Journal Description
Viruses
Viruses
is a peer-reviewed, open access journal of virology, published monthly online by MDPI. The American Society for Virology (ASV), Spanish Society for Virology (SEV), Canadian Society for Virology (CSV), Italian Society for Virology (SIV-ISV), Australasian Virology Society (AVS) and others are affiliated with Viruses and their members receive a discount on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, MEDLINE, PMC, Embase, PubAg, AGRIS, and other databases.
- Journal Rank: JCR - Q2 (Virology) / CiteScore - Q1 (Infectious Diseases)
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 16.1 days after submission; acceptance to publication is undertaken in 2.6 days (median values for papers published in this journal in the first half of 2024).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
- Companion journal: Zoonotic Diseases.
Impact Factor:
3.8 (2023);
5-Year Impact Factor:
4.0 (2023)
Latest Articles
Interactions between Common Bean Viruses and Their Whitefly Vector
Viruses 2024, 16(10), 1567; https://doi.org/10.3390/v16101567 - 2 Oct 2024
Abstract
Common bean (Phaseolus vulgaris L.) is a widely cultivated crop, representing an important protein source in the human diet in developing countries. The production of this crop faces serious challenges, such as virus diseases transmitted by the whitefly Bemisia tabaci. Although
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Common bean (Phaseolus vulgaris L.) is a widely cultivated crop, representing an important protein source in the human diet in developing countries. The production of this crop faces serious challenges, such as virus diseases transmitted by the whitefly Bemisia tabaci. Although there is a lot of information about some of these viruses, most of what we know has been developed using model systems, such as tomato plants and tomato yellow leaf curl virus (TYLCV). There is still very little information on the most relevant common bean viruses, such as bean golden mosaic virus (BGMV), bean golden yellow mosaic virus (BGYMV), bean dwarf mosaic virus (BDMV), cowpea mild mottle virus (CPMMV), and bean yellow disorder virus (BnYDV). In this review, we discuss the available data in the most up-to-date literature and suggest future research avenues to contribute to the development of management tools for preventing or reducing the damage caused by viruses in this important crop.
Full article
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
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Open AccessArticle
Tsg101 UEV Interaction with Nedd4 HECT Relieves E3 Ligase Auto-Inhibition, Promoting HIV-1 Assembly and CA-SP1 Maturation Cleavage
by
Susan M. Watanabe, David A. Nyenhuis, Mahfuz Khan, Lorna S. Ehrlich, Irene Ischenko, Michael D. Powell, Nico Tjandra and Carol A. Carter
Viruses 2024, 16(10), 1566; https://doi.org/10.3390/v16101566 - 2 Oct 2024
Abstract
Tsg101, a component of the endosomal sorting complex required for transport (ESCRT), is responsible for recognition of events requiring the machinery, as signaled by cargo tagging with ubiquitin (Ub), and for recruitment of downstream acting subunits to the site. Although much is known
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Tsg101, a component of the endosomal sorting complex required for transport (ESCRT), is responsible for recognition of events requiring the machinery, as signaled by cargo tagging with ubiquitin (Ub), and for recruitment of downstream acting subunits to the site. Although much is known about the latter function, little is known about its role in the earlier event. The N-terminal domain of Tsg101 is a structural homologue of Ub conjugases (E2 enzymes) and the protein associates with Ub ligases (E3 enzymes) that regulate several cellular processes including virus budding. A pocket in the domain recognizes a motif, PT/SAP, that permits its recruitment. PT/SAP disruption makes budding dependent on Nedd4L E3 ligases. Using HIV-1 encoding a PT/SAP mutation that makes budding Nedd4L-dependent, we identified as critical for rescue the residues in the catalytic (HECT) domain of the E3 enzyme that lie in proximity to sites in Tsg101 that bind Ub non-covalently. Mutation of these residues impaired rescue by Nedd4L but the same mutations had no apparent effect in the context of a Nedd4 isomer, Nedd4-2s, whose N-terminal (C2) domain is naturally truncated, precluding C2-HECT auto-inhibition. Surprisingly, like small molecules that disrupt Tsg101 Ub-binding, small molecules that interfered with Nedd4 substrate recognition arrested budding at an early stage, supporting the conclusion that Tsg101–Ub–Nedd4 interaction promotes enzyme activation and regulates Nedd4 signaling for viral egress. Tsg101 regulation of E3 ligases may underlie its broad ability to function as an effector in various cellular activities, including viral particle assembly and budding.
Full article
(This article belongs to the Special Issue 12th International Retroviral Symposium: Assembly, Maturation and Uncoating)
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Open AccessReview
Applications of CRISPR/Cas as a Toolbox for Hepatitis B Virus Detection and Therapeutics
by
Anuj Kumar, Emmanuel Combe, Léa Mougené, Fabien Zoulim and Barbara Testoni
Viruses 2024, 16(10), 1565; https://doi.org/10.3390/v16101565 - 2 Oct 2024
Abstract
Hepatitis B virus (HBV) infection remains a significant global health challenge, leading to chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). Covalently closed circular DNA (cccDNA) and integrated HBV DNA are pivotal in maintaining viral persistence. Recent advances in CRISPR/Cas technology offer innovative
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Hepatitis B virus (HBV) infection remains a significant global health challenge, leading to chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). Covalently closed circular DNA (cccDNA) and integrated HBV DNA are pivotal in maintaining viral persistence. Recent advances in CRISPR/Cas technology offer innovative strategies to inhibit HBV by directly targeting both cccDNA and integrated HBV DNA or indirectly by degrading HBV RNAs or targeting host proteins. This review provides a comprehensive overview of the latest advancements in using CRISPR/Cas to inhibit HBV, with a special highlight on newer non-double-strand (non-DSB) break approaches. Beyond the canonical use of CRISPR/Cas for target inhibition, we discuss additional applications, including HBV diagnosis and developing models to understand cccDNA biology, highlighting the diverse use of this technology in the HBV field.
Full article
(This article belongs to the Special Issue CRISPR/Cas in Viral Research 2024)
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Open AccessCommunication
Modulation of ADAM17 Levels by Pestiviruses Is Species-Specific
by
Hann-Wei Chen, Marianne Zaruba, Aroosa Dawood, Stefan Düsterhöft, Benjamin Lamp, Till Ruemenapf and Christiane Riedel
Viruses 2024, 16(10), 1564; https://doi.org/10.3390/v16101564 - 2 Oct 2024
Abstract
Upon host cell infection, viruses modulate their host cells to better suit their needs, including the downregulation of virus entry receptors. ADAM17, a cell surface sheddase, is an essential factor for infection of bovine cells with several pestiviruses. To assess the effect of
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Upon host cell infection, viruses modulate their host cells to better suit their needs, including the downregulation of virus entry receptors. ADAM17, a cell surface sheddase, is an essential factor for infection of bovine cells with several pestiviruses. To assess the effect of pestivirus infection on ADAM17, the amounts of cellular ADAM17 and its presence at the cell surface were determined. Mature ADAM17 levels were reduced upon infection with a cytopathic pestivirus bovis (bovine viral diarrhea virus, cpBVDV), pestivirus suis (classical swine fever virus, CSFV) or pestivirus giraffae (strain giraffe), but not negatively affected by pestivirus L (Linda virus, LindaV). A comparable reduction of ADAM17 surface levels, which represents the bioactive form, could be observed in the presence of E2 of BVDV and CSFV, but not LindaV or atypical porcine pestivirus (pestivirus scrofae) E2. Superinfection exclusion in BVDV infection is caused by at least two proteins, glycoprotein E2 and protease/helicase NS3. To evaluate whether the lowered ADAM17 levels could be involved in superinfection exclusion, persistently CSFV- or LindaV-infected cells were challenged with different pestiviruses. Persistently LindaV-infected cells were significantly more susceptible to cpBVDV infection than persistently CSFV-infected cells, whilst the other pestiviruses tested were not or only hardly able to infect the persistently infected cells. These results provide evidence of a pestivirus species-specific effect on ADAM17 levels and hints at the possibility of its involvement in superinfection exclusion.
Full article
(This article belongs to the Special Issue Pestivirus 2024)
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Open AccessReview
The Role of Macrophages in Airway Disease Focusing on Porcine Reproductive and Respiratory Syndrome Virus and the Treatment with Antioxidant Nanoparticles
by
Kyuhyung Choi
Viruses 2024, 16(10), 1563; https://doi.org/10.3390/v16101563 - 1 Oct 2024
Abstract
Lung macrophage cells play a critical role in various lung diseases, and their state can change depending on the progression of the disease by inducing either an inflammatory or anti-inflammatory state. In this review, the potential therapeutic effects of treatment with antioxidant nanoparticles
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Lung macrophage cells play a critical role in various lung diseases, and their state can change depending on the progression of the disease by inducing either an inflammatory or anti-inflammatory state. In this review, the potential therapeutic effects of treatment with antioxidant nanoparticles in air-borne diseases focusing on porcine reproductive and respiratory virus (PRRSV), considering reactive oxygen species (ROS) as one of the factors that regulate M1 and M2 macrophages in the inflammatory and anti-inflammatory states, respectively, was described. In addition, the author examines the status of protein structure research on CD163 (one of the markers of anti-inflammatory M2 macrophages) in human and veterinary lung diseases.
Full article
(This article belongs to the Special Issue Viruses and Virus-Like Particles as Nanoplatforms for Vaccines, Diagnostic and Therapeutic Nanomedicine)
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Open AccessReview
A Journey through the Minefield of the Discovery and Characterization of Latency-Related RNA/Latency-Associated Transcript
by
Homayon Ghiasi
Viruses 2024, 16(10), 1562; https://doi.org/10.3390/v16101562 - 30 Sep 2024
Abstract
Scientific knowledge evolves in small steps, with occasional backsteps to correct inaccuracies, all occurring within a competitive environment. This perspective for the first time looks at the history of latency-related RNA (LR-RNA) that was later renamed latency-associated transcript (LAT). At the 1986 International
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Scientific knowledge evolves in small steps, with occasional backsteps to correct inaccuracies, all occurring within a competitive environment. This perspective for the first time looks at the history of latency-related RNA (LR-RNA) that was later renamed latency-associated transcript (LAT). At the 1986 International Herpesvirus Workshop (IHW) meeting in Leeds, England, Daniel L Rock and Anthony B Nesburn first reported the discovery of human herpes virus 1 (HSV-1) latency-related (LR) RNA that is antisense to ICP0. Less than a month after the IHW meeting, a paper was submitted to Science magazine and 8 months later appeared in print thanking “D. Rock for suggesting RNA complementary to the ICP0 message may be present in latently infected cells”. This perspective is not a review of the LAT literature but intends to clarify the timeline of LAT discovery and subsequent breakthroughs such as reactivation, apoptosis, CD8+ T cell exhaustion, and LAT expression in different cell types detected during latency. While many review articles have been written about LAT since 1987, the most comprehensive and balanced review about LAT was written by Dr. David Bloom’s group. In this overview, I will discuss our original collaboration with Dr. Dan Rock and subsequent work that our group performed, which is still ongoing. Finally, I will discuss the controversies associated with LAT from its inception to current times.
Full article
(This article belongs to the Special Issue Viruses and Eye Diseases)
Open AccessArticle
The First Pseudomonas Phage vB_PseuGesM_254 Active against Proteolytic Pseudomonas gessardii Strains
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Vera Morozova, Igor Babkin, Alina Mogileva, Yuliya Kozlova, Artem Tikunov, Alevtina Bardasheva, Valeria Fedorets, Elena Zhirakovskaya, Tatiana Ushakova and Nina Tikunova
Viruses 2024, 16(10), 1561; https://doi.org/10.3390/v16101561 - 30 Sep 2024
Abstract
Bacteria of the Pseudomonas genus, including the Pseudomonas gessardii subgroup, play an important role in the environmental microbial communities. Psychrotolerant isolates of P. gessardii can produce thermostable proteases and lipases. When contaminating refrigerated raw milk, these bacteria spoil it by producing enzymes resistant
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Bacteria of the Pseudomonas genus, including the Pseudomonas gessardii subgroup, play an important role in the environmental microbial communities. Psychrotolerant isolates of P. gessardii can produce thermostable proteases and lipases. When contaminating refrigerated raw milk, these bacteria spoil it by producing enzymes resistant to pasteurization. One possible way to prevent spoilage of raw milk is to use Pseudomonas lytic phages specific to undesirable P. gessardii isolates. The first phage, Pseudomonas vB_PseuGesM_254, was isolated and characterized, which is active against several proteolytic P. gessardii strains. This lytic myophage can infect and lyse its host strain at 24 °C and at low temperature (8 °C); so, it has the potential to prevent contamination of raw milk. The vB_PseuGesM_254 genome, 95,072 bp, shows a low level of intergenomic similarity with the genomes of known phages. Comparative proteomic ViPTree analysis indicated that vB_PseuGesM_254 is associated with a large group of Pseudomonas phages that are members of the Skurskavirinae and Gorskivirinae subfamilies and the Nankokuvirus genus. The alignment constructed using ViPTree shows that the vB_PseuGesM_254 genome has a large inversion between ~53,100 and ~70,700 bp, which is possibly a distinctive feature of a new taxonomic unit within this large group of Pseudomonas phages.
Full article
(This article belongs to the Special Issue Bacteriophage Diversity)
Open AccessReview
The Management of Hematopoietic Stem Cell Transplant in People with HIV
by
Jana K. Dickter and Courtney Moc Willeford
Viruses 2024, 16(10), 1560; https://doi.org/10.3390/v16101560 - 30 Sep 2024
Abstract
Hematopoietic stem cell transplant (HSCT) is now recognized as a standard treatment option for people with HIV (PWH) who develop high-risk hematologic malignancies. However, the involved polypharmacy can lead to complications from drug interactions and toxicities, affecting the efficacy and safety of chemotherapy
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Hematopoietic stem cell transplant (HSCT) is now recognized as a standard treatment option for people with HIV (PWH) who develop high-risk hematologic malignancies. However, the involved polypharmacy can lead to complications from drug interactions and toxicities, affecting the efficacy and safety of chemotherapy and antiretroviral therapy (ART). Managing these patients requires a personalized approach, including the careful selection of ART based on previous therapies and potential interactions, alongside risk assessment for infections. This discussion will address the history of HSCT in PWH and management considerations for this group.
Full article
(This article belongs to the Special Issue Viral Infections in Hematopoietic Stem Cell Transplant and Cellular Therapy Recipients)
Open AccessArticle
GPCR Inhibitors Have Antiviral Properties against JC Polyomavirus Infection
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Amanda L. Sandberg, Avery C. S. Bond, Lucas J. Bennett, Sophie E. Craig, David P. Winski, Lara C. Kirkby, Abby R. Kraemer, Kristina G. Kelly, Samuel T. Hess and Melissa S. Maginnis
Viruses 2024, 16(10), 1559; https://doi.org/10.3390/v16101559 (registering DOI) - 30 Sep 2024
Abstract
JC polyomavirus (JCPyV) infects the majority of the population and initially establishes a persistent but asymptomatic infection of the kidneys. In healthy individuals, the infection remains controlled by the host immune system, but for individuals experiencing prolonged immunosuppression, the infection can reactivate and
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JC polyomavirus (JCPyV) infects the majority of the population and initially establishes a persistent but asymptomatic infection of the kidneys. In healthy individuals, the infection remains controlled by the host immune system, but for individuals experiencing prolonged immunosuppression, the infection can reactivate and spread to the brain, where it causes progressive multifocal leukoencephalopathy (PML), which is a fatal neurodegenerative disease. Currently, there are no approved therapies to treat PML, and affected individuals suffer rapid motor weakness and cognitive deterioration. To identify novel therapeutic treatments for JCPyV infection, receptor agonists/antagonists identified in a previously published drug screen were evaluated for their antiviral properties. Seven drugs were selected and validated using infectivity assays, and the mechanism of inhibition was further explored for G protein coupled receptor (GPCR)-associated inhibitors due to the role of the GPCR 5-hydroxytryptamine 2 receptors (5-HT2Rs) in JCPyV entry. The inhibitors cetirizine and paroxetine both reduced infection early in the JCPyV infectious cycle. Paroxetine specifically reduced viral internalization through altering the receptor density of 5-HT2CR, inhibiting β-arrestin recruitment to the receptor, and reducing MAPK signaling through ERK. These findings highlight the potential of receptor signaling and viral entry mechanisms as possible targets for antiviral drug development. Further, this research suggests that FDA-approved receptor agonists/antagonists currently used to treat other medical conditions could be repurposed into antivirals for the possible treatment of JCPyV infection and the fatal disease PML.
Full article
(This article belongs to the Special Issue JC Polyomavirus)
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Molecular Detection by Rolling Circle Amplification Combined with Deep Sequencing of Mixed Infection by Bovine Papillomaviruses 2 and 4 in Carcinoma In Situ of the Bovine Esophageal Mucosa
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Bruna F. Matias, Michele Lunardi, Kátia C. B. Gonçalves, Laurival A. Vilas-Boas, Emanuele Gustani-Buss, Ana Paula F. R. L. Bracarense, Luiz Fernando C. Cunha Filho, Alice F. Alfieri and Amauri A. Alfieri
Viruses 2024, 16(10), 1558; https://doi.org/10.3390/v16101558 - 30 Sep 2024
Abstract
Papillomaviruses (PVs) are oncogenic and infect the skin and mucosa of various host species. Considering the recent advances in research on PVs using rolling circle amplification (RCA) followed by high-throughput sequencing (HTS), in this study, we aimed to investigate the bovine papillomavirus (BPV)
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Papillomaviruses (PVs) are oncogenic and infect the skin and mucosa of various host species. Considering the recent advances in research on PVs using rolling circle amplification (RCA) followed by high-throughput sequencing (HTS), in this study, we aimed to investigate the bovine papillomavirus (BPV) types associated with proliferative lesions in the upper alimentary tract of an affected bull and characterize the viral strains through complete genome sequencing using this strategy. We analyzed the PV strains associated with two hyperplastic esophageal lesions through PCR using degenerate primer pairs and RCA, followed by HTS. HTS of the libraries generated using RCA products provided the whole genome sequence of BPV4 present in squamous papilloma, whereas the complete genome sequence of BPV2 and subgenomic fragments of BPV4 were identified in carcinoma in situ (CIS). For the first time, we have sequenced BPV2 identified from the CIS of the bovine upper alimentary canal. Additionally, RCA followed by HTS allowed characterization of the mixed infection by BPV2 and BPV4 in this lesion. These data reveal that BPV4 is not the only BPV type present in CIS of the esophageal mucous membrane; moreover, a mixed infection caused by BPV2 and BPV4 at the tested anatomical site was demonstrated.
Full article
(This article belongs to the Special Issue Animal Papillomaviruses Research)
Open AccessArticle
Discriminating North American Swine Influenza Viruses with a Portable, One-Step, Triplex Real-Time RT-PCR Assay, and Portable Sequencing
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Marie K. Kirby, Bo Shu, Matthew W. Keller, Malania M. Wilson, Benjamin L. Rambo-Martin, Yunho Jang, Jimma Liddell, Eduardo Salinas Duron, Jacqueline M. Nolting, Andrew S. Bowman, C. Todd Davis, David E. Wentworth and John R. Barnes
Viruses 2024, 16(10), 1557; https://doi.org/10.3390/v16101557 - 30 Sep 2024
Abstract
Swine harbors a genetically diverse population of swine influenza A viruses (IAV-S), with demonstrated potential to transmit to the human population, causing outbreaks and pandemics. Here, we describe the development of a one-step, triplex real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay that detects
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Swine harbors a genetically diverse population of swine influenza A viruses (IAV-S), with demonstrated potential to transmit to the human population, causing outbreaks and pandemics. Here, we describe the development of a one-step, triplex real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay that detects and distinguishes the majority of the antigenically distinct influenza A virus hemagglutinin (HA) clades currently circulating in North American swine, including the IAV-S H1 1A.1 (α), 1A.2 (β), 1A.3 (γ), 1B.2.2 (δ1) and 1B.2.1 (δ2) clades, and the IAV-S H3 2010.1 clade. We performed an in-field test at an exhibition swine show using in-field viral concentration and RNA extraction methodologies and a portable real-time PCR instrument, and rapidly identified three distinct IAV-S clades circulating within the N.A. swine population. Portable sequencing is used to further confirm the results of the in-field test of the swine triplex assay. The IAV-S triplex rRT-PCR assay can be easily transported and used in-field to characterize circulating IAV-S clades in North America, allowing for surveillance and early detection of North American IAV-S with human outbreak and pandemic potential.
Full article
(This article belongs to the Special Issue Advances in Animal Influenza Virus Research: Third Edition)
Open AccessArticle
Understanding the Omicron Variant Impact in Healthcare Workers: Insights from the Prospective COVID-19 Post-Immunization Serological Cohort in Munich (KoCo-Impf) on Risk Factors for Breakthrough and Reinfections
by
Christian Janke, Raquel Rubio-Acero, Maximilian Weigert, Christina Reinkemeyer, Yeganeh Khazaei, Lisa Kleinlein, Ronan Le Gleut, Katja Radon, Marlene Hannes, Francesco Picasso, Anne Elisabeth Lucke, Michael Plank, Irene Charlotte Kotta, Ivana Paunovic, Ana Zhelyazkova, Ivan Noreña, Simon Winter, Michael Hoelscher, Andreas Wieser, Helmut Küchenhoff, Noemi Castelletti and on behalf of the ORCHESTRA workingadd
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Viruses 2024, 16(10), 1556; https://doi.org/10.3390/v16101556 - 30 Sep 2024
Abstract
This study analyzes immune responses to SARS-CoV-2 vaccination and infection, including asymptomatic cases, focusing on infection risks during the Omicron wave, particularly among high-risk healthcare workers. In the KoCo-Impf study, we monitored 6088 vaccinated participants in Munich aged 18 and above. From 13
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This study analyzes immune responses to SARS-CoV-2 vaccination and infection, including asymptomatic cases, focusing on infection risks during the Omicron wave, particularly among high-risk healthcare workers. In the KoCo-Impf study, we monitored 6088 vaccinated participants in Munich aged 18 and above. From 13 May to 31 July 2022, 2351 participants were follow-uped. Logistic regression models evaluated primary, secondary, and breakthrough infections (BTIs). Roche Elecsys® Anti-SARS-CoV-2 assays detected prior infections (via anti-Nucleocapsid antibodies) and assessed vaccination/infection impact (via anti-Spike antibodies) using dried blood spots. Our findings revealed an anti-Nucleocapsid seroprevalence of 44.1%. BTIs occurred in 38.8% of participants, with reinfections in 48.0%. Follow-up participation was inversely associated with current smoking and non-vaccination, while significantly increasing with age and receipt of three vaccine doses. Larger household sizes and younger age increased infection risks, whereas multiple vaccinations and older age reduced them. Household size and specific institutional subgroups were risk factors for BTIs. The anti-Nucleocapsid value prior to the second infection was significantly associated with reinfection risk. Institutional subgroups influenced all models, underscoring the importance of tailored outbreak responses. The KoCo-Impf study underscores the importance of vaccination, demographic factors, and institutional settings in understanding SARS-CoV-2 infection risks during the Omicron wave.
Full article
(This article belongs to the Section Coronaviruses)
Open AccessReview
Viral Infections and Their Ability to Modulate Endoplasmic Reticulum Stress Response Pathways
by
Flávio Guimarães da Fonseca, Ângela Vieira Serufo, Thiago Lima Leão and Karine Lima Lourenço
Viruses 2024, 16(10), 1555; https://doi.org/10.3390/v16101555 - 30 Sep 2024
Abstract
In eukaryotic cells, the endoplasmic reticulum is particularly important in post-translational modification of proteins before they are released extracellularly or sent to another endomembrane system. The correct three-dimensional folding of most proteins occurs in the ER lumen, which has an oxidative environment that
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In eukaryotic cells, the endoplasmic reticulum is particularly important in post-translational modification of proteins before they are released extracellularly or sent to another endomembrane system. The correct three-dimensional folding of most proteins occurs in the ER lumen, which has an oxidative environment that is essential for the formation of disulfide bridges, which are important in maintaining protein structure. The ER is a versatile organelle that ensures the correct structure of proteins and is essential in the synthesis of lipids and sterols, in addition to offering support in the maintenance of intracellular calcium. Consequently, the cells needed to respond to demands caused by physiological conditions and pathological disturbances in the organelle homeostasis, leading to proper functioning of the cell or even programmed cell death. Disturbances to the ER function trigger a response to the accumulation of unfolded or misfolded proteins, known as the unfolded protein response. Such disturbances include abiotic stress, pharmacological agents, and intracellular pathogens, such as viruses. When misfolded proteins accumulate in the ER, they can undergo ubiquitination and proteasomal degradation through components of the ER-associated degradation system. Once a prolonged activity of the UPR pathway occurs, indicating that homeostasis cannot be reestablished, components of this pathway induce cell death by apoptosis. Here, we discuss how viruses have evolved ways to counteract UPR responses to maximize replication. This evolutionary viral ability is important to understand cell pathology and should be taken into account when designing therapeutic interventions and vaccines.
Full article
(This article belongs to the Section General Virology)
Open AccessArticle
Selection Pressure Profile Suggests Species Criteria among Tick-Borne Orthoflaviviruses
by
Andrei A. Deviatkin, Yulia A. Aleshina, Galina G. Karganova and Alexander N. Lukashev
Viruses 2024, 16(10), 1554; https://doi.org/10.3390/v16101554 - 30 Sep 2024
Abstract
Orthoflaviviruses are arthropod-borne viruses that are transmitted by mosquitoes or ticks and cause a range of significant human diseases. Among the most important tick-borne orthoflaviviruses (TBFVs) is tick-borne encephalitis virus (TBEV), which is endemic in Eurasia, and Powassan virus, which is endemic in
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Orthoflaviviruses are arthropod-borne viruses that are transmitted by mosquitoes or ticks and cause a range of significant human diseases. Among the most important tick-borne orthoflaviviruses (TBFVs) is tick-borne encephalitis virus (TBEV), which is endemic in Eurasia, and Powassan virus, which is endemic in Asia and North America. There is a significant controversy regarding species assignment in the tick-borne encephalitis virus complex due to the complex phylogenetic, serological, ecological, and pathogenetic properties of viruses. Comparing the rate of non-synonymous to synonymous substitutions (dN/dS) over the course of tick-borne orthoflavivirus diversification suggests that there is a very strong stabilizing selection (Nei-Gojobori dN/dS < 0.1) among tick-borne orthoflaviviruses that differ by less than 13.5% amino acid/21.4% nucleotide sequences, and discretely more rapid accumulation of non-synonymous substitutions (dN/dS > 0.13) among more divergent viruses that belong to distinct species. This pattern was similarly observed in genome regions encoding structural (E) and non-structural (NS3) proteins. Below this distance threshold, viruses appear fit and strongly tied to their ecological niche, whereas above the threshold, a greater degree of adaptation appears necessary. This species criterion suggests that all subtypes of TBEV, all related ovine/caprine encephalomyelitis viruses, and Omsk hemorrhagic fever virus (OHFV) together correspond to a single species. Within this species, viruses make up 11 subtypes that are reliably segregated by a 10% nucleotide distance cut-off suggested earlier for TBEV. The same 10% subtype cut-off suggests that Powassan virus includes two subtypes, Powassan and Deer Tick virus.
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(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Dispersion of Flaviviruses (2nd Edition))
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Open AccessArticle
Surveillance of Wildlife Viruses: Insights from South Australia’s Monitoring of Rabbit Haemorrhagic Disease Virus (RHDV GI.1 and GI.2)
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David E. Peacock, Amy Iannella, Ron G. Sinclair and John Kovaliski
Viruses 2024, 16(10), 1553; https://doi.org/10.3390/v16101553 - 30 Sep 2024
Abstract
Surveillance of wildlife virus impacts can be passive or active. Both approaches have their strengths and weaknesses, especially regarding cost and knowledge that can be gained. Monitoring of rabbit haemorrhagic disease virus (GI.1 and GI.2) in South Australia has utilised both strategies and
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Surveillance of wildlife virus impacts can be passive or active. Both approaches have their strengths and weaknesses, especially regarding cost and knowledge that can be gained. Monitoring of rabbit haemorrhagic disease virus (GI.1 and GI.2) in South Australia has utilised both strategies and their methods and gained insights are discussed. Active strategies to monitor the continuing impact of rabbit haemorrhagic disease virus 2 (GI.2) on susceptible lagomorphs in countries such as the USA, Mexico, South Africa, Spain, France and Portugal are encouraged to gain critical insights into the evolution, spread and impact of this virus. Furthermore, there are lessons here for the international monitoring of diseases in wildlife, particularly where there is a risk of them becoming zoonotic.
Full article
(This article belongs to the Special Issue Monitoring New Viral Diseases in Wild Rabbit and Hares (Lagomorphs))
Open AccessSystematic Review
Intrauterine Fetal Demise, Spontaneous Abortion and Congenital Cytomegalovirus: A Systematic Review of the Incidence and Histopathologic Features
by
Megan H. Pesch, Jonathan Mowers, Anh Huynh and Mark R. Schleiss
Viruses 2024, 16(10), 1552; https://doi.org/10.3390/v16101552 - 30 Sep 2024
Abstract
The objective was to review the existing literature reporting on spontaneous abortion (SA) and intrauterine fetal demise (IUFD) associated with cytomegalovirus (CMV) infection. A review using standardized terminology such as ‘intrauterine fetal death’, ‘congenital cytomegalovirus’ and ‘CMV’ was performed using PubMed and Embase
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The objective was to review the existing literature reporting on spontaneous abortion (SA) and intrauterine fetal demise (IUFD) associated with cytomegalovirus (CMV) infection. A review using standardized terminology such as ‘intrauterine fetal death’, ‘congenital cytomegalovirus’ and ‘CMV’ was performed using PubMed and Embase (Medline) using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology. Twenty-one studies met inclusion criteria. CMV was identified as a potential or likely factor in a median of 7.1% of SA or IUFD in study cohorts. Of the studies, 11 used fetal remains, 18 used placenta, 6 used serum, and 1 used post-mortem dried blood spot as specimens for testing for CMV. Features commonly observed were fetal thrombotic vasculopathy, hydrops fetalis and chronic villitis. CMV is frequently noted in studies evaluating viral etiologies of SA or IUFD. Large population-based studies are needed to estimate the incidence of CMV-associated SA or IUFD. CMV and congenital CMV should be included on the differential diagnosis in all cases of SA or IUFD of unknown etiology.
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(This article belongs to the Special Issue Congenital Viral Infections: Mechanisms of Vertical Transmission and Pathology Findings)
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Variability of Hepatitis C Treatment Cascade Outcomes among People Who Inject Drugs across Geographically Diverse Clinics in the US: The HERO Study
by
Snehal S. Lopes, Moonseong Heo, Irene Pericot-Valverde, Brianna L. Norton, Lynn E. Taylor, Judith I. Tsui, Shruti H. Mehta, Judith Feinberg, Arthur Y. Kim, Paula J. Lum, Kimberly Page, Cristina Murray-Krezan, Jessica Anderson, Alain H. Litwin and the HERO Study Group
Viruses 2024, 16(10), 1551; https://doi.org/10.3390/v16101551 - 30 Sep 2024
Abstract
Heterogeneity of outcomes across different clinical trial study sites is often inevitable. Understanding how outcomes differ by site is important for planning future programs and studies. We examined the extent of heterogeneity of hepatitis C virus (HCV) treatment cascade outcomes among persons who
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Heterogeneity of outcomes across different clinical trial study sites is often inevitable. Understanding how outcomes differ by site is important for planning future programs and studies. We examined the extent of heterogeneity of hepatitis C virus (HCV) treatment cascade outcomes among persons who inject drugs (PWIDs) across sixteen clinical sites utilized in the HERO Study—a pragmatic randomized trial of HCV treatment support. Treatment cascade outcomes included averages of overall treatment adherence and proportions of treatment initiation, treatment completion, sustained virologic response (SVR) test completion, and SVR achievement. The HERO study utilized 16 clinical sites across the United States (US): eight opioid treatment programs (OTPs) and eight community health centers (CHCs). Variability of the outcomes across the 16 clinical sites was assessed using ranges and intraclass correlation coefficients (ICC) estimated from mixed-effects linear or logistic regression models. Treatment initiation was analyzed in the intention-to-treat (ITT) sample (N = 755); treatment completion, adherence, and SVR test completion in the modified ITT (mITT) sample, which is the sample that initiated treatment (N = 623); and SVR achievement in the mITT and per-protocol (PP, N = 501) samples. Across the 16 clinical sites, the range observed in the averages of overall treatment adherence was from 68% to 81% [ICC = 0.026 (0.005, 0.054)], and the ranges of proportions observed were from 68% to 96% for treatment initiation [ICC (95% CI) = 0.086 (0.051, 0.155)], 60% to 100% for treatment completion [ICC = 0.049 (0.008, 0.215)], 54% to 95% for SVR test completion [ICC = 0.096 (0.006, 0.177)], 46% to 90% for SVR achievement in the mITT sample [ICC = 0.070 (0.014, 0.122)], and 76% to 100% for SVR achievement in the PP sample [ICC = 0.143 (0.021, 0.422)]. The variability of the outcomes across 16 US sites treating HCV among PWIDs appears to be substantial in view of the ranges and ICC values of the outcomes. It is imperative to develop tailored interventions to target the sources of variability and reduce barriers at the patient, provider, clinic, and state policy levels to facilitate more equitable access to HCV treatment and reduce heterogeneity in treatment outcomes.
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(This article belongs to the Special Issue Hepatitis C Virus Infection among People Who Inject Drugs)
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Open AccessArticle
High-Throughput Sequencing Methods for the Detection of Two Strawberry Viruses in Post-Entry Quarantine
by
Luciano Nunes-Leite, Lia W. Liefting, David W. Waite, Subuhi Khan and Jeremy R. Thompson
Viruses 2024, 16(10), 1550; https://doi.org/10.3390/v16101550 - 30 Sep 2024
Abstract
High-throughput sequencing (HTS) technologies may be a useful tool for testing imported plant germplasm for multiple pathogens present in a sample, offering strain-generic detection not offered by most PCR-based assays. Metatranscriptomics (RNAseq) and tiled amplicon PCR (TA-PCR) were tested as HTS-based techniques to
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High-throughput sequencing (HTS) technologies may be a useful tool for testing imported plant germplasm for multiple pathogens present in a sample, offering strain-generic detection not offered by most PCR-based assays. Metatranscriptomics (RNAseq) and tiled amplicon PCR (TA-PCR) were tested as HTS-based techniques to detect viruses present in low titres. Strawberry mottle virus (SMoV), an RNA virus, and strawberry vein banding virus (SVBV), a DNA virus, were selected for comparison of RNAseq and TA-PCR with quantitative PCR assays. RNAseq of plant ribosomal RNA-depleted samples of low viral titre was used to obtain datasets from 3 M to 120 M paired-end (PE) reads. RNAseq demonstrated PCR-like sensitivity, able to detect as few as 10 viral copies/µL when 60 million (M) PE reads were generated. The custom TA-PCR primer panels designed for each virus were successfully used to recover most of the reference genomes for each virus. Single- and multiple-target TA-PCR allowed the detection of viruses in samples with around 10 viral copies/µL with a minimum continuous sequence length recovery of 500 bp. The limit of detection of the HTS-based protocols described here is comparable to that of quantitative PCR assays. This work lays the groundwork for an increased flexibility in HTS detection of plant viruses.
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(This article belongs to the Special Issue Advances in Plant Virus/Viroid Detection and Identification Methods)
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Open AccessArticle
Bovine Transcription Factor POU Class 2 Homeobox 1 (POU2F1/Oct1) Protein Promotes BoHV-1 Replication in MDBK Cells
by
Enguang Rong, Inga Dry, Robert G. Dalziel and Wenfang Spring Tan
Viruses 2024, 16(10), 1549; https://doi.org/10.3390/v16101549 - 30 Sep 2024
Abstract
Bovine herpesvirus type 1 (BoHV-1) causes severe diseases in bovine species and great economic burden to the cattle industry worldwide. Due to its complex life cycle, many host factors that affect BoHV-1 replication remain to be explored. To understand the possible roles that
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Bovine herpesvirus type 1 (BoHV-1) causes severe diseases in bovine species and great economic burden to the cattle industry worldwide. Due to its complex life cycle, many host factors that affect BoHV-1 replication remain to be explored. To understand the possible roles that the Oct1 cellular protein could play in this process, we first created Oct1-deficient MDBK cells using CRISPR/Cas9-mediated genome editing. Upon infection, the absence of Oct1 in MDBK cells significantly impacted BoHV-1 replication, a phenotype rescued by over-expressing the wild-type Oct1 protein in the deficient cells. We further found that the expression of all three classes of temporal genes, including essential and non-essential viral genes, were significantly reduced in Oct1 knockout MDBK cells, following both high and low multiplicity of infection. In summary, our findings confirm that the bovine Oct1 protein acts as a pro-viral factor for BoHV-1 replication by promoting its viral gene transcription in MDBK cells.
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(This article belongs to the Special Issue Animal Herpesvirus)
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Open AccessReview
Detection of Porcine Circovirus (PCV) Using CRISPR-Cas12a/13a Coupled with Isothermal Amplification
by
Huijuan Wang, Gang Zhou, Huiming Liu, Ruqun Peng, Tingli Sun, Sujuan Li, Mingjie Chen, Yingsi Wang, Qingshan Shi and Xiaobao Xie
Viruses 2024, 16(10), 1548; https://doi.org/10.3390/v16101548 - 30 Sep 2024
Abstract
The impact of porcine circovirus (PCV) on the worldwide pig industry is profound, leading to notable economic losses. Early and prompt identification of PCV is essential in managing and controlling this disease effectively. A range of detection techniques for PCV have been developed
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The impact of porcine circovirus (PCV) on the worldwide pig industry is profound, leading to notable economic losses. Early and prompt identification of PCV is essential in managing and controlling this disease effectively. A range of detection techniques for PCV have been developed and primarily divided into two categories focusing on nucleic acid or serum antibody identification. The methodologies encompass conventional polymerase chain reaction (PCR), real-time fluorescence quantitative PCR (qPCR), fluorescence in situ hybridization (FISH), loop-mediated isothermal amplification (LAMP), immunofluorescence assay (IFA), immunohistochemistry (IHC), and enzyme-linked immunosorbent assay (ELISA). Despite their efficacy, these techniques are often impeded by the necessity for substantial investment in equipment, specialized knowledge, and intricate procedural steps, which complicate their application in real-time field detections. To surmount these challenges, a sensitive, rapid, and specific PCV detection method using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas12a/13a coupled with isothermal amplification, such as enzymatic recombinase amplification (ERA), recombinase polymerase amplification (RPA), and loop-mediated isothermal amplification (LAMP), has been developed. This novel method has undergone meticulous optimization for detecting PCV types 2, 3, and 4, boasting a remarkable sensitivity to identify a single copy per microliter. The specificity of this technique is exemplary, with no observable interaction with other porcine viruses such as PEDV, PRRSV, PRV, and CSFV. Its reliability has been validated with clinical samples, where it produced a perfect alignment with qPCR findings, showcasing a 100% coincidence rate. The elegance of merging CRISPR-Cas technology with isothermal amplification assays lies in its on-site testing without the need for expensive tools or trained personnel, rendering it exceptionally suitable for on-site applications, especially in resource-constrained swine farming environments. This review assesses and compares the process and characteristics inherent in the utilization of ERA/LAMP/RPA-CRISPR-Cas12a/Cas13a methodologies for the detection of PCV, providing critical insights into their practicality and effectiveness.
Full article
(This article belongs to the Section Animal Viruses)
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