Viruses

Editorial

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3 pages, 174 KiB

Open AccessEditorial

The COVID-19 Pandemic Enhanced Virology Research in Greece

by Apostolos Beloukas, Serafeim C. Chaintoutis and Ioannis Karakasiliotis

Viruses 2023, 15(1), 69; https://doi.org/10.3390/v15010069 - 25 Dec 2022

Viewed by 1639

Abstract

The emergence of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presented an unprecedented public health threat, being the cause of one of the most devastating pandemics in history [...] Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

Research

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14 pages, 1514 KiB

Open AccessArticle

Hepatitis C Core Protein Induces a Genotype-Specific Susceptibility of Hepatocytes to TNF-Induced Death In Vitro and In Vivo

by Savvina Moustafa, Katerina Kassela, Maria Bampali, Nikolas Dovrolis, Athanassios Kakkanas, Apostolos Beloukas, Penelope Mavromara and Ioannis Karakasiliotis

Viruses 2022, 14(11), 2521; https://doi.org/10.3390/v14112521 - 14 Nov 2022

Cited by 1 | Viewed by 2167

Abstract

Hepatitis C virus (HCV) core protein is a multifunctional protein that is involved in the proliferation, inflammation, and apoptosis mechanism of hepatocytes. HCV core protein genetic variability has been implicated in various outcomes of HCV pathology and treatment. In the present study, we [...] Read more.

Hepatitis C virus (HCV) core protein is a multifunctional protein that is involved in the proliferation, inflammation, and apoptosis mechanism of hepatocytes. HCV core protein genetic variability has been implicated in various outcomes of HCV pathology and treatment. In the present study, we aimed to analyze the role of the HCV core protein in tumor necrosis factor α (TNFα)-induced death under the viewpoint of HCV genetic variability. Immortalized hepatocytes (IHH), and not the Huh 7.5 hepatoma cell line, stably expressing HCV subtype 4a and HCV subtype 4f core proteins showed that only the HCV 4a core protein could increase sensitivity to TNFα-induced death. Development of two transgenic mice expressing the two different core proteins under the liver-specific promoter of transthyretin (TTR) allowed for the in vivo assessment of the role of the core in TNFα-induced death. Using the TNFα-dependent model of lipopolysaccharide/D-galactosamine (LPS/Dgal), we were able to recapitulate the in vitro results in IHH cells in vivo. Transgenic mice expressing the HCV 4a core protein were more susceptible to the LPS/Dgal model, while mice expressing the HCV 4f core protein had the same susceptibility as their littermate controls. Transcriptome analysis in liver biopsies from these transgenic mice gave insights into HCV core molecular pathogenesis while linking HCV core protein genetic variability to differential pathology in vivo. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

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17 pages, 2524 KiB

Open AccessArticle

A Proteomic Approach to Study the Biological Role of Hepatitis C Virus Protein Core+1/ARFP

by Vasileios Vrazas, Savvina Moustafa, Manousos Makridakis, Ioannis Karakasiliotis, Antonia Vlahou, Penelope Mavromara and Katerina R. Katsani

Viruses 2022, 14(8), 1694; https://doi.org/10.3390/v14081694 - 31 Jul 2022

Cited by 3 | Viewed by 2454

Abstract

Hepatitis C virus is the major cause of chronic liver diseases and the only cytoplasmic RNA virus known to be oncogenic in humans. The viral genome gives rise to ten mature proteins and to additional proteins, which are the products of alternative translation [...] Read more.

Hepatitis C virus is the major cause of chronic liver diseases and the only cytoplasmic RNA virus known to be oncogenic in humans. The viral genome gives rise to ten mature proteins and to additional proteins, which are the products of alternative translation initiation mechanisms. A protein—known as ARFP (alternative reading frame protein) or Core+1 protein—is synthesized by an open reading frame overlapping the HCV Core coding region in the (+1) frame of genotype 1a. Almost 20 years after its discovery, we still know little of the biological role of the ARFP/Core+1 protein. Here, our differential proteomic analysis of stable hepatoma cell lines expressing the Core+1/Long isoform of HCV-1a relates the expression of the Core+1/Long isoform with the progression of the pathology of HCV liver disease to cancer. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

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15 pages, 1090 KiB

Open AccessArticle

Changes in Body Mass Index after Initiation of Antiretroviral Treatment: Differences by Class of Core Drug

by Nikos Pantazis, Vasilios Papastamopoulos, Anastasia Antoniadou, Georgios Adamis, Vasilios Paparizos, Simeon Metallidis, Helen Sambatakou, Mina Psichogiou, Maria Chini, Georgios Chrysos, Periklis Panagopoulos, Nikolaos V. Sipsas, Emmanouil Barbunakis, Charalambos Gogos and Giota Touloumi

Viruses 2022, 14(8), 1677; https://doi.org/10.3390/v14081677 - 29 Jul 2022

Cited by 10 | Viewed by 2110

Abstract

Recent research on antiretroviral treatment (ART) for HIV suggests that integrase strand transfer inhibitors (INSTIs) cause faster weight gain compared to other drug classes. Here, we investigated changes in body mass index (BMI) and obesity prevalence after treatment initiation and corresponding differences between [...] Read more.

Recent research on antiretroviral treatment (ART) for HIV suggests that integrase strand transfer inhibitors (INSTIs) cause faster weight gain compared to other drug classes. Here, we investigated changes in body mass index (BMI) and obesity prevalence after treatment initiation and corresponding differences between drug classes. Data were derived from a large collaborative cohort in Greece. Included individuals were adults who started ART, in or after 2010, while previously ART naïve and achieved virologic response within the first year of ART. Data were analysed using mixed fractional polynomial models. INSTI regimens led to the more pronounced BMI increases, followed by boosted PI and NNRTI based regimens. Individuals with normal initial BMI are expected to gain 6 kg with an INSTI regimen compared to 4 kg with a boosted PI and less than 3 kg with a NNRTI regimen after four years of treatment. Prevalence of obesity was 5.7% at ART initiation and 12.2%, 14.2% and 18.1% after four years of treatment with NNRTIs, PIs, and INSTIs, respectively. Dolutegravir or Raltegravir were associated with marginally faster BMI increase compared to Elvitegravir. INSTIs are associated with faster weight gain. INSTIs’ increased risk of treatment emergent obesity and, possibly, weight-related co-morbidities should be judged against their improved efficacy and tolerability but increased clinical attention is required. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

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31 pages, 12017 KiB

Open AccessArticle

Understanding the Driving Forces That Trigger Mutations in SARS-CoV-2: Mutational Energetics and the Role of Arginine Blockers in COVID-19 Therapy

by Harry Ridgway, Christos T. Chasapis, Konstantinos Kelaidonis, Irene Ligielli, Graham J. Moore, Laura Kate Gadanec, Anthony Zulli, Vasso Apostolopoulos, Thomas Mavromoustakos and John M. Matsoukas

Viruses 2022, 14(5), 1029; https://doi.org/10.3390/v14051029 - 11 May 2022

Cited by 29 | Viewed by 4386

Abstract

SARS-CoV-2 is a global challenge due to its ability to mutate into variants that spread more rapidly than the wild-type virus. Because the molecular biology of this virus has been studied in such great detail, it represents an archetypal paradigm for research into [...] Read more.

SARS-CoV-2 is a global challenge due to its ability to mutate into variants that spread more rapidly than the wild-type virus. Because the molecular biology of this virus has been studied in such great detail, it represents an archetypal paradigm for research into new antiviral drug therapies. The rapid evolution of SARS-CoV-2 in the human population is driven, in part, by mutations in the receptor-binding domain (RBD) of the spike (S-) protein, some of which enable tighter binding to angiotensin-converting enzyme (ACE2). More stable RBD-ACE2 association is coupled with accelerated hydrolysis of furin and 3CLpro cleavage sites that augment infection. Non-RBD and non-interfacial mutations assist the S-protein in adopting thermodynamically favorable conformations for stronger binding. The driving forces of key mutations for Alpha, Beta, Gamma, Delta, Kappa, Lambda and Omicron variants, which stabilize the RBD-ACE2 complex, are investigated by free-energy computational approaches, as well as equilibrium and steered molecular dynamic simulations. Considered also are the structural hydropathy traits of the residues in the interface between SARS-CoV-2 RBD and ACE2 protein. Salt bridges and π-π interactions are critical forces that create stronger complexes between the RBD and ACE2. The trend of mutations is the replacement of non-polar hydrophobic interactions with polar hydrophilic interactions, which enhance binding of RBD with ACE2. However, this is not always the case, as conformational landscapes also contribute to a stronger binding. Arginine, the most polar and hydrophilic among the natural amino acids, is the most aggressive mutant amino acid for stronger binding. Arginine blockers, such as traditional sartans that bear anionic tetrazoles and carboxylates, may be ideal candidate drugs for retarding viral infection by weakening S-protein RBD binding to ACE2 and discouraging hydrolysis of cleavage sites. Based on our computational results it is suggested that a new generation of “supersartans”, called “bisartans”, bearing two anionic biphenyl-tetrazole pharmacophores, are superior to carboxylates in terms of their interactions with viral targets, suggesting their potential as drugs in the treatment of COVID-19. In Brief: This in silico study reviews our understanding of molecular driving forces that trigger mutations in the SARS-CoV-2 virus. It also reports further studies on a new class of “supersartans” referred to herein as “bisartans”, bearing two anionic biphenyltetrazole moieties that show potential in models for blocking critical amino acids of mutants, such as arginine, in the Delta variant. Bisartans may also act at other targets essential for viral infection and replication (i.e., ACE2, furin cleavage site and 3CLpro), rendering them potential new drugs for additional experimentation and translation to human clinical trials. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

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16 pages, 3529 KiB

Open AccessArticle

Characterizing Kinetics and Avidity of SARS-CoV-2 Antibody Responses in COVID-19 Greek Patients

by Stavroula Labropoulou, Niki Vassilaki, Raphaela S. Milona, Evangelos Terpos, Marianna Politou, Vasiliki Pappa, Maria Pagoni, Elisavet Grouzi, Meletios A. Dimopoulos, Andreas Mentis, Mary Emmanouil and Emmanouil Angelakis

Viruses 2022, 14(4), 758; https://doi.org/10.3390/v14040758 - 5 Apr 2022

Cited by 4 | Viewed by 2384

Abstract

In-depth understanding of the immune response provoked by SARS-CoV-2 infection is necessary, as there is a great risk of reinfection and a difficulty in achieving herd immunity due to a decline in both antibody concentration and avidity. Avidity testing, however, could overcome variability [...] Read more.

In-depth understanding of the immune response provoked by SARS-CoV-2 infection is necessary, as there is a great risk of reinfection and a difficulty in achieving herd immunity due to a decline in both antibody concentration and avidity. Avidity testing, however, could overcome variability in the immune response associated with sex or clinical symptoms, and thus differentiate between recent and past infections. In this context, here, we analyzed SARS-CoV-2 antibody kinetics and avidity in Greek hospitalized (26%) and non-hospitalized (74%) COVID-19 patients (N = 71) in the course of up to 15 months after their infection to improve the accuracy of the serological diagnosis in dating the onset of the infection. The results showed that IgG-S1 levels decline significantly at four months (p = 0.0239) in both groups of patients and are higher in hospitalized ones (up to 2.1-fold, p < 0.001). Additionally, hospitalized patients’ titers drop greatly and are equalized to non-hospitalized ones only at a time-point of twelve to fifteen months. Antibody levels of women in total remain more stable months after infection, compared to men. Furthermore, we examined the differential maturation of IgG avidity after SARS-CoV-2 infection, showing an incomplete maturation of avidity that results in a plateau at four months after infection. We also defined 38.2% avidity (sensitivity: 58.9%, specificity: 90.91%) as an appropriate “cut-off” that could be used to determine the stage of infection before avidity reaches a plateau. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

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21 pages, 1916 KiB

Open AccessArticle

Comparative Analysis of SARS-CoV-2 Variants of Concern, Including Omicron, Highlights Their Common and Distinctive Amino Acid Substitution Patterns, Especially at the Spike ORF

by Marios Nikolaidis, Athanasios Papakyriakou, Katerina Chlichlia, Panayotis Markoulatos, Stephen G. Oliver and Grigorios D. Amoutzias

Viruses 2022, 14(4), 707; https://doi.org/10.3390/v14040707 - 29 Mar 2022

Cited by 34 | Viewed by 4176

Abstract

In order to gain a deeper understanding of the recently emerged and highly divergent Omicron variant of concern (VoC), a study of amino acid substitution (AAS) patterns was performed and compared with those of the other four successful variants of concern (Alpha, Beta, [...] Read more.

In order to gain a deeper understanding of the recently emerged and highly divergent Omicron variant of concern (VoC), a study of amino acid substitution (AAS) patterns was performed and compared with those of the other four successful variants of concern (Alpha, Beta, Gamma, Delta) and one closely related variant of interest (VoI—Lambda). The Spike ORF consistently emerges as an AAS hotspot in all six lineages, but in Omicron this enrichment is significantly higher. The progenitors of each of these VoC/VoI lineages underwent positive selection in the Spike ORF. However, once they were established, their Spike ORFs have been undergoing purifying selection, despite the application of global vaccination schemes from 2021 onwards. Our analyses reject the hypothesis that the heavily mutated receptor binding domain (RBD) of the Omicron Spike was introduced via recombination from another closely related Sarbecovirus. Thus, successive point mutations appear as the most parsimonious scenario. Intriguingly, in each of the six lineages, we observed a significant number of AAS wherein the new residue is not present at any homologous site among the other known Sarbecoviruses. Such AAS should be further investigated as potential adaptations to the human host. By studying the phylogenetic distribution of AAS shared between the six lineages, we observed that the Omicron (BA.1) lineage had the highest number (8/10) of recurrent mutations. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

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15 pages, 3756 KiB

Open AccessArticle

Identifying Country-Level Risk Factors for the Spread of COVID-19 in Europe Using Machine Learning

by Serafeim Moustakidis, Christos Kokkotis, Dimitrios Tsaopoulos, Petros Sfikakis, Sotirios Tsiodras, Vana Sypsa, Theoklis E. Zaoutis and Dimitrios Paraskevis

Viruses 2022, 14(3), 625; https://doi.org/10.3390/v14030625 - 17 Mar 2022

Cited by 1 | Viewed by 2578

Abstract

Coronavirus disease 2019 (COVID-19) has resulted in approximately 5 million deaths around the world with unprecedented consequences in people’s daily routines and in the global economy. Despite vast increases in time and money spent on COVID-19-related research, there is still limited information about [...] Read more.

Coronavirus disease 2019 (COVID-19) has resulted in approximately 5 million deaths around the world with unprecedented consequences in people’s daily routines and in the global economy. Despite vast increases in time and money spent on COVID-19-related research, there is still limited information about the factors at the country level that affected COVID-19 transmission and fatality in EU. The paper focuses on the identification of these risk factors using a machine learning (ML) predictive pipeline and an associated explainability analysis. To achieve this, a hybrid dataset was created employing publicly available sources comprising heterogeneous parameters from the majority of EU countries, e.g., mobility measures, policy responses, vaccinations, and demographics/generic country-level parameters. Data pre-processing and data exploration techniques were initially applied to normalize the available data and decrease the feature dimensionality of the data problem considered. Then, a linear ε-Support Vector Machine (ε-SVM) model was employed to implement the regression task of predicting the number of deaths for each one of the three first pandemic waves (with mean square error of 0.027 for wave 1 and less than 0.02 for waves 2 and 3). Post hoc explainability analysis was finally applied to uncover the rationale behind the decision-making mechanisms of the ML pipeline and thus enhance our understanding with respect to the contribution of the selected country-level parameters to the prediction of COVID-19 deaths in EU. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

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33 pages, 5131 KiB

Open AccessArticle

Dengue Virus Replication Is Associated with Catecholamine Biosynthesis and Metabolism in Hepatocytes

by George Mpekoulis, Vassilina Tsopela, Anna Chalari, Katerina I. Kalliampakou, Georgios Panos, Efseveia Frakolaki, Raphaela S. Milona, Diamantis C. Sideris, Dido Vassilacopoulou and Niki Vassilaki

Viruses 2022, 14(3), 564; https://doi.org/10.3390/v14030564 - 9 Mar 2022

Cited by 6 | Viewed by 3330

Abstract

Previously, the association between the catecholamine biosynthetic enzyme L-Dopa decarboxylase (DDC) and Dengue virus (DV) replication was demonstrated in liver cells and was found to be mediated at least by the interaction between DDC and phosphoinositide 3-kinase (PI3K). Here, we show that biogenic [...] Read more.

Previously, the association between the catecholamine biosynthetic enzyme L-Dopa decarboxylase (DDC) and Dengue virus (DV) replication was demonstrated in liver cells and was found to be mediated at least by the interaction between DDC and phosphoinositide 3-kinase (PI3K). Here, we show that biogenic amines production and uptake impede DV replication in hepatocytes and monocytes, while the virus reduces catecholamine biosynthesis, metabolism, and transport. To examine how catecholamine biosynthesis/metabolism influences DV, first, we verified the role of DDC by altering DDC expression. DDC silencing enhanced virus replication, but not translation, attenuated the negative effect of DDC substrates on the virus and reduced the infection related cell death. Then, the role of the downstream steps of the catecholamine biosynthesis/metabolism was analyzed by chemical inhibition of the respective enzymes, application of their substrates and/or their products; moreover, reserpine, the inhibitor of the vesicular monoamine transporter 2 (VMAT2), was used to examine the role of uptake/storage of catecholamines on DV. Apart from the role of each enzyme/transporter, these studies revealed that the dopamine uptake, and not the dopamine-signaling, is responsible for the negative effect on DV. Accordingly, all treatments expected to enhance the accumulation of catecholamines in the cell cytosol suppressed DV replication. This was verified by the use of chemical inducers of catecholamine biosynthesis. Last, the cellular redox alterations due to catecholamine oxidation were not related with the inhibition of DV replication. In turn, DV apart from its negative impact on DDC, inhibits tyrosine hydroxylase, dopamine beta-hydroxylase, monoamine oxidase, and VMAT2 expression. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

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26 pages, 2623 KiB

Open AccessArticle

Association of Hepatitis C Virus Replication with the Catecholamine Biosynthetic Pathway

by George Mpekoulis, Vassilina Tsopela, Georgios Panos, Vasileiοs Siozos, Katerina I. Kalliampakou, Efseveia Frakolaki, Constantinos D. Sideris, Alice G. Vassiliou, Diamantis C. Sideris, Dido Vassilacopoulou and Niki Vassilaki

Viruses 2021, 13(11), 2139; https://doi.org/10.3390/v13112139 - 23 Oct 2021

Cited by 8 | Viewed by 3512

Abstract

A bidirectional negative relationship between Hepatitis C virus (HCV) replication and gene expression of the catecholamine biosynthetic enzyme L-Dopa decarboxylase (DDC) was previously shown in the liver and attributed at least to an association of DDC with phosphatidylinositol 3-kinase (PI3K). Here, we report [...] Read more.

A bidirectional negative relationship between Hepatitis C virus (HCV) replication and gene expression of the catecholamine biosynthetic enzyme L-Dopa decarboxylase (DDC) was previously shown in the liver and attributed at least to an association of DDC with phosphatidylinositol 3-kinase (PI3K). Here, we report that the biosynthesis and uptake of catecholamines restrict HCV replication in hepatocytes, while HCV has developed ways to reduce catecholamine production. By employing gene silencing, chemical inhibition or induction of the catecholamine biosynthetic and metabolic enzymes and transporters, and by applying the substrates or the products of the respective enzymes, we unravel the role of the different steps of the pathway in viral infection. We also provide evidence that the effect of catecholamines on HCV is strongly related with oxidative stress that is generated by their autoxidation in the cytosol, while antioxidants or treatments that lower cytosolic catecholamine levels positively affect the virus. To counteract the effect of catecholamines, HCV, apart from the already reported effects on DDC, causes the down-regulation of tyrosine hydroxylase that encodes the rate-limiting enzyme of catecholamine biosynthesis and suppresses dopamine beta-hydroxylase mRNA and protein amounts, while increasing the catecholamine degradation enzyme monoamine oxidase. Moreover, the NS4B viral protein is implicated in the effect of HCV on the ratio of the ~50 kDa DDC monomer and a ~120 kDa DDC complex, while the NS5A protein has a negative effect on total DDC protein levels. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

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8 pages, 219 KiB

Open AccessCommunication

Prevalence of Common Viral Skin Infections in Beach Volleyball Athletes

by Niki Tertipi, Vasiliki Kefala, Effie Papageorgiou and Efstathios Rallis

Viruses 2021, 13(11), 2107; https://doi.org/10.3390/v13112107 - 20 Oct 2021

Cited by 7 | Viewed by 3616

Abstract

Viral skin infections often affect the sports community. The aim of this study was to assess the rates, location sites, and seasons of appearance of common viral cutaneous diseases in beach volleyball athletes in Greece. Five hundred and forty-nine beach volleyball athletes participated [...] Read more.

Viral skin infections often affect the sports community. The aim of this study was to assess the rates, location sites, and seasons of appearance of common viral cutaneous diseases in beach volleyball athletes in Greece. Five hundred and forty-nine beach volleyball athletes participated in this study. The average age was 28.4 years. The viral infections were herpes simplex (type 1), molluscum contagiosum and warts. The measured parameters included: gender, age, the season when athletes may be more susceptible to infections and the location of infection in the body. Practicing information such as the number of training years, number of weekly trainings, and average hours of daily training was also recorded. Incidence rates correlated in relation to age: (a) warts (p < 0.001), molluscum contagiosum (p < 0.001), and herpes simplex (p = 0.001); (b) years of training: warts (p < 0.001), molluscum contagiosum (p < 0.001), and herpes simplex (p = 0.004); (c) average hours of daily training: molluscum contagiosum (p = 0.006) and herpes simplex (p < 0.010). The skin is the largest organ, and the risk of infection should not be underestimated. Prevention, early detection, recognition, and treatment are related to health and athletic performance, but also to the risk of transmission. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

Review

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18 pages, 955 KiB

Open AccessReview

Viral Infections and Schizophrenia: A Comprehensive Review

by Ioanna Kotsiri, Panagiota Resta, Alexandros Spyrantis, Charalampos Panotopoulos, Dimitrios Chaniotis, Apostolos Beloukas and Emmanouil Magiorkinis

Viruses 2023, 15(6), 1345; https://doi.org/10.3390/v15061345 - 9 Jun 2023

Cited by 14 | Viewed by 6311

Abstract

Schizophrenia is a complex mental disorder with multiple genetic and environmental factors contributing to its pathogenesis. Viral infections have been suggested to be one of the environmental factors associated with the development of this disorder. We comprehensively review all relevant published literature focusing [...] Read more.

Schizophrenia is a complex mental disorder with multiple genetic and environmental factors contributing to its pathogenesis. Viral infections have been suggested to be one of the environmental factors associated with the development of this disorder. We comprehensively review all relevant published literature focusing on the relationship between schizophrenia and various viral infections, such as influenza virus, herpes virus 1 and 2 (HSV-1 and HSV-2), cytomegalovirus (CMV), Epstein-Barr virus (EBV), retrovirus, coronavirus, and Borna virus. These viruses may interfere with the normal maturation of the brain directly or through immune-induced mediators, such as cytokines, leading to the onset of schizophrenia. Changes in the expression of critical genes and elevated levels of inflammatory cytokines have been linked to virally-induced infections and relevant immune activities in schizophrenia. Future research is necessary to understand this relationship better and provide insight into the molecular mechanisms underlying the pathophysiology of schizophrenia. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

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24 pages, 1058 KiB

Open AccessReview

The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the COVID-19 Pandemic and the Future Evolutionary Paths of SARS-CoV-2

by Grigorios D. Amoutzias, Marios Nikolaidis, Eleni Tryfonopoulou, Katerina Chlichlia, Panayotis Markoulatos and Stephen G. Oliver

Viruses 2022, 14(1), 78; https://doi.org/10.3390/v14010078 - 2 Jan 2022

Cited by 72 | Viewed by 12010

Abstract

Coronaviruses (CoVs) constitute a large and diverse subfamily of positive-sense single-stranded RNA viruses. They are found in many mammals and birds and have great importance for the health of humans and farm animals. The current SARS-CoV-2 pandemic, as well as many previous epidemics [...] Read more.

Coronaviruses (CoVs) constitute a large and diverse subfamily of positive-sense single-stranded RNA viruses. They are found in many mammals and birds and have great importance for the health of humans and farm animals. The current SARS-CoV-2 pandemic, as well as many previous epidemics in humans that were of zoonotic origin, highlights the importance of studying the evolution of the entire CoV subfamily in order to understand how novel strains emerge and which molecular processes affect their adaptation, transmissibility, host/tissue tropism, and patho non-homologous genicity. In this review, we focus on studies over the last two years that reveal the impact of point mutations, insertions/deletions, and intratypic/intertypic homologous and non-homologous recombination events on the evolution of CoVs. We discuss whether the next generations of CoV vaccines should be directed against other CoV proteins in addition to or instead of spike. Based on the observed patterns of molecular evolution for the entire subfamily, we discuss five scenarios for the future evolutionary path of SARS-CoV-2 and the COVID-19 pandemic. Finally, within this evolutionary context, we discuss the recently emerged Omicron (B.1.1.529) VoC. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

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Other

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8 pages, 628 KiB

Open AccessBrief Report

The T350G Variation of Human Papillomavirus 16 E6 Gene Prevails in Oropharyngeal Cancer from a Small Cohort of Greek Patients

by Christine Kottaridi, Panagiota Resta, Danai Leventakou, Katerina Gioti, Ioannis Zygouras, Alina-Roxani Gouloumi, Georgios Sakagiannis, Khalid J. Alzahrani, Maria S. Venetikou, Fragkiski Anthouli-Anagnostopoulou and Apostolos Beloukas

Viruses 2022, 14(8), 1724; https://doi.org/10.3390/v14081724 - 4 Aug 2022

Cited by 4 | Viewed by 2788

Abstract

Recent trends have shown a dramatic rise in the incidence of oropharyngeal squamous cell carcinoma strongly associated with high-risk human papillomavirus (HPV) of type 16. The genetic variability of HPV16 has been extensively studied in cervical cancer but there are very limited published [...] Read more.

Recent trends have shown a dramatic rise in the incidence of oropharyngeal squamous cell carcinoma strongly associated with high-risk human papillomavirus (HPV) of type 16. The genetic variability of HPV16 has been extensively studied in cervical cancer but there are very limited published data concerning the genetic variations of this HPV type in oropharyngeal cancer. In the present study, the genetic variations of HPV16 E6 gene sequences originated from a small cohort of Greek patients diagnosed with oropharyngeal cancer were assessed. The vast majority of the sequences clustered within the European variant branch. The T350G variation was found to be the predominant one. This finding may indicate the need for further studies that could explain the possible impact of this variant in the pathomechanisms of oropharyngeal cancer. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

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16 pages, 1575 KiB

Open AccessSystematic Review

Global Burden of Cyclospora cayetanensis Infection and Associated Risk Factors in People Living with HIV and/or AIDS

by Saba Ramezanzadeh, Apostolos Beloukas, Abdol Sattar Pagheh, Mohammad Taghi Rahimi, Seyed Abdollah Hosseini, Sonia M. Rodrigues Oliveira, Maria de Lourdes Pereira and Ehsan Ahmadpour

Viruses 2022, 14(6), 1279; https://doi.org/10.3390/v14061279 - 12 Jun 2022

Cited by 10 | Viewed by 3514

Abstract

Cyclospora cayetanensis infections remain one of the most common protozoan opportunistic causes of gastrointestinal diseases and diarrhea among people living with HIV and/or AIDS (PLWHA). This study was conducted to provide a summary of the evidence on the global burden of C. cayetanensis [...] Read more.

Cyclospora cayetanensis infections remain one of the most common protozoan opportunistic causes of gastrointestinal diseases and diarrhea among people living with HIV and/or AIDS (PLWHA). This study was conducted to provide a summary of the evidence on the global burden of C. cayetanensis infection and associated risk factors among PLWHA. Scopus, PubMed, Science Direct, and EMBASE were searched up to February 2022. All original peer-reviewed original research articles were considered, including descriptive and cross-sectional studies describing C. cayetanensis in PLWHA. Incoherence and heterogeneity between studies were quantified by I index and Cochran’s Q test. Publication and population bias were assessed with funnel plots and Egger’s asymmetry regression test. All statistical analyses were performed using StatsDirect. The pooled prevalence of C. cayetanensis infection among PLWHA was 3.89% (95% CI, 2.62–5.40). The highest prevalence found in South America was 7.87% and the lowest in Asia 2.77%. In addition, the prevalence of C. cayetanensis was higher in PLWHA compared to healthy individuals. There was a relationship between a higher C. cayetanensis prevalence in PLWHA with a CD4 cell count below 200 cells/mL and people with diarrhea. The results show that PLWHA are more vulnerable to C. cayetanensis infection and emphasizes the need to implement the screening and prophylaxis tailored to the local context. Owing to the serious and significant clinical manifestations of the parasite, an early identification of seropositivity is recommended to initiate prophylaxis between PLWHA with a CD4 count ≤200 cells/mL and PLWHA who do not receive antiviral therapy. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

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11 pages, 1185 KiB

Open AccessCase Report

SARS-CoV-2 Antigenemia as a Confounding Factor in Immunodiagnostic Assays: A Case Study

by Konstantinos Belogiannis, Venetia A. Florou, Paraskevi C. Fragkou, Stefanos Ferous, Loukas Chatzis, Aikaterini Polyzou, Nefeli Lagopati, Demetrios Vassilakos, Christos Kittas, Athanasios G. Tzioufas, Sotirios Tsiodras, George Sourvinos and Vassilis G. Gorgoulis

Viruses 2021, 13(6), 1143; https://doi.org/10.3390/v13061143 - 14 Jun 2021

Cited by 14 | Viewed by 4503

Abstract

Humoral immunity has emerged as a vital immune component against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nevertheless, a subset of recovered Coronavirus Disease-2019 (COVID-19) paucisymptomatic/asymptomatic individuals do not generate an antibody response, constituting a paradox. We assumed that immunodiagnostic assays may operate [...] Read more.

Humoral immunity has emerged as a vital immune component against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nevertheless, a subset of recovered Coronavirus Disease-2019 (COVID-19) paucisymptomatic/asymptomatic individuals do not generate an antibody response, constituting a paradox. We assumed that immunodiagnostic assays may operate under a competitive format within the context of antigenemia, potentially explaining this phenomenon. We present a case where persistent antigenemia/viremia was documented for at least 73 days post-symptom onset using ‘in-house’ methodology, and as it progressively declined, seroconversion took place late, around day 55, supporting our hypothesis. Thus, prolonged SARS-CoV-2 antigenemia/viremia could mask humoral responses, rendering, in certain cases, the phenomenon of ‘non-responders’ a misnomer. Full article

(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)

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