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Kebriaei A, Besharati R, Namdar Ahmad Abad H, Havakhah S, Khosrojerdi M, Azimian A. The relationship between microRNAs and COVID-19 complications. Noncoding RNA Res 2025; 10:16-24. [PMID: 39296641 PMCID: PMC11406673 DOI: 10.1016/j.ncrna.2024.08.007] [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: 04/02/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/21/2024] Open
Abstract
Over the past three years, since the onset of COVID-19, several scientific studies have concentrated on understanding susceptibility to the virus, the progression of the illness, and possible long-term complexity. COVID-19 is broadly recognized with effects on multiple systems in the body, and various factors related to society, medicine, and genetics/epigenetics may contribute to the intensity and results of the disease. Additionally, a SARS-CoV-2 infection can activate pathological activities and expedite the emergence of existing health issues into clinical problems. Forming easily accessible, distinctive, and permeable biomarkers is essential for categorizing patients, preventing the disease, predicting its course, and tailoring treatments for COVID-19 individually. One promising candidate for such biomarkers is microRNAs, which could serve various purposes in understanding diverse forms of COVID-19, including susceptibility, intensity, disease progression, outcomes, and potential therapeutic options. This review provides an overview of the most significant findings related to the involvement of microRNAs in COVID-19 pathogenesis. Furthermore, it explores the function of microRNAs in a broad span of effects that may arise from accompanying or underlying health status. It underscores the value of comprehending how diverse conditions, such as neurological disorders, diabetes, cardiovascular diseases, and obesity, interact with COVID-19.
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Affiliation(s)
- Abdollah Kebriaei
- Department of Pathobiology and Laboratory Sciences, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Reza Besharati
- Department of Pathobiology and Laboratory Sciences, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Hasan Namdar Ahmad Abad
- Department of Pathobiology and Laboratory Sciences, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Shahrzad Havakhah
- Department of Physiology, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mahsa Khosrojerdi
- Department of Immunology and Allergy, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Azimian
- Department of Pathobiology and Laboratory Sciences, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
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2
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Yang Y, Azzuolo A, Fodil N, Gros P. Gene: environment interactions in immune and inflammatory responses to severe acute respiratory syndrome coronavirus 2 infection. Curr Opin Immunol 2024; 90:102459. [PMID: 39243725 DOI: 10.1016/j.coi.2024.102459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 08/07/2024] [Accepted: 08/19/2024] [Indexed: 09/09/2024]
Abstract
Despite its devastating human cost, the rapid spread and global establishment of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) pandemic had the benefit of providing unique insights into the intricate interplay between genetic, environmental, and socioeconomic factors, which collectively impact susceptibility to infection with SARS-CoV-2. Preceding the implementation of broad vaccination programs and assuming the absence of significant acquired immunity, examining the innate vulnerability to the virus becomes essential. There is indeed considerable heterogeneity observed at both the population and individual levels for various SARS-CoV-2 infection phenotypes, including emergence, progression, and survival from the coronavirus disease 2019 (COVID-19) syndrome. Particularly intriguing is the seemingly milder course of COVID-19 disease reported for the African continent early during the pandemic. This was characterized by significantly lower mortality rates in SARS-CoV-2 patients compared with the European and American continents and globally. We will discuss some of the demographic and socioeconomic factors that may have contributed to these observations. We review the mapped COVID-19 genetic architecture, including the remarkable association of type I interferon as a single protective mechanism and a major determinant of susceptibility. Furthermore, we speculate on potential 'environmental' modulators of penetrance and expressivity of intrinsic vulnerability factors, with a focus on the microbiome and associated metabolomes. Additionally, this review explores the potential immunomodulatory contribution of helminth parasites to the human host immune and inflammatory responses to respiratory viral infections.
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Affiliation(s)
- Yunxiang Yang
- Department of Biochemistry, McGill Research Center of Complex Traits, and Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC, Canada
| | - Alessia Azzuolo
- Department of Biochemistry, McGill Research Center of Complex Traits, and Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC, Canada
| | - Nassima Fodil
- Department of Biochemistry, McGill Research Center of Complex Traits, and Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC, Canada
| | - Philippe Gros
- Department of Biochemistry, McGill Research Center of Complex Traits, and Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC, Canada.
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3
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Kumari P, Singh HP, Singh S. Mathematical model for understanding the relationship between diabetes and novel coronavirus. Gene 2024:148970. [PMID: 39357581 DOI: 10.1016/j.gene.2024.148970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 09/15/2024] [Accepted: 09/25/2024] [Indexed: 10/04/2024]
Abstract
A new model is proposed to explore interactions between diabetes and novel coronavirus. The model accounted for both the omicron variant and variants varying from omicron. The model investigated compartments such as hospitalization, diabetes, co-infection, omicron variant, and quarantine. Additionally, the impact of different vaccination doses is assessed. Sensitivity analysis is carried out to determine disease prevalence and control options, emphasizing the significance of knowing epidemics and their characteristics. The model is validated using actual data from Japan. The parameters are fitted with the help of "Least Square Curve Fitting" method to describe the dynamic behavior of the proposed model. Simulation results and theoretical findings demonstrate the dynamic behavior of novel coronavirus and diabetes mellitus (DM). Biological illustrations that illustrate impact of model parameters are evaluated. Furthermore, effect of vaccine efficacy and vaccination rates for the vaccine's first, second, and booster doses is conducted. The impact of various preventive measures, such as hospitalization rate, quarantine or self-isolation rate, vaccine dose-1, dose-2, and booster dose, is considered for diabetic individuals in contact with symptomatic or asymptomatic COVID-19 infectious people in the proposed model. The findings demonstrate the significance of vaccine doses on people with diabetes and individuals infectious with omicron variant. The proposed work helps with subsequent prevention efforts and the design of a vaccination policy to mitigate the effect of the novel coronavirus.
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Affiliation(s)
- Preety Kumari
- Faculty of Mathematical Science, University of Delhi, Delhi 110007, India; School of Engineering & Technology, Central University of Haryana, Mahendergarh 123031, India.
| | | | - Swarn Singh
- Sri Venkateswara College, University of Delhi, Delhi 110021, India.
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4
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Altmann DM, Boyton RJ. Protective immunity to repeated COVID-19 breakthrough infections. Clin Immunol 2024; 268:110374. [PMID: 39357633 DOI: 10.1016/j.clim.2024.110374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 09/26/2024] [Accepted: 09/27/2024] [Indexed: 10/04/2024]
Affiliation(s)
- Daniel M Altmann
- Departments of Immunology and Inflammation, Faculty of Medicine, Imperial College London, UK.
| | - Rosemary J Boyton
- Departments of Infectious Disease, Faculty of Medicine, Imperial College London, UK
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Milostić-Srb A, Srb N, Talapko J, Meštrović T, Žiger T, Pačarić S, Fureš R, Makarović V, Škrlec I. The Effect of COVID-19 and COVID-19 Vaccination on Assisted Human Reproduction Outcomes: A Systematic Review and Meta-Analysis. Diseases 2024; 12:201. [PMID: 39329870 PMCID: PMC11431602 DOI: 10.3390/diseases12090201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/24/2024] [Accepted: 08/25/2024] [Indexed: 09/28/2024] Open
Abstract
The most discussed infectious disease is coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Many research endeavors have focused on the effects of the virus on reproductive organs, as these have also been shown to carry the receptors to which the virus attaches. The results of assisted reproductive technology (ART) have been significantly affected by the pandemic, with some in vitro fertilization (IVF) centers being closed due to the risk of further spread of the disease. According to World Health Organization statistics, 17.5% of adults worldwide suffered from fertility problems in 2023; in other words, one in six people in the world have reproductive health problems. As infertility is a growing problem in the modern world and new developments in assisted reproduction are always a topic of profound interest, it is important to understand the impact of SARS-CoV-2 on reproductive health. This systematic review aimed to examine studies describing patients undergoing ART procedures with a COVID-19-positive history and to shed light on the recent evidence on the safety of COVID-19 vaccination in the ART context. A meta-analysis was conducted to confirm the results of the systematic review. The results showed a significant difference in clinical pregnancy rates between the vaccinated and unvaccinated groups and an increased miscarriage rate in those with a COVID-19-positive history. However, no significant difference in clinical pregnancy and birth rates was found in participants with a previous COVID-19 infection. The results show that further studies and research are needed, even though the spread and impact of the virus have decreased. Evidence-based information for individuals and couples undergoing infertility treatment is vital to enable informed decision-making.
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Affiliation(s)
- Andrea Milostić-Srb
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Nika Srb
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Jasminka Talapko
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Tomislav Meštrović
- University Centre Varaždin, University North, 42000 Varaždin, Croatia
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA 98195, USA
- Department for Health Metrics Sciences, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tihomil Žiger
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Stana Pačarić
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Surgery, University Hospital Centre Osijek, 31000 Osijek, Croatia
| | - Rajko Fureš
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Department of Gynecology and Obstetrics, Zabok General Hospital and Croatian Veterans Hospital, 49210 Zabok, Croatia
| | - Vedrana Makarović
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- University Hospital Center Osijek, 31000 Osijek, Croatia
| | - Ivana Škrlec
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
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Ramonfaur D, Ayad N, Liu PHZ, Zhou J, Wu Y, Li J, Chen G. The global clinical studies of long COVID. Int J Infect Dis 2024; 146:107105. [PMID: 38782355 DOI: 10.1016/j.ijid.2024.107105] [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: 03/11/2024] [Revised: 05/06/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024] Open
Abstract
People with long COVID are those who still have symptoms, signs, and conditions after the initial phase of infection of SARS-CoV-2. The incidence of long COVID varies among regions-31% in North America, 44% in Europe, and 51% in Asia, which is challenging the healthcare system, but there is limited guidelines for its treatment. With more and more nationwide projects funded by the government such as the RECOVER initiative in the United States and National Institute for Health Research funding in the United Kingdom, an increasing number of ongoing clinical trials are investigating the efficacy of diverse therapies on reversing long COVID. After searching the World Health Organization International Clinical Trial Registry Platform, 587 clinical studies are identified as long COVID studies. Among these, 312 studies (53.2%) are testing potential therapies. Most of the long COVID trials were conducted in the United States (58 trials [18.6%]), followed by India (55 trials [17.6%]), and Spain (20 trials [6.4%]). Interventions in these clinical trials include physical exercise, rehabilitation therapy, behavioral therapy, and pharmacological therapies including herbs, paxlovid, and fluvoxamine. These trials are aiming to deal with these long COVID symptoms and signs including fatigue, decreased pulmonary function, reduced cognitive function, and others. To date, only 11 of these 312 studies have published their results that were not confirmative, unfortunately. Future studies should be designed to address sleep disorders which were seldomly included in registered clinical studies. Moreover, interventions aimed at treating the underlying pathophysiology of long COVID are also necessary but currently lacking.
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Affiliation(s)
| | - Nardeen Ayad
- Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, Massachusetts, United States
| | | | - Jiayan Zhou
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States
| | - Ying Wu
- Harvard Law School, Harvard University, Cambridge, Massachusetts, United States
| | - Jinlin Li
- Harvard Kennedy School, Harvard University, Cambridge, Massachusetts, United States
| | - Guang Chen
- LKS Faculty of Medicine, The University of Hong Kong, Kong Hong, China; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States.
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Lindo J, Coelho P, Gavinhos C, Martins M, Liberal J, Ferreira AJ, Gonçalves T, Rodrigues F. Health Status and COVID-19 Epidemiology in an Inland Region of Portugal: A Retrospective Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2024; 21:1033. [PMID: 39200643 PMCID: PMC11353782 DOI: 10.3390/ijerph21081033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/24/2024] [Accepted: 07/31/2024] [Indexed: 09/02/2024]
Abstract
Multiple factors, from socioeconomic development to genetic background, can affect the regional impact of some diseases, and this has also been seen during the COVID-19 pandemic. The objective of this retrospective study was to characterize a population in the interior of Portugal regarding health status and COVID-19 epidemiology. Between October 2021 and January 2023, 1553 subjects residing in Beira Baixa, Portugal, were included. Using a self-report approach, demographic and clinical data were obtained. Blood group, blood pressure, peripheral oxygen saturation and anti-spike protein immunoglobulin concentration were also analyzed. Statistical analysis was performed using IBM SPSS Statistics. The average age of the participants was 48.95 (±14.43) years, with 64% being male and 36% being female. The most prevalent comorbidities were hypertension (19.2%), dyslipidemia (12.6%) and diabetes mellitus (6.6%). Half of the population was overweight, and more than half of the subjects had no history of tobacco consumption. Among the participants, 33% were infected with SARS-CoV-2: 70.1% had mild disease, 14.1% moderate disease and 1.4% severe disease. There was a very significant adherence to vaccination (97%). Previously infected or vaccinated people had higher anti-spike protein immunoglobulin values; this value depended on the vaccine administered (p < 0.001). Patients with autoimmune diseases and smokers had lower levels of anti-S IgG antibodies (p = 0.030 and p = 0.024, respectively). The severity of COVID-19 did not affect the concentration of anti-S IgG (p = 0.430). This study highlights the general health statuses and the impact of COVID-19 on a population in the Portuguese interior. Knowledge of the circulation and impact of the virus in this specific population can alert and assist in better interventions being conducted by health authorities.
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Affiliation(s)
- Jorge Lindo
- FMUC—Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal; (J.L.)
- CNC-UC—Centre for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
- Dermatology Department, Coimbra’s Hospital and University Center, Unidade Local de Saúde de Coimbra, 3004-561 Coimbra, Portugal
| | - Patrícia Coelho
- Sport Physical Activity and Health Research & Innovation Center (Sprint), Polytechnic Institute of Castelo Branco, 6000-084 Castelo Branco, Portugal;
| | - Catarina Gavinhos
- IPCB/ESALD—Instituto Politécnico de Castelo Branco, Escola Superior Agrária, UID-QRural, 6000-084 Castelo Branco, Portugal; (C.G.); (M.M.)
| | - Manuel Martins
- IPCB/ESALD—Instituto Politécnico de Castelo Branco, Escola Superior Agrária, UID-QRural, 6000-084 Castelo Branco, Portugal; (C.G.); (M.M.)
| | - Joana Liberal
- IPC/ESTSC—Instituto Politécnico de Coimbra, Escola Superior Tecnologia da Saúde de Coimbra, 3046-854 Coimbra, Portugal;
| | - António Jorge Ferreira
- FMUC—Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal; (J.L.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Teresa Gonçalves
- FMUC—Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal; (J.L.)
- CNC-UC—Centre for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Francisco Rodrigues
- Sport Physical Activity and Health Research & Innovation Center (Sprint), Polytechnic Institute of Castelo Branco, 6000-084 Castelo Branco, Portugal;
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8
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Robertson SJ, Best SM. Interfer-on time: lessons from genetically diverse mouse models of SARS-CoV-2 infection. Genes Immun 2024; 25:341-342. [PMID: 38158396 DOI: 10.1038/s41435-023-00250-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Affiliation(s)
- Shelly J Robertson
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Sonja M Best
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA.
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Baker CN, Duso D, Kothapalli N, Hart T, Casey S, Cookenham T, Kummer L, Hvizdos J, Lanzer K, Vats P, Shanbhag P, Bell I, Tighe M, Travis K, Szaba F, Bedard O, Oberding N, Ward JM, Adams MD, Lutz C, Bradrick SS, Reiley WW, Rosenthal N. Characterization of Collaborative Cross mouse founder strain CAST/EiJ as a novel model for lethal COVID-19. RESEARCH SQUARE 2024:rs.3.rs-4675061. [PMID: 39149485 PMCID: PMC11326417 DOI: 10.21203/rs.3.rs-4675061/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Mutations in SARS-CoV-2 variants of concern (VOCs) have expanded the viral host range beyond primates, and a limited range of other mammals, to mice, affording the opportunity to exploit genetically diverse mouse panels to model the broad range of responses to infection in patient populations. Here we surveyed responses to VOC infection in genetically diverse Collaborative Cross (CC) founder strains. Infection of wild-derived CC founder strains produced a broad range of viral burden, disease susceptibility and survival, whereas most other strains were resistant to disease despite measurable lung viral titers. In particular, CAST/EiJ, a wild-derived strain, developed high lung viral burdens, more severe lung pathology than seen in other CC strains, and a dysregulated cytokine profile resulting in morbidity and mortality. These inbred mouse strains may serve as a valuable platform to evaluate therapeutic countermeasures against severe COVID-19 and other coronavirus pandemics in the future.
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Marchal A, Cirulli ET, Neveux I, Bellos E, Thwaites RS, Schiabor Barrett KM, Zhang Y, Nemes-Bokun I, Kalinova M, Catchpole A, Tangye SG, Spaan AN, Lack JB, Ghosn J, Burdet C, Gorochov G, Tubach F, Hausfater P, Dalgard CL, Zhang SY, Zhang Q, Chiu C, Fellay J, Grzymski JJ, Sancho-Shimizu V, Abel L, Casanova JL, Cobat A, Bolze A. Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection. HGG ADVANCES 2024; 5:100300. [PMID: 38678364 PMCID: PMC11215417 DOI: 10.1016/j.xhgg.2024.100300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 04/29/2024] Open
Abstract
Human genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B∗15:01 allele and asymptomatic SARS-CoV-2 infection in unvaccinated individuals was recently reported, suggesting a contribution of pre-existing T cell-dependent adaptive immunity. We report a lack of association of classical HLA alleles, including HLA-B∗15:01, with pre-omicron asymptomatic SARS-CoV-2 infection in unvaccinated participants in a prospective population-based study in the United States (191 asymptomatic vs. 945 symptomatic COVID-19 cases). Moreover, we found no such association in the international COVID Human Genetic Effort cohort (206 asymptomatic vs. 574 mild or moderate COVID-19 cases and 1,625 severe or critical COVID-19 cases). Finally, in the Human Challenge Characterisation study, the three HLA-B∗15:01 individuals infected with SARS-CoV-2 developed symptoms. As with other acute primary infections studied, no classical HLA alleles favoring an asymptomatic course of SARS-CoV-2 infection were identified.
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Affiliation(s)
- Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France
| | | | - Iva Neveux
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA
| | - Evangelos Bellos
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Ivana Nemes-Bokun
- Department of Infectious Disease, Imperial College London, London, UK
| | | | | | - Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, New South Wales, Australia
| | - András N Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Justin B Lack
- NIAID Collaborative Bioinformatics Resource, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD, USA
| | - Jade Ghosn
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University Paris Cité, Paris, France; AP-HP, Bichat-Claude Bernard Hospital, Infectious and Tropical Diseases Department, Paris, France
| | - Charles Burdet
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University Paris Cité, Paris, France; AP-HP, Hôpital Bichat, Centre d'Investigation Clinique, INSERM CIC 1425, Paris, France; Département Epidémiologie, Biostatistiques et Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, 75018 Paris, France
| | - Guy Gorochov
- Sorbonne Université, INSERM Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Département d'immunologie Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Florence Tubach
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Département de Santé Publique, Unitéde Recherche Clinique PSL-CFX, CIC-1901, Paris, France
| | - Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France; GRC-14 BIOSFAST Sorbonne Université, UMR INSERM 1135, CIMI, Sorbonne Université, Paris, France
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Joseph J Grzymski
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA; Renown Health, Reno, NV, USA
| | - Vanessa Sancho-Shimizu
- Department of Infectious Disease, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Department of Pediatrics, Necker Hospital for Sick Children, Paris, France; Howard Hughes Medical Institute, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
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11
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Zhang Z, Zhou J, Peng X, Li P, Meng X, Hu M, Zhao M, Lin Q, Ru K. Completion rates and myelosuppression degrees of cancer patients receiving radiotherapy or chemoradiotherapy unchanged regardless of delay duration after Omicron infection. Sci Rep 2024; 14:14226. [PMID: 38902401 PMCID: PMC11190149 DOI: 10.1038/s41598-024-65019-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024] Open
Abstract
This study aimed to investigate impacts of Omicron infection on cancer patients in China. A retrospective study was conducted, including 347 cancer patients undergoing radiotherapy or chemoradiotherapy between July 2022 and March 2023. Three groups involved: 108 patients without SARS-CoV-2 infection (non-COVID-19 group), 102 patients beginning treatment 10 days after first SARS-CoV-2 infection (≥ 10 days COVID-19 group), and 137 patients beginning treatment less than 10 days after first SARS-CoV-2 infection (< 10 days COVID-19 group). SAA, hsCRP, ALT, etc., were used to assess COVID-19 infection. Serum levels of SAA, hsCRP and IL-6 were all raised in two COVID-19-infected groups (SAA < 0.01, hsCRP < 0.01, IL-6 < 0.05), but PCT, ALT, LDH and HBDH levels were only elevated in ≥ 10 days COVID-19 group (PCT = 0.0478, ALT = 0.0022, LDH = 0.0313, HBDH = 0.0077). Moreover, moderate and severe infected cases were higher in ≥ 10 days COVID-19 group than < 10 days COVID-19 group (12/102 vs 5/137, p = 0.0211), but no significance in myelosuppression and completion rates among three groups. Omicron infection led to inflammation, liver and cardiovascular injury on cancer patients, but delay duration of radiotherapy or chemoradiotherapy after infection did not affect the completion rates and myelosuppression of current therapy. Besides, severity of Omicron infection was even worse among cancer patients who received delayed treatment.
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Affiliation(s)
- Zhenyu Zhang
- Department of Pathology and Lab Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Juan Zhou
- Department of Pathology and Lab Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Xun Peng
- Department of Pathology and Lab Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Ping Li
- Department of Hematology and Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China
| | - Xue Meng
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China
| | - Man Hu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China
| | - Miaoqing Zhao
- Department of Pathology and Lab Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Qinghai Lin
- Department of Pathology and Lab Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China.
| | - Kun Ru
- Department of Pathology and Lab Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China.
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12
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Waman VP, Ashford P, Lam SD, Sen N, Abbasian M, Woodridge L, Goldtzvik Y, Bordin N, Wu J, Sillitoe I, Orengo CA. Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics. Sci Rep 2024; 14:14208. [PMID: 38902252 PMCID: PMC11190248 DOI: 10.1038/s41598-024-61541-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/07/2024] [Indexed: 06/22/2024] Open
Abstract
The COVID-19 disease is an ongoing global health concern. Although vaccination provides some protection, people are still susceptible to re-infection. Ostensibly, certain populations or clinical groups may be more vulnerable. Factors causing these differences are unclear and whilst socioeconomic and cultural differences are likely to be important, human genetic factors could influence susceptibility. Experimental studies indicate SARS-CoV-2 uses innate immune suppression as a strategy to speed-up entry and replication into the host cell. Therefore, it is necessary to understand the impact of variants in immunity-associated human proteins on susceptibility to COVID-19. In this work, we analysed missense coding variants in several SARS-CoV-2 proteins and their human protein interactors that could enhance binding affinity to SARS-CoV-2. We curated a dataset of 19 SARS-CoV-2: human protein 3D-complexes, from the experimentally determined structures in the Protein Data Bank and models built using AlphaFold2-multimer, and analysed the impact of missense variants occurring in the protein-protein interface region. We analysed 468 missense variants from human proteins and 212 variants from SARS-CoV-2 proteins and computationally predicted their impacts on binding affinities for the human viral protein complexes. We predicted a total of 26 affinity-enhancing variants from 13 human proteins implicated in increased binding affinity to SARS-CoV-2. These include key-immunity associated genes (TOMM70, ISG15, IFIH1, IFIT2, RPS3, PALS1, NUP98, AXL, ARF6, TRIMM, TRIM25) as well as important spike receptors (KREMEN1, AXL and ACE2). We report both common (e.g., Y13N in IFIH1) and rare variants in these proteins and discuss their likely structural and functional impact, using information on known and predicted functional sites. Potential mechanisms associated with immune suppression implicated by these variants are discussed. Occurrence of certain predicted affinity-enhancing variants should be monitored as they could lead to increased susceptibility and reduced immune response to SARS-CoV-2 infection in individuals/populations carrying them. Our analyses aid in understanding the potential impact of genetic variation in immunity-associated proteins on COVID-19 susceptibility and help guide drug-repurposing strategies.
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Affiliation(s)
- Vaishali P Waman
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Paul Ashford
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Su Datt Lam
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Neeladri Sen
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Mahnaz Abbasian
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Laurel Woodridge
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Yonathan Goldtzvik
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Nicola Bordin
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Jiaxin Wu
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Christine A Orengo
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
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13
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Tane M, Kosako H, Sonoki T, Hosoi H. TAFRO Syndrome and COVID-19. Biomedicines 2024; 12:1287. [PMID: 38927495 PMCID: PMC11200813 DOI: 10.3390/biomedicines12061287] [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: 04/30/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
TAFRO syndrome is a systemic inflammatory disease characterized by thrombocytopenia and anasarca. It results from hyperinflammation and produces severe cytokine storms. Severe acute respiratory syndrome coronavirus 2, which led to the coronavirus disease 2019 (COVID-19) pandemic, also causes cytokine storms. COVID-19 was reported to be associated with various immune-related manifestations, including multisystem inflammatory syndrome, hemophagocytic syndrome, vasculitis, and immune thrombocytopenia. Although the pathogenesis and complications of COVID-19 have not been fully elucidated, the pathogeneses of excessive immunoreaction after COVID-19 and TAFRO syndrome both involve cytokine storms. Since the COVID-19 pandemic, there have been a few case reports about the onset of TAFRO syndrome after COVID-19 or COVID-19 vaccination. Castleman disease also presents with excessive cytokine production. We reviewed the literature about the association between TAFRO syndrome or Castleman disease and COVID-19 or vaccination against it. While the similarities and differences between the pathogeneses of TAFRO syndrome and COVID-19 have not been investigated previously, the cytokines and genetic factors associated with TAFRO syndrome and COVID-19 were reviewed by examining case reports. Investigation of TAFRO-like manifestations after COVID-19 or vaccination against COVID-19 may contribute to understanding the pathogenesis of TAFRO syndrome.
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Affiliation(s)
- Misato Tane
- Department of Hematology/Oncology, Wakayama Medical University, Wakayama 641-8509, Japan; (M.T.)
- Department of Hematology, Kinan Hospital, Wakayama 646-8588, Japan
| | - Hideki Kosako
- Department of Hematology/Oncology, Wakayama Medical University, Wakayama 641-8509, Japan; (M.T.)
- Department of Hematology, Kinan Hospital, Wakayama 646-8588, Japan
| | - Takashi Sonoki
- Department of Hematology/Oncology, Wakayama Medical University, Wakayama 641-8509, Japan; (M.T.)
- Department of Transfusion Medicine, Wakayama Medical University Hospital, Wakayama 641-8510, Japan
| | - Hiroki Hosoi
- Department of Hematology/Oncology, Wakayama Medical University, Wakayama 641-8509, Japan; (M.T.)
- Department of Transfusion Medicine, Wakayama Medical University Hospital, Wakayama 641-8510, Japan
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14
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Tomasa-Irriguible TM, Monfà R, Miranda-Jiménez C, Morros R, Robert N, Bordejé-Laguna L, Vidal S, Torán-Monserrat P, Barriocanal AM. Preventive Intake of a Multiple Micronutrient Supplement during Mild, Acute SARS-CoV-2 Infection to Reduce the Post-Acute COVID-19 Condition: A Double-Blind, Placebo-Controlled, Randomized Clinical Trial. Nutrients 2024; 16:1631. [PMID: 38892564 PMCID: PMC11174626 DOI: 10.3390/nu16111631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Patients hospitalized with COVID-19 have low levels of vitamins and trace elements. This could lead to a post-acute COVID-19 condition (PCC) that can worsen a patient's quality of life. We aimed to study the baseline micronutrient status of patients and assess whether a multiple micronutrient supplement (MMS) taken for 2 weeks at the first sign of COVID-19 symptoms would be able to reduce the incidence of PCC. This double-blind, placebo-controlled, randomized clinical trial was conducted in adult outpatients with acute COVID-19, recruited between 2021 and 2023 in Spain. Of the 285 patients assessed for eligibility, 267 were randomized and 246 were included in the intent-to-treat population. The mean age was 46.8 years, and 68% were female. Overall, 54.6% had micronutrient deficiencies in the acute phase of COVID-19 at baseline, and 26.2% had PCC after 180 days of follow-up (D180). The most frequently recorded PCC symptoms were neurological (14.1%), with 24% patients scoring worse in the cognitive tests compared to their baseline status. The rate of PCC at D180 was similar between the placebo (25.0%) and intervention (27.7%) groups, without significant differences (p = 0.785). Age over 50 years was the most relevant risk factor for developing PCC, followed by female sex. The most important protective factor against PCC was SARS-CoV-2 vaccination. In this population of predominantly middle-aged, white women with acute COVID-19 not requiring hospital admission, MMS intake for 14 days at symptom onset did not prevent PCC nor improve their micronutrient status at D180.
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Affiliation(s)
| | - Ramon Monfà
- Jordi Gol University Research Institute in Primary Care (IDIAP Jordi Gol), 08007 Barcelona, Spain; (R.M.); (C.M.-J.)
| | - Cristina Miranda-Jiménez
- Jordi Gol University Research Institute in Primary Care (IDIAP Jordi Gol), 08007 Barcelona, Spain; (R.M.); (C.M.-J.)
| | - Rosa Morros
- Department of Pharmacology, Therapeutics and Toxicology, Autonomous University of Barcelona (UAB), 08193 Bellaterra, Spain;
| | - Neus Robert
- Emergency Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain;
| | - Luisa Bordejé-Laguna
- Intensive Care Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain;
| | - Sandra Vidal
- Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain; (S.V.); (A.M.B.)
| | - Pere Torán-Monserrat
- North Metropolitan Research Support Unit, Jordi Gol University Research Institute in Primary Care (NM-IDIAP Jordi Gol), 08303 Mataró, Spain;
| | - Ana Maria Barriocanal
- Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain; (S.V.); (A.M.B.)
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15
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González-Fernández M, Vázquez-Coto D, Albaiceta GM, Amado-Rodríguez L, Clemente MG, Velázquez-Cuervo L, García-Lago C, Gómez J, Coto E. Chromosome-Y haplogroups in Asturias (Northern Spain) and their association with severe COVID-19. Mol Genet Genomics 2024; 299:49. [PMID: 38704518 PMCID: PMC11069473 DOI: 10.1007/s00438-024-02143-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
The main objective of this study was to determine whether the common Y-haplogroups were be associated with the risk of developing severe COVID-19 in Spanish male. We studied 479 patients who required hospitalization due to COVID-19 and 285 population controls from the region of Asturias (northern Spain), They were genotyped for several polymorphisms that define the common European Y-haplogroups. We compared the frequencies between patients and controls aged ≤ 65 and >65 years. There were no different haplogroup frequencies between the two age groups of controls. Haplogroup R1b was less common in patients aged ≤65 years. Haplogroup I was more common in the two patient´s groups compared to controls (p = 0.02). Haplogroup R1b was significantly more frequent among hypertensive patients, without difference between the hypertensive and normotensive controls. This suggested that R1b could increase the risk for severe COVID-19 among male with pre-existing hypertension. In conclusion, we described the Y-haplogroup structure among Asturians. We found an increased risk of severe COVID-19 among haplogroup I carriers, and a significantly higher frequency of R1b among hypertensive patients. These results indicate that Y-chromosome variants could serve as markers to define the risk of developing a severe form of COVID-19.
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Affiliation(s)
| | - Daniel Vázquez-Coto
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
| | - Guillermo M Albaiceta
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central Asturias, Oviedo, Spain
- Universidad de Oviedo, Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Laura Amado-Rodríguez
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central Asturias, Oviedo, Spain
- Universidad de Oviedo, Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Marta G Clemente
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
- Neumología, Hospital Universitario Central Asturias, Oviedo, Spain
| | | | - Claudia García-Lago
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
| | - Juan Gómez
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Eliecer Coto
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain.
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain.
- Universidad de Oviedo, Oviedo, Spain.
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16
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Chávez-Vélez E, Álvarez-Nava F, Torres-Vinueza A, Balarezo-Díaz T, Pilataxi K, Acosta-López C, Peña IZ, Narváez K. Single nucleotide variants in the CCL2, OAS1 and DPP9 genes and their association with the severity of COVID-19 in an Ecuadorian population. Front Cell Infect Microbiol 2024; 14:1322882. [PMID: 38694517 PMCID: PMC11061356 DOI: 10.3389/fcimb.2024.1322882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/15/2024] [Indexed: 05/04/2024] Open
Abstract
COVID-19 has a broad clinical spectrum, ranging from asymptomatic-mild form to severe phenotype. The severity of COVID-19 is a complex trait influenced by various genetic and environmental factors. Ethnic differences have been observed in relation to COVID-19 severity during the pandemic. It is currently unknown whether genetic variations may contribute to the increased risk of severity observed in Latin-American individuals The aim of this study is to investigate the potential correlation between gene variants at CCL2, OAS1, and DPP9 genes and the severity of COVID-19 in a population from Quito, Ecuador. This observational case-control study was conducted at the Carrera de Biologia from the Universidad Central del Ecuador and the Hospital Quito Sur of the Instituto Ecuatoriano de Seguridad Social (Quito-SUR-IESS), Quito, Ecuador. Genotyping for gene variants at rs1024611 (A>G), rs10774671 (A>G), and rs10406145 (G>C) of CCL2, OAS1, and DPP9 genes was performed on 100 COVID-19 patients (43 with severe form and 57 asymptomatic-mild) using RFLP-PCR. The genotype distribution of all SNVs throughout the entire sample of 100 individuals showed Hardy Weinberg equilibrium (P=0.53, 0.35, and 0.4 for CCL2, OAS1, and DPP9, respectively). The HWE test did not find any statistically significant difference in genotype distribution between the study and control groups for any of the three SNVs. The multivariable logistic regression analysis showed that individuals with the GG of the CCL2 rs1024611 gene variant had an increased association with the severe COVID-19 phenotype in a recessive model (P = 0.0003, OR = 6.43, 95% CI 2.19-18.89) and for the OAS1 rs10774671 gene variant, the log-additive model showed a significant association with the severe phenotype of COVID-19 (P=0.0084, OR=3.85, 95% CI 1.33-11.12). Analysis of haplotype frequencies revealed that the coexistence of GAG at CCL2, OAS1, and DPP9 variants, respectively, in the same individual increased the presence of the severe COVID-19 phenotype (OR=2.273, 95% CI: 1.271-4.068, P=0.005305). The findings of the current study suggests that the ethnic background affects the allele and genotype frequencies of genes associated with the severity of COVID-19. The experience with COVID-19 has provided an opportunity to identify an ethnicity-based approach to recognize genetically high-risk individuals in different populations for emerging diseases.
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Affiliation(s)
- Erik Chávez-Vélez
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Francisco Álvarez-Nava
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Alisson Torres-Vinueza
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Thalía Balarezo-Díaz
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Kathya Pilataxi
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Camila Acosta-López
- Carrera de Biología, Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Ivonne Z. Peña
- Unidad de Cuidados Críticos de Adultos, Hospital Quito Sur del Instituto Ecuatoriano de Securidad Social, Quito, Ecuador
| | - Katherin Narváez
- Unidad de Cuidados Críticos de Adultos, Hospital Quito Sur del Instituto Ecuatoriano de Securidad Social, Quito, Ecuador
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17
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Gamero-de-Luna EJ, Sánchez-Jaén MR. [Genetic factors associated with long COVID]. Semergen 2024; 50:102187. [PMID: 38277732 DOI: 10.1016/j.semerg.2023.102187] [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: 09/19/2023] [Accepted: 10/01/2023] [Indexed: 01/28/2024]
Abstract
INTRODUCTION The variability in expression and evolution of COVID is not completely explained by clinical factors. In fact, genetic factors play an important role. Moreover, it is unknown whether the genetic factor that contribute to susceptibility and severity are also involved in the onset and evolution of long-COVID. The objective of this review is to gather information from literature to understand which genetic factors are involved in the onset of persistent COVID. MATERIAL AND METHODS Systematic review in PubMed and bioRxiv and medRxiv repositories based on MeSH-descriptors and MeSH-terms related to COVID and genetic factors. Using these terms 2715 articles were pooled. An initial screening performed by authors independently, selected 205 articles of interest. A final deeper screening a total of 85 articles were chosen for complete reading and summarized in this review. RESULTS Although ACE2 and TMPSS6 are involved in COVID susceptibility, their involvement in long-COVID has not been found. On the other hand, the severity of the disease and the onset of long-COVID has been associated with different genes involved in the inflammatory and immune response. Particularly interesting has been the association found with the FOXP4 locus. CONCLUSIONS Although studies on long-COVID are insufficient to fully comprehend the cause, it is clear that the current identified genetic factors do not fully explain the progression and onset of long-COVID. Other factors such as polygenic action, pleiotropic genes, the microbiota and epigenetic changes must be considered and studied.
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Affiliation(s)
- E J Gamero-de-Luna
- Medicina Familiar y Comunitaria, Centro de Salud El Juncal, Sevilla, España; GT Medicina Genómica Personalizada y Enfermedades Raras, SEMERGEN, España.
| | - M R Sánchez-Jaén
- GT Medicina Genómica Personalizada y Enfermedades Raras, SEMERGEN, España; Medicina Familiar y Comunitaria, Centro de Salud de Fabero, León, España
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18
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Montserrat-Capdevila J, Fornells-Barberà I, Roso-Llorach A, Olivares-Sanzo P, Romero-Gracia A, Ichart JX. [Impact of COVID-19 on the mental health of the population: Study in primary care]. Aten Primaria 2024; 56:102813. [PMID: 38039619 PMCID: PMC10711385 DOI: 10.1016/j.aprim.2023.102813] [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: 07/19/2023] [Revised: 10/25/2023] [Accepted: 10/29/2023] [Indexed: 12/03/2023] Open
Abstract
OBJECTIVE To determine the prevalence of COVID-19 and the characteristics of infected patients, as well as the prevalence of mental disorders associated with the infection and the associated risk factors. Secondary: to know the prevalence of the long COVID syndrome and the characteristics of this cohort. DESIGN Incidence study of mental disorder in patients diagnosed with COVID-19 and case-control study of long COVID syndrome in the subsample of patients diagnosed with COVID-19 without a history of mental disorder. SITE: Primary care setting in Lleida. PARTICIPANTS The 46,258 patients diagnosed of COVID-19 without a history of mental disorder were followed for 2 years. MAIN MEASUREMENTS The dependent variable was the mental disorder in the period 03/11/2020 to 03/11/2022; and the independent variables were clinical and social variables. Its association with mental disorder was analyzed by calculating the adjusted hazard ratio using a logistic regression model. RESULTS The average age of 46,258 patients at the beginning of the study was 43±17.9 years. 47% were women. The mental disorder rate for all period was 3.46% (59.20% anxiety). A predictive score was elaborated. The long COVID syndrome was more common in older women, without toxic habits, with obesity and associated comorbidity. CONCLUSIONS COVID-19 has had an impact on the mental health of patients. Knowing the risk factors for developing these mental disorders and the long COVID syndrome would allow the clinician to be able to identify patients at risk in order to establish preventive measures and avoid their appearance.
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Affiliation(s)
- Josep Montserrat-Capdevila
- Unitat Docent Multiprofessional d'Atenció Familiar i Comunitària (UDMAFIC) Lleida, Lleida, España; Fundació d'Investigació en Atenció Primària Jordi Gol, Institut per a la recerca a l'Atenció Primària de Salut (IDIAP), Barcelona, España; Atenció Primària Lleida, Institut Català de la Salut (ICS), Lleida, España; Facultat de Medicina, Universitat de Lleida (UdL), Lleida, España.
| | - Immaculada Fornells-Barberà
- Equip d'Assessorament i d'Orientació Psicopedagògic (EAP) Ll-02 Segrià (Sector B). Departament d'Educació, Generalitat de Catalunya, España
| | - Albert Roso-Llorach
- Fundació d'Investigació en Atenció Primària Jordi Gol, Institut per a la recerca a l'Atenció Primària de Salut (IDIAP), Barcelona, España; Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Barcelona, España
| | - Pau Olivares-Sanzo
- Unitat Docent Multiprofessional d'Atenció Familiar i Comunitària (UDMAFIC) Lleida, Lleida, España; Fundació d'Investigació en Atenció Primària Jordi Gol, Institut per a la recerca a l'Atenció Primària de Salut (IDIAP), Barcelona, España; Atenció Primària Lleida, Institut Català de la Salut (ICS), Lleida, España
| | - Albert Romero-Gracia
- Fundació d'Investigació en Atenció Primària Jordi Gol, Institut per a la recerca a l'Atenció Primària de Salut (IDIAP), Barcelona, España; Atenció Primària Lleida, Institut Català de la Salut (ICS), Lleida, España
| | - J Xavier Ichart
- Àrea de Gestió Clínica, Direcció d'Atenció Primària Lleida, Institut Català de la Salut (ICS), Lleida, España; Fundació d'Investigació en Atenció Primària Jordi Gol, Institut per a la recerca a l'Atenció Primària de Salut (IDIAP), Barcelona, España
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19
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Skerenova M, Cibulka M, Dankova Z, Holubekova V, Kolkova Z, Lucansky V, Dvorska D, Kapinova A, Krivosova M, Petras M, Baranovicova E, Baranova I, Novakova E, Liptak P, Banovcin P, Bobcakova A, Rosolanka R, Janickova M, Stanclova A, Gaspar L, Caprnda M, Prosecky R, Labudova M, Gabbasov Z, Rodrigo L, Kruzliak P, Lasabova Z, Matakova T, Halasova E. Host genetic variants associated with COVID-19 reconsidered in a Slovak cohort. Adv Med Sci 2024; 69:198-207. [PMID: 38555007 DOI: 10.1016/j.advms.2024.03.007] [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: 06/28/2023] [Revised: 11/15/2023] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
We present the results of an association study involving hospitalized coronavirus disease 2019 (COVID-19) patients with a clinical background during the 3rd pandemic wave of COVID-19 in Slovakia. Seventeen single nucleotide variants (SNVs) in the eleven most relevant genes, according to the COVID-19 Host Genetics Initiative, were investigated. Our study confirms the validity of the influence of LZTFL1 and 2'-5'-oligoadenylate synthetase (OAS)1/OAS3 genetic variants on the severity of COVID-19. For two LZTFL1 SNVs in complete linkage disequilibrium, rs17713054 and rs73064425, the odds ratios of baseline allelic associations and logistic regressions (LR) adjusted for age and sex ranged in the four tested designs from 2.04 to 2.41 and from 2.05 to 3.98, respectively. The OAS1/OAS3 haplotype 'gttg' carrying a functional allele G of splice-acceptor variant rs10774671 manifested its protective function in the Delta pandemic wave. Significant baseline allelic associations of two DPP9 variants in all tested designs and two IFNAR2 variants in the Omicron pandemic wave were not confirmed by adjusted LR. Nevertheless, adjusted LR showed significant associations of NOTCH4 rs3131294 and TYK2 rs2304256 variants with severity of COVID-19. Hospitalized patients' reported comorbidities were not correlated with genetic variants, except for obesity, smoking (IFNAR2), and hypertension (NOTCH4). The results of our study suggest that host genetic variations have an impact on the severity and duration of acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Considering the differences in allelic associations between pandemic waves, they support the hypothesis that every new SARS-CoV-2 variant may modify the host immune response by reconfiguring involved pathways.
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Affiliation(s)
- Maria Skerenova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Michal Cibulka
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Zuzana Dankova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Veronika Holubekova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Zuzana Kolkova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Vincent Lucansky
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Dana Dvorska
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Kapinova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Michaela Krivosova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Martin Petras
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Eva Baranovicova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Ivana Baranova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Elena Novakova
- Department of Microbiology and Immunology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Peter Liptak
- Clinic of Internal Medicine- Gastroenterology, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Peter Banovcin
- Clinic of Internal Medicine- Gastroenterology, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Anna Bobcakova
- Clinic of Pneumology and Phthisiology, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Robert Rosolanka
- Clinic of Infectology and Travel Medicine, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Maria Janickova
- Clinic of Stomatology and Maxillofacial Surgery, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Stanclova
- Department of Pathological Anatomy, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Ludovit Gaspar
- Faculty of Health Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Martin Caprnda
- 1st Department of Internal Medicine, Faculty of Medicine, Comenius University and University Hospital, Bratislava, Slovakia
| | - Robert Prosecky
- 2nd Department of Internal Medicine, Faculty of Medicine, Masaryk University and St. Anne'S University Hospital, Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital and Masaryk University, Brno, Czech Republic
| | - Monika Labudova
- Faculty of Health Care and Social Work, University of Trnava in Trnava, Slovakia
| | - Zufar Gabbasov
- National Medical Research Centre for Cardiology, Moscow, Russia
| | - Luis Rodrigo
- Faculty of Medicine, University of Oviedo and Central University Hospital of Asturias (HUCA), Oviedo, Spain
| | - Peter Kruzliak
- Faculty of Medicine, University of Oviedo and Central University Hospital of Asturias (HUCA), Oviedo, Spain; Research and Development Services, Olomouc, Czech Republic.
| | - Zora Lasabova
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Tatiana Matakova
- Department of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Erika Halasova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia.
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20
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Zhang Z, Wang S, Jiang L, Wei J, Lu C, Li S, Diao Y, Fang Z, He S, Tan T, Yang Y, Zou K, Shi J, Lin J, Chen L, Bao C, Fei J, Fang H. Priority index for critical Covid-19 identifies clinically actionable targets and drugs. Commun Biol 2024; 7:189. [PMID: 38366110 PMCID: PMC10873402 DOI: 10.1038/s42003-024-05897-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 02/07/2024] [Indexed: 02/18/2024] Open
Abstract
While genome-wide studies have identified genomic loci in hosts associated with life-threatening Covid-19 (critical Covid-19), the challenge of resolving these loci hinders further identification of clinically actionable targets and drugs. Building upon our previous success, we here present a priority index solution designed to address this challenge, generating the target and drug resource that consists of two indexes: the target index and the drug index. The primary purpose of the target index is to identify clinically actionable targets by prioritising genes associated with Covid-19. We illustrate the validity of the target index by demonstrating its ability to identify pre-existing Covid-19 phase-III drug targets, with the majority of these targets being found at the leading prioritisation (leading targets). These leading targets have their evolutionary origins in Amniota ('four-leg vertebrates') and are predominantly involved in cytokine-cytokine receptor interactions and JAK-STAT signaling. The drug index highlights opportunities for repurposing clinically approved JAK-STAT inhibitors, either individually or in combination. This proposed strategic focus on the JAK-STAT pathway is supported by the active pursuit of therapeutic agents targeting this pathway in ongoing phase-II/III clinical trials for Covid-19.
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Affiliation(s)
- Zhiqiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lulu Jiang
- Translational Health Sciences, University of Bristol, Bristol, BS1 3NY, UK
| | - Jianwen Wei
- Network and Information Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chang Lu
- MRC London Institute of Medical Sciences, Imperial College London, London, W12 0HS, UK
| | - Shengli Li
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201620, China
| | - Yizhu Diao
- College of Finance and Statistics, Hunan University, Changsha, 410079, Hunan, China
| | - Zhongcheng Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuo He
- College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Tingting Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yisheng Yang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Kexin Zou
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiantao Shi
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - James Lin
- Network and Information Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liye Chen
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK.
| | - Chaohui Bao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Department of General Surgery, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, 200020, China.
| | - Jian Fei
- Department of General Surgery, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, 200020, China.
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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21
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Asteris PG, Gandomi AH, Armaghani DJ, Tsoukalas MZ, Gavriilaki E, Gerber G, Konstantakatos G, Skentou AD, Triantafyllidis L, Kotsiou N, Braunstein E, Chen H, Brodsky R, Touloumenidou T, Sakellari I, Alkayem NF, Bardhan A, Cao M, Cavaleri L, Formisano A, Guney D, Hasanipanah M, Khandelwal M, Mohammed AS, Samui P, Zhou J, Terpos E, Dimopoulos MA. Genetic justification of COVID-19 patient outcomes using DERGA, a novel data ensemble refinement greedy algorithm. J Cell Mol Med 2024; 28:e18105. [PMID: 38339761 PMCID: PMC10863978 DOI: 10.1111/jcmm.18105] [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: 06/12/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 02/12/2024] Open
Abstract
Complement inhibition has shown promise in various disorders, including COVID-19. A prediction tool including complement genetic variants is vital. This study aims to identify crucial complement-related variants and determine an optimal pattern for accurate disease outcome prediction. Genetic data from 204 COVID-19 patients hospitalized between April 2020 and April 2021 at three referral centres were analysed using an artificial intelligence-based algorithm to predict disease outcome (ICU vs. non-ICU admission). A recently introduced alpha-index identified the 30 most predictive genetic variants. DERGA algorithm, which employs multiple classification algorithms, determined the optimal pattern of these key variants, resulting in 97% accuracy for predicting disease outcome. Individual variations ranged from 40 to 161 variants per patient, with 977 total variants detected. This study demonstrates the utility of alpha-index in ranking a substantial number of genetic variants. This approach enables the implementation of well-established classification algorithms that effectively determine the relevance of genetic variants in predicting outcomes with high accuracy.
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Affiliation(s)
- Panagiotis G. Asteris
- Computational Mechanics Laboratory, School of Pedagogical and Technological EducationAthensGreece
| | - Amir H. Gandomi
- Faculty of Engineering & ITUniversity of Technology SydneySydneyNew South WalesAustralia
- University Research and Innovation Center (EKIK), Óbuda UniversityBudapestHungary
| | - Danial J. Armaghani
- School of Civil and Environmental EngineeringUniversity of Technology SydneySydneyNew South WalesAustralia
| | - Markos Z. Tsoukalas
- Computational Mechanics Laboratory, School of Pedagogical and Technological EducationAthensGreece
| | - Eleni Gavriilaki
- 2nd Propedeutic Department of Internal MedicineAristotle University of ThessalonikiThessalonikiGreece
| | - Gloria Gerber
- Hematology DivisionJohns Hopkins UniversityBaltimoreUSA
| | - Gerasimos Konstantakatos
- Computational Mechanics Laboratory, School of Pedagogical and Technological EducationAthensGreece
| | - Athanasia D. Skentou
- Computational Mechanics Laboratory, School of Pedagogical and Technological EducationAthensGreece
| | - Leonidas Triantafyllidis
- Computational Mechanics Laboratory, School of Pedagogical and Technological EducationAthensGreece
| | - Nikolaos Kotsiou
- 2nd Propedeutic Department of Internal MedicineAristotle University of ThessalonikiThessalonikiGreece
| | | | - Hang Chen
- Hematology DivisionJohns Hopkins UniversityBaltimoreUSA
| | | | | | - Ioanna Sakellari
- Hematology Department – BMT UnitG Papanicolaou HospitalThessalonikiGreece
| | | | - Abidhan Bardhan
- Civil Engineering DepartmentNational Institute of Technology PatnaPatnaIndia
| | - Maosen Cao
- Department of Engineering MechanicsHohai UniversityNanjingChina
| | - Liborio Cavaleri
- Department of Civil, Environmental, Aerospace and Materials EngineeringUniversity of PalermoPalermoItaly
| | - Antonio Formisano
- Department of Structures for Engineering and ArchitectureUniversity of Naples “Federico II”NaplesItaly
| | - Deniz Guney
- Engineering FacultySan Diego State UniversitySan DiegoCaliforniaUSA
| | - Mahdi Hasanipanah
- Department of Geotechnics and Transportation, Faculty of Civil EngineeringUniversiti Teknologi MalaysiaJohor BahruMalaysia
| | - Manoj Khandelwal
- Institute of Innovation, Science and SustainabilityFederation University AustraliaBallaratVictoriaAustralia
| | | | - Pijush Samui
- Civil Engineering DepartmentNational Institute of Technology PatnaPatnaIndia
| | - Jian Zhou
- School of Resources and Safety EngineeringCentral South UniversityChangshaChina
| | - Evangelos Terpos
- Department of Clinical Therapeutics, Medical School, Faculty of MedicineNational Kapodistrian University of AthensAthensGreece
| | - Meletios A. Dimopoulos
- Department of Clinical Therapeutics, Medical School, Faculty of MedicineNational Kapodistrian University of AthensAthensGreece
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22
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Camps-Vilaró A, Pinsach-Abuin ML, Degano IR, Ramos R, Martí-Lluch R, Elosua R, Subirana I, Solà-Richarte C, Puigmulé M, Pérez A, Vilaró I, Cruz R, Diz-de Almeida S, Nogues X, Masclans JR, Güerri-Fernández R, Marin J, Tizon-Marcos H, Vaquerizo B, Brugada R, Marrugat J. Genetic characteristics involved in COVID-19 severity. The CARGENCORS case-control study and meta-analysis. J Med Virol 2024; 96:e29404. [PMID: 38293834 DOI: 10.1002/jmv.29404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/30/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
Pre-existing coronary artery disease (CAD), and thrombotic, inflammatory, or virus infectivity response phenomena have been associated with COVID-19 disease severity. However, the association of candidate single nucleotide variants (SNVs) related to mechanisms of COVID-19 complications has been seldom analysed. Our aim was to test and validate the effect of candidate SNVs on COVID-19 severity. CARGENCORS (CARdiovascular GENetic risk score for Risk Stratification of patients positive for SARS-CoV-2 [COVID-19] virus) is an age- and sex-matched case-control study with 818 COVID-19 cases hospitalized with hypoxemia, and 1636 controls with COVID-19 treated at home. The association between severity and SNVs related to CAD (n = 32), inflammation (n = 19), thrombosis (n = 14), virus infectivity (n = 11), and two published to be related to COVID-19 severity was tested with adjusted logistic regression models. Two external independent cohorts were used for meta-analysis (SCOURGE and UK Biobank). After adjustment for potential confounders, 14 new SNVs were associated with COVID-19 severity in the CARGENCORS Study. These SNVs were related to CAD (n = 10), thrombosis (n = 2), and inflammation (n = 2). We also confirmed eight SNVs previously related to severe COVID-19 and virus infectivity. The meta-analysis showed five SNVs associated with severe COVID-19 in adjusted analyses (rs11385942, rs1561198, rs6632704, rs6629110, and rs12329760). We identified 14 novel SNVs and confirmed eight previously related to COVID-19 severity in the CARGENCORS data. In the meta-analysis, five SNVs were significantly associated to COVID-19 severity, one of them previously related to CAD.
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Affiliation(s)
- Anna Camps-Vilaró
- Registre Gironí del Cor (REGICOR) Study Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Doctoral College, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Mel Lina Pinsach-Abuin
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IdIBGi), Salt, Spain
| | - Irene R Degano
- Registre Gironí del Cor (REGICOR) Study Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Institute for Research and Innovation in Life Sciences and Health in Central Catalonia (IRIS-CC), Vic, Spain
| | - Rafel Ramos
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain
- Vascular Health Research Group, Institut Universitari per a la Recerca en Atenció Primària Jordi Gol i Gurina, Girona, Spain
- Girona Biomedical Research Institute, Girona, Spain
- Primary Care Services, Catalan Institute of Health, Girona, Spain
| | - Ruth Martí-Lluch
- Vascular Health Research Group, Institut Universitari per a la Recerca en Atenció Primària Jordi Gol i Gurina, Girona, Spain
- Girona Biomedical Research Institute, Girona, Spain
| | - Roberto Elosua
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Cardiovascular Epidemiology and Genetics Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Isaac Subirana
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Cardiovascular Epidemiology and Genetics Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Clàudia Solà-Richarte
- Registre Gironí del Cor (REGICOR) Study Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Marta Puigmulé
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
| | - Alexandra Pérez
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IdIBGi), Salt, Spain
| | | | - Raquel Cruz
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia Diz-de Almeida
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Xavier Nogues
- Musculoskeletal Research Unit, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Internal Medicine, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable, Instituto de Salud Carlos III, Madrid, Spain
- Department of Medicine, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Joan R Masclans
- Critical Illness Research Group (GREPAC), Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Critical Care, Hospital del Mar, Barcelona, Spain
- Medicine and Life Sciences department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roberto Güerri-Fernández
- Department of Medicine, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Department of Infectious Diseases, Hospital del Mar Research Institute, Barcelona, Spain
| | - Judith Marin
- Critical Illness Research Group (GREPAC), Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Critical Care, Hospital del Mar, Barcelona, Spain
| | - Helena Tizon-Marcos
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Biomedical Research in Heart Diseases Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Cardiology, Hospital del Mar, Barcelona, Spain
| | - Beatriz Vaquerizo
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Department of Medicine, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Biomedical Research in Heart Diseases Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Cardiology, Hospital del Mar, Barcelona, Spain
| | - Ramon Brugada
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta (IdIBGi), Salt, Spain
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain
- Department of Cardiology, Hospital Josep Trueta & University of Girona, Girona, Spain
| | - Jaume Marrugat
- Registre Gironí del Cor (REGICOR) Study Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
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23
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Lee A, Seo J, Park S, Cho Y, Kim G, Li J, Liang L, Park T, Chung W. Type 2 diabetes and its genetic susceptibility are associated with increased severity and mortality of COVID-19 in UK Biobank. Commun Biol 2024; 7:122. [PMID: 38267566 PMCID: PMC10808197 DOI: 10.1038/s42003-024-05799-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
Type 2 diabetes (T2D) is known as one of the important risk factors for the severity and mortality of COVID-19. Here, we evaluate the impact of T2D and its genetic susceptibility on the severity and mortality of COVID-19, using 459,119 individuals in UK Biobank. Utilizing the polygenic risk scores (PRS) for T2D, we identified a significant association between T2D or T2D PRS, and COVID-19 severity. We further discovered the efficacy of vaccination and the pivotal role of T2D-related genetics in the pathogenesis of severe COVID-19. Moreover, we found that individuals with T2D or those in the high T2D PRS group had a significantly increased mortality rate. We also observed that the mortality rate for SARS-CoV-2-infected patients was approximately 2 to 7 times higher than for those not infected, depending on the time of infection. These findings emphasize the potential of T2D PRS in estimating the severity and mortality of COVID-19.
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Affiliation(s)
- Aeyeon Lee
- Department of Statistics and Actuarial Science, Soongsil University, Seoul, 06978, Korea
| | - Jieun Seo
- Department of Statistics and Actuarial Science, Soongsil University, Seoul, 06978, Korea
| | - Seunghwan Park
- Department of Statistics and Actuarial Science, Soongsil University, Seoul, 06978, Korea
- Institute of Genetic Epidemiology, Basgenbio Co. Ltd., Seoul, 04167, Korea
| | - Youngkwang Cho
- Department of Statistics and Actuarial Science, Soongsil University, Seoul, 06978, Korea
| | - Gaeun Kim
- Department of Statistics and Actuarial Science, Soongsil University, Seoul, 06978, Korea
| | - Jun Li
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Liming Liang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul, 08826, Korea.
| | - Wonil Chung
- Department of Statistics and Actuarial Science, Soongsil University, Seoul, 06978, Korea.
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
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24
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Zapico SC, Roca G. Making the Most of Lateral Flow Immunochromatographic Tests: An Efficient Protocol to Recover DNA. Methods Protoc 2024; 7:8. [PMID: 38251201 PMCID: PMC10801598 DOI: 10.3390/mps7010008] [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: 11/22/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Lateral flow immunochromatographic (LFI) tests are widely used in both biomedical and forensic sciences for different applications. In forensic sciences, their main use is to detect body fluids at crime scenes. However, there are situations in which the amount of potential biological evidence is so low that DNA extraction is favored with respect to the identification of body fluids. Here, an efficient and quick protocol is presented to integrate the detection of body fluids through LFI with DNA extraction from a sample swab and buffer, providing a complete characterization of the biological evidence. This protocol is a modification of a general DNA extraction silica-based kit, whose main application is for blood and tissues. Thus, it could be carried out in different settings (forensic labs, hospitals, other testing labs) without the necessity of buying a specific kit for swabs. The validation of this protocol is supported by the results presented here and previous publications from our group, obtaining DNA in good quantity and with good quality. This proves the potential application of the protocol in both forensic scenarios, to fully characterize biological evidence, and biomedical settings, to molecularly confirm the results of LFI tests.
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Affiliation(s)
- Sara C. Zapico
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
- Anthropology Department and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Gabriela Roca
- SERATEC Gesellschaft für Biotechnologie mbH, 37079 Göttingen, Germany;
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25
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Liu F, Deng P, He J, Chen X, Jiang X, Yan Q, Xu J, Hu S, Yan J. A regional genomic surveillance program is implemented to monitor the occurrence and emergence of SARS-CoV-2 variants in Yubei District, China. Virol J 2024; 21:13. [PMID: 38191416 PMCID: PMC10775548 DOI: 10.1186/s12985-023-02279-6] [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: 07/06/2023] [Accepted: 12/27/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND In December 2022, Chongqing experienced a significant surge in coronavirus disease 2019 (COVID-19) epidemic after adjusting control measures in China. Given the widespread immunization of the population with the BA.5 variant, it is crucial to actively monitor severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant evolution in Chongqing's Yubei district. METHODS In this retrospective study based on whole genome sequencing, we collected oropharyngeal and nasal swab of native COVID-19 cases from Yubei district between January to May 2023, along with imported cases from January 2022 to January 2023. Through second-generation sequencing, we generated a total of 578 genomes. RESULTS Phylogenetic analyses revealed these genomes belong to 47 SARS-CoV-2 Pango lineages. BA.5.2.48 was dominant from January to April 2023, rapidly replaced by XBB* variants from April to May 2023. Bayesian Skyline Plot reconstructions indicated a higher evolutionary rate (6.973 × 10-4 subs/site/year) for the XBB.1.5* lineage compared to others. The mean time to the most recent common ancestor (tMRCA) of BA.5.2.48* closely matched BA.2.75* (May 27, 2022). Using multinomial logistic regression, we estimated growth advantages, with XBB.1.9.1 showing the highest growth advantage (1.2, 95% HPI:1.1-1.2), followed by lineage FR.1 (1.1, 95% HPI:1.1-1.2). CONCLUSIONS Our monitoring reveals the rapid replacement of the previously prevalent BA.5.2.48 variant by XBB and its sub-variants, underscoring the ineffectiveness of herd immunity and breakthrough BA.5 infections against XBB variants. Given the ongoing evolutionary pressure, sustaining a SARS-CoV-2 genomic surveillance program is imperative.
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Affiliation(s)
- Fangyuan Liu
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Peng Deng
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Jiuhong He
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Xiaofeng Chen
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Xinyu Jiang
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Qi Yan
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Jing Xu
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Sihan Hu
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China
| | - Jin Yan
- Chongqing Yubei Center for Disease Control and Prevention, Chongqing, China.
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26
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Boccellino M. COVID-19 Pandemic: Therapeutic Strategies and Vaccines. Int J Mol Sci 2023; 25:556. [PMID: 38203727 PMCID: PMC10778581 DOI: 10.3390/ijms25010556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 01/12/2024] Open
Abstract
Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), a highly pathogenic and transmissible virus, has spurred an impressive accumulation of knowledge [...].
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Affiliation(s)
- Mariarosaria Boccellino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
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27
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Marchal A, Cirulli ET, Neveux I, Bellos E, Thwaites RS, Schiabor Barrett KM, Zhang Y, Nemes-Bokun I, Kalinova M, Catchpole A, Tangye SG, Spaan AN, Lack JB, Ghosn J, Burdet C, Gorochov G, Tubach F, Hausfater P, Dalgard CL, Zhang SY, Zhang Q, Chiu C, Fellay J, Grzymski JJ, Sancho-Shimizu V, Abel L, Casanova JL, Cobat A, Bolze A. Lack of association between HLA and asymptomatic SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.06.23299623. [PMID: 38168184 PMCID: PMC10760282 DOI: 10.1101/2023.12.06.23299623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Human genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B*15:01 allele and asymptomatic SARS-CoV-2 infection in unvaccinated individuals was recently reported, suggesting a contribution of pre-existing T cell-dependent adaptive immunity. We report a lack of association of classical HLA alleles, including HLA-B*15:01, with pre-omicron asymptomatic SARS-CoV-2 infection in unvaccinated participants in a prospective population-based study in the US (191 asymptomatic vs. 945 symptomatic COVID-19 cases). Moreover, we found no such association in the international COVID Human Genetic Effort cohort (206 asymptomatic vs. 574 mild or moderate COVID-19 cases and 1,625 severe or critical COVID-19 cases). Finally, in the Human Challenge Characterisation study, the three HLA-B*15:01 individuals infected with SARS-CoV-2 developed symptoms. As with other acute primary infections, no classical HLA alleles favoring an asymptomatic course of SARS-CoV-2 infection were identified. These findings suggest that memory T-cell immunity to seasonal coronaviruses does not strongly influence the outcome of SARS-CoV-2 infection in unvaccinated individuals.
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Affiliation(s)
- Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
| | | | - Iva Neveux
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA
| | - Evangelos Bellos
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Ryan S. Thwaites
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Ivana Nemes-Bokun
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | | | | | - Stuart G. Tangye
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, NSW, Australia
| | - András N. Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands, EU
| | - Justin B. Lack
- NIAID Collaborative Bioinformatics Resource, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Jade Ghosn
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University of Paris, Paris, France, EU
- AP-HP, Bichat Claude Bernard Hospital, Infectious and Tropical Diseases Department, Paris, France, EU
| | - Charles Burdet
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University of Paris, Paris, France, EU
- Epidémiologie clinique du Centre d’Investigation Clinique (CIC-EP), INSERM CIC 1425, Hôpital Bichat, 75018 Paris, France, EU
- Département Epidémiologie, Biostatistiques et Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, 75018 Paris, France, EU
| | - Guy Gorochov
- Sorbonne Université, INSERM Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Département d’immunologie Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France, EU
| | - Florence Tubach
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié Salpêtrière, Département de Santé Publique, Unité de Recherche Clinique PSL-CFX, CIC-1901, Paris, France, EU
| | - Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France, EU
- GRC-14 BIOFAST Sorbonne Université, UMR INSERM 1135, CIMI, Sorbonne Université, Paris, France, EU
| | | | | | | | | | | | | | | | | | | | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Christopher Chiu
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Joseph J. Grzymski
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA
- Renown Health, Reno, NV, USA
| | - Vanessa Sancho-Shimizu
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
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Fritsche LG, Nam K, Du J, Kundu R, Salvatore M, Shi X, Lee S, Burgess S, Mukherjee B. Uncovering associations between pre-existing conditions and COVID-19 Severity: A polygenic risk score approach across three large biobanks. PLoS Genet 2023; 19:e1010907. [PMID: 38113267 PMCID: PMC10763941 DOI: 10.1371/journal.pgen.1010907] [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: 08/09/2023] [Revised: 01/03/2024] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
OBJECTIVE To overcome the limitations associated with the collection and curation of COVID-19 outcome data in biobanks, this study proposes the use of polygenic risk scores (PRS) as reliable proxies of COVID-19 severity across three large biobanks: the Michigan Genomics Initiative (MGI), UK Biobank (UKB), and NIH All of Us. The goal is to identify associations between pre-existing conditions and COVID-19 severity. METHODS Drawing on a sample of more than 500,000 individuals from the three biobanks, we conducted a phenome-wide association study (PheWAS) to identify associations between a PRS for COVID-19 severity, derived from a genome-wide association study on COVID-19 hospitalization, and clinical pre-existing, pre-pandemic phenotypes. We performed cohort-specific PRS PheWAS and a subsequent fixed-effects meta-analysis. RESULTS The current study uncovered 23 pre-existing conditions significantly associated with the COVID-19 severity PRS in cohort-specific analyses, of which 21 were observed in the UKB cohort and two in the MGI cohort. The meta-analysis yielded 27 significant phenotypes predominantly related to obesity, metabolic disorders, and cardiovascular conditions. After adjusting for body mass index, several clinical phenotypes, such as hypercholesterolemia and gastrointestinal disorders, remained associated with an increased risk of hospitalization following COVID-19 infection. CONCLUSION By employing PRS as a proxy for COVID-19 severity, we corroborated known risk factors and identified novel associations between pre-existing clinical phenotypes and COVID-19 severity. Our study highlights the potential value of using PRS when actual outcome data may be limited or inadequate for robust analyses.
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Affiliation(s)
- Lars G. Fritsche
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Kisung Nam
- Graduate School of Data Science, Seoul National University, Seoul, South Korea
| | - Jiacong Du
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Ritoban Kundu
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Maxwell Salvatore
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Xu Shi
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Seunggeun Lee
- Graduate School of Data Science, Seoul National University, Seoul, South Korea
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
- Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Bhramar Mukherjee
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Michigan Institute for Data Science, University of Michigan, Ann Arbor, Michigan, United States of America
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29
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Ferri C, Raimondo V, Giuggioli D, Gragnani L, Lorini S, Dagna L, Bosello SL, Foti R, Riccieri V, Guiducci S, Cuomo G, Tavoni A, De Angelis R, Cacciapaglia F, Zanatta E, Cozzi F, Murdaca G, Cavazzana I, Romeo N, Codullo V, Pellegrini R, Varcasia G, De Santis M, Selmi C, Abignano G, Caminiti M, L'Andolina M, Olivo D, Lubrano E, Spinella A, Lumetti F, De Luca G, Ruscitti P, Urraro T, Visentini M, Bellando-Randone S, Visalli E, Testa D, Sciascia G, Masini F, Pellegrino G, Saccon F, Balestri E, Elia G, Ferrari SM, Tonutti A, Dall’Ara F, Pagano Mariano G, Pettiti G, Zanframundo G, Brittelli R, Aiello V, Dal Bosco Y, Foti R, Di Cola I, Scorpiniti D, Fusaro E, Ferrari T, Gigliotti P, Campochiaro C, Francioso F, Iandoli C, Caira V, Zignego AL, D'Angelo S, Franceschini F, Matucci-Cerinic M, Giacomelli R, Doria A, Santini SA, Fallahi P, Iannone F, Antonelli A. Impact of COVID-19 and vaccination campaign on 1,755 systemic sclerosis patients during first three years of pandemic. Possible risks for individuals with impaired immunoreactivity to vaccine, ongoing immunomodulating treatments, and disease-related lung involvement during the next pandemic phase. J Transl Autoimmun 2023; 7:100212. [PMID: 37854035 PMCID: PMC10580042 DOI: 10.1016/j.jtauto.2023.100212] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Introduction The impact of COVID-19 pandemic represents a serious challenge for 'frail' patients' populations with inflammatory autoimmune systemic diseases such as systemic sclerosis (SSc). We investigated the prevalence and severity of COVID-19, as well the effects of COVID-19 vaccination campaign in a large series of SSc patients followed for the entire period (first 38 months) of pandemic. Patients and method This prospective survey study included 1755 unselected SSc patients (186 M, 1,569F; mean age 58.7 ± 13.4SD years, mean disease duration 8.8 ± 7.3SD years) recruited in part by telephone survey at 37 referral centers from February 2020 to April 2023. The following parameters were carefully evaluated: i. demographic, clinical, serological, and therapeutical features; ii. prevalence and severity of COVID-19; and iii. safety, immunogenicity, and efficacy of COVID-19 vaccines. Results The prevalence of COVID-19 recorded during the whole pandemic was significantly higher compared to Italian general population (47.3 % vs 43.3 %, p < 0.000), as well the COVID-19-related mortality (1.91 % vs 0.72 %, p < 0.001). As regards the putative prognostic factors of worse outcome, COVID-19 positive patients with SSc-related interstitial lung involvement showed significantly higher percentage of COVID-19-related hospitalization compared to those without (5.85 % vs 1.73 %; p < 0.0001), as well as of mortality rate (2.01 % vs 0.4 %; p = 0.002). Over half of patients (56.3 %) received the first two plus one booster dose of vaccine; while a fourth dose was administered to 35.6 %, and only few of them (1.99 %) had five or more doses of vaccine. Of note, an impaired seroconversion was recorded in 25.6 % of individuals after the first 2 doses of vaccine, and in 8.4 % of patients also after the booster dose. Furthermore, the absence of T-cell immunoreactivity was observed in 3/7 patients tested by QuantiFERON® SARSCoV-2 Starter Set (Qiagen). The efficacy of vaccines, evaluated by comparing the COVID-19-related death rate recorded during pre- and post-vaccination pandemic periods, revealed a quite stable outcome in SSc patients (death rate from 2.54 % to 1.76 %; p = ns), despite the significant drop of mortality observed in the Italian general population (from 2.95 % to 0.29 %; p < 0.0001). Conclusions An increased COVID-19 prevalence and mortality rate was recorded in SSc patients; moreover, the efficacy of vaccines in term of improved outcomes was less evident in SSc compared to Italian general population. This discrepancy might be explained by concomitant adverse prognostic factors: increased rate of non-responders to vaccine in SSc series, low percentage of individuals with four or more doses of vaccine, ongoing immunomodulating treatments, disease-related interstitial lung disease, and/or reduced preventive measures in the second half of pandemic. A careful monitoring of response to COVID-19 vaccines together with adequate preventive/therapeutical strategies are highly recommendable in the near course of pandemic in this frail patients' population.
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Affiliation(s)
- Clodoveo Ferri
- Rheumatology Unit, University of Modena & RE., School of Medicine, Modena, Italy
- Rheumatology Clinic ‘Madonna Dello Scoglio’ Cotronei, Crotone, Italy
| | - Vincenzo Raimondo
- Rheumatology Clinic ‘Madonna Dello Scoglio’ Cotronei, Crotone, Italy
| | - Dilia Giuggioli
- Rheumatology Unit, University of Modena & RE., School of Medicine, Modena, Italy
| | - Laura Gragnani
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Italy
| | - Serena Lorini
- MASVE Interdepartmental Hepatology Center, Department of Experimental and Clinical Medicine, University of Florence, Center for Research and Innovation CRIA-MASVE, AOU Careggi, Florence, Italy
| | | | - Silvia Laura Bosello
- Division of Rheumatology, Catholic University of the Sacred Heart, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
| | - Rosario Foti
- AOU Policlinico Vittorio Emanuele, Catania, Italy
| | | | | | | | | | - Rossella De Angelis
- Rheumatology Clinic, Department of Clinical & Molecular Sciences, Marche Polytechnic University, Ancona, Italy
| | | | | | | | - Giuseppe Murdaca
- Ospedale Policlinico S. Martino-University of Genova, Genova, Italy
| | | | | | | | | | | | - Maria De Santis
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Rheumatology and Clinical Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Carlo Selmi
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Rheumatology and Clinical Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | | | - Maurizio Caminiti
- UOD Reumatologia- Grande Ospedale Metropolitano, Reggio Calabria, Italy
| | - Massimo L'Andolina
- Rheumatology Outpatient Clinic, ASP- Vibo Valentia-Tropea Hospital, Italy
| | - Domenico Olivo
- Rheumatology Outpatient Clinic, San Giovanni di Dio Hospital, Crotone, Italy
| | - Ennio Lubrano
- Rheumatology, Università Del Molise, Campobasso, Italy
| | - Amelia Spinella
- Rheumatology Unit, University of Modena & RE., School of Medicine, Modena, Italy
| | - Federica Lumetti
- Rheumatology Unit, University of Modena & RE., School of Medicine, Modena, Italy
| | | | - Piero Ruscitti
- Rheumatology Unit, Department of Biotechnological & Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Teresa Urraro
- Rheumatology Unit, "M. Scarlato" Hospital, Scafati, Italy
| | - Marcella Visentini
- Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | | | | | - Davide Testa
- Clinical Immunology, University of Pisa, Pisa, Italy
| | | | | | | | | | - Eugenia Balestri
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Giusy Elia
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Silvia Martina Ferrari
- Department of Clinical and Experimental Medicine, University of Pisa, School of Medicine, Pisa, Italy
| | - Antonio Tonutti
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Rheumatology and Clinical Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Francesca Dall’Ara
- Child and Adolescent Neuropsychiatric Service (UONPIA) Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | | | | | | | - Vincenzo Aiello
- Rheumatology Clinic ‘Madonna Dello Scoglio’ Cotronei, Crotone, Italy
| | | | - Roberta Foti
- AOU Policlinico Vittorio Emanuele, Catania, Italy
| | - Ilenia Di Cola
- Rheumatology Unit, Department of Biotechnological & Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Enrico Fusaro
- Rheumatology Unit, Azienda Ospedaliero Universitaria Città Della Salute e Della Scienza, Torino, Italy
| | | | | | | | - Francesca Francioso
- Rheumatology Clinic, Department of Clinical & Molecular Sciences, Marche Polytechnic University, Ancona, Italy
| | - Carlo Iandoli
- University of Campania, Luigi Vanvitelli, Napoli, Italy
| | - Virginia Caira
- U.O.S. Reumatologia, Ospedale Castrovillari, Cosenza, Italy
| | - Anna Linda Zignego
- MASVE Interdepartmental Hepatology Center, Department of Experimental and Clinical Medicine, University of Florence, Center for Research and Innovation CRIA-MASVE, AOU Careggi, Florence, Italy
| | | | | | | | - Roberto Giacomelli
- Clinical and Research Section of Rheumatology and Clinical Immunology, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - Andrea Doria
- Rheumatology, University of Padova, Padova, Italy
| | - Stefano Angelo Santini
- Department of Basic, Clinical, Intensive and Perioperative Biotechnological Sciences, Catholic University School of Medicine, Rome, Italy
- Synlab Lazio, Roma, Italy
| | - Poupak Fallahi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Italy
| | | | - Alessandro Antonelli
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - for the COVID-19 & ASD Italian Study Group
- Rheumatology Unit, University of Modena & RE., School of Medicine, Modena, Italy
- Rheumatology Clinic ‘Madonna Dello Scoglio’ Cotronei, Crotone, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Italy
- MASVE Interdepartmental Hepatology Center, Department of Experimental and Clinical Medicine, University of Florence, Center for Research and Innovation CRIA-MASVE, AOU Careggi, Florence, Italy
- Department of Ospedale S. Raffaele, Milano, Italy
- Division of Rheumatology, Catholic University of the Sacred Heart, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
- AOU Policlinico Vittorio Emanuele, Catania, Italy
- Rheumatology, Sapienza-University of Rome, Roma, Italy
- Rheumatology, University of Florence, Italy
- University of Campania, Luigi Vanvitelli, Napoli, Italy
- Clinical Immunology, University of Pisa, Pisa, Italy
- Rheumatology Clinic, Department of Clinical & Molecular Sciences, Marche Polytechnic University, Ancona, Italy
- UO Reumatologia - DETO, Università di Bari, Bari, Italy
- Rheumatology, University of Padova, Padova, Italy
- Ospedale "Villa Salus", Mestre, Italy
- Ospedale Policlinico S. Martino-University of Genova, Genova, Italy
- Rheumatology, Spedali Civili di Brescia, Brescia, Italy
- ASO S. Croce e Carle, Cuneo, Italy
- Rheumatology, Policlinico San Matteo, Pavia, Italy
- U.O.C. Medicina Interna 'M.Valentini" P.O, Annunziata, Cosenza, Italy
- U.O.S. Reumatologia, Ospedale Castrovillari, Cosenza, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Rheumatology and Clinical Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
- AOR San Carlo di Potenza, Potenza, Italy
- UOD Reumatologia- Grande Ospedale Metropolitano, Reggio Calabria, Italy
- Rheumatology Outpatient Clinic, ASP- Vibo Valentia-Tropea Hospital, Italy
- Rheumatology Outpatient Clinic, San Giovanni di Dio Hospital, Crotone, Italy
- Rheumatology, Università Del Molise, Campobasso, Italy
- Rheumatology Unit, Department of Biotechnological & Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
- Rheumatology Unit, "M. Scarlato" Hospital, Scafati, Italy
- Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
- Department of Clinical and Experimental Medicine, University of Pisa, School of Medicine, Pisa, Italy
- Child and Adolescent Neuropsychiatric Service (UONPIA) Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Rheumatology Unit, Azienda Ospedaliero Universitaria Città Della Salute e Della Scienza, Torino, Italy
- U.O.T. Specialistica Ambulatoriale ASP 201, Cosenza, Italy
- Clinical and Research Section of Rheumatology and Clinical Immunology, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Basic, Clinical, Intensive and Perioperative Biotechnological Sciences, Catholic University School of Medicine, Rome, Italy
- Synlab Lazio, Roma, Italy
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Jin W, Hao W, Shi X, Fritsche LG, Salvatore M, Admon AJ, Friese CR, Mukherjee B. Using Multi-Modal Electronic Health Record Data for the Development and Validation of Risk Prediction Models for Long COVID Using the Super Learner Algorithm. J Clin Med 2023; 12:7313. [PMID: 38068365 PMCID: PMC10707399 DOI: 10.3390/jcm12237313] [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: 09/29/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Post-Acute Sequelae of COVID-19 (PASC) have emerged as a global public health and healthcare challenge. This study aimed to uncover predictive factors for PASC from multi-modal data to develop a predictive model for PASC diagnoses. METHODS We analyzed electronic health records from 92,301 COVID-19 patients, covering medical phenotypes, medications, and lab results. We used a Super Learner-based prediction approach to identify predictive factors. We integrated the model outputs into individual and composite risk scores and evaluated their predictive performance. RESULTS Our analysis identified several factors predictive of diagnoses of PASC, including being overweight/obese and the use of HMG CoA reductase inhibitors prior to COVID-19 infection, and respiratory system symptoms during COVID-19 infection. We developed a composite risk score with a moderate discriminatory ability for PASC (covariate-adjusted AUC (95% confidence interval): 0.66 (0.63, 0.69)) by combining the risk scores based on phenotype and medication records. The combined risk score could identify 10% of individuals with a 2.2-fold increased risk for PASC. CONCLUSIONS We identified several factors predictive of diagnoses of PASC and integrated the information into a composite risk score for PASC prediction, which could contribute to the identification of individuals at higher risk for PASC and inform preventive efforts.
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Affiliation(s)
- Weijia Jin
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; (W.J.)
- Center for Precision Health Data Science, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wei Hao
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; (W.J.)
- Center for Precision Health Data Science, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xu Shi
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; (W.J.)
| | - Lars G. Fritsche
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; (W.J.)
| | - Maxwell Salvatore
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; (W.J.)
- Center for Precision Health Data Science, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew J. Admon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- VA Center for Clinical Management Research, Ann Arbor, MI 48109, USA
- LTC Charles S. Kettles VA Medical Center, Ann Arbor, MI 48109, USA
| | - Christopher R. Friese
- School of Nursing, University of Michigan, Ann Arbor, MI 48109, USA
- Institute for Healthcare Policy and Innovation, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bhramar Mukherjee
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; (W.J.)
- Center for Precision Health Data Science, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48109, USA
- Institute for Healthcare Policy and Innovation, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
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Xu J, Luo C, Huang L, Xiao X, Liu L, Yang Z. Clinical Efficacy and Safety Evaluation of Ceftazidime-Avibactam in the Treatment of Klebsiella pneumoniae Infection: A Retrospective Analysis from a Hospital in China. Infect Drug Resist 2023; 16:7227-7237. [PMID: 38023408 PMCID: PMC10656859 DOI: 10.2147/idr.s435882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/04/2023] [Indexed: 12/01/2023] Open
Abstract
Background Ceftazidime-avibactam (CAZ-AVI) is a new cephalosporin/β-lactamase inhibitor combination that received clinical approval in China in 2019. This study aims to investigate the efficacy and safety of CAZ-AVI in the treatment of Klebsiella pneumoniae (KP) infection in a hospital, and differences in efficacy among various infection sites and between monotherapy and combination therapy, providing valuable insights for its further application. Methods Patients who used CAZ-AVI between January 2019 and April 2023 were identified through the hospital information system. Demographic information, details of the infection site, KP strain's drug sensitivity report, treatment duration, combination therapies, adverse drug reactions (ADR), and 28-day survival were recorded. Clinical and microbiological efficacies were analyzed using SPSS 23.0 software to compare different infection sites and combination therapies. Results The overall effective clinical response (CR) rate of CAZ-AVI against KP infection was 62.13%, with a favorable microbial response (MR) rate was 65.68% and a 28-day survival rate was 63.91%. No significant difference occurred in effective CR and 28-day survival rate among different infection sites (P = 0.709 and 0.862, respectively). The favorable MR rate for abdominal infections was slightly lower than that for other sites of infection (P = 0.021). No significant differences in effective CR, favorable MR, and 28-day survival between monotherapy and combination therapy were present (P values were 0.649, 0.123, and 0.280, respectively). The incidence of ADR was 1.78%, including increased creatinine, elevated transaminase, hematuria, and thrombocytopenia. Conclusion CAZ-AVI demonstrates good clinical efficacy and safety in the treatment of KP infections. The clinical efficacy of CAZ-AVI was similar across different infection sites, and combination therapy did not show an advantage over monotherapy. Further studies are warranted. It should be noted that CAZ-AVI may induce thrombocytopenia and hematuria.
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Affiliation(s)
- Jia Xu
- Department of Clinical Pharmacy, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, 410016, People’s Republic of China
| | - Chengjia Luo
- Department of Clinical Pharmacy, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, 410016, People’s Republic of China
| | - Liang Huang
- Department of Rehabilitation, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, 410016, People’s Republic of China
| | - Xi Xiao
- Department of Clinical Laboratory, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, 410016, People’s Republic of China
| | - Ling Liu
- Department of Clinical Pharmacy, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, 410016, People’s Republic of China
| | - Zhiling Yang
- Department of Clinical Pharmacy, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, 410016, People’s Republic of China
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Jones RP, Ponomarenko A. COVID-19-Related Age Profiles for SARS-CoV-2 Variants in England and Wales and States of the USA (2020 to 2022): Impact on All-Cause Mortality. Infect Dis Rep 2023; 15:600-634. [PMID: 37888139 PMCID: PMC10606787 DOI: 10.3390/idr15050058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 10/28/2023] Open
Abstract
Since 2020, COVID-19 has caused serious mortality around the world. Given the ambiguity in establishing COVID-19 as the direct cause of death, we first investigate the effects of age and sex on all-cause mortality during 2020 and 2021 in England and Wales. Since infectious agents have their own unique age profile for death, we use a 9-year time series and several different methods to adjust single-year-of-age deaths in England and Wales during 2019 (the pre-COVID-19 base year) to a pathogen-neutral single-year-of-age baseline. This adjusted base year is then used to confirm the widely reported higher deaths in males for most ages above 43 in both 2020 and 2021. During 2020 (+COVID-19 but no vaccination), both male and female population-adjusted deaths significantly increased above age 35. A significant reduction in all-cause mortality among both males and females aged 75+ could be demonstrated in 2021 during the widespread COVID-19 vaccination period; however, deaths below age 75 progressively increased. This finding arises from a mix of vaccination coverage and year-of-age profiles of deaths for the different SARS-CoV-2 variants. In addition, specific effects of age around puberty were demonstrated, where females had higher deaths than males. There is evidence that year-of-birth cohorts may also be involved, indicating that immune priming to specific pathogen outbreaks in the past may have led to lower deaths for some birth cohorts. To specifically identify the age profile for the COVID-19 variants from 2020 to 2023, we employ the proportion of total deaths at each age that are potentially due to or 'with' COVID-19. The original Wuhan strain and the Alpha variant show somewhat limited divergence in the age profile, with the Alpha variant shifting to a moderately higher proportion of deaths below age 84. The Delta variant specifically targeted individuals below age 65. The Omicron variants showed a significantly lower proportion of overall mortality, with a markedly higher relative proportion of deaths above age 65, steeply increasing with age to a maximum around 100 years of age. A similar age profile for the variants can be seen in the age-banded deaths in US states, although they are slightly obscured by using age bands rather than single years of age. However, the US data shows that higher male deaths are greatly dependent on age and the COVID variant. Deaths assessed to be 'due to' COVID-19 (as opposed to 'involving' COVID-19) in England and Wales were especially overestimated in 2021 relative to the change in all-cause mortality. This arose as a by-product of an increase in COVID-19 testing capacity in late 2020. Potential structure-function mechanisms for the age-specificity of SARS-CoV-2 variants are discussed, along with potential roles for small noncoding RNAs (miRNAs). Using data from England, it is possible to show that the unvaccinated do indeed have a unique age profile for death from each variant and that vaccination alters the shape of the age profile in a manner dependent on age, sex, and the variant. The question is posed as to whether vaccines based on different variants carry a specific age profile.
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Affiliation(s)
| | - Andrey Ponomarenko
- Department of Biophysics, Informatics and Medical Instrumentation, Odessa National Medical University, Valikhovsky Lane 2, 65082 Odessa, Ukraine
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Gatti G, Brandolini M, Mancini A, Taddei F, Zannoli S, Dirani G, Manera M, Arfilli V, Denicolò A, Marzucco A, Montanari MS, Zaghi I, Guerra M, Tennina R, Marino MM, Grumiro L, Cricca M, Sambri V. Genomic and Temporal Analysis of Deletions Correlated to qRT-PCR Dropout in N Gene in Alpha, Delta and Omicron Variants. Viruses 2023; 15:1630. [PMID: 37631974 PMCID: PMC10458892 DOI: 10.3390/v15081630] [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: 07/05/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Since the first SARS-CoV-2 outbreak, mutations such as single nucleotide polymorphisms (SNPs) and insertion/deletions (INDELs) have changed and characterized the viral genome sequence, structure and protein folding leading to the onset of new variants. The presence of those alterations challenges not only the clinical field but also the diagnostic demand due to failures in gene detection or incompleteness of polymerase chain reaction (PCR) results. In particular, the analysis of understudied genes such as N and the investigation through whole-genome next generation sequencing (WG-NGS) of regions more prone to mutate can help in the identification of new or reacquired mutations, with the aim of designing robust and long-lasting primers. In 48 samples of SARS-CoV-2 (including Alpha, Delta and Omicron variants), a lack of N gene amplification was observed in the genomes analyzed through WG-NGS. Three gene regions were detected hosting the highest number of SNPs and INDELs. In several cases, the latter can interfere deeply with both the sensitivity of diagnostic methodologies and the final protein folding. The monitoring over time of the viral evolution and the reacquisition among different variants of the same mutations or different alterations within the same genomic positions can be relevant to avoid unnecessary consumption of resources.
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Affiliation(s)
- Giulia Gatti
- Department of Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, 40138 Bologna, Italy; (G.G.); (M.B.); (M.C.)
| | - Martina Brandolini
- Department of Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, 40138 Bologna, Italy; (G.G.); (M.B.); (M.C.)
| | - Andrea Mancini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Francesca Taddei
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Silvia Zannoli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Giorgio Dirani
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Martina Manera
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Valentina Arfilli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Agnese Denicolò
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Anna Marzucco
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Maria Sofia Montanari
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Irene Zaghi
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Massimiliano Guerra
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Rita Tennina
- Unit of Laboratory Medicine—Local Health Authority 1 Complex Operative Unit, 67051 L’Aquila, Italy
| | - Maria Michela Marino
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Laura Grumiro
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Monica Cricca
- Department of Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, 40138 Bologna, Italy; (G.G.); (M.B.); (M.C.)
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
| | - Vittorio Sambri
- Department of Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, 40138 Bologna, Italy; (G.G.); (M.B.); (M.C.)
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522 Cesena, Italy; (A.M.); (F.T.); (S.Z.); (G.D.); (M.M.); (V.A.); (A.D.); (A.M.); (M.S.M.); (I.Z.); (M.G.); (L.G.)
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Wilson GN. A Clinical Qualification Protocol Highlights Overlapping Genomic Influences and Neuro-Autonomic Mechanisms in Ehlers-Danlos and Long COVID-19 Syndromes. Curr Issues Mol Biol 2023; 45:6003-6023. [PMID: 37504295 PMCID: PMC10378515 DOI: 10.3390/cimb45070379] [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: 06/05/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
A substantial fraction of the 15% with double-jointedness or hypermobility have the traditionally ascertained joint-skeletal, cutaneous, and cardiovascular symptoms of connective tissue dysplasia and its particular manifestation as Ehlers-Danlos syndrome (EDS). The holistic ascertainment of 120 findings in 1261 EDS patients added neuro-autonomic symptoms like headaches, muscle weakness, brain fog, chronic fatigue, dyspnea, and bowel irregularity to those of arthralgia and skin laxity, 15 of these symptoms shared with those of post-infectious SARS-CoV-2 (long COVID-19). Underlying articulo-autonomic mechanisms guided a clinical qualification protocol that qualified DNA variants in 317 genes as having diagnostic utility for EDS, six of them identical (F2-LIFR-NLRP3-STAT1-T1CAM1-TNFRSF13B) and eighteen similar to those modifying COVID-19 severity/EDS, including ADAMTS13/ADAMTS2-C3/C1R-IKBKG/IKBKAP-PIK3C3/PIK3R1-POLD4/POLG-TMPRSS2/TMPRSS6-WNT3/WNT10A. Also, contributing to EDS and COVID-19 severity were forty and three genes, respectively, impacting mitochondrial functions as well as parts of an overlapping gene network, or entome, that are hypothesized to mediate the cognitive-behavioral, neuro-autonomic, and immune-inflammatory alterations of connective tissue in these conditions. The further characterization of long COVID-19 natural history and genetic predisposition will be necessary before these parallels to EDS can be carefully delineated and translated into therapies.
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Affiliation(s)
- Golder N Wilson
- Department of Pediatrics, Texas Tech University Health Sciences Center, Lubbock, and KinderGenome Genetics Private Practice, 5347 W Mockingbird, Dallas, TX 75209, USA
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Farooqi R, Kooner JS, Zhang W. Associations between polygenic risk score and covid-19 susceptibility and severity across ethnic groups: UK Biobank analysis. BMC Med Genomics 2023; 16:150. [PMID: 37386504 PMCID: PMC10311902 DOI: 10.1186/s12920-023-01584-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND COVID-19 manifests with huge heterogeneity in susceptibility and severity outcomes. UK Black Asian and Minority Ethnic (BAME) groups have demonstrated disproportionate burdens. Some variability remains unexplained, suggesting potential genetic contribution. Polygenic Risk Scores (PRS) can determine genetic predisposition to disease based on Single Nucleotide Polymorphisms (SNPs) within the genome. COVID-19 PRS analyses within non-European samples are extremely limited. We applied a multi-ethnic PRS to a UK-based cohort to understand genetic contribution to COVID-19 variability. METHODS We constructed two PRS for susceptibility and severity outcomes based on leading risk-variants from the COVID-19 Host Genetics Initiative. Scores were applied to 447,382 participants from the UK-Biobank. Associations with COVID-19 outcomes were assessed using binary logistic regression and discriminative power was validated using incremental area under receiver operating curve (ΔAUC). Variance explained was compared between ethnic groups via incremental pseudo-R2 (ΔR2). RESULTS Compared to those at low genetic risk, those at high risk had a significantly greater risk of severe COVID-19 for White (odds ratio [OR] 1.57, 95% confidence interval [CI] 1.42-1.74), Asian (OR 2.88, 95% CI 1.63-5.09) and Black (OR 1.98, 95% CI 1.11-3.53) ethnic groups. Severity PRS performed best within Asian (ΔAUC 0.9%, ΔR2 0.98%) and Black (ΔAUC 0.6%, ΔR2 0.61%) cohorts. For susceptibility, higher genetic risk was significantly associated with COVID-19 infection risk for the White cohort (OR 1.31, 95% CI 1.26-1.36), but not for Black or Asian groups. CONCLUSIONS Significant associations between PRS and COVID-19 outcomes were elicited, establishing a genetic basis for variability in COVID-19. PRS showed utility in identifying high-risk individuals. The multi-ethnic approach allowed applicability of PRS to diverse populations, with the severity model performing well within Black and Asian cohorts. Further studies with larger sample sizes of non-White samples are required to increase statistical power and better assess impacts within BAME populations.
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Affiliation(s)
- Raabia Farooqi
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK.
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, W2 1PG, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
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Luo H, Chen J, Jiang Q, Yu Y, Yang M, Luo Y, Wang X. Comprehensive DNA methylation profiling of COVID-19 and hepatocellular carcinoma to identify common pathogenesis and potential therapeutic targets. Clin Epigenetics 2023; 15:100. [PMID: 37309005 DOI: 10.1186/s13148-023-01515-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND & AIMS The effects of SARS-CoV-2 infection can be more complex and severe in patients with hepatocellular carcinoma (HCC) as compared to other cancers. This is due to several factors, including pre-existing conditions such as viral hepatitis and cirrhosis, which are commonly associated with HCC. METHODS We conducted an analysis of epigenomics in SARS-CoV-2 infection and HCC patients, and identified common pathogenic mechanisms using weighted gene co-expression network analysis (WGCNA) and other analyses. Hub genes were identified and analyzed using LASSO regression. Additionally, drug candidates and their binding modes to key macromolecular targets of COVID-19 were identified using molecular docking. RESULTS The epigenomic analysis of the relationship between SARS-CoV-2 infection and HCC patients revealed that the co-pathogenesis was closely linked to immune response, particularly T cell differentiation, regulation of T cell activation and monocyte differentiation. Further analysis indicated that CD4+ T cells and monocytes play essential roles in the immunoreaction triggered by both conditions. The expression levels of hub genes MYLK2, FAM83D, STC2, CCDC112, EPHX4 and MMP1 were strongly correlated with SARS-CoV-2 infection and the prognosis of HCC patients. In our study, mefloquine and thioridazine were identified as potential therapeutic agents for COVID-19 in combined with HCC. CONCLUSIONS In this research, we conducted an epigenomics analysis to identify common pathogenetic processes between SARS-CoV-2 infection and HCC patients, providing new insights into the pathogenesis and treatment of HCC patients infected with SARS-CoV-2.
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Affiliation(s)
- Huiyan Luo
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jixin Chen
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiyin Jiang
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yifan Yu
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Miaolun Yang
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuehua Luo
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiongwen Wang
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
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Liu Z, Song L, Chen J, Zhou Y, Wang Y, Tang L, Li Y. Causal associations between chronic hepatitis B and COVID-19 in East Asian populations. Virol J 2023; 20:109. [PMID: 37264390 DOI: 10.1186/s12985-023-02081-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/25/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND The relationship between chronic hepatitis B (CHB) and Coronavirus disease 2019 (COVID-19) has been inconsistent in traditional observational studies. METHODS We explored the total causal and direct causal associations between CHB and the three COVID-19 outcomes using univariate and multivariate Mendelian randomization (MR) analyses, respectively. Genome-wide association study datasets for CHB and COVID-19 were obtained from the Japan Biobank and the COVID-19 Host Genetics Initiative, respectively. RESULTS Univariate MR analysis showed that CHB increased the risk of SARS-CoV-2 infection (OR = 1.04, 95% CI 1.01-1.07, P = 3.39E-03), hospitalized COVID-19 (OR = 1.10, 95% CI 1.06-1.13, P = 7.31E-08), and severe COVID-19 (OR = 1.16, 95%CI 1.08-1.26, P = 1.43E-04). A series of subsequent sensitivity analyses ensured the stability and reliability of these results. In multivariable MR analyses adjusting for type 2 diabetes, body mass index, basophil count, and smoking, genetically related CHB is still positively associated with increased risk of SARS-CoV-2 infection (OR = 1.06, 95% CI 1.02-1.11, P = 1.44E-03) and hospitalized COVID-19 (OR = 1.12, 95% CI 1.07-1.16, P = 5.13E-07). However, the causal link between CHB and severe COVID-19 was attenuated after adjustment for the above variables. In addition, the MR analysis did not support the causal effect of COVID-19 on CHB. CONCLUSIONS This study provides evidence that CHB increases COVID-19 susceptibility and severity among individuals of East Asian ancestry.
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Affiliation(s)
- Zhenguo Liu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, No. 1838 North Guangzhou Avenue, Guangzhou, 510515, China
| | - Linnan Song
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, No. 1838 North Guangzhou Avenue, Guangzhou, 510515, China
| | - Junling Chen
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, No. 1838 North Guangzhou Avenue, Guangzhou, 510515, China
| | - Yongjun Zhou
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, No. 1838 North Guangzhou Avenue, Guangzhou, 510515, China
| | - Yuhao Wang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, No. 1838 North Guangzhou Avenue, Guangzhou, 510515, China
| | - Libo Tang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, No. 1838 North Guangzhou Avenue, Guangzhou, 510515, China.
| | - Yongyin Li
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, No. 1838 North Guangzhou Avenue, Guangzhou, 510515, China.
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Abstract
Autoimmune diseases display a high degree of comorbidity within individuals and families, suggesting shared risk factors. Over the past 15 years, genome-wide association studies have established the polygenic basis of these common conditions and revealed widespread sharing of genetic effects, indicative of a shared immunopathology. Despite ongoing challenges in determining the precise genes and molecular consequences of these risk variants, functional experiments and integration with multimodal genomic data are providing valuable insights into key immune cells and pathways driving these diseases, with potential therapeutic implications. Moreover, genetic studies of ancient populations are shedding light on the contribution of pathogen-driven selection pressures to the increased prevalence of autoimmune disease. This Review summarizes the current understanding of autoimmune disease genetics, including shared effects, mechanisms, and evolutionary origins.
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Affiliation(s)
- Adil Harroud
- Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
- The Neuro (Montreal Neurological Institute and Hospital), McGill University, Montréal, Quebec, Canada
| | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
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Gonzalez-Garcia P, Fiorillo Moreno O, Zarate Peñata E, Calderon-Villalba A, Pacheco Lugo L, Acosta Hoyos A, Villarreal Camacho JL, Navarro Quiroz R, Pacheco Londoño L, Aroca Martinez G, Moares N, Gabucio A, Fernandez-Ponce C, Garcia-Cozar F, Navarro Quiroz E. From Cell to Symptoms: The Role of SARS-CoV-2 Cytopathic Effects in the Pathogenesis of COVID-19 and Long COVID. Int J Mol Sci 2023; 24:ijms24098290. [PMID: 37175995 PMCID: PMC10179575 DOI: 10.3390/ijms24098290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) infection triggers various events from molecular to tissue level, which in turn is given by the intrinsic characteristics of each patient. Given the molecular diversity characteristic of each cellular phenotype, the possible cytopathic, tissue and clinical effects are difficult to predict, which determines the heterogeneity of COVID-19 symptoms. The purpose of this article is to provide a comprehensive review of the cytopathic effects of SARS-CoV-2 on various cell types, focusing on the development of COVID-19, which in turn may lead, in some patients, to a persistence of symptoms after recovery from the disease, a condition known as long COVID. We describe the molecular mechanisms underlying virus-host interactions, including alterations in protein expression, intracellular signaling pathways, and immune responses. In particular, the article highlights the potential impact of these cytopathies on cellular function and clinical outcomes, such as immune dysregulation, neuropsychiatric disorders, and organ damage. The article concludes by discussing future directions for research and implications for the management and treatment of COVID-19 and long COVID.
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Affiliation(s)
| | - Ornella Fiorillo Moreno
- Clínica Iberoamerica, Barranquilla 080001, Colombia
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
| | - Eloina Zarate Peñata
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
| | | | - Lisandro Pacheco Lugo
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
| | - Antonio Acosta Hoyos
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
| | | | - Roberto Navarro Quiroz
- Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona, Spanish National Research Council, 08028 Barcelona, Spain
| | | | - Gustavo Aroca Martinez
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
- School of Medicine, Universidad del Norte, Barranquilla 080001, Colombia
| | - Noelia Moares
- Department of Biomedicine, Biotechnology and Public Health, Faculty of Medicine, University of Cadiz, 11003 Cádiz, Spain
| | - Antonio Gabucio
- Department of Biomedicine, Biotechnology and Public Health, Faculty of Medicine, University of Cadiz, 11003 Cádiz, Spain
| | - Cecilia Fernandez-Ponce
- Institute of Biomedical Research Cadiz (INIBICA), 11009 Cádiz, Spain
- Department of Biomedicine, Biotechnology and Public Health, Faculty of Medicine, University of Cadiz, 11003 Cádiz, Spain
| | - Francisco Garcia-Cozar
- Institute of Biomedical Research Cadiz (INIBICA), 11009 Cádiz, Spain
- Department of Biomedicine, Biotechnology and Public Health, Faculty of Medicine, University of Cadiz, 11003 Cádiz, Spain
| | - Elkin Navarro Quiroz
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
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Yoo S, Garg E, Elliott LT, Hung RJ, Halevy AR, Brooks JD, Bull SB, Gagnon F, Greenwood C, Lawless JF, Paterson AD, Sun L, Zawati MH, Lerner-Ellis J, Abraham R, Birol I, Bourque G, Garant JM, Gosselin C, Li J, Whitney J, Thiruvahindrapuram B, Herbrick JA, Lorenti M, Reuter MS, Adeoye OO, Liu S, Allen U, Bernier FP, Biggs CM, Cheung AM, Cowan J, Herridge M, Maslove DM, Modi BP, Mooser V, Morris SK, Ostrowski M, Parekh RS, Pfeffer G, Suchowersky O, Taher J, Upton J, Warren RL, Yeung R, Aziz N, Turvey SE, Knoppers BM, Lathrop M, Jones S, Scherer SW, Strug LJ. HostSeq: a Canadian whole genome sequencing and clinical data resource. BMC Genom Data 2023; 24:26. [PMID: 37131148 PMCID: PMC10152008 DOI: 10.1186/s12863-023-01128-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/22/2023] [Indexed: 05/04/2023] Open
Abstract
HostSeq was launched in April 2020 as a national initiative to integrate whole genome sequencing data from 10,000 Canadians infected with SARS-CoV-2 with clinical information related to their disease experience. The mandate of HostSeq is to support the Canadian and international research communities in their efforts to understand the risk factors for disease and associated health outcomes and support the development of interventions such as vaccines and therapeutics. HostSeq is a collaboration among 13 independent epidemiological studies of SARS-CoV-2 across five provinces in Canada. Aggregated data collected by HostSeq are made available to the public through two data portals: a phenotype portal showing summaries of major variables and their distributions, and a variant search portal enabling queries in a genomic region. Individual-level data is available to the global research community for health research through a Data Access Agreement and Data Access Compliance Office approval. Here we provide an overview of the collective project design along with summary level information for HostSeq. We highlight several statistical considerations for researchers using the HostSeq platform regarding data aggregation, sampling mechanism, covariate adjustment, and X chromosome analysis. In addition to serving as a rich data source, the diversity of study designs, sample sizes, and research objectives among the participating studies provides unique opportunities for the research community.
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Affiliation(s)
- S Yoo
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Ottawa, Ottawa, ON, Canada
| | - E Garg
- Simon Fraser University, Burnaby, BC, Canada
| | - L T Elliott
- Simon Fraser University, Burnaby, BC, Canada
| | - R J Hung
- University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - A R Halevy
- The Hospital for Sick Children, Toronto, ON, Canada
| | - J D Brooks
- University of Toronto, Toronto, ON, Canada
| | - S B Bull
- University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - F Gagnon
- University of Toronto, Toronto, ON, Canada
| | - Cmt Greenwood
- McGill University, Montreal, QC, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - J F Lawless
- University of Waterloo, Waterloo, ON, Canada
| | - A D Paterson
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - L Sun
- University of Toronto, Toronto, ON, Canada
| | | | - J Lerner-Ellis
- University of Toronto, Toronto, ON, Canada
- Sinai Health System, Toronto, ON, Canada
| | - Rjs Abraham
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - I Birol
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - G Bourque
- McGill University, Montreal, QC, Canada
| | - J-M Garant
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - C Gosselin
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - J Li
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - J Whitney
- The Hospital for Sick Children, Toronto, ON, Canada
| | | | - J-A Herbrick
- The Hospital for Sick Children, Toronto, ON, Canada
| | - M Lorenti
- The Hospital for Sick Children, Toronto, ON, Canada
| | - M S Reuter
- The Hospital for Sick Children, Toronto, ON, Canada
| | - O O Adeoye
- The Hospital for Sick Children, Toronto, ON, Canada
| | - S Liu
- The Hospital for Sick Children, Toronto, ON, Canada
| | - U Allen
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - F P Bernier
- University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital, Calgary, AB, Canada
| | - C M Biggs
- University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital, Vancouver, BC, Canada
- St. Paul's Hospital, Vancouver, BC, Canada
| | - A M Cheung
- University Health Network, Toronto, ON, Canada
| | - J Cowan
- University of Ottawa, Ottawa, ON, Canada
- The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - M Herridge
- University Health Network, Toronto, ON, Canada
| | | | - B P Modi
- BC Children's Hospital, Vancouver, BC, Canada
| | - V Mooser
- McGill University, Montreal, QC, Canada
| | - S K Morris
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - M Ostrowski
- University of Toronto, Toronto, ON, Canada
- St. Michael's Hospital, Unity Health, Toronto, ON, Canada
| | - R S Parekh
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
- Women's College Hospital, Toronto, ON, Canada
| | - G Pfeffer
- University of Calgary, Calgary, AB, Canada
| | | | - J Taher
- University of Toronto, Toronto, ON, Canada
- Sinai Health System, Toronto, ON, Canada
| | - J Upton
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - R L Warren
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Rsm Yeung
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - N Aziz
- The Hospital for Sick Children, Toronto, ON, Canada
| | - S E Turvey
- University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital, Vancouver, BC, Canada
| | | | - M Lathrop
- McGill University, Montreal, QC, Canada
| | - Sjm Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - S W Scherer
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - L J Strug
- The Hospital for Sick Children, Toronto, ON, Canada.
- University of Toronto, Toronto, ON, Canada.
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41
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Li Y, Yu Q, Huang R, Chen H, Ren H, Ma L, He Y, Li W. SARS-CoV-2 SUD2 and Nsp5 Conspire to Boost Apoptosis of Respiratory Epithelial Cells via an Augmented Interaction with the G-Quadruplex of BclII. mBio 2023; 14:e0335922. [PMID: 36853058 PMCID: PMC10127692 DOI: 10.1128/mbio.03359-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/09/2023] [Indexed: 03/01/2023] Open
Abstract
The molecular mechanisms underlying how SUD2 recruits other proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to exert its G-quadruplex (G4)-dependent pathogenic function is unknown. Herein, Nsp5 was singled out as a binding partner of the SUD2-N+M domains (SUD2core) with high affinity, through the surface located crossing these two domains. Biochemical and fluorescent assays demonstrated that this complex also formed in the nucleus of living host cells. Moreover, the SUD2core-Nsp5 complex displayed significantly enhanced selective binding affinity for the G4 structure in the BclII promoter than did SUD2core alone. This increased stability exhibited by the tertiary complex was rationalized by AlphaFold2 and molecular dynamics analysis. In line with these molecular interactions, downregulation of BclII and subsequent augmented apoptosis of respiratory cells were both observed. These results provide novel information and a new avenue to explore therapeutic strategies targeting SARS-CoV-2. IMPORTANCE SUD2, a unique protein domain closely related to the pathogenesis of SARS-CoV-2, has been reported to bind with the G-quadruplex (G4), a special noncanonical DNA structure endowed with important functions in regulating gene expression. However, the interacting partner of SUD2, among other SARS-CoV-2 Nsps, and the resulting functional consequences remain unknown. Here, a stable complex formed between SUD2 and Nsp5 was fully characterized both in vitro and in host cells. Moreover, this complex had a significantly enhanced binding affinity specifically targeting the Bcl2G4 in the promoter region of the antiapoptotic gene BclII, compared with SUD2 alone. In respiratory epithelial cells, the SUD2-Nsp5 complex promoted BclII-mediated apoptosis in a G4-dependent manner. These results reveal fresh information about matched multicomponent interactions, which can be parlayed to develop new therapeutics for future relevant viral disease.
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Affiliation(s)
- Ying Li
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, China
- Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Quanwei Yu
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, China
- Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ridong Huang
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, China
- Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hai Chen
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, China
- Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hequan Ren
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, China
- Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lingling Ma
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, China
- Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yang He
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, China
- Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, China
- Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
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42
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Wolday D, Fung CYJ, Morgan G, Casalino S, Frangione E, Taher J, Lerner-Ellis JP. HLA Variation and SARS-CoV-2 Specific Antibody Response. Viruses 2023; 15:906. [PMID: 37112884 PMCID: PMC10143129 DOI: 10.3390/v15040906] [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: 03/15/2023] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Differences in SARS-CoV-2-specific immune responses have been observed between individuals following natural infection or vaccination. In addition to already known factors, such as age, sex, COVID-19 severity, comorbidity, vaccination status, hybrid immunity, and duration of infection, inter-individual variations in SARS-CoV-2 immune responses may, in part, be explained by structural differences brought about by genetic variation in the human leukocyte antigen (HLA) molecules responsible for the presentation of SARS-CoV-2 antigens to T effector cells. While dendritic cells present peptides with HLA class I molecules to CD8+ T cells to induce cytotoxic T lymphocyte responses (CTLs), they present peptides with HLA class II molecules to T follicular helper cells to induce B cell differentiation followed by memory B cell and plasma cell maturation. Plasma cells then produce SARS-CoV-2-specific antibodies. Here, we review published data linking HLA genetic variation or polymorphisms with differences in SARS-CoV-2-specific antibody responses. While there is evidence that heterogeneity in antibody response might be related to HLA variation, there are conflicting findings due in part to differences in study designs. We provide insight into why more research is needed in this area. Elucidating the genetic basis of variability in the SARS-CoV-2 immune response will help to optimize diagnostic tools and lead to the development of new vaccines and therapeutics against SARS-CoV-2 and other infectious diseases.
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Affiliation(s)
- Dawit Wolday
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1Z5, Canada; (C.Y.J.F.); (G.M.); (S.C.); (E.F.); (J.T.)
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1Z5, Canada
| | - Chun Yiu Jordan Fung
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1Z5, Canada; (C.Y.J.F.); (G.M.); (S.C.); (E.F.); (J.T.)
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1Z5, Canada
| | - Gregory Morgan
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1Z5, Canada; (C.Y.J.F.); (G.M.); (S.C.); (E.F.); (J.T.)
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1Z5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1Z5, Canada
| | - Selina Casalino
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1Z5, Canada; (C.Y.J.F.); (G.M.); (S.C.); (E.F.); (J.T.)
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1Z5, Canada
| | - Erika Frangione
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1Z5, Canada; (C.Y.J.F.); (G.M.); (S.C.); (E.F.); (J.T.)
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1Z5, Canada
| | - Jennifer Taher
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1Z5, Canada; (C.Y.J.F.); (G.M.); (S.C.); (E.F.); (J.T.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1Z5, Canada
| | - Jordan P. Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1Z5, Canada; (C.Y.J.F.); (G.M.); (S.C.); (E.F.); (J.T.)
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON M5G 1Z5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1Z5, Canada
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43
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Scaramuzzo G, Nucera F, Asmundo A, Messina R, Mari M, Montanaro F, Johansen MD, Monaco F, Fadda G, Tuccari G, Hansbro NG, Hansbro PM, Hansel TT, Adcock IM, David A, Kirkham P, Caramori G, Volta CA, Spadaro S. Cellular and molecular features of COVID-19 associated ARDS: therapeutic relevance. J Inflamm (Lond) 2023; 20:11. [PMID: 36941580 PMCID: PMC10027286 DOI: 10.1186/s12950-023-00333-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/08/2023] [Indexed: 03/23/2023] Open
Abstract
The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection can be asymptomatic or cause a disease (COVID-19) characterized by different levels of severity. The main cause of severe COVID-19 and death is represented by acute (or acute on chronic) respiratory failure and acute respiratory distress syndrome (ARDS), often requiring hospital admission and ventilator support.The molecular pathogenesis of COVID-19-related ARDS (by now termed c-ARDS) is still poorly understood. In this review we will discuss the genetic susceptibility to COVID-19, the pathogenesis and the local and systemic biomarkers correlated with c-ARDS and the therapeutic options that target the cell signalling pathways of c-ARDS.
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Affiliation(s)
- Gaetano Scaramuzzo
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant’Anna, Ferrara, Italy
| | - Francesco Nucera
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Alessio Asmundo
- Medicina Legale, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Roberto Messina
- Intensive Care Unit, Dipartimento di Patologia Umana e dell’Età Evolutiva Gaetano Barresi, Università di Messina, Messina, Italy
| | - Matilde Mari
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant’Anna, Ferrara, Italy
| | - Federica Montanaro
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant’Anna, Ferrara, Italy
| | - Matt D. Johansen
- Centre for Inflammation, School of Life Sciences, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW Australia
| | - Francesco Monaco
- Chirurgia Toracica, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Guido Fadda
- Section of Pathological Anatomy, Department of Human Pathology of Adult and Developmental Age “Gaetano Barresi”, University of Messina, Messina, Italy
| | - Giovanni Tuccari
- Section of Pathological Anatomy, Department of Human Pathology of Adult and Developmental Age “Gaetano Barresi”, University of Messina, Messina, Italy
| | - Nicole G. Hansbro
- Centre for Inflammation, School of Life Sciences, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW Australia
| | - Philip M. Hansbro
- Centre for Inflammation, School of Life Sciences, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW Australia
| | - Trevor T. Hansel
- Medical Research Council and Asthma, UK Centre in Allergic Mechanisms of Asthma, London, UK
| | - Ian M. Adcock
- Airway Disease Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Antonio David
- Intensive Care Unit, Dipartimento di Patologia Umana e dell’Età Evolutiva Gaetano Barresi, Università di Messina, Messina, Italy
| | - Paul Kirkham
- Department of Biomedical Sciences, Faculty of Sciences and Engineering, University of Wolverhampton, West Midlands, Wolverhampton, UK
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Carlo Alberto Volta
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant’Anna, Ferrara, Italy
| | - Savino Spadaro
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant’Anna, Ferrara, Italy
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Abstract
OBJECTIVE Interindividual variability in the clinical progression of COVID-19 may be explained by host genetics. Emerging literature supports a potential inherited predisposition to severe forms of COVID-19. Demographic and inflammatory characteristics of COVID-19 suggest that acquired hematologic mutations leading to clonal hematopoiesis (CH) may further increase vulnerability to adverse sequelae. This review summarizes the available literature examining genetic predispositions to severe COVID-19 and describes how these findings could eventually be used to improve its clinical management. DATA SOURCES A PubMed literature search was performed. STUDY SELECTION Studies examining the significance of inherited genetic variation or acquired CH mutations in severe COVID-19 were selected for inclusion. DATA EXTRACTION Relevant genetic association data and aspects of study design were qualitatively assessed and narratively synthesized. DATA SYNTHESIS Genetic variants affecting inflammatory responses may increase susceptibility to severe COVID-19. Genome-wide association studies and candidate gene approaches have identified a list of inherited mutations, which likely alter cytokine and interferon secretion, and lung-specific mechanisms of immunity in COVID-19. The potential role of CH in COVID-19 is more uncertain at present; however, the available evidence suggests that the various types of acquired mutations and their differential influence on immune cell function must be carefully considered. CONCLUSIONS The current literature supports the hypothesis that host genetic factors affect vulnerability to severe COVID-19. Further research is required to confirm the full scope of relevant variants and the causal mechanisms underlying these associations. Clinical approaches, which consider the genetic basis of interindividual variability in COVID-19 and potentially other causes of critical illness, could optimize hospital resource allocation, predict responsiveness to treatment, identify more efficacious drug targets, and ultimately improve outcomes.
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Cappadona C, Rimoldi V, Paraboschi EM, Asselta R. Genetic susceptibility to severe COVID-19. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 110:105426. [PMID: 36934789 PMCID: PMC10022467 DOI: 10.1016/j.meegid.2023.105426] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the coronavirus disease 2019 (COVID-19) pandemic. Clinical manifestations of the disease range from an asymptomatic condition to life-threatening events and death, with more severe courses being associated with age, male sex, and comorbidities. Besides these risk factors, intrinsic characteristics of the virus as well as genetic factors of the host are expected to account for COVID-19 clinical heterogeneity. Genetic studies have long been recognized as fundamental to identify biological mechanisms underlying congenital diseases, to pinpoint genes/proteins responsible for the susceptibility to different inherited conditions, to highlight targets of therapeutic relevance, to suggest drug repurposing, and even to clarify causal relationships that make modifiable some environmental risk factors. Though these studies usually take long time to be concluded and, above all, to translate their discoveries to patients' bedside, the scientific community moved really fast to deliver genetic signals underlying different COVID-19 phenotypes. In this Review, besides a concise description of COVID-19 symptomatology and of SARS-CoV-2 mechanism of infection, we aimed to recapitulate the current literature in terms of host genetic factors that specifically associate with an increased severity of the disease.
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Affiliation(s)
- Claudio Cappadona
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele - Milan 20090, Italy
| | - Valeria Rimoldi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele - Milan 20090, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan 20089, Italy
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele - Milan 20090, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan 20089, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele - Milan 20090, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan 20089, Italy.
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46
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Jankovic M, Nikolic D, Novakovic I, Petrovic B, Lackovic M, Santric-Milicevic M. miRNAs as a Potential Biomarker in the COVID-19 Infection and Complications Course, Severity, and Outcome. Diagnostics (Basel) 2023; 13:1091. [PMID: 36980399 PMCID: PMC10047241 DOI: 10.3390/diagnostics13061091] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/08/2023] [Accepted: 03/12/2023] [Indexed: 03/15/2023] Open
Abstract
During the last three years, since the emergence of the COVID-19 pandemic, a significant number of scientific publications have focused on resolving susceptibility to the infection, as well as the course of the disease and potential long-term complications. COVID-19 is widely considered as a multisystem disease and a variety of socioeconomic, medical, and genetic/epigenetic factors may contribute to the disease severity and outcome. Furthermore, the SARS-COV-2 infection may trigger pathological processes and accelerate underlying conditions to clinical entities. The development of specific and sensitive biomarkers that are easy to obtain will allow for patient stratification, prevention, prognosis, and more individualized treatments for COVID-19. miRNAs are proposed as promising biomarkers for different aspects of COVID-19 disease (susceptibility, severity, complication course, outcome, and therapeutic possibilities). This review summarizes the most relevant findings concerning miRNA involvement in COVID-19 pathology. Additionally, the role of miRNAs in wide range of complications due to accompanied and/or underlying health conditions is discussed. The importance of understanding the functional relationships between different conditions, such as pregnancy, obesity, or neurological diseases, with COVID-19 is also highlighted.
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Affiliation(s)
- Milena Jankovic
- Neurology Clinic, University Clinical Center of Serbia, 11000 Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Dejan Nikolic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Department of Physical Medicine and Rehabilitation, University Children's Hospital, 11000 Belgrade, Serbia
| | - Ivana Novakovic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Bojana Petrovic
- Clinic of Gynecology and Obstetrics, University Clinical Center of Serbia, 11000 Belgrade, Serbia
| | - Milan Lackovic
- Department of Obstetrics and Gynecology, University Hospital "Dragisa Misovic", 11000 Belgrade, Serbia
| | - Milena Santric-Milicevic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Institute of Social Medicine, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Faculty of Medicine, School of Public Health and Health Management, University of Belgrade, 11000 Belgrade, Serbia
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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: 279] [Impact Index Per Article: 279.0] [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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48
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Francisco Junior RDS, Temerozo JR, Ferreira CDS, Martins Y, Souza TML, Medina-Acosta E, de Vasconcelos ATR. Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines. Front Immunol 2023; 13:1101526. [PMID: 36818472 PMCID: PMC9929942 DOI: 10.3389/fimmu.2022.1101526] [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: 11/17/2022] [Accepted: 12/19/2022] [Indexed: 02/05/2023] Open
Abstract
Introduction Cell entry of SARS-CoV-2 causes genome-wide disruption of the transcriptional profiles of genes and biological pathways involved in the pathogenesis of COVID-19. Expression allelic imbalance is characterized by a deviation from the Mendelian expected 1:1 expression ratio and is an important source of allele-specific heterogeneity. Expression allelic imbalance can be measured by allele-specific expression analysis (ASE) across heterozygous informative expressed single nucleotide variants (eSNVs). ASE reflects many regulatory biological phenomena that can be assessed by combining genome and transcriptome information. ASE contributes to the interindividual variability associated with the disease. We aim to estimate the transcriptome-wide impact of SARS-CoV-2 infection by analyzing eSNVs. Methods We compared ASE profiles in the human lung cell lines Calu-3, A459, and H522 before and after infection with SARS-CoV-2 using RNA-Seq experiments. Results We identified 34 differential ASE (DASE) sites in 13 genes (HLA-A, HLA-B, HLA-C, BRD2, EHD2, GFM2, GSPT1, HAVCR1, MAT2A, NQO2, SUPT6H, TNFRSF11A, UMPS), all of which are enriched in protein binding functions and play a role in COVID-19. Most DASE sites were assigned to the MHC class I locus and were predominantly upregulated upon infection. DASE sites in the MHC class I locus also occur in iPSC-derived airway epithelium basal cells infected with SARS-CoV-2. Using an RNA-Seq haplotype reconstruction approach, we found DASE sites and adjacent eSNVs in phase (i.e., predicted on the same DNA strand), demonstrating differential haplotype expression upon infection. We found a bias towards the expression of the HLA alleles with a higher binding affinity to SARS-CoV-2 epitopes. Discussion Independent of gene expression compensation, SARS-CoV-2 infection of human lung cell lines induces transcriptional allelic switching at the MHC loci. This suggests a response mechanism to SARS-CoV-2 infection that swaps HLA alleles with poor epitope binding affinity, an expectation supported by publicly available proteome data.
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Affiliation(s)
| | - Jairo R. Temerozo
- Laboratory on Thymus Research, Oswaldo Cruz Institute (Fiocruz), Rio de Janeiro, Brazil
- National Institute of Science and Technology on Neuroimmunomodulation, Rio de Janeiro, Brazil
| | - Cristina dos Santos Ferreira
- Bioinformatics Laboratory (LABINFO), National Laboratory of Scientific Computation (LNCC/MCTIC), Petrópolis, Brazil
| | - Yasmmin Martins
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA), Buenos Aires, Argentina
| | - Thiago Moreno L. Souza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
- Center for Technological Development in Health (CDTS), National Institute for Science and Technology on Innovation on Neglected Diseases Neglected Populations (INCT/IDNP), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Enrique Medina-Acosta
- Molecular Identification and Diagnostics Unit (NUDIM), Laboratory of Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Brazil
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49
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Yoshiji S, Butler-Laporte G, Lu T, Willett JDS, Su CY, Nakanishi T, Morrison DR, Chen Y, Liang K, Hultström M, Ilboudo Y, Afrasiabi Z, Lan S, Duggan N, DeLuca C, Vaezi M, Tselios C, Xue X, Bouab M, Shi F, Laurent L, Münter HM, Afilalo M, Afilalo J, Mooser V, Timpson NJ, Zeberg H, Zhou S, Forgetta V, Farjoun Y, Richards JB. Proteome-wide Mendelian randomization implicates nephronectin as an actionable mediator of the effect of obesity on COVID-19 severity. Nat Metab 2023; 5:248-264. [PMID: 36805566 PMCID: PMC9940690 DOI: 10.1038/s42255-023-00742-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/10/2023] [Indexed: 02/22/2023]
Abstract
Obesity is a major risk factor for Coronavirus disease (COVID-19) severity; however, the mechanisms underlying this relationship are not fully understood. As obesity influences the plasma proteome, we sought to identify circulating proteins mediating the effects of obesity on COVID-19 severity in humans. Here, we screened 4,907 plasma proteins to identify proteins influenced by body mass index using Mendelian randomization. This yielded 1,216 proteins, whose effect on COVID-19 severity was assessed, again using Mendelian randomization. We found that an s.d. increase in nephronectin (NPNT) was associated with increased odds of critically ill COVID-19 (OR = 1.71, P = 1.63 × 10-10). The effect was driven by an NPNT splice isoform. Mediation analyses supported NPNT as a mediator. In single-cell RNA-sequencing, NPNT was expressed in alveolar cells and fibroblasts of the lung in individuals who died of COVID-19. Finally, decreasing body fat mass and increasing fat-free mass were found to lower NPNT levels. These findings provide actionable insights into how obesity influences COVID-19 severity.
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Grants
- C18281/A29019 Cancer Research UK
- 365825 CIHR
- 409511 CIHR
- 100558 CIHR
- 169303 CIHR
- The Richards research group is supported by the Canadian Institutes of Health Research (CIHR: 365825, 409511, 100558, 169303), the McGill Interdisciplinary Initiative in Infection and Immunity (MI4), the Lady Davis Institute of the Jewish General Hospital, the Jewish General Hospital Foundation, the Canadian Foundation for Innovation, the NIH Foundation, Cancer Research UK, Genome Québec, the Public Health Agency of Canada, McGill University, Cancer Research UK [grant number C18281/A29019] and the Fonds de Recherche Québec Santé (FRQS). J.B.R. is supported by an FRQS Mérite Clinical Research Scholarship. Support from Calcul Québec and Compute Canada is acknowledged. TwinsUK is funded by the Welcome Trust, Medical Research Council, European Union, the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London. S.Y. is supported by the Japan Society for the Promotion of Science. T.L. has been supported by a Vanier Canada Graduate Scholarship, an FRQS doctoral training fellowship, and a McGill University Faculty of Medicine Studentship. These funding agencies mentioned above had no role in the design, implementation, or interpretation of this study.
- MEXT | Japan Society for the Promotion of Science (JSPS)
- Gouvernement du Canada | Instituts de Recherche en Santé du Canada | CIHR Skin Research Training Centre (Skin Research Training Centre)
- Fonds de Recherche du Québec-Société et Culture (FRQSC)
- Cancer Research UK (CRUK)
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Affiliation(s)
- Satoshi Yoshiji
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Guillaume Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
| | - Tianyuan Lu
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Quebec, Canada
- 5 Prime Sciences, Montréal, Quebec, Canada
| | - Julian Daniel Sunday Willett
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Quebec, Canada
| | - Chen-Yang Su
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Computer Science, McGill University, Montréal, Quebec, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - David R Morrison
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Yiheng Chen
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Kevin Liang
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Quebec, Canada
| | - Michael Hultström
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Yann Ilboudo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Zaman Afrasiabi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Shanshan Lan
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Naomi Duggan
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Chantal DeLuca
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Mitra Vaezi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Chris Tselios
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Xiaoqing Xue
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Meriem Bouab
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Fangyi Shi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Laetitia Laurent
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | | | - Marc Afilalo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Emergency Medicine, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Jonathan Afilalo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
- Division of Cardiology, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
- McGill Genome Centre, McGill University, Montréal, Quebec, Canada
| | | | - Hugo Zeberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sirui Zhou
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
- McGill Genome Centre, McGill University, Montréal, Quebec, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- 5 Prime Sciences, Montréal, Quebec, Canada
| | - Yossi Farjoun
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada.
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada.
- 5 Prime Sciences, Montréal, Quebec, Canada.
- Department of Twin Research, King's College London, London, UK.
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50
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Fano-Sizgorich D, Vásquez-Velásquez C, Orellana LR, Ponce-Torres C, Gamboa-Serpa H, Alvarez-Huambachano K, Gonzales GF. Risk of death, hospitalization and intensive care unit admission by SARS-CoV-2 variants in Peru: a retrospective study. Int J Infect Dis 2023; 127:144-149. [PMID: 36563957 PMCID: PMC9763211 DOI: 10.1016/j.ijid.2022.12.020] [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: 08/22/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Peru has had the highest death toll from the pandemic worldwide; however, it is not clear what the effects of the different variants on these outcomes are. The study aimed to evaluate the risk of death, hospitalization, and intensive care unit (ICU) admission rates of COVID-19 according to the SARS-CoV-2 variants detected in Peru from March 2020-February 2022. METHODS Retrospective study using open-access databases were published by the Peruvian Ministry of Health. Databases of genomic sequencing, death, COVID-19 cases, hospitalization and ICU, and vaccination were used. Crude and adjusted Cox proportional hazards regressions with clustered variances were modeled to calculate the hazard ratio (HR) of outcomes by variant. RESULTS Lambda variant had the highest risk of death (HR 1.92, 95% CI 1.37-2.68), whereas the Delta variant had the lowest risk (HR 0.50, 95% CI 0.31-0.82). Mu variant had the highest risk of hospitalization (HR: 2.39, 95% CI 1.56-3.67), Omicron the lowest (HR 0.45, 95%CI 0.23-0.90), and Gamma had the highest ICU admission rate (HR 1.95, 95%CI 1.40-2.71). CONCLUSION SARS-CoV-2 variants showed distinctive risks of clinical outcomes, which could have implications for the management of infected persons during the pandemic.
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Affiliation(s)
- Diego Fano-Sizgorich
- Laboratorio de Endocrinología y Reproducción, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru; Latin American Center of Excellence for Climate Change and Health, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Cinthya Vásquez-Velásquez
- Laboratorio de Endocrinología y Reproducción, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru; Dirección de Laboratorio de Salud Pública, Dirección Regional de Salud del Callao, Callao, Peru
| | - Laura R Orellana
- EMERGE, Emerging Diseases and Climate Change Research Unit, Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Christian Ponce-Torres
- Latin American Center of Excellence for Climate Change and Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | - Gustavo F Gonzales
- Laboratorio de Endocrinología y Reproducción, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
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