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Das R, Sinnarasan VSP, Paul D, Venkatesan A. A Machine Learning Approach to Identify Potential miRNA-Gene Regulatory Network Contributing to the Pathogenesis of SARS-CoV-2 Infection. Biochem Genet 2024; 62:987-1006. [PMID: 37515735 DOI: 10.1007/s10528-023-10458-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/14/2023] [Indexed: 07/31/2023]
Abstract
Worldwide, many lives have been lost in the recent outbreak of coronavirus disease. The pathogen responsible for this disease takes advantage of the host machinery to replicate itself and, in turn, causes pathogenesis in humans. Human miRNAs are seen to have a major role in the pathogenesis and progression of viral diseases. Hence, an in-silico approach has been used in this study to uncover the role of miRNAs and their target genes in coronavirus disease pathogenesis. This study attempts to perform the miRNA seq data analysis to identify the potential differentially expressed miRNAs. Considering only the experimentally proven interaction databases TarBase, miRTarBase, and miRecords, the target genes of the miRNAs have been identified from the mirNET analytics platform. The identified hub genes were subjected to gene ontology and pathway enrichment analysis using EnrichR. It is found that a total of 9 miRNAs are deregulated, out of which 2 were upregulated (hsa-mir-3614-5p and hsa-mir-3614-3p) and 7 were downregulated (hsa-mir-17-5p, hsa-mir-106a-5p, hsa-mir-17-3p, hsa-mir-181d-5p, hsa-mir-93-3p, hsa-mir-28-5p, and hsa-mir-100-5p). These miRNAs help us to classify the diseased and healthy control patients accurately. Moreover, it is also found that crucial target genes (UBC and UBB) of 4 signature miRNAs interact with viral replicase polyprotein 1ab of SARS-Coronavirus. As a result, it is noted that the virus hijacks key immune pathways like various cancer and virus infection pathways and molecular functions such as ubiquitin ligase binding and transcription corepressor and coregulator binding.
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Affiliation(s)
- Rajesh Das
- Department of Bioinformatics, Pondicherry University, RV Nagar, Kalapet, Puducherry, 605014, India
| | | | - Dahrii Paul
- Department of Bioinformatics, Pondicherry University, RV Nagar, Kalapet, Puducherry, 605014, India
| | - Amouda Venkatesan
- Department of Bioinformatics, Pondicherry University, RV Nagar, Kalapet, Puducherry, 605014, India.
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2
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Grubelnik G, Korva M, Kogoj R, Polanc T, Mavrič M, Jevšnik Virant M, Uršič T, Keše D, Seme K, Petrovec M, Jereb M, Avšič-Županc T. Herpesviridae and Atypical Bacteria Co-Detections in Lower Respiratory Tract Samples of SARS-CoV-2-Positive Patients Admitted to an Intensive Care Unit. Microorganisms 2024; 12:714. [PMID: 38674658 PMCID: PMC11051806 DOI: 10.3390/microorganisms12040714] [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: 02/05/2024] [Revised: 03/20/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
Shortly after the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), cases of viral, bacterial, and fungal coinfections in hospitalized patients became evident. This retrospective study investigates the prevalence of multiple pathogen co-detections in 1472 lower respiratory tract (LRT) samples from 229 SARS-CoV-2-positive patients treated in the largest intensive care unit (ICU) in Slovenia. In addition to SARS-CoV-2, (rt)RT-PCR tests were used to detect cytomegalovirus (CMV), Epstein-Barr virus (EBV), herpes simplex virus 1 (HSV-1), herpes simplex virus 2 (HSV-2), varicella zoster virus (VZV), and atypical bacteria: Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella pneumophila/spp. At least one co-detection was observed in 89.1% of patients. EBV, HSV-1, and CMV were the most common, with 74.7%, 58.1%, and 38.0% of positive patients, respectively. The median detection time of EBV, HSV-1, and CMV after initial SARS-CoV-2 confirmation was 11 to 20 days. Bronchoalveolar lavage (BAL) and tracheal aspirate (TA) samples showed equivalent performance for the detection of EBV, CMV, and HSV-1 in patients with both available samples. Our results indicate that SARS-CoV-2 infection could be a risk factor for latent herpesvirus reactivation, especially HSV-1, EBV, and CMV. However, additional studies are needed to elucidate the clinical importance of these findings.
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Affiliation(s)
- Gašper Grubelnik
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, 1000 Ljubljana, Slovenia; (G.G.); (M.K.); (R.K.); (M.J.V.); (T.U.); (D.K.); (K.S.); (M.P.)
| | - Miša Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, 1000 Ljubljana, Slovenia; (G.G.); (M.K.); (R.K.); (M.J.V.); (T.U.); (D.K.); (K.S.); (M.P.)
| | - Rok Kogoj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, 1000 Ljubljana, Slovenia; (G.G.); (M.K.); (R.K.); (M.J.V.); (T.U.); (D.K.); (K.S.); (M.P.)
| | - Tina Polanc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, 1000 Ljubljana, Slovenia; (G.G.); (M.K.); (R.K.); (M.J.V.); (T.U.); (D.K.); (K.S.); (M.P.)
| | - Matej Mavrič
- Department of Infectious Diseases, Ljubljana University Medical Center, Japljeva Ulica 2, 1000 Ljubljana, Slovenia; (M.M.); (M.J.)
| | - Monika Jevšnik Virant
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, 1000 Ljubljana, Slovenia; (G.G.); (M.K.); (R.K.); (M.J.V.); (T.U.); (D.K.); (K.S.); (M.P.)
| | - Tina Uršič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, 1000 Ljubljana, Slovenia; (G.G.); (M.K.); (R.K.); (M.J.V.); (T.U.); (D.K.); (K.S.); (M.P.)
| | - Darja Keše
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, 1000 Ljubljana, Slovenia; (G.G.); (M.K.); (R.K.); (M.J.V.); (T.U.); (D.K.); (K.S.); (M.P.)
| | - Katja Seme
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, 1000 Ljubljana, Slovenia; (G.G.); (M.K.); (R.K.); (M.J.V.); (T.U.); (D.K.); (K.S.); (M.P.)
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, 1000 Ljubljana, Slovenia; (G.G.); (M.K.); (R.K.); (M.J.V.); (T.U.); (D.K.); (K.S.); (M.P.)
| | - Matjaž Jereb
- Department of Infectious Diseases, Ljubljana University Medical Center, Japljeva Ulica 2, 1000 Ljubljana, Slovenia; (M.M.); (M.J.)
- Faculty of Medicine, University of Ljubljana, Vrazov Trg 2, 1000 Ljubljana, Slovenia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, 1000 Ljubljana, Slovenia; (G.G.); (M.K.); (R.K.); (M.J.V.); (T.U.); (D.K.); (K.S.); (M.P.)
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Naidu AS, Wang CK, Rao P, Mancini F, Clemens RA, Wirakartakusumah A, Chiu HF, Yen CH, Porretta S, Mathai I, Naidu SAG. Precision nutrition to reset virus-induced human metabolic reprogramming and dysregulation (HMRD) in long-COVID. NPJ Sci Food 2024; 8:19. [PMID: 38555403 PMCID: PMC10981760 DOI: 10.1038/s41538-024-00261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/15/2024] [Indexed: 04/02/2024] Open
Abstract
SARS-CoV-2, the etiological agent of COVID-19, is devoid of any metabolic capacity; therefore, it is critical for the viral pathogen to hijack host cellular metabolic machinery for its replication and propagation. This single-stranded RNA virus with a 29.9 kb genome encodes 14 open reading frames (ORFs) and initiates a plethora of virus-host protein-protein interactions in the human body. These extensive viral protein interactions with host-specific cellular targets could trigger severe human metabolic reprogramming/dysregulation (HMRD), a rewiring of sugar-, amino acid-, lipid-, and nucleotide-metabolism(s), as well as altered or impaired bioenergetics, immune dysfunction, and redox imbalance in the body. In the infectious process, the viral pathogen hijacks two major human receptors, angiotensin-converting enzyme (ACE)-2 and/or neuropilin (NRP)-1, for initial adhesion to cell surface; then utilizes two major host proteases, TMPRSS2 and/or furin, to gain cellular entry; and finally employs an endosomal enzyme, cathepsin L (CTSL) for fusogenic release of its viral genome. The virus-induced HMRD results in 5 possible infectious outcomes: asymptomatic, mild, moderate, severe to fatal episodes; while the symptomatic acute COVID-19 condition could manifest into 3 clinical phases: (i) hypoxia and hypoxemia (Warburg effect), (ii) hyperferritinemia ('cytokine storm'), and (iii) thrombocytosis (coagulopathy). The mean incubation period for COVID-19 onset was estimated to be 5.1 days, and most cases develop symptoms after 14 days. The mean viral clearance times were 24, 30, and 39 days for acute, severe, and ICU-admitted COVID-19 patients, respectively. However, about 25-70% of virus-free COVID-19 survivors continue to sustain virus-induced HMRD and exhibit a wide range of symptoms that are persistent, exacerbated, or new 'onset' clinical incidents, collectively termed as post-acute sequelae of COVID-19 (PASC) or long COVID. PASC patients experience several debilitating clinical condition(s) with >200 different and overlapping symptoms that may last for weeks to months. Chronic PASC is a cumulative outcome of at least 10 different HMRD-related pathophysiological mechanisms involving both virus-derived virulence factors and a multitude of innate host responses. Based on HMRD and virus-free clinical impairments of different human organs/systems, PASC patients can be categorized into 4 different clusters or sub-phenotypes: sub-phenotype-1 (33.8%) with cardiac and renal manifestations; sub-phenotype-2 (32.8%) with respiratory, sleep and anxiety disorders; sub-phenotype-3 (23.4%) with skeleto-muscular and nervous disorders; and sub-phenotype-4 (10.1%) with digestive and pulmonary dysfunctions. This narrative review elucidates the effects of viral hijack on host cellular machinery during SARS-CoV-2 infection, ensuing detrimental effect(s) of virus-induced HMRD on human metabolism, consequential symptomatic clinical implications, and damage to multiple organ systems; as well as chronic pathophysiological sequelae in virus-free PASC patients. We have also provided a few evidence-based, human randomized controlled trial (RCT)-tested, precision nutrients to reset HMRD for health recovery of PASC patients.
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Affiliation(s)
- A Satyanarayan Naidu
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA.
- N-terminus Research Laboratory, 232659 Via del Rio, Yorba Linda, CA, 92887, USA.
| | - Chin-Kun Wang
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- School of Nutrition, Chung Shan Medical University, 110, Section 1, Jianguo North Road, Taichung, 40201, Taiwan
| | - Pingfan Rao
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- College of Food and Bioengineering, Fujian Polytechnic Normal University, No.1, Campus New Village, Longjiang Street, Fuqing City, Fujian, China
| | - Fabrizio Mancini
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- President-Emeritus, Parker University, 2540 Walnut Hill Lane, Dallas, TX, 75229, USA
| | - Roger A Clemens
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- University of Southern California, Alfred E. Mann School of Pharmacy/D. K. Kim International Center for Regulatory & Quality Sciences, 1540 Alcazar St., CHP 140, Los Angeles, CA, 90089, USA
| | - Aman Wirakartakusumah
- International Union of Food Science and Technology (IUFoST), Guelph, ON, Canada
- IPMI International Business School Jakarta; South East Asian Food and Agriculture Science and Technology, IPB University, Bogor, Indonesia
| | - Hui-Fang Chiu
- Department of Chinese Medicine, Taichung Hospital, Ministry of Health & Well-being, Taichung, Taiwan
| | - Chi-Hua Yen
- Department of Family and Community Medicine, Chung Shan Medical University Hospital; School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Sebastiano Porretta
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- President, Italian Association of Food Technology (AITA), Milan, Italy
- Experimental Station for the Food Preserving Industry, Department of Consumer Science, Viale Tanara 31/a, I-43121, Parma, Italy
| | - Issac Mathai
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- Soukya International Holistic Health Center, Whitefield, Bengaluru, India
| | - Sreus A G Naidu
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- N-terminus Research Laboratory, 232659 Via del Rio, Yorba Linda, CA, 92887, USA
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Lambarey H, Blumenthal MJ, Chetram A, Joyimbana W, Jennings L, Orrell C, Schäfer G. Reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV) by SARS-CoV-2 in non-hospitalised HIV-infected patients. EBioMedicine 2024; 100:104986. [PMID: 38306893 PMCID: PMC10850403 DOI: 10.1016/j.ebiom.2024.104986] [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: 09/22/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND While acute SARS-CoV-2 infection and associated inflammation resulted in substantial morbidity and mortality during the COVID-19 pandemic, particularly in unvaccinated patients, long-term effects of SARS-CoV-2 exposure for reactivation of latent oncogenic herpesviruses, such as KSHV, is unknown. METHODS We performed a longitudinal observational cross-sectional study on 407 non-hospitalised adult HIV-infected (CD4 count <350 cells/μL) patients attending antiretroviral therapy services in Gugulethu, South Africa, from October 2020 to April 2023. FINDINGS KSHV seroprevalence was 53.5%; the quarterly SARS-CoV-2 seroprevalence increased from 76.2% (before roll-out of COVID-19 vaccinations) to 94.9%, with 32.2% being self-reportedly vaccinated against COVID-19. Over the course of recruitment, the quarterly percentage of patients with detectable KSHV viral load (VL) in the peripheral blood increased from 3.3% to 69.2%. The presence of KSHV VL was significantly associated with SARS-CoV-2 RBD antibody titers in unvaccinated (median RBD IgG OD 1.24 [IQR 0.82-2.42] in non-reactivated versus 2.83 [IQR 1.08-4.72] in reactivated patients, p = 0.0030) but not in vaccinated patients (median RBD IgG OD 5.13 [IQR 4.11-6.36] in non-reactivated versus 4.53 [IQR 2.90-5.92] in reactivated patients, p = 0.086). Further logistic regression revealed significantly higher odds of KSHV reactivation in unvaccinated, previously SARS-CoV-2 exposed patients (p = 0.015, adjusted OR 1.28 [95% CI: 1.05-1.55]), but not vaccinated patients (p = 0.080, adjusted OR 0.83 [95% CI: 0.67-1.02]). Interestingly, detectable KSHV VL was not associated with increased inflammatory markers such as C-reactive protein and interleukin-6. INTERPRETATION High, and most likely repeated, exposure to SARS-CoV-2 in unvaccinated individuals may have long-term consequences for reactivation of KSHV infection as shown here in the context of HIV-infected patients with impaired immune functions. Post-pandemic prevention and/or monitoring strategies of potential KSHV-associated pathologies in high-risk patients with immunodeficiencies are therefore highly recommended. FUNDING This research was funded by the EDCTP2 programme (Training and Mobility Action TMA2018SF-2446).
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Affiliation(s)
- Humaira Lambarey
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, South Africa; Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Melissa J Blumenthal
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, South Africa; Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Abeen Chetram
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa
| | | | | | - Catherine Orrell
- Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, South Africa; Desmond Tutu Health Foundation, Cape Town, South Africa
| | - Georgia Schäfer
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, South Africa; Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, South Africa.
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5
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Fappani C, Gori M, Bianchi S, Terraneo M, Bilardi E, Colzani D, Tanzi E, Canuti M, Amendola A. Differential diagnosis of fever and rash cases negative for measles and rubella to complement surveillance activities. J Med Virol 2023; 95:e29141. [PMID: 37796084 DOI: 10.1002/jmv.29141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/09/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023]
Abstract
In the quest to eliminate measles virus (MV) and rubella virus (Ruv), every suspected case must be properly identified and diagnosed. Since 2017, in Milan (Italy), a total of 978 measles and rubella suspected cases (fever and rash) were investigated and 310 were not laboratory confirmed (discarded cases). To improve surveillance activities, we investigated the presence in discarded cases of 8 other viral pathogens commonly associated with rash: human herpesvirus 6 (HHV-6) and 7 (HHV-7), parvovirus B19 (B19V), enterovirus (EV), Epstein-Barr virus (EBV), human adenovirus (HAdV), cytomegalovirus (HCMV), and SARS-CoV-2. Differential diagnosis was carried out on 289 discarded cases by multiplex real-time PCR assays. At least one pathogen was detected in 188 cases (65.1%) with HHV-7 being the most frequently detected virus. No difference in the number of detected infections overtime was observed and infections were identified in all age groups. As expected, most HHV-6, EV, HAdV, and HCMV-positive cases were found in children aged 0-4 years and HHV-7 was most frequent in the 15-39 age group. In light of the World Health Organization measles elimination goal, the introduction of laboratory methods for differential diagnosis is required for the final classification of clinically compatible cases. The used screening panel allowed us to increase the percentage of virus-positive cases to 87.5%, allowing us to clarify viral involvement and epidemiology, improve diagnosis, and strengthen surveillance activities. As all investigated pathogens were detected, this diagnostic panel was a suitable tool to complement MV and RuV surveillance activities.
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Affiliation(s)
- Clara Fappani
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
| | - Maria Gori
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
| | - Silvia Bianchi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
| | - Mara Terraneo
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Erica Bilardi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Daniela Colzani
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Elisabetta Tanzi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
- Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy
| | - Marta Canuti
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
- Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Antonella Amendola
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinate Research Centre EpiSoMI (Epidemiology and Molecular Surveillance of Infections), Università degli Studi di Milano, Milan, Italy
- Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy
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6
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Nunes JM, Kell DB, Pretorius E. Cardiovascular and haematological pathology in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS): A role for viruses. Blood Rev 2023; 60:101075. [PMID: 36963989 PMCID: PMC10027292 DOI: 10.1016/j.blre.2023.101075] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/25/2023]
Abstract
ME/CFS is a debilitating chronic condition that often develops after viral or bacterial infection. Insight from the study of Long COVID/Post Acute Sequelae of COVID-19 (PASC), the post-viral syndrome associated with SARS-CoV-2 infection, might prove to be useful for understanding pathophysiological mechanisms of ME/CFS. Disease presentation is similar between the two conditions, and a subset of Long COVID patients meet the diagnostic criteria for ME/CFS. Since Long COVID is characterized by significant vascular pathology - including endothelial dysfunction, coagulopathy, and vascular dysregulation - the question of whether or not the same biological abnormalities are of significance in ME/CFS arises. Cardiac abnormalities have for a while now been documented in ME/CFS cohorts, with recent studies demonstrating major deficits in cerebral blood flow, and hence vascular dysregulation. A growing body of research is demonstrating that ME/CFS is accompanied by platelet hyperactivation, anomalous clotting, a procoagulant phenotype, and endothelial dysfunction. Endothelial damage and dysregulated clotting can impair substance exchange between blood and tissues, and result in hypoperfusion, which may contribute to the manifestation of certain ME/CFS symptoms. Here we review the ME/CFS literature to summarize cardiovascular and haematological findings documented in patients with the condition, and, in this context, briefly discuss the potential role of previously-implicated pathogens. Overall, cardiac and haematological abnormalities are present within ME/CFS cohorts. While atherosclerotic heart disease is not significantly associated with ME/CFS, suboptimal cardiovascular function defined by reduced cardiac output, impaired cerebral blood flow, and vascular dysregulation are, and these abnormalities do not appear to be influenced by deconditioning. Rather, these cardiac abnormalities may result from dysfunction in the (autonomic) nervous system. Plenty of recently published studies are demonstrating significant platelet hyperactivity and endothelial dysfunction in ME/CFS, as well as anomalous clotting processes. It is of particular importance to determine to what extent these cardiovascular and haematological abnormalities contribute to symptom severity, and if these two systems can be targeted for therapeutic purposes. Viral reservoirs of herpesviruses exist in ME/CFS, and most likely contribute to cardiovascular and haematological dysfunction directly or indirectly. This review highlights the potential of studying cardiac functioning, the vasculature, and coagulation system in ME/CFS.
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Affiliation(s)
- Jean M Nunes
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1, Matieland 7602, South Africa.
| | - Douglas B Kell
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1, Matieland 7602, South Africa; Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK; The Novo Nordisk Foundation Centre for Biosustainability, Building 220, Chemitorvet 200, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Etheresia Pretorius
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1, Matieland 7602, South Africa; Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK.
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Moynan D, Barkat R, Avramovic G, Morley D, O'Kelly B, Lambert JS. The reactivation of herpesviruses in severe COVID-19; a retrospective analysis of a critical care cohort. CLINICAL INFECTION IN PRACTICE 2023; 19:100232. [PMID: 37251495 PMCID: PMC10204275 DOI: 10.1016/j.clinpr.2023.100232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023] Open
Affiliation(s)
- David Moynan
- Department of Infectious Diseases, Mater Misericordiae University Hospital, Dublin, 44 Eccles St, Dublin 7 D07 AX57, Ireland
| | - Rizwan Barkat
- Department of Critical Care Medicine, Mater Misericordiae University Hospital, Dublin, 44 Eccles St, Dublin 7 D07 AX57, Ireland
| | - Gordana Avramovic
- University College Dublin, Catherine McAuley Centre, 21 Nelson St, Dublin 7 D07 KX5K, Ireland
| | - Deirdre Morley
- Department of Infectious Diseases, Mater Misericordiae University Hospital, Dublin, 44 Eccles St, Dublin 7 D07 AX57, Ireland
- Department of Critical Care Medicine, Mater Misericordiae University Hospital, Dublin, 44 Eccles St, Dublin 7 D07 AX57, Ireland
| | - Brendan O'Kelly
- Department of Infectious Diseases, Mater Misericordiae University Hospital, Dublin, 44 Eccles St, Dublin 7 D07 AX57, Ireland
| | - John S Lambert
- Department of Infectious Diseases, Mater Misericordiae University Hospital, Dublin, 44 Eccles St, Dublin 7 D07 AX57, Ireland
- University College Dublin, Catherine McAuley Centre, 21 Nelson St, Dublin 7 D07 KX5K, Ireland
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8
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Sweet DR, Freeman ML, Zidar DA. Immunohematologic Biomarkers in COVID-19: Insights into Pathogenesis, Prognosis, and Prevention. Pathog Immun 2023; 8:17-50. [PMID: 37427016 PMCID: PMC10324469 DOI: 10.20411/pai.v8i1.572] [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: 02/24/2023] [Accepted: 05/24/2023] [Indexed: 07/11/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has had profound effects on the health of individuals and on healthcare systems worldwide. While healthcare workers on the frontlines have fought to quell multiple waves of infection, the efforts of the larger research community have changed the arch of this pandemic as well. This review will focus on biomarker discovery and other efforts to identify features that predict outcomes, and in so doing, identify possible effector and passenger mechanisms of adverse outcomes. Identifying measurable soluble factors, cell-types, and clinical parameters that predict a patient's disease course will have a legacy for the study of immunologic responses, especially stimuli, which induce an overactive, yet ineffectual immune system. As prognostic biomarkers were identified, some have served to represent pathways of therapeutic interest in clinical trials. The pandemic conditions have created urgency for accelerated target identification and validation. Collectively, these COVID-19 studies of biomarkers, disease outcomes, and therapeutic efficacy have revealed that immunologic systems and responses to stimuli are more heterogeneous than previously assumed. Understanding the genetic and acquired features that mediate divergent immunologic outcomes in response to this global exposure is ongoing and will ultimately improve our preparedness for future pandemics, as well as impact preventive approaches to other immunologic diseases.
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Affiliation(s)
- David R. Sweet
- Case Western Reserve University School of Medicine, Cleveland, OH
| | - Michael L. Freeman
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, OH
| | - David A. Zidar
- Harrington Heart and Vascular Institute, University Hospitals Cleveland Medical Center, Cleveland, OH
- Cardiology Section, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University School of Medicine, Case Western Reserve University, Cleveland, OH
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9
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Abstract
Wang et al. found that elderly COVID-19 patients were at risk of AD. The following facts suggest a possible explanation: reactivation of herpes simplex virus type 1 (HSV1) and other herpesviruses can occur in SARS-CoV-2 patients; in cell cultures, HSV1 infection causes occurrence of many AD-like features, as does reactivation of latent HSV1 after addition of certain infectious agents; recurrent experimental reactivation of HSV1-infected mice leads to formation of the main features of AD brains, and to cognitive decline. These suggest that COVID-19 results in repeated reactivation of HSV1 in brain, with subsequent accumulation of damage and eventual development of AD.
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Affiliation(s)
- Ruth F Itzhaki
- Institute of Population Ageing, University of Oxford, Oxford, UK
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10
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Zsichla L, Müller V. Risk Factors of Severe COVID-19: A Review of Host, Viral and Environmental Factors. Viruses 2023; 15:175. [PMID: 36680215 PMCID: PMC9863423 DOI: 10.3390/v15010175] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The clinical course and outcome of COVID-19 are highly variable, ranging from asymptomatic infections to severe disease and death. Understanding the risk factors of severe COVID-19 is relevant both in the clinical setting and at the epidemiological level. Here, we provide an overview of host, viral and environmental factors that have been shown or (in some cases) hypothesized to be associated with severe clinical outcomes. The factors considered in detail include the age and frailty, genetic polymorphisms, biological sex (and pregnancy), co- and superinfections, non-communicable comorbidities, immunological history, microbiota, and lifestyle of the patient; viral genetic variation and infecting dose; socioeconomic factors; and air pollution. For each category, we compile (sometimes conflicting) evidence for the association of the factor with COVID-19 outcomes (including the strength of the effect) and outline possible action mechanisms. We also discuss the complex interactions between the various risk factors.
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Affiliation(s)
- Levente Zsichla
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
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11
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Karpov DS, Demidova NA, Kulagin KA, Shuvalova AI, Kovalev MA, Simonov RA, Karpov VL, Snezhkina AV, Kudryavtseva AV, Klimova RR, Kushch AA. Complete and Prolonged Inhibition of Herpes Simplex Virus Type 1 Infection In Vitro by CRISPR/Cas9 and CRISPR/CasX Systems. Int J Mol Sci 2022; 23:ijms232314847. [PMID: 36499174 PMCID: PMC9738314 DOI: 10.3390/ijms232314847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Almost all people become infected with herpes viruses, including herpes simplex virus type 1 (HSV-1), during their lifetime. Typically, these viruses persist in a latent form that is resistant to all available antiviral medications. Under certain conditions, such as immunosuppression, the latent forms reactivate and cause disease. Moreover, strains of herpesviruses that are drug-resistant have rapidly emerged. Therefore, it is important to develop alternative methods capable of eradicating herpesvirus infections. One promising direction is the development of CRISPR/Cas systems for the therapy of herpesvirus infections. We aimed to design a CRISPR/Cas system for relatively effective long-term and safe control of HSV-1 infection. Here, we show that plasmids encoding the CRISPR/Cas9 system from Streptococcus pyogenes with a single sgRNA targeting the UL30 gene can completely suppress HSV-1 infection of the Vero cell line within 6 days and provide substantial protection within 9 days. For the first time, we show that CRISPR/CasX from Deltaproteobacteria with a single guide RNA against UL30 almost completely suppresses HSV-1 infection of the Vero cell line for 3 days and provides substantial protection for 6 days. We also found that the Cas9 protein without sgRNAs attenuates HSV-1 infection. Our results show that the developed CRISPR/Cas systems are promising therapeutic approaches to control HSV-1 infections.
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Affiliation(s)
- Dmitry S. Karpov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
- Correspondence: ; Tel.: +7-(499)-135-98-01
| | - Natalia A. Demidova
- N.F. Gamaleya National Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya Str., 18, 123098 Moscow, Russia
| | - Kirill A. Kulagin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Anastasija I. Shuvalova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Maxim A. Kovalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Ruslan A. Simonov
- N.F. Gamaleya National Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya Str., 18, 123098 Moscow, Russia
| | - Vadim L. Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Anastasiya V. Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Anna V. Kudryavtseva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Regina R. Klimova
- N.F. Gamaleya National Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya Str., 18, 123098 Moscow, Russia
| | - Alla A. Kushch
- N.F. Gamaleya National Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya Str., 18, 123098 Moscow, Russia
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12
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Chen J, Song J, Dai L, Post SR, Qin Z. SARS-CoV-2 infection and lytic reactivation of herpesviruses: A potential threat in the postpandemic era? J Med Virol 2022; 94:5103-5111. [PMID: 35819034 PMCID: PMC9350099 DOI: 10.1002/jmv.27994] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 02/06/2023]
Abstract
The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative pathogen for the coronavirus disease 2019 (COVID-19) pandemic, has greatly stressed our healthcare system. In addition to severe respiratory and systematic symptoms, several comorbidities increase the risk of fatal disease outcomes, including chronic viral infections. Increasing cases of lytic reactivation of human herpesviruses in COVID-19 patients and vaccinated people have been reported recently. SARS-CoV2 coinfection, COVID-19 treatments, and vaccination may aggravate those herpesvirus-associated diseases by reactivating the viruses in latently infected host cells. In this review, we summarize recent clinical findings and limited mechanistic studies regarding the relationship between SARS-CoV-2 and different human herpesviruses that suggest an ongoing potential threat to human health in the postpandemic era.
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Affiliation(s)
- Jungang Chen
- Department of Pathology, Winthrop P. Rockefeller Cancer InstituteUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Jiao Song
- Department of Pathology, Winthrop P. Rockefeller Cancer InstituteUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Lu Dai
- Department of Pathology, Winthrop P. Rockefeller Cancer InstituteUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Steven R. Post
- Department of Pathology, Winthrop P. Rockefeller Cancer InstituteUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Zhiqiang Qin
- Department of Pathology, Winthrop P. Rockefeller Cancer InstituteUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
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