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Berdygulova Z, Maltseva E, Perfilyeva Y, Nizkorodova A, Zhigailov A, Naizabayeva D, Ostapchuk YO, Kuatbekova S, Dosmagambet Z, Kuatbek M, Bissenbay A, Cherusheva A, Mashzhan A, Abdolla N, Ashimbekov S, Ismagulova G, Dmitrovskiy A, Mamadaliyev S, Skiba Y. RT-qPCR investigation of post-mortem tissues during COVID-19. J Appl Biomed 2024; 22:115-122. [PMID: 38912867 DOI: 10.32725/jab.2024.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 06/20/2024] [Indexed: 06/25/2024] Open
Abstract
In 2020, there were numerous cases in Kazakhstan with clinical symptoms of COVID-19 but negative PCR results in nasopharyngeal and oropharyngeal swabs. The diagnosis was confirmed clinically and by CT scans (computed tomography). The problem with such negative PCR results for SARS-CoV-2 infection confirmation still exists and indicates the need to confirm the diagnosis in the bronchoalveolar lavage in such cases. There is also a lack of information about confirmation of SARS-CoV-2 infection in deceased patients. In this study, various tissue materials, including lungs, bronchi, and trachea, were examined from eight patients who died, presumably from SARS-CoV-2 infection, between 2020 and 2022. Naso/oropharyngeal swabs taken from these patients in hospitals tested PCR negative for SARS-CoV-2. This study presents a modified RNA isolation method based on a comparison of the most used methods for RNA isolation in laboratories: QIAamp Viral RNA Mini Kit and TRIzol-based method. This modified nucleic acid extraction protocol can be used to confirm SARS-CoV-2 infection by RT-qPCR in the tissues of deceased patients in disputed cases. RT-qPCR with RNA of SARS-CoV-2 re-extracted with such method from post-mortem tissues that were stored at -80 °C for more than 32 months still demonstrated high-yielding positive results.
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Affiliation(s)
- Zhanna Berdygulova
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
- M. A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Elina Maltseva
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
- M. A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
- Tethys Scientific Society, Almaty, Kazakhstan
| | - Yuliya Perfilyeva
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
- M. A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Anna Nizkorodova
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
- M. A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Andrey Zhigailov
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
- M. A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Dinara Naizabayeva
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
- M. A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
- Tethys Scientific Society, Almaty, Kazakhstan
| | - Yekaterina O Ostapchuk
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
- M. A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Saltanat Kuatbekova
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
| | - Zhaniya Dosmagambet
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
- Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Moldir Kuatbek
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
- Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Akerke Bissenbay
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
- M. A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Alena Cherusheva
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
| | - Akzhigit Mashzhan
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
| | - Nurshat Abdolla
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
- M. A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | | | - Gulnara Ismagulova
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
- M. A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Andrey Dmitrovskiy
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
| | - Seidigapbar Mamadaliyev
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
| | - Yuriy Skiba
- Almaty Branch of the National Center for Biotechnology, Central Reference Laboratory, Almaty, Kazakhstan
- M. A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
- Tethys Scientific Society, Almaty, Kazakhstan
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Kwiatkowska B, Krajewska-Włodarczyk M, Batko B, Maślińska M, Stajszczyk M, Świerkot J, Wiland P, Żuber Z, Tomasiewicz K. COVID-19 prophylaxis, diagnostics, and treatment in patients with rheumatic diseases. The Polish experts panel opinion. Reumatologia 2024; 62:4-17. [PMID: 38558893 PMCID: PMC10979375 DOI: 10.5114/reum/183469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 01/30/2024] [Indexed: 04/04/2024] Open
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolves, infection management in vulnerable populations requires formalized guidance. Although low-virulence variants of SARS-CoV-2 remain predominant, they pose an increased risk of severe illness in adults with rheumatic and musculoskeletal diseases (RMDs). Several disease-specific (chronic long-grade inflammation, concomitant immunosuppression) and individual (advanced age, multimorbidity, pregnancy, vaccination status) factors contribute to excess risk in RMD populations. Various post-COVID-19 manifestations are also increasingly reported and appear more commonly than in the general population. At a pathogenetic level, complex interplay involving innate and acquired immune dysregulation, viral persistence, and genetic predisposition shapes a unique susceptibility profile. Moreover, incident cases of SARS-CoV-2 infection as a trigger factor for the development of autoimmune conditions have been reported. Vaccination remains a key preventive strategy, and encouraging active education and awareness will be crucial for rheumatologists in the upcoming years. In patients with RMDs, COVID-19 vaccines' benefits outweigh the risks. Derivation of specialized diagnostic and therapeutic protocols within a comprehensive COVID-19 care plan represents an ideal scenario for healthcare system organization. Vigilance for symptoms of infection and rapid diagnosis are key for introducing antiviral treatment in patients with RMDs in a timely manner. This review provides updated guidance on optimal immunization, diagnosis, and antiviral treatment strategies.
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Affiliation(s)
- Brygida Kwiatkowska
- Early Arthritis Clinic, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
| | | | - Bogdan Batko
- Department of Rheumatology and Immunology, Faculty of Medicine and Health Sciences, Andrzej Frycz Modrzewski University, Krakow, Poland
| | - Maria Maślińska
- Early Arthritis Clinic, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
| | - Marcin Stajszczyk
- Department of Rheumatology and Autoimmune Diseases, Silesian Center for Rheumatology, Orthopedics and Rehabilitation, Ustron, Poland
| | - Jerzy Świerkot
- Department of Rheumatology and Internal Medicine, Wroclaw Medical University, Poland
| | - Piotr Wiland
- Department of Rheumatology and Internal Medicine, Wroclaw Medical University, Poland
| | - Zbigniew Żuber
- Department of Rheumatology, St. Louis Voivodeship Specialist Children’s Hospital, Krakow, Poland
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3
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Eltayeb A, Al-Sarraj F, Alharbi M, Albiheyri R, Mattar EH, Abu Zeid IM, Bouback TA, Bamagoos A, Uversky VN, Rubio-Casillas A, Redwan EM. Intrinsic factors behind long COVID: IV. Hypothetical roles of the SARS-CoV-2 nucleocapsid protein and its liquid-liquid phase separation. J Cell Biochem 2024; 125:e30530. [PMID: 38349116 DOI: 10.1002/jcb.30530] [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: 09/09/2023] [Revised: 01/10/2024] [Accepted: 01/24/2024] [Indexed: 03/12/2024]
Abstract
When the SARS-CoV-2 virus infects humans, it leads to a condition called COVID-19 that has a wide spectrum of clinical manifestations, from no symptoms to acute respiratory distress syndrome. The virus initiates damage by attaching to the ACE-2 protein on the surface of endothelial cells that line the blood vessels and using these cells as hosts for replication. Reactive oxygen species levels are increased during viral replication, which leads to oxidative stress. About three-fifths (~60%) of the people who get infected with the virus eradicate it from their body after 28 days and recover their normal activity. However, a large fraction (~40%) of the people who are infected with the virus suffer from various symptoms (anosmia and/or ageusia, fatigue, cough, myalgia, cognitive impairment, insomnia, dyspnea, and tachycardia) beyond 12 weeks and are diagnosed with a syndrome called long COVID. Long-term clinical studies in a group of people who contracted SARS-CoV-2 have been contrasted with a noninfected matched group of people. A subset of infected people can be distinguished by a set of cytokine markers to have persistent, low-grade inflammation and often self-report two or more bothersome symptoms. No medication can alleviate their symptoms efficiently. Coronavirus nucleocapsid proteins have been investigated extensively as potential drug targets due to their key roles in virus replication, among which is their ability to bind their respective genomic RNAs for incorporation into emerging virions. This review highlights basic studies of the nucleocapsid protein and its ability to undergo liquid-liquid phase separation. We hypothesize that this ability of the nucleocapsid protein for phase separation may contribute to long COVID. This hypothesis unlocks new investigation angles and could potentially open novel avenues for a better understanding of long COVID and treating this condition.
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Affiliation(s)
- Ahmed Eltayeb
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Faisal Al-Sarraj
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Raed Albiheyri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ehab H Mattar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Isam M Abu Zeid
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thamer A Bouback
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Atif Bamagoos
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Moscow Region, Russia
| | - Alberto Rubio-Casillas
- Autlan Regional Hospital, Health Secretariat, Autlan, Jalisco, Mexico
- Biology Laboratory, Autlan Regional Preparatory School, University of Guadalajara, Autlan, Jalisco, Mexico
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
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Troxel AB, Bind MAC, Flotte TJ, Cordon-Cardo C, Decker LA, Finn AV, Padera RF, Reichard RR, Stone JR, Adolphi NL, Casimero FVC, Crary JF, Elifritz J, Faustin A, Ghosh SKB, Krausert A, Martinez-Lage M, Melamed J, Mitchell RA, Sampson BA, Seifert AC, Simsir A, Adams C, Haasnoot S, Hafner S, Siciliano MA, Vallejos BB, Del Boccio P, Lamendola-Essel MF, Young CE, Kewlani D, Akinbo PA, Parent B, Chung A, Cato TC, Mudumbi PC, Esquenazi-Karonika S, Wood MJ, Chan J, Monteiro J, Shinnick DJ, Thaweethai T, Nguyen AN, Fitzgerald ML, Perlowski AA, Stiles LE, Paskett ML, Katz SD, Foulkes AS. Researching COVID to enhance recovery (RECOVER) tissue pathology study protocol: Rationale, objectives, and design. PLoS One 2024; 19:e0285645. [PMID: 38198481 PMCID: PMC10781091 DOI: 10.1371/journal.pone.0285645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/23/2023] [Indexed: 01/12/2024] Open
Abstract
IMPORTANCE SARS-CoV-2 infection can result in ongoing, relapsing, or new symptoms or organ dysfunction after the acute phase of infection, termed Post-Acute Sequelae of SARS-CoV-2 (PASC), or long COVID. The characteristics, prevalence, trajectory and mechanisms of PASC are poorly understood. The objectives of the Researching COVID to Enhance Recovery (RECOVER) tissue pathology study (RECOVER-Pathology) are to: (1) characterize prevalence and types of organ injury/disease and pathology occurring with PASC; (2) characterize the association of pathologic findings with clinical and other characteristics; (3) define the pathophysiology and mechanisms of PASC, and possible mediation via viral persistence; and (4) establish a post-mortem tissue biobank and post-mortem brain imaging biorepository. METHODS RECOVER-Pathology is a cross-sectional study of decedents dying at least 15 days following initial SARS-CoV-2 infection. Eligible decedents must meet WHO criteria for suspected, probable, or confirmed infection and must be aged 18 years or more at the time of death. Enrollment occurs at 7 sites in four U.S. states and Washington, DC. Comprehensive autopsies are conducted according to a standardized protocol within 24 hours of death; tissue samples are sent to the PASC Biorepository for later analyses. Data on clinical history are collected from the medical records and/or next of kin. The primary study outcomes include an array of pathologic features organized by organ system. Causal inference methods will be employed to investigate associations between risk factors and pathologic outcomes. DISCUSSION RECOVER-Pathology is the largest autopsy study addressing PASC among US adults. Results of this study are intended to elucidate mechanisms of organ injury and disease and enhance our understanding of the pathophysiology of PASC.
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Affiliation(s)
- Andrea B. Troxel
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Marie-Abele C. Bind
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, United States of America
| | - Thomas J. Flotte
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, United States of America
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular and Cell-Based Medicine, Mount Sinai Health System, New York, NY, United States of America
| | - Lauren A. Decker
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM, United States of America
| | - Aloke V. Finn
- Department of Pathology, CVPath Institute, Gaithersburg, MD, United States of America
| | - Robert F. Padera
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States of America
| | - R. Ross Reichard
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, United States of America
| | - James R. Stone
- Department of Pathology, Massachusetts General Hospital, Boston, MA, United States of America
| | - Natalie L. Adolphi
- Office of the Medical Investigator, University of New Mexico School of Medicine, Albuquerque, NM, United States of America
| | | | - John F. Crary
- Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States of America
| | - Jamie Elifritz
- Departments of Radiology and Pathology, University of New Mexico, Albuquerque, NM, United States of America
| | - Arline Faustin
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Saikat Kumar B. Ghosh
- Department of Molecular Biology and Genomics, CVPath Institute, Gaithersburg, MD, United States of America
| | - Amanda Krausert
- Department of Pathology, Molecular and Cell-Based Medicine, Mount Sinai Health System, New York, NY, United States of America
| | - Maria Martinez-Lage
- Department of Pathology, Massachusetts General Hospital, Boston, MA, United States of America
| | - Jonathan Melamed
- Department of Anatomical Pathology, NYU Langone Hospital—Long Island, Mineola, NY, United States of America
| | - Roger A. Mitchell
- Department of Pathology, Howard University College of Medicine, Washington DC, United States of America
| | - Barbara A. Sampson
- Department of Pathology, Molecular and Cell-Based Medicine, Mount Sinai Health System, New York, NY, United States of America
| | - Alan C. Seifert
- Biomedical Engineering and Imaging Institute, Department of Radiology, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Aylin Simsir
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Cheryle Adams
- Department of Pathology, Howard University College of Medicine, Washington DC, United States of America
| | - Stephanie Haasnoot
- Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States of America
| | - Stephanie Hafner
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, United States of America
| | - Michelle A. Siciliano
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Brittany B. Vallejos
- Office of the Medical Investigators, Department of Research, University of New Mexico, Albuquerque, NM, United States of America
| | - Phoebe Del Boccio
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Michelle F. Lamendola-Essel
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Chloe E. Young
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Deepshikha Kewlani
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Precious A. Akinbo
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Brendan Parent
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Alicia Chung
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Teresa C. Cato
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Praveen C. Mudumbi
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Shari Esquenazi-Karonika
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Marion J. Wood
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States of America
| | - James Chan
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, United States of America
| | - Jonathan Monteiro
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, United States of America
| | - Daniel J. Shinnick
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, United States of America
| | - Tanayott Thaweethai
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, United States of America
| | - Amber N. Nguyen
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, United States of America
| | - Megan L. Fitzgerald
- Patient-Led Research Collaborative on COVID-19, Washington DC, United States of America
| | | | - Lauren E. Stiles
- Department of Neurology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, United States of America
| | - Moira L. Paskett
- Department of Anatomical Pathology, NYU Langone Hospital—Long Island, Mineola, NY, United States of America
| | - Stuart D. Katz
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Andrea S. Foulkes
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, United States of America
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Noack P, Grosse C, Bodingbauer J, Almeder M, Lohfink-Schumm S, Salzer HJF, Meier J, Lamprecht B, Schmitt CA, Langer R. Minimally invasive autopsies for the investigation of pulmonary pathology of COVID-19-experiences of a longitudinal series of 92 patients. Virchows Arch 2023; 483:611-619. [PMID: 37653260 PMCID: PMC10673967 DOI: 10.1007/s00428-023-03622-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/20/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023]
Abstract
Minimally invasive autopsies (MIAs) allow the collection of tissue samples for diagnostic and research purposes in special situations, e.g., when there is a high risk of infection which is the case in the context of COVID-19 or restrictions due to legal or personal reasons. We performed MIA to analyze lung tissue from 92 COVID-19 patients (mean age 78 years; range 48-98; 35 women, 57 men), representing 44% of all patients who died from the disease between October 2020 and April 2021. An intercostal approach was used with removal of a 5-cm rib section followed by manual collection of four lung tissue samples (5-8 cm in size). Diffuse alveolar damage (DAD) was found in 89 (97%) patients at various stages. Exudative DAD (eDAD) predominated in 18 (20%) patients, proliferative DAD (pDAD) in 43 (47%) patients, and mixed DAD (mDAD) in 31 (34%) patients. There were no significant differences in the predominant DAD pattern between tissue samples from the same patient. Additional purulent components were present in 46 (50%) cases. Fungi were detected in 11 (12%) patients. The pDAD pattern was associated with longer hospital stay including intensive care unit (p=0.026 and p<0.001) and younger age (p=0.019). Positive bronchoalveolar lavage and blood cultures were observed more frequently in pDAD patterns (p<0.001; p=0.018). In contrast, there was no significant association between intravital positive microbiological results and superimposed bronchopneumonia or fungal infection at autopsy. Having demonstrated the characteristic lung changes in a large longitudinal autopsy series, we conclude that the presented MIA approach can be considered a reliable and safe method for performing post mortem lung diagnostics in COVID-19 and other high-risk situations. The lack of correlation between histological changes indicative of bacterial or fungal superinfection and microbiology could have clinical implications for disease and treatment surveillance.
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Affiliation(s)
- Petar Noack
- Institute of Clinical Pathology, Kepler University Hospital, Krankenhausstr. 9, 4021, Linz, Austria
- Medical Faculty, Johannes Kepler University, Linz, Austria
| | - Claudia Grosse
- Institute of Clinical Pathology, Kepler University Hospital, Krankenhausstr. 9, 4021, Linz, Austria
| | - Jacob Bodingbauer
- Institute of Clinical Pathology, Kepler University Hospital, Krankenhausstr. 9, 4021, Linz, Austria
- Medical Faculty, Johannes Kepler University, Linz, Austria
| | - Marion Almeder
- Institute of Clinical Pathology, Kepler University Hospital, Krankenhausstr. 9, 4021, Linz, Austria
- Medical Faculty, Johannes Kepler University, Linz, Austria
| | - Sylvia Lohfink-Schumm
- Institute of Clinical Pathology, Kepler University Hospital, Krankenhausstr. 9, 4021, Linz, Austria
- Medical Faculty, Johannes Kepler University, Linz, Austria
| | - Helmut J F Salzer
- Medical Faculty, Johannes Kepler University, Linz, Austria
- Division of Infectious Diseases and Tropical Medicine, Department of Pulmonary Medicine, Kepler University Hospital, Linz, Austria
- Ignaz-Semmelweis-Institute, Interuniversity Institute for Infection Research, Vienna, Austria
| | - Jens Meier
- Medical Faculty, Johannes Kepler University, Linz, Austria
- Department of Anesthesiology and Intensive Care Medicine, Kepler University Hospital, Linz, Austria
| | - Bernd Lamprecht
- Medical Faculty, Johannes Kepler University, Linz, Austria
- Department of Pulmonary Medicine, Kepler University Hospital, Linz, Austria
| | - Clemens A Schmitt
- Medical Faculty, Johannes Kepler University, Linz, Austria
- Department of Hematology and Medical Oncology, Kepler University Hospital, Linz, Austria
| | - Rupert Langer
- Institute of Clinical Pathology, Kepler University Hospital, Krankenhausstr. 9, 4021, Linz, Austria.
- Medical Faculty, Johannes Kepler University, Linz, Austria.
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6
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Tedesco I, Zito Marino F, Ronchi A, Duarte Neto AN, Dolhnikoff M, Municinò M, Campobasso CP, Pannone G, Franco R. COVID-19: detection methods in post-mortem samples. Pathologica 2023; 115:263-274. [PMID: 38054901 DOI: 10.32074/1591-951x-933] [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: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 12/07/2023] Open
Abstract
COVID-19 identification is routinely performed on fresh samples, such as nasopharyngeal and oropharyngeal swabs, even if, the detection of the virus in formalin-fixed paraffin-embedded (FFPE) autopsy tissues could help to underlie mechanisms of the pathogenesis that are not well understood. The gold standard for COVID-19 detection in FFPE samples remains the qRT-PCR as in swab samples, contextually other methods have been developed, including immunohistochemistry (IHC), and in situ hybridization (ISH). In this manuscript, we summarize the main data regarding the methods of COVID-19 detection in pulmonary and extra-pulmonary post-mortem samples, and especially the sensitivity and specificity of these assays will be discussed.
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Affiliation(s)
- Ilaria Tedesco
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania "L. Vanvitelli", Naples, Italy
| | - Federica Zito Marino
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania "L. Vanvitelli", Naples, Italy
| | - Andrea Ronchi
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania "L. Vanvitelli", Naples, Italy
| | - Amaro Nunes Duarte Neto
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo, Brazil
| | - Marisa Dolhnikoff
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo, Brazil
| | - Maurizio Municinò
- Forensic Medicine Unit, "S. Giuliano" Hospital, Giugliano in Campania, Italy
| | - Carlo Pietro Campobasso
- Department of Experimental Medicine, University of Campania, Luigi Vanvitelli, Naples, Italy
| | - Giuseppe Pannone
- Anatomic Pathology Unit, Department of Clinic and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Renato Franco
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania "L. Vanvitelli", Naples, Italy
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7
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Perumal R, Shunmugam L, Naidoo K, Wilkins D, Garzino-Demo A, Brechot C, Vahlne A, Nikolich J. Biological mechanisms underpinning the development of long COVID. iScience 2023; 26:106935. [PMID: 37265584 PMCID: PMC10193768 DOI: 10.1016/j.isci.2023.106935] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
As COVID-19 evolves from a pandemic to an endemic disease, the already staggering number of people that have been or will be infected with SARS-CoV-2 is only destined to increase, and the majority of humanity will be infected. It is well understood that COVID-19, like many other viral infections, leaves a significant fraction of the infected with prolonged consequences. Continued high number of SARS-CoV-2 infections, viral evolution with escape from post-infection and vaccinal immunity, and reinfections heighten the potential impact of Long COVID. Hence, the impact of COVID-19 on human health will be seen for years to come until more effective vaccines and pharmaceutical treatments become available. To that effect, it is imperative that the mechanisms underlying the clinical manifestations of Long COVID be elucidated. In this article, we provide an in-depth analysis of the evidence on several potential mechanisms of Long COVID and discuss their relevance to its pathogenesis.
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Affiliation(s)
- Rubeshan Perumal
- South African Medical Research Council (SAMRC)-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4001, South Africa
- Department of Pulmonology and Critical Care, Division of Internal Medicine, School of Clinical Medicine, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Department of Immunobiology and the University of Arizona Center on Aging, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724, USA
| | - Letitia Shunmugam
- South African Medical Research Council (SAMRC)-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4001, South Africa
| | - Kogieleum Naidoo
- South African Medical Research Council (SAMRC)-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4001, South Africa
| | - Dave Wilkins
- The Global Virus Network, Baltimore, MD 21201, USA
| | - Alfredo Garzino-Demo
- The Global Virus Network, Baltimore, MD 21201, USA
- Department of Molecular Medicine, University of Padova, Padova 1- 35129, Italy
| | - Christian Brechot
- The Global Virus Network, Baltimore, MD 21201, USA
- Infectious Disease and International Health, University of South Florida, Tampa, FL 33620, USA
| | - Anders Vahlne
- The Global Virus Network, Baltimore, MD 21201, USA
- Division of Clinical Microbiology, Karolinska Institute, Stockholm 17165, Sweden
| | - Janko Nikolich
- The Global Virus Network, Baltimore, MD 21201, USA
- The Aegis Consortium for Pandemic-Free Future, University of Arizona Health Sciences, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724, USA
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8
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Van Slambrouck J, Khan M, Verbeken E, Choi S, Geudens V, Vanluyten C, Feys S, Vanhulle E, Wollants E, Vermeire K, De Fays C, Aversa L, Kaes J, Van Raemdonck D, Vos R, Vanaudenaerde B, De Hertogh G, Wauters E, Wauters J, Ceulemans LJ, Mombaerts P. Visualising SARS-CoV-2 infection of the lung in deceased COVID-19 patients. EBioMedicine 2023; 92:104608. [PMID: 37224768 PMCID: PMC10202122 DOI: 10.1016/j.ebiom.2023.104608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/21/2023] [Accepted: 04/21/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND SARS-CoV-2 is a single-stranded positive-sense RNA virus. Several negative-sense SARS-CoV-2 RNA species, both full-length genomic and subgenomic, are produced transiently during viral replication. Methodologies for rigorously characterising cell tropism and visualising ongoing viral replication at single-cell resolution in histological sections are needed to assess the virological and pathological phenotypes of future SARS-CoV-2 variants. We aimed to provide a robust methodology for examining the human lung, the major target organ of this RNA virus. METHODS A prospective cohort study took place at the University Hospitals Leuven in Leuven, Belgium. Lung samples were procured postmortem from 22 patients who died from or with COVID-19. Tissue sections were fluorescently stained with the ultrasensitive single-molecule RNA in situ hybridisation platform of RNAscope combined with immunohistochemistry followed by confocal imaging. FINDINGS We visualised perinuclear RNAscope signal for negative-sense SARS-CoV-2 RNA species in ciliated cells of the bronchiolar epithelium of a patient who died with COVID-19 in the hyperacute phase of the infection, and in ciliated cells of a primary culture of human airway epithelium that had been infected experimentally with SARS-CoV-2. In patients who died between 5 and 13 days after diagnosis of the infection, we detected RNAscope signal for positive-sense but not for negative-sense SARS-CoV-2 RNA species in pneumocytes, macrophages, and among debris in the alveoli. SARS-CoV-2 RNA levels decreased after a disease course of 2-3 weeks, concomitant with a histopathological change from exudative to fibroproliferative diffuse alveolar damage. Taken together, our confocal images illustrate the complexities stemming from traditional approaches in the literature to characterise cell tropism and visualise ongoing viral replication solely by the surrogate parameters of nucleocapsid-immunoreactive signal or in situ hybridisation for positive-sense SARS-CoV-2 RNA species. INTERPRETATION Confocal imaging of human lung sections stained fluorescently with commercially available RNAscope probes for negative-sense SARS-CoV-2 RNA species enables the visualisation of viral replication at single-cell resolution during the acute phase of the infection in COVID-19. This methodology will be valuable for research on future SARS-CoV-2 variants and other respiratory viruses. FUNDING Max Planck Society, Coronafonds UZ/KU Leuven, European Society for Organ Transplantation.
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Affiliation(s)
- Jan Van Slambrouck
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium; Department of Thoracic Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Mona Khan
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | - Erik Verbeken
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium; Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Sumin Choi
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | - Vincent Geudens
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium
| | - Cedric Vanluyten
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium; Department of Thoracic Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Simon Feys
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium; Medical Intensive Care Unit, University Hospitals Leuven, Leuven, Belgium
| | - Emiel Vanhulle
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Elke Wollants
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Kurt Vermeire
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Charlotte De Fays
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium; Pole of Pneumology, ENT, and Dermatology, Institute of Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium
| | - Lucia Aversa
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium
| | - Janne Kaes
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium
| | - Dirk Van Raemdonck
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium; Department of Thoracic Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Robin Vos
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium; Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Bart Vanaudenaerde
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium
| | - Gert De Hertogh
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium; Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Els Wauters
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium; Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Joost Wauters
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium; Medical Intensive Care Unit, University Hospitals Leuven, Leuven, Belgium
| | - Laurens J Ceulemans
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium; Department of Thoracic Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Peter Mombaerts
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany.
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9
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Yang C, Zhao H, Espín E, Tebbutt SJ. Association of SARS-CoV-2 infection and persistence with long COVID. THE LANCET. RESPIRATORY MEDICINE 2023:S2213-2600(23)00142-X. [PMID: 37178694 PMCID: PMC10171832 DOI: 10.1016/s2213-2600(23)00142-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/27/2023] [Accepted: 04/05/2023] [Indexed: 05/15/2023]
Affiliation(s)
- Chengliang Yang
- Prevention of Organ Failure Centre of Excellence, Vancouver, BC, Canada; Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Hedi Zhao
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Estefanía Espín
- Prevention of Organ Failure Centre of Excellence, Vancouver, BC, Canada; Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure Centre of Excellence, Vancouver, BC, Canada; Centre for Heart Lung Innovation, Providence Research, St Paul's Hospital, Vancouver, BC, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada.
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10
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Saharia KK, Ramelli SC, Stein SR, Roder AE, Kreitman A, Banakis S, Chung JY, Burbelo PD, Singh M, Reed RM, Patel V, Rabin J, Krupnick AS, Cohen JI, de Wit E, Ghedin E, Hewitt SM, Vannella KM, Chertow DS, Grazioli A. Successful lung transplantation using an allograft from a COVID-19-recovered donor: a potential role for subgenomic RNA to guide organ utilization. Am J Transplant 2023; 23:101-107. [PMID: 36695611 PMCID: PMC9833374 DOI: 10.1016/j.ajt.2022.09.001] [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: 06/13/2022] [Revised: 08/31/2022] [Accepted: 09/23/2022] [Indexed: 01/13/2023]
Abstract
Although the risk of SARS-CoV-2 transmission through lung transplantation from acutely infected donors is high, the risks of virus transmission and long-term lung allograft outcomes are not as well described when using pulmonary organs from COVID-19-recovered donors. We describe successful lung transplantation for a COVID-19-related lung injury using lungs from a COVID-19-recovered donor who was retrospectively found to have detectable genomic SARS-CoV-2 RNA in the lung tissue by multiple highly sensitive assays. However, SARS-CoV-2 subgenomic RNA (sgRNA), a marker of viral replication, was not detectable in the donor respiratory tissues. One year after lung transplantation, the recipient has a good functional status, walking 1 mile several times per week without the need for supplemental oxygen and without any evidence of donor-derived SARS-CoV-2 transmission. Our findings highlight the limitations of current clinical laboratory diagnostic assays in detecting the persistence of SARS-CoV-2 RNA in the lung tissue. The persistence of SARS-CoV-2 RNA in the donor tissue did not appear to represent active viral replication via sgRNA testing and, most importantly, did not negatively impact the allograft outcome in the first year after lung transplantation. sgRNA is easily performed and may be a useful assay for assessing viral infectivity in organs from donors with a recent infection.
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Affiliation(s)
- Kapil K Saharia
- Division of Infectious Diseases, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA.
| | - Sabrina C Ramelli
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA; Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sydney R Stein
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA; Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Allison E Roder
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Allie Kreitman
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephanie Banakis
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Joon-Yong Chung
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Manmeet Singh
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, Montana, USA
| | - Robert M Reed
- Division of Pulmonary and Critical Care, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Vipul Patel
- Division of Pulmonary and Critical Care, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Joseph Rabin
- Department of Surgery, R Adams Cowley Shock Trauma Center, University of Maryland School of Medicine, Baltimore, Maryland,USA
| | - Alexander S Krupnick
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Emmie de Wit
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, Montana, USA
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kevin M Vannella
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA; Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Daniel S Chertow
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA; Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
| | - Alison Grazioli
- Department of Medicine, R Adams Cowley Shock Trauma Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
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11
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Pérez-Mies B, Caniego-Casas T, Bardi T, Carretero-Barrio I, Benito A, García-Cosío M, González-García I, Pizarro D, Rosas M, Cristóbal E, Ruano Y, Garrido MC, Rigual-Bobillo J, de Pablo R, Galán JC, Pestaña D, Palacios J. Progression to lung fibrosis in severe COVID-19 patients: A morphological and transcriptomic study in postmortem samples. Front Med (Lausanne) 2022; 9:976759. [PMID: 36405615 PMCID: PMC9669577 DOI: 10.3389/fmed.2022.976759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/17/2022] [Indexed: 09/02/2023] Open
Abstract
The development of lung fibrosis is a major concern in patients recovered from severe COVID-19 pneumonia. This study aimed to document the evolution of diffuse alveolar damage (DAD) to the fibrosing pattern and define the transcriptional programs involved. Morphological, immunohistochemical and transcriptional analysis were performed in lung samples obtained from autopsy of 33 severe COVID-19 patients (median illness duration: 36 days). Normal lung and idiopathic pulmonary fibrosis (IPF) were used for comparison. Twenty-seven patients with DAD and disease evolution of more than 2 weeks had fibrosis. Pathways and genes related with collagen biosynthesis and extracellular matrix (ECM) biosynthesis and degradation, myofibroblastic differentiation and epithelial to mesenchymal transition (EMT) were overexpressed in COVID-19. This pattern had similarities with that observed in IPF. By immunohistochemistry, pathological fibroblasts (pFBs), with CTHRC1 and SPARC expression, increased in areas of proliferative DAD and decreased in areas of mature fibrosis. Immunohistochemical analysis demonstrated constitutive expression of cadherin-11 in normal epithelial cells and a similar pattern of cadherin and catenin expression in epithelial cells from both normal and COVID-19 samples. Transcriptomic analysis revealed downregulation of the Hippo pathway, concordant with the observation of YAP overexpression in hyperplastic alveolar epithelial cells. Progression to fibrosis in severe COVID-19 is associated with overexpression of fibrogenic pathways and increased in CTHRC1- and SPARC-positive pFBs. Whereas the Hippo pathway seemed to be implicated in the response to epithelial cell damage, EMT was not a major process implicated in COVID-19 mediated lung fibrosis.
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Affiliation(s)
- Belén Pérez-Mies
- Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Medicine, Alcalá University, Alcalá de Henares, Spain
| | - Tamara Caniego-Casas
- Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Tommaso Bardi
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
- Department of Anesthesiology and Surgical Critical Care, Hospital Ramón y Cajal, Madrid, Spain
| | - Irene Carretero-Barrio
- Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
- Faculty of Medicine, Alcalá University, Alcalá de Henares, Spain
| | - Amparo Benito
- Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
- Faculty of Medicine, Alcalá University, Alcalá de Henares, Spain
| | - Mónica García-Cosío
- Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
- Faculty of Medicine, Alcalá University, Alcalá de Henares, Spain
| | - Irene González-García
- Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
| | - David Pizarro
- Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Rosas
- Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Eva Cristóbal
- Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Yolanda Ruano
- Department of Pathology, Medical School, Universidad Complutense, Instituto i + 12, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - María Concepción Garrido
- Department of Pathology, Medical School, Universidad Complutense, Instituto i + 12, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Juan Rigual-Bobillo
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
- Department of Respiratory, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Raúl de Pablo
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
- Faculty of Medicine, Alcalá University, Alcalá de Henares, Spain
- Medical Intensive Care Unit, Hospital Ramón y Cajal, Madrid, Spain
| | - Juan Carlos Galán
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
- Clinical Microbiology Unit, Hospital Ramón y Cajal, Madrid, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - David Pestaña
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
- Faculty of Medicine, Alcalá University, Alcalá de Henares, Spain
- Department of Anesthesiology and Surgical Critical Care, Hospital Ramón y Cajal, Madrid, Spain
| | - José Palacios
- Pathology, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Instituto Ramon y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Medicine, Alcalá University, Alcalá de Henares, Spain
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12
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Ruiz MJ, Siracusano G, Cottignies-Calamarte A, Tudor D, Real F, Zhu A, Pastori C, Capron C, Rosenberg AR, Temperton N, Cantoni D, Liao H, Ternette N, Moine P, Godement M, Geri G, Chiche JD, Annane D, Cramer Bordé E, Lopalco L, Bomsel M. Persistent but dysfunctional mucosal SARS-CoV-2-specific IgA and low lung IL-1β associate with COVID-19 fatal outcome: A cross-sectional analysis. Front Immunol 2022; 13:842468. [PMID: 36248831 PMCID: PMC9560774 DOI: 10.3389/fimmu.2022.842468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
The role of the mucosal pulmonary antibody response in coronavirus disease 2019 (COVID-19) outcome remains unclear. Here, we found that in bronchoalveolar lavage (BAL) samples from 48 patients with severe COVID-19-infected with the ancestral Wuhan virus, mucosal IgG and IgA specific for S1, receptor-binding domain (RBD), S2, and nucleocapsid protein (NP) emerged in BAL containing viruses early in infection and persist after virus elimination, with more IgA than IgG for all antigens tested. Furthermore, spike-IgA and spike-IgG immune complexes were detected in BAL, especially when the lung virus has been cleared. BAL IgG and IgA recognized the four main RBD variants. BAL neutralizing titers were higher early in COVID-19 when virus replicates in the lung than later in infection after viral clearance. Patients with fatal COVID-19, in contrast to survivors, developed higher levels of mucosal spike-specific IgA than IgG but lost neutralizing activities over time and had reduced IL-1β in the lung. Altogether, mucosal spike and NP-specific IgG and S1-specific IgA persisting after lung severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance and low pulmonary IL-1β correlate with COVID-19 fatal outcome. Thus, mucosal SARS-CoV-2-specific antibodies may have adverse functions in addition to protective neutralization.
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Affiliation(s)
- Maria Julia Ruiz
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Paris-Descartes University, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Gabriel Siracusano
- Immunobiology of HIV Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Andréa Cottignies-Calamarte
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Paris-Descartes University, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Daniela Tudor
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Paris-Descartes University, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Fernando Real
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Paris-Descartes University, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Aiwei Zhu
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Paris-Descartes University, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Claudia Pastori
- Immunobiology of HIV Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Claude Capron
- AP-HP, Hôpital Ambroise Paré, Service d'Hématologie, Boulogne-Billancourt, France
| | - Arielle R. Rosenberg
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Paris-Descartes University, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
- AP-HP, Hôpital Cochin, Service de Virologie, Paris, France
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, United Kingdom
| | - Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, United Kingdom
| | - Hanqing Liao
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicola Ternette
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Pierre Moine
- FHU SEPSIS (Saclay and Paris Seine Nord Endeavour to PerSonalize Interventions for Sepsis), RHU RECORDS (Rapid rEcognition of CORticosteroiD resistant or sensitive Sepsis), Department of Intensive Care, Hôpital Raymond Poincaré (APHP), Laboratory of Infection and Inflammation – U1173, School of Medicine Simone Veil, University Versailles Saint Quentin – University Paris Saclay, INSERM, Garches, France
| | - Mathieu Godement
- FHU SEPSIS (Saclay and Paris Seine Nord Endeavour to PerSonalize Interventions for Sepsis), RHU RECORDS (Rapid rEcognition of CORticosteroiD resistant or sensitive Sepsis), Department of Intensive Care, Hôpital Raymond Poincaré (APHP), Laboratory of Infection and Inflammation – U1173, School of Medicine Simone Veil, University Versailles Saint Quentin – University Paris Saclay, INSERM, Garches, France
| | - Guillaume Geri
- AP-HP, Hôpital Ambroise Paré, Service de Réanimation, Boulogne-Billancourt, France
- Université de Versailles-St Quentin en Yvelines, Versailles, France
| | | | - Djillali Annane
- FHU SEPSIS (Saclay and Paris Seine Nord Endeavour to PerSonalize Interventions for Sepsis), RHU RECORDS (Rapid rEcognition of CORticosteroiD resistant or sensitive Sepsis), Department of Intensive Care, Hôpital Raymond Poincaré (APHP), Laboratory of Infection and Inflammation – U1173, School of Medicine Simone Veil, University Versailles Saint Quentin – University Paris Saclay, INSERM, Garches, France
| | | | - Lucia Lopalco
- Immunobiology of HIV Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Morgane Bomsel
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Paris-Descartes University, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
- *Correspondence: Morgane Bomsel,
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13
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Ilieva M, Tschaikowski M, Vandin A, Uchida S. The current status of gene expression profilings in COVID‐19 patients. CLINICAL AND TRANSLATIONAL DISCOVERY 2022; 2:e104. [PMID: 35942159 PMCID: PMC9350144 DOI: 10.1002/ctd2.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 11/26/2022]
Abstract
Background The global pandemic of coronavirus disease 2019 (COVID‐19) caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has swept through every part of the world. Because of its impact, international efforts have been underway to identify the variants of SARS‐CoV‐2 by genome sequencing and to understand the gene expression changes in COVID‐19 patients compared to healthy donors using RNA sequencing (RNA‐seq) assay. Within the last two and half years since the emergence of SARS‐CoV‐2, a large number of OMICS data of COVID‐19 patients have accumulated. Yet, we are still far from understanding the disease mechanism. Further, many people suffer from long‐term effects of COVID‐19; calling for a more systematic way to data mine the generated OMICS data, especially RNA‐seq data. Methods By searching gene expression omnibus (GEO) using the key terms, COVID‐19 and RNA‐seq, 108 GEO entries were identified. Each of these studies was manually examined to categorize the studies into bulk or single‐cell RNA‐seq (scRNA‐seq) followed by an inspection of their original articles. Results The currently available RNA‐seq data were generated from various types of patients’ samples, and COVID‐19 related sample materials have been sequenced at the level of RNA, including whole blood, different components of blood [e.g., plasma, peripheral blood mononuclear cells (PBMCs), leukocytes, lymphocytes, monocytes, T cells], nasal swabs, and autopsy samples (e.g., lung, heart, liver, kidney). Of these, RNA‐seq studies using whole blood, PBMCs, nasal swabs and autopsy/biopsy samples were reviewed to highlight the major findings from RNA‐seq data analysis. Conclusions Based on the bulk and scRNA‐seq data analysis, severe COVID‐19 patients display shifts in cell populations, especially those of leukocytes and monocytes, possibly leading to cytokine storms and immune silence. These RNA‐seq data form the foundation for further gene expression analysis using samples from individuals suffering from long COVID.
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Affiliation(s)
- Mirolyuba Ilieva
- Center for RNA Medicine, Department of Clinical Medicine Aalborg University Copenhagen Denmark
| | - Max Tschaikowski
- Department of Computer Science Aalborg University Aalborg Denmark
| | - Andrea Vandin
- Institute of Economics and EMbeDS Sant'Anna School of Advanced Studies Pisa Italy
- Department of Applied Mathematics and Computer Science Technical University of Denmark Kongens Lyngby Denmark
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine Aalborg University Copenhagen Denmark
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14
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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15
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Lai A, Tambuzzi S, Bergna A, Battistini A, Della Ventura C, Galli M, Zoja R, Zehender G, Cattaneo C. Evidence of SARS-CoV-2 Antibodies and RNA on Autopsy Cases in the Pre-Pandemic Period in Milan (Italy). Front Microbiol 2022; 13:886317. [PMID: 35783409 PMCID: PMC9240701 DOI: 10.3389/fmicb.2022.886317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/17/2022] [Indexed: 12/31/2022] Open
Abstract
In this study, we analyzed blood samples obtained from 169 cadavers subjected to an autopsy from 1 October 2019 to 27 March 2020. The presence of anti-severe acute respiratory syndrome coronavirus 2 (anti-SARS-CoV-2) antibodies was searched by lateral flow immunochromatographic assay (LFIA) and ELISA tests and the SARS-CoV-2 RNA was tested in blood and available lung tissues by real-time PCR (RT-PCR) and droplet digital PCR (ddPCR). Five cases resulted in positives at the serological screening for anti-SARS-CoV-2. Three results were weakly positive for IgM while only one showed strong reactivity for IgG antibodies. The fifth subject (who died in December 2019) resulted positive for the ELISA test. The detection of SARS-CoV-2 RNA resulted in positive only in the blood and lung tissues of such cases. These data suggest that cadaveric blood may be a suitable substrate for the assessment of SARS-CoV-2 infection; moreover, they extend the observations of sporadic cases of SARS-CoV-2 infection in North Italy prior to the first confirmed cases.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
- *Correspondence: Alessia Lai
| | - Stefano Tambuzzi
- Department of Biomedical Sciences for Health, Institute of Forensic Medicine, University of Milan, Milan, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Alessio Battistini
- Department of Biomedical Sciences for Health, Institute of Forensic Medicine, University of Milan, Milan, Italy
| | - Carla Della Ventura
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Riccardo Zoja
- Department of Biomedical Sciences for Health, Institute of Forensic Medicine, University of Milan, Milan, Italy
| | | | - Cristina Cattaneo
- Department of Biomedical Sciences for Health, Institute of Forensic Medicine, University of Milan, Milan, Italy
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