cell entry phenotypes assisted by reverse genetics, mutational mapping of spike in lentiviral pseudotypes, viral and cellular gene expression studies, and infectivity stability assays in an enhanced range of cell and epithelial culture models. In almost all models, VOC Alpha spread less or equally efficiently as ancestral (B.1) SARS-CoV-2. B.1. and VOC Alpha shared similar susceptibility to serum neutralization. Despite increased relative abundance of specific sgRNAs in the context of VOC Alpha infection, immune gene expression in infected cells did not differ between VOC Alpha and B.1. However, inferior spreading and entry efficiencies of VOC Alpha corresponded to lower abundance of proteolytically cleaved spike products presumably linked to the T716I mutation. In addition, we identified a bronchial cell line, NCI-H1299, which supported 24-fold increased growth of VOC Alpha and is to our knowledge the only cell line to recapitulate the fitness advantage of VOC Alpha compared to B.1. Interestingly, also VOC Delta showed a strong (595-fold) fitness advantage over B.1 in these cells. Comparative analysis of chimeric viruses expressing VOC Alpha spike in the backbone of B.1, and vice versa, showed that the specific replication phenotype of VOC Alpha in NCI-H1299 cells is largely determined by its spike protein. Despite undetectable ACE2 protein expression in NCI-H1299 cells, CRISPR/Cas9 knock-out and antibody-mediated blocking experiments revealed that multicycle spread of B.1 and VOC Alpha required ACE2 expression. Interestingly, entry of VOC Alpha, as opposed to B.1 virions, was largely unaffected by treatment with exogenous trypsin or saliva prior to infection, suggesting enhanced resistance of VOC Alpha spike to premature proteolytic cleavage in the extracellular environment of the human respiratory tract. This property may result in delayed degradation of VOC Alpha particle infectivity in conditions typical of mucosal fluids of the upper respiratory tract that may be recapitulated in NCI-H1299 cells closer than in highly ACE2-expressing cell lines and models. Our study highlights the importance of cell model evaluation and comparison for in-depth characterization of virus variant-specific phenotypes and uncovers a fine-tuned interrelationship between VOC Alpha- and host cell-specific determinants that may underlie the increased and prolonged virus shedding detected in patients infected with VOC Alpha.
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Affiliation(s)
- Daniela Niemeyer
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
| | - Saskia Stenzel
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Talitha Veith
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
| | - Simon Schroeder
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Kirstin Friedmann
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Friderike Weege
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Julian Heinze
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
| | - Anja Richter
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Jenny Jansen
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Jackson Emanuel
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Julia Kazmierski
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Fabian Pott
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Lara M. Jeworowski
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Ruth Olmer
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH — Center for Translational Regenerative Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Mark-Christian Jaboreck
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH — Center for Translational Regenerative Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Beate Tenner
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Papies
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Walper
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Marie L. Schmidt
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Nicolas Heinemann
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Elisabeth Möncke-Buchner
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Morris Baumgardt
- Department of Infectious Diseases and Respiratory Medicine, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Karen Hoffmann
- Department of Infectious Diseases and Respiratory Medicine, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | | | - Anita Balázs
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jessica Schulze
- Unit 17 “Influenza and other Respiratory Viruses", Robert Koch Institute, Berlin, Germany
| | - Christin Mache
- Unit 17 “Influenza and other Respiratory Viruses", Robert Koch Institute, Berlin, Germany
| | - Terry C. Jones
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Morkel
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, Berlin, Germany
- BIH Bioportal Single Cells, Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- German Center for Infection Research, DZIF, Braunschweig, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, Frankfurt am Main, Germany
| | - Leif G. Hanitsch
- Institute of Medical Immunology, Charité — Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Marcus A. Mall
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Centre for Lung Research (DZL), associated partner Charité, Berlin, Germany
| | - Andreas C. Hocke
- Department of Infectious Diseases and Respiratory Medicine, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern, Switzerland
| | - Klaus Osterrieder
- Berlin Institute of Health, Berlin, Germany
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Thorsten Wolff
- Unit 17 “Influenza and other Respiratory Viruses", Robert Koch Institute, Berlin, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH — Center for Translational Regenerative Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Victor M. Corman
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
- Labor Berlin – Charité Vivantes GmbH, Berlin, Germany
| | - Marcel A. Müller
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
| | - Christine Goffinet
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- Labor Berlin – Charité Vivantes GmbH, Berlin, Germany
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138
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Capsid adaptation defines pandemic HIV. Nat Microbiol 2022; 7:1715-1716. [PMID: 36289398 DOI: 10.1038/s41564-022-01253-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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139
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Cruz CAK, Medina PMB. Temporal changes in the accessory protein mutations of SARS-CoV-2 variants and their predicted structural and functional effects. J Med Virol 2022; 94:5189-5200. [PMID: 35764775 PMCID: PMC9349927 DOI: 10.1002/jmv.27964] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/22/2022] [Accepted: 06/26/2022] [Indexed: 12/15/2022]
Abstract
Emerging variants enable the continuous spread of SARS-CoV-2 in humans. The factors contributing to behavioral differences in variants remain elusive despite associations with several Spike protein mutations. Exploring accessory proteins may provide a wider understanding of these differences since these proteins may affect viral processes that occur beyond infection. Various bioinformatics tools were utilized to identify significant accessory protein mutations and determine their structural and functional effects over time. The ViruClust web application was used to retrieve accessory protein amino acid sequences and determine mutation frequencies in these sequences across time. The structural and functional effects of the mutations were determined using Missense3D and PROVEAN, respectively. The accessory and Spike protein mutations were compared using mutation densities. Q57H and T151I of ORF3a; T21I and W27L of ORF6; G38V, V82A, and T120I of ORF7a; S31P and T40I of ORF7b; and R52I, C61F, and I121L of ORF8 were highly frequent in most variants of concern and were within known functional domains. Thus, these are good candidates for further experimental evaluation. Among the accessory proteins, ORF6 and ORF8 were highlighted because of their strong and weak correlation with Spike protein mutations, respectively.
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Affiliation(s)
- Christian Alfredo K. Cruz
- Biological Models Laboratory, Department of Biochemistry and Molecular Biology, College of MedicineUniversity of the Philippines ManilaManila, Metro ManilaPhilippines
| | - Paul Mark B. Medina
- Biological Models Laboratory, Department of Biochemistry and Molecular Biology, College of MedicineUniversity of the Philippines ManilaManila, Metro ManilaPhilippines
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140
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Zhang Z. Genomic Transcriptome Benefits and Potential Harms of COVID-19 Vaccines Indicated from Optimized Genomic Biomarkers. Vaccines (Basel) 2022; 10:1774. [PMID: 36366282 PMCID: PMC9692407 DOI: 10.3390/vaccines10111774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/28/2022] [Accepted: 10/20/2022] [Indexed: 11/07/2023] Open
Abstract
COVID-19 vaccines can be the tugboats for preventing SARS-CoV-2 infections when they are practical and, more importantly, without adverse effects. However, the reality is that they may result in short-term or long-term impacts on COVID-19-related diseases and even trigger the formation of new variants of SARS-CoV-2. Using published data, we use a set of optimized-performance COVID-19 genomic biomarkers (MND1, CDC6, ZNF282) to study the benefits and adverse effects of the BNT162b2 vaccine. We found that the vaccine lowered the expression values of genes MND1 and CDC6 while heightening the expression values of ZNF282 in individuals who are SARS-CoV-2 naïve, which is expected and satisfies the biological equivalence between the COVID-19 disease and the genomic signature patterns established in the literature. However, we also found that COVID-19-convalescent octogenarians responded reversely. The vaccine heightened the expression values of MND1 and CDC6. In addition, it lowered the expression values of ZNF282. Such adverse effects raise outstanding concerns about whether or not COVID-19-convalescent individuals should take the current vaccine or when they can take it. These findings are new at the genomic level and can provide insights into developing next-generation vaccines, antiviral drugs, and pandemic management guidance.
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Affiliation(s)
- Zhengjun Zhang
- Department of Statistics, School of Computer, Data & Information Sciences, University of Wisconsin, Madison, WI 53706, USA
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141
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Chen Q, Zhang J, Wang P, Zhang Z. The mechanisms of immune response and evasion by the main SARS-CoV-2 variants. iScience 2022; 25:105044. [PMID: 36068846 PMCID: PMC9436868 DOI: 10.1016/j.isci.2022.105044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. SARS-CoV-2 carries a unique group of mutations, and the transmission of the virus has led to the emergence of other mutants such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Kappa (B.1.617.1), Delta (B.1.617.2) and Omicron (B.1.1.529). The advent of a vaccine has raised hopes of ending the pandemic. However, the mutation variants of SARS-CoV-2 have raised concerns about the effectiveness of vaccines because the data showed that the vaccine was less effective against mutation variants compared to the previous variants. Mutation variants could easily mutate the N-segment structure and receptor domain of its spike glycoprotein (S) protein to escape antibody recognition. Therefore, it is vital to understand the potential immune response and evasion mechanism of SARS-CoV-2 variants. In this review, immune response and evasion mechanisms of several SARS-CoV-2 variants are described, which could provide some helpful advice for future vaccines.
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Affiliation(s)
- Qiuli Chen
- Department of Research and Development, Zhejiang Zhongwei Medical Research Center, Hangzhou, Zhejiang 310018, China
| | - Jiawei Zhang
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Peter Wang
- Department of Research and Development, Zhejiang Zhongwei Medical Research Center, Hangzhou, Zhejiang 310018, China
| | - Zuyong Zhang
- The Affiliated Hangzhou Xixi Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310023, China
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142
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SARS-CoV-2 Variant-Specific Infectivity and Immune Profiles Are Detectable in a Humanized Lung Mouse Model. Viruses 2022; 14:v14102272. [PMID: 36298826 PMCID: PMC9612296 DOI: 10.3390/v14102272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/09/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Small animal models that accurately model pathogenesis of SARS-CoV-2 variants are required for ongoing research efforts. We modified our human immune system mouse model to support replication of SARS-CoV-2 by implantation of human lung tissue into the mice to create TKO-BLT-Lung (L) mice and compared infection with two different variants in a humanized lung model. Infection of TKO-BLT-L mice with SARS-CoV-2 recapitulated the higher infectivity of the B.1.1.7 variant with more animals becoming infected and higher sustained viral loads compared to mice challenged with an early B lineage (614D) virus. Viral lesions were observed in lung organoids but no differences were detected between the viral variants as expected. Partially overlapping but distinct immune profiles were also observed between the variants with a greater Th1 profile in VIDO-01 and greater Th2 profile in B.1.1.7 infection. Overall, the TKO-BLT-L mouse supported SARS-CoV-2 infection, recapitulated key known similarities and differences in infectivity and pathogenesis as well as revealing previously unreported differences in immune responses between the two viral variants. Thus, the TKO-BLT-L model may serve as a useful animal model to study the immunopathobiology of newly emerging variants in the context of genuine human lung tissue and immune cells.
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143
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Bendall EE, Callear A, Getz A, Goforth K, Edwards D, Monto AS, Martin ET, Lauring AS. Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.12.511991. [PMID: 36263068 PMCID: PMC9580385 DOI: 10.1101/2022.10.12.511991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Transmission bottlenecks limit the spread of novel mutations and reduce the efficiency of natural selection along a transmission chain. Many viruses exhibit tight bottlenecks, and studies of early SARS-CoV-2 lineages identified a bottleneck of 1-3 infectious virions. While increased force of infection, host receptor binding, or immune evasion may influence bottleneck size, the relationship between transmissibility and the transmission bottleneck is unclear. Here, we compare the transmission bottleneck of non-variant-of-concern (non-VOC) SARS-CoV-2 lineages to those of the Alpha, Delta, and Omicron variants. We sequenced viruses from 168 individuals in 65 multiply infected households in duplicate to high depth of coverage. In 110 specimens collected close to the time of transmission, within-host diversity was extremely low. At a 2% frequency threshold, 51% had no intrahost single nucleotide variants (iSNV), and 42% had 1-2 iSNV. In 64 possible transmission pairs with detectable iSNV, we identified a bottleneck of 1 infectious virion (95% CI 1-1) for Alpha, Delta, and Omicron lineages and 2 (95% CI 2-2) in non-VOC lineages. The latter was driven by a single iSNV shared in one non-VOC household. The tight transmission bottleneck in SARS-CoV-2 is due to low genetic diversity at the time of transmission, a relationship that may be more pronounced in rapidly transmissible variants. The tight bottlenecks identified here will limit the development of highly mutated VOC in typical transmission chains, adding to the evidence that selection over prolonged infections in immunocompromised patients may drive their evolution.
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Affiliation(s)
- Emily E. Bendall
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Amy Callear
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Amy Getz
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Kendra Goforth
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Drew Edwards
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Arnold S. Monto
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Emily T. Martin
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Adam S. Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
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144
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Jalloh S, Olejnik J, Berrigan J, Nisa A, Suder EL, Akiyama H, Lei M, Ramaswamy S, Tyagi S, Bushkin Y, Mühlberger E, Gummuluru S. CD169-mediated restrictive SARS-CoV-2 infection of macrophages induces pro-inflammatory responses. PLoS Pathog 2022; 18:e1010479. [PMID: 36279285 PMCID: PMC9632919 DOI: 10.1371/journal.ppat.1010479] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 11/03/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
Exacerbated and persistent innate immune response marked by pro-inflammatory cytokine expression is thought to be a major driver of chronic COVID-19 pathology. Although macrophages are not the primary target cells of SARS-CoV-2 infection in humans, viral RNA and antigens in activated monocytes and macrophages have been detected in post-mortem samples, and dysfunctional monocytes and macrophages have been hypothesized to contribute to a protracted hyper-inflammatory state in COVID-19 patients. In this study, we demonstrate that CD169, a myeloid cell specific I-type lectin, facilitated ACE2-independent SARS-CoV-2 fusion and entry in macrophages. CD169-mediated SARS-CoV-2 entry in macrophages resulted in expression of viral genomic and subgenomic RNAs with minimal viral protein expression and no infectious viral particle release, suggesting a post-entry restriction of the SARS-CoV-2 replication cycle. Intriguingly this post-entry replication block was alleviated by exogenous ACE2 expression in macrophages. Restricted expression of viral genomic and subgenomic RNA in CD169+ macrophages elicited a pro-inflammatory cytokine expression (TNFα, IL-6 and IL-1β) in a RIG-I, MDA-5 and MAVS-dependent manner, which was suppressed by remdesivir treatment. These findings suggest that de novo expression of SARS-CoV-2 RNA in macrophages contributes to the pro-inflammatory cytokine signature and that blocking CD169-mediated ACE2 independent infection and subsequent activation of macrophages by viral RNA might alleviate COVID-19-associated hyperinflammatory response.
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Affiliation(s)
- Sallieu Jalloh
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Judith Olejnik
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
| | - Jacob Berrigan
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Annuurun Nisa
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Ellen L. Suder
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
| | - Hisashi Akiyama
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Maohua Lei
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Sita Ramaswamy
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Yuri Bushkin
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
| | - Suryaram Gummuluru
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
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145
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Liu G, Gack MU. Insights into pandemic respiratory viruses: manipulation of the antiviral interferon response by SARS-CoV-2 and influenza A virus. Curr Opin Immunol 2022; 78:102252. [PMID: 36215931 PMCID: PMC9472579 DOI: 10.1016/j.coi.2022.102252] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 01/29/2023]
Abstract
The outbreak of the COVID-19 pandemic one year after the centennial of the 1918 influenza pandemic reaffirms the catastrophic impact respiratory viruses can have on global health and economy. A key feature of SARS-CoV-2 and influenza A viruses (IAV) is their remarkable ability to suppress or dysregulate human immune responses. Here, we summarize the growing knowledge about the interplay of SARS-CoV-2 and antiviral innate immunity, with an emphasis on the regulation of type-I or -III interferon responses that are critically implicated in COVID-19 pathogenesis. Furthermore, we draw parallels to IAV infection and discuss shared innate immune sensing mechanisms and the respective viral countermeasures.
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Affiliation(s)
- GuanQun Liu
- Cleveland Clinic Florida Research and Innovation Center, Port St. Lucie, FL, USA
| | - Michaela U Gack
- Cleveland Clinic Florida Research and Innovation Center, Port St. Lucie, FL, USA.
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146
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Aggarwal A, Akerman A, Milogiannakis V, Silva MR, Walker G, Stella AO, Kindinger A, Angelovich T, Waring E, Amatayakul-Chantler S, Roth N, Manni S, Hauser T, Barnes T, Condylios A, Yeang M, Wong M, Jean T, Foster CSP, Christ D, Hoppe AC, Munier ML, Darley D, Churchill M, Stark DJ, Matthews G, Rawlinson WD, Kelleher AD, Turville SG. SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern. EBioMedicine 2022; 84:104270. [PMID: 36130476 PMCID: PMC9482529 DOI: 10.1016/j.ebiom.2022.104270] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/09/2022] [Accepted: 09/02/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Genetically distinct viral variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been recorded since January 2020. The introduction of global vaccine programs has contributed to lower COVID-19 hospitalisation and mortality rates, particularly in developed countries. In late 2021, Omicron BA.1 emerged, with substantially altered genetic differences and clinical effects from other variants of concern. Shortly after dominating global spread in early 2022, BA.1 was supplanted by the genetically distinct Omicron lineage BA.2. A sub-lineage of BA.2, designated BA.5, presently has an outgrowth advantage over BA.2 and other BA.2 sub-lineages. Here we study the neutralisation of Omicron BA.1, BA.2 and BA.5 and pre-Omicron variants using a range of vaccine and convalescent sera and therapeutic monoclonal antibodies using a live virus neutralisation assay. Using primary nasopharyngeal swabs, we also tested the relative fitness of BA.5 compared to pre-Omicron and Omicron viral lineages in their ability to use the ACE2-TMPRSS2 pathway. METHODS Using low passage clinical isolates of Clade A.2.2, Beta, Delta, BA.1, BA.2 and BA.5, we determined humoral neutralisation in vitro in vaccinated and convalescent cohorts, using concentrated human IgG pooled from thousands of plasma donors, and licensed monoclonal antibody therapies. We then determined infectivity to particle ratios in primary nasopharyngeal samples and expanded low passage isolates in a genetically engineered ACE2/TMPRSS2 cell line in the presence and absence of the TMPRSS2 inhibitor Nafamostat. FINDINGS Peak responses to 3 doses of BNT162b2 vaccine were associated with a 9-fold reduction in neutralisation for Omicron lineages BA.1, BA.2 and BA.5. Concentrated pooled human IgG from convalescent and vaccinated donors and BNT162b2 vaccination with BA.1 breakthrough infections were associated with greater breadth of neutralisation, although the potency was still reduced 7-fold across all Omicron lineages. Testing of clinical grade antibodies revealed a 14.3-fold reduction using Evusheld and 16.8-fold reduction using Sotrovimab for the BA.5. Whilst the infectivity of BA.1 and BA.2 was attenuated in ACE2/TMPRSS2 entry, BA.5 was observed to be equivalent to that of an early 2020 circulating clade and had greater sensitivity to the TMPRSS2 inhibitor Nafamostat. INTERPRETATION Observations support all Omicron variants to significantly escape neutralising antibodies across a range of vaccination and/or convalescent responses. Potency of therapeutic monoclonal antibodies is also reduced and differs across Omicron lineages. The key difference of BA.5 from other Omicron sub-variants is the reversion in tropism back to using the well-known ACE2-TMPRSS2 pathway, utilised efficiently by pre-Omicron lineages. Monitoring if these changes influence transmission and/or disease severity will be key for ongoing tracking and management of Omicron waves globally. FUNDING This work was primarily supported by Australian Medical Foundation research grants MRF2005760 (ST, GM & WDR), MRF2001684 (ADK and ST) and Medical Research Future Fund Antiviral Development Call grant (WDR), Medical Research Future Fund COVID-19 grant (MRFF2001684, ADK & SGT) and the New South Wales Health COVID-19 Research Grants Round 2 (SGT).
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Affiliation(s)
- Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Anouschka Akerman
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | | | - Mariana Ruiz Silva
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Gregory Walker
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | | | - Andrea Kindinger
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Thomas Angelovich
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | - Emily Waring
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | | | - Nathan Roth
- Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Sandro Manni
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Thomas Hauser
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Thomas Barnes
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Anna Condylios
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Malinna Yeang
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Maureen Wong
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Tyra Jean
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Charles S P Foster
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | | | - Mee Ling Munier
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - David Darley
- St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Melissa Churchill
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | - Damien J Stark
- Molecular Diagnostic Medicine Laboratory, Sydpath, St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Gail Matthews
- The Kirby Institute, University of New South Wales, New South Wales, Australia; St Vincent's Hospital, Sydney, New South Wales, Australia
| | - William D Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Anthony D Kelleher
- The Kirby Institute, University of New South Wales, New South Wales, Australia; St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Stuart G Turville
- The Kirby Institute, University of New South Wales, New South Wales, Australia.
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147
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Aggarwal A, Akerman A, Milogiannakis V, Silva MR, Walker G, Stella AO, Kindinger A, Angelovich T, Waring E, Amatayakul-Chantler S, Roth N, Manni S, Hauser T, Barnes T, Condylios A, Yeang M, Wong M, Jean T, Foster CSP, Christ D, Hoppe AC, Munier ML, Darley D, Churchill M, Stark DJ, Matthews G, Rawlinson WD, Kelleher AD, Turville SG. SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern. EBioMedicine 2022; 84:104270. [PMID: 36130476 DOI: 10.1101/2021.12.14.21267772] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/09/2022] [Accepted: 09/02/2022] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Genetically distinct viral variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been recorded since January 2020. The introduction of global vaccine programs has contributed to lower COVID-19 hospitalisation and mortality rates, particularly in developed countries. In late 2021, Omicron BA.1 emerged, with substantially altered genetic differences and clinical effects from other variants of concern. Shortly after dominating global spread in early 2022, BA.1 was supplanted by the genetically distinct Omicron lineage BA.2. A sub-lineage of BA.2, designated BA.5, presently has an outgrowth advantage over BA.2 and other BA.2 sub-lineages. Here we study the neutralisation of Omicron BA.1, BA.2 and BA.5 and pre-Omicron variants using a range of vaccine and convalescent sera and therapeutic monoclonal antibodies using a live virus neutralisation assay. Using primary nasopharyngeal swabs, we also tested the relative fitness of BA.5 compared to pre-Omicron and Omicron viral lineages in their ability to use the ACE2-TMPRSS2 pathway. METHODS Using low passage clinical isolates of Clade A.2.2, Beta, Delta, BA.1, BA.2 and BA.5, we determined humoral neutralisation in vitro in vaccinated and convalescent cohorts, using concentrated human IgG pooled from thousands of plasma donors, and licensed monoclonal antibody therapies. We then determined infectivity to particle ratios in primary nasopharyngeal samples and expanded low passage isolates in a genetically engineered ACE2/TMPRSS2 cell line in the presence and absence of the TMPRSS2 inhibitor Nafamostat. FINDINGS Peak responses to 3 doses of BNT162b2 vaccine were associated with a 9-fold reduction in neutralisation for Omicron lineages BA.1, BA.2 and BA.5. Concentrated pooled human IgG from convalescent and vaccinated donors and BNT162b2 vaccination with BA.1 breakthrough infections were associated with greater breadth of neutralisation, although the potency was still reduced 7-fold across all Omicron lineages. Testing of clinical grade antibodies revealed a 14.3-fold reduction using Evusheld and 16.8-fold reduction using Sotrovimab for the BA.5. Whilst the infectivity of BA.1 and BA.2 was attenuated in ACE2/TMPRSS2 entry, BA.5 was observed to be equivalent to that of an early 2020 circulating clade and had greater sensitivity to the TMPRSS2 inhibitor Nafamostat. INTERPRETATION Observations support all Omicron variants to significantly escape neutralising antibodies across a range of vaccination and/or convalescent responses. Potency of therapeutic monoclonal antibodies is also reduced and differs across Omicron lineages. The key difference of BA.5 from other Omicron sub-variants is the reversion in tropism back to using the well-known ACE2-TMPRSS2 pathway, utilised efficiently by pre-Omicron lineages. Monitoring if these changes influence transmission and/or disease severity will be key for ongoing tracking and management of Omicron waves globally. FUNDING This work was primarily supported by Australian Medical Foundation research grants MRF2005760 (ST, GM & WDR), MRF2001684 (ADK and ST) and Medical Research Future Fund Antiviral Development Call grant (WDR), Medical Research Future Fund COVID-19 grant (MRFF2001684, ADK & SGT) and the New South Wales Health COVID-19 Research Grants Round 2 (SGT).
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Affiliation(s)
- Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Anouschka Akerman
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | | | - Mariana Ruiz Silva
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Gregory Walker
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | | | - Andrea Kindinger
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Thomas Angelovich
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | - Emily Waring
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | | | - Nathan Roth
- Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Sandro Manni
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Thomas Hauser
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Thomas Barnes
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Anna Condylios
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Malinna Yeang
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Maureen Wong
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Tyra Jean
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Charles S P Foster
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | | | - Mee Ling Munier
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - David Darley
- St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Melissa Churchill
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | - Damien J Stark
- Molecular Diagnostic Medicine Laboratory, Sydpath, St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Gail Matthews
- The Kirby Institute, University of New South Wales, New South Wales, Australia; St Vincent's Hospital, Sydney, New South Wales, Australia
| | - William D Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Anthony D Kelleher
- The Kirby Institute, University of New South Wales, New South Wales, Australia; St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Stuart G Turville
- The Kirby Institute, University of New South Wales, New South Wales, Australia.
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148
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Laine L, Skön M, Väisänen E, Julkunen I, Österlund P. SARS-CoV-2 variants Alpha, Beta, Delta and Omicron show a slower host cell interferon response compared to an early pandemic variant. Front Immunol 2022; 13:1016108. [PMID: 36248817 PMCID: PMC9561549 DOI: 10.3389/fimmu.2022.1016108] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/15/2022] [Indexed: 11/15/2022] Open
Abstract
Since the start of the pandemic at the end of 2019, arising mutations in SARS-CoV-2 have improved its transmission and ability to circumvent the immunity induced by vaccination and previous COVID-19 infection. Studies on the effects of SARS-CoV-2 genomic mutations on replication and innate immunity will give us valuable insight into the evolution of the virus which can aid in further development of vaccines and new treatment modalities. Here we systematically analyzed the kinetics of virus replication, innate immune activation, and host cell antiviral response patterns in Alpha, Beta, Delta, Kappa, Omicron and two early pandemic SARS-CoV-2 variant-infected human lung epithelial Calu-3 cells. We observed overall comparable replication patterns for these variants with modest variations. Particularly, the sublineages of Omicron BA.1, BA.2 and a recombinant sublineage, XJ, all showed attenuated replication in Calu-3 cells compared to Alpha and Delta. Furthermore, there was relatively weak activation of primary innate immune signaling pathways, however, all variants produced enough interferons to induce the activation of STAT2 and production of interferon stimulated genes (ISGs). While interferon mRNA expression and STAT2 activation correlated with cellular viral RNA levels, ISG production did not. Although clear cut effects of specific SARS-CoV-2 genomic mutations could not be concluded, the variants of concern, including Omicron, showed a lower replication efficiency and a slower interferon response compared to an early pandemic variant in the study.
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Affiliation(s)
- Larissa Laine
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- *Correspondence: Larissa Laine,
| | - Marika Skön
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Elina Väisänen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- Infection and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Ilkka Julkunen
- Infection and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Pamela Österlund
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
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149
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Rhabdomyolysis in Pediatric Patients with SARS-CoV-2 Infection. CHILDREN 2022; 9:children9101441. [PMID: 36291377 PMCID: PMC9600903 DOI: 10.3390/children9101441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 02/06/2023]
Abstract
Background: Rhabdomyolysis is a rare but severe complication in adult patients with Coronavirus disease 2019 (COVID-19), which can result in acute kidney injury and death; however, it is rarely reported in pediatric patients. Methods: In this study, we retrospectively reviewed the clinical features and outcomes of rhabdomyolysis in pediatric patients aged 0–18 years with COVID-19 who were hospitalized at Taipei Tzu Chi Hospital, an epicenter of COVID-19 in northern Taiwan. Results: We treated eight patients with rhabdomyolysis during the omicron variant-Severe acute respiratory syndrome coronavirus 2 (omicron variant-SARS-CoV-2) community outbreak and none during the alpha variant endemic. These eight patients shared stereotypical presentations, including the presence of bilateral calf pain after defervescence. The creatinine kinase (CK) levels were between 1346 and 6937 U/L on admission, and clinical course was uneventful after aggressive saline hydration. Conclusion: Rhabdomyolysis is not a rare complication in pediatric patients with the omicron-SARS-CoV-2 infection, and reassurance of a good prognosis is important to alleviate family anxiety.
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150
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The Spike-Stabilizing D614G Mutation Interacts with S1/S2 Cleavage Site Mutations To Promote the Infectious Potential of SARS-CoV-2 Variants. J Virol 2022; 96:e0130122. [PMID: 36121299 PMCID: PMC9555207 DOI: 10.1128/jvi.01301-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remained genetically stable during the first 3 months of the pandemic, before acquiring a D614G spike mutation that rapidly spread worldwide and then generating successive waves of viral variants with increasingly high transmissibility. We set out to evaluate possible epistatic interactions between the early-occurring D614G mutation and the more recently emerged cleavage site mutations present in spike of the Alpha, Delta, and Omicron variants of concern. The P681H/R mutations at the S1/S2 cleavage site increased spike processing and fusogenicity but limited its incorporation into pseudoviruses. In addition, the higher cleavage rate led to higher shedding of the spike S1 subunit, resulting in a lower infectivity of the P681H/R-carrying pseudoviruses compared to those expressing the Wuhan wild-type spike. The D614G mutation increased spike expression at the cell surface and limited S1 shedding from pseudovirions. As a consequence, the D614G mutation preferentially increased the infectivity of P681H/R-carrying pseudoviruses. This enhancement was more marked in cells where the endosomal route predominated, suggesting that more stable spikes could better withstand the endosomal environment. Taken together, these findings suggest that the D614G mutation stabilized S1/S2 association and enabled the selection of mutations that increased S1/S2 cleavage, leading to the emergence of SARS-CoV-2 variants expressing highly fusogenic spikes. IMPORTANCE The first SARS-CoV-2 variant that spread worldwide in early 2020 carried a D614G mutation in the viral spike, making this protein more stable in its cleaved form at the surface of virions. The Alpha and Delta variants, which spread in late 2020 and early 2021, respectively, proved increasingly transmissible and pathogenic compared to the original strain. Interestingly, Alpha and Delta both carried the mutations P681H/R in a cleavage site that made the spike more cleaved and more efficient at mediating viral fusion. We show here that variants with increased spike cleavage due to P681H/R were even more dependent on the stabilizing effect of the D614G mutation, which limited the shedding of cleaved S1 subunits from viral particles. These findings suggest that the worldwide spread of the D614G mutation was a prerequisite for the emergence of more pathogenic SARS-CoV-2 variants with highly fusogenic spikes.
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