Viruses

20 pages, 5806 KB

Open AccessArticle

Development and Validation of a Passive Surveillance System for Early Detection of Pepino Mosaic Virus in Commercial Greenhouse Facilities

by Hester Roberts, David W. Waite, Subuhi Khan, Stella Veerakone, Joe Tang and Jeremy R. Thompson

Viruses 2026, 18(8), 866; https://doi.org/10.3390/v18080866 - 7 Aug 2026

Abstract

The use of environmental nucleic acid (eNA), both DNA and RNA, as a means for surveillance has been a fixture in the scientific literature for many years. The application of environmental screening for genomic signatures of organisms of interest—particularly those of diagnostic concern—is [...] Read more.

The use of environmental nucleic acid (eNA), both DNA and RNA, as a means for surveillance has been a fixture in the scientific literature for many years. The application of environmental screening for genomic signatures of organisms of interest—particularly those of diagnostic concern—is a promising yet still under-utilised tool for sample screening. While the literature tends to focus on the use of high-throughput sequencing (HTS) to detect organisms of interest using metagenomic or metatranscriptomic sampling, this approach is not cost-competitive with more traditional targeted molecular test methods. Consequently, eNA sampling still has not gained significant traction in practical settings despite its popularity in ecological research. To address these issues in a biosecurity context, we report here the development of a testing protocol to monitor irrigation water for the presence of pepino mosaic virus (PepMV) that also includes an endogenous Sphingomonas control. We employed passive sampling through the immersion of filtering devices into the water system at three commercial growing operations at two time points to collect samples with minimal hands-on effort, while simultaneously developing and validating molecular methods for the recovery of RNA competent for both PCR and high-throughput sequencing. We demonstrate not only the ability to detect PepMV from water collections, but also that the method is robust to the accumulation of non-target material and does not lose signal if viruses are only transiently present in the water system. Finally, we developed a capsid-integrity pre-treatment protocol for differentiating between intact and denatured (non-viable) virus particles during PCR testing. This work presents a low-cost and low-effort technique for proactive screening of commercial greenhouse facilities to facilitate early detection of harmful crop pests and pathogens. Full article

(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)

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28 pages, 5203 KB

Open AccessReview

Mpox in Europe, 2022–2026: A Scoping Review of Viral Clades, Host Determinants of Severity and Antiviral Therapy

by Filippos Sofos, Zoi D. Pana and Dimitris Drikakis

Viruses 2026, 18(8), 865; https://doi.org/10.3390/v18080865 - 7 Aug 2026

Abstract

The 2022–2024 mpox outbreak in Europe was dominated by MPXV Clade IIb and generally mild, but recent Clade I/Ib detections and early local transmission have changed preparedness needs. We performed a PRISMA-ScR scoping review of European mpox evidence from 2022 to 2026, supplemented [...] Read more.

The 2022–2024 mpox outbreak in Europe was dominated by MPXV Clade IIb and generally mild, but recent Clade I/Ib detections and early local transmission have changed preparedness needs. We performed a PRISMA-ScR scoping review of European mpox evidence from 2022 to 2026, supplemented by global and African data where regional evidence was sparse, covering clades, host determinants of severe disease, and antiviral efficacy and resistance, and ranking the evidence gaps. European Clade IIb surveillance showed very low mortality (10 deaths among 22,662 cases; case fatality 0.04%), contrasting with 3–11% estimates for Clade I/Ib in affected African settings, although comparisons are confounded by age, health-system access and comorbidity. Severe European disease was driven mainly by immune compromise: non-HIV immunosuppression, uncontrolled HIV and CD4 counts < 200 cells/µL were the most consistent markers, while women were a small minority of cases, with higher hospitalisation risk, especially in pregnancy. Tecovirimat failed to improve outcomes in four randomised trials, F13L-associated resistance was reported in advanced HIV, and its European mpox use was subsequently restricted. The evidence base is strongest for mild Clade IIb infection in immunocompetent adults and weakest for the groups most likely to need treatment. Preparedness should prioritise harmonised genomic surveillance, severity-stratified cohort data and adaptive therapeutic trials enrolling immunocompromised, paediatric, pregnant and older patients. Full article

(This article belongs to the Section Human Virology and Viral Diseases)

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21 pages, 31862 KB

Open AccessArticle

Isolation, Characterization and Reverse Genetic System Establishment of a Highly Virulent PEDV Strain

by Fan Zhang, Helu Liu, Linlong Ji, Yanyang Zhou, Heng Chen, Jiyong Zhou and Jinyan Gu

Viruses 2026, 18(8), 864; https://doi.org/10.3390/v18080864 - 7 Aug 2026

Abstract

Porcine epidemic diarrhea virus (PEDV) G2c variants have recently emerged, posing significant challenges to swine health management. As a major coronavirus affecting the swine industry, PEDV exhibits extensive genetic variability, which has greatly complicated disease control. Current vaccines provide suboptimal protection under field [...] Read more.

Porcine epidemic diarrhea virus (PEDV) G2c variants have recently emerged, posing significant challenges to swine health management. As a major coronavirus affecting the swine industry, PEDV exhibits extensive genetic variability, which has greatly complicated disease control. Current vaccines provide suboptimal protection under field conditions. Therefore, the isolation of recently circulating strains and the establishment of a robust reverse genetics system are critical for advancing the study of emerging variants and facilitating rational vaccine development. In this study, a PEDV field strain designated PEDV-BJ-2023 was isolated from diarrheic piglets in Guizhou, China. Phylogenetic analysis based on the complete genome and spike gene classified PEDV-BJ-2023 within the emerging G2c lineage. To facilitate functional studies, a full-length infectious cDNA clone was constructed using transformation-associated recombination cloning in yeast. Furthermore, an enhanced green fluorescent protein reporter virus was generated via CRISPR/Cas9-assisted homologous recombination by inserting an EGFP-2A cassette upstream of the nucleocapsid gene. The recombinant viruses displayed virion morphology and plaque characteristics similar to those of the parental wild-type PEDV-BJ-2023 strain, although the parental virus exhibited faster replication during the early stage of infection in vitro. In 5-day-old piglets, all three viruses caused severe diarrhea, weight loss, and intestinal lesions; however, recombinant viruses exhibited slightly reduced viral shedding and pathogenicity, with rPEDV-EGFP being the most attenuated. Notably, rPEDV-EGFP maintained stable EGFP expression over eight serial passages. This study establishes a reverse genetics platform for an emerging G2c PEDV strain and provides a stable fluorescent reporter virus, offering valuable tools for visualizing viral infection and investigating virus–host interactions. Full article

(This article belongs to the Special Issue Viruses of Swine and Companion Animals: Pathogenesis, Prevalence, Evolution and Control)

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31 pages, 7737 KB

Open AccessReview

Current Strategies for Selecting Recombinant Orthopoxvirus Proteins for Immunobiological and Diagnostic Applications

by Aigerim Zhakypbek, Lespek Kutumbetov, Gulnur Kuzembekova, Kamshat Shorayeva, Nurlan Kozhabergenov, Bekbolat Usserbayev, Gulnur Nakhanova, Kuanysh Jekebekov, Gaukhar Shynybekova, Akbope Abdykalyk, Aknur Ulankyzy, Temirlan Baiseit, Balzhan Myrzakhmetova, Olga Chervyakova and Kuandyk Zhugunissov

Viruses 2026, 18(8), 863; https://doi.org/10.3390/v18080863 - 7 Aug 2026

Abstract

Orthopoxviruses are zoonotic DNA viruses of continuing public health importance, as highlighted by recent global mpox outbreaks. The high antigenic similarity among orthopoxviruses enables cross-reactive immune responses but complicates the development of serological diagnostic systems for serosurveillance, assessment of previous exposure, evaluation of [...] Read more.

Orthopoxviruses are zoonotic DNA viruses of continuing public health importance, as highlighted by recent global mpox outbreaks. The high antigenic similarity among orthopoxviruses enables cross-reactive immune responses but complicates the development of serological diagnostic systems for serosurveillance, assessment of previous exposure, evaluation of vaccine-induced immunity, and species differentiation. This review summarizes current knowledge regarding the structure, biological functions, and diagnostic and vaccine potential of major orthopoxvirus recombinant antigens. Particular attention is given to the genomic organization of Orthopoxvirus, differences between intracellular mature virion (IMV) and extracellular enveloped virion (EV) forms, and the characteristics of key antigens, including A29, M1, H3, A35, and B6. Comparative phylogenetic analyses demonstrated a high degree of conservation among structurally important orthopoxvirus proteins while also identifying variable regions potentially relevant for differential diagnostics. Available evidence indicates that IMV-associated proteins are primarily involved in virus neutralization, whereas EV-associated antigens contribute mainly to limiting viral dissemination. Consequently, multicomponent antigen strategies combining IMV- and EV-associated proteins appear to provide the greatest potential for the development of effective serological assays and next-generation subunit vaccines. Overall, rational antigen selection should be based on integrated evaluation of structural, functional, and immunological properties to optimize orthopoxvirus diagnostic and vaccine platforms. Full article

(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)

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8 pages, 1404 KB

Open AccessBrief Report

Pan-Viral Sequencing Surveillance Identifies Mammalian Orthoreovirus 2 in United States Wastewater

by John P. Collins, Michael A. Mechikoff, Thomas A. Pressley, Catherine R. Jarriel, Riley E. M. Russell, Cullen Ingersoll, Xiang-Jun Lu, Thomas Briese, Armand L. Balboni and J. Kenneth Wickiser

Viruses 2026, 18(8), 862; https://doi.org/10.3390/v18080862 - 6 Aug 2026

Abstract

Mammalian orthoreoviruses (MRVs) are segmented, double-stranded RNA viruses that infect a broad range of mammalian hosts, including humans. Although MRVs have been detected in wastewater in parts of Southeast Asia, they have not previously been reported in U.S. wastewater. Using the VirCapSeq-VERT pan-viral [...] Read more.

Mammalian orthoreoviruses (MRVs) are segmented, double-stranded RNA viruses that infect a broad range of mammalian hosts, including humans. Although MRVs have been detected in wastewater in parts of Southeast Asia, they have not previously been reported in U.S. wastewater. Using the VirCapSeq-VERT pan-viral sequencing assay, we identified MRV type 2 (MRV-2) in a wastewater sample collected in March 2024 from the United States Air Force Academy. Complete genome sequences were recovered for all 10 segments. Phylogenetic analyses showed that the virus clustered most closely with an MRV isolate recovered from a big brown bat (Eptesicus fuscus) in Pennsylvania, with additional genomic similarity to a second bat-derived isolate from Nebraska. The MRV sequence signal declined rapidly in subsequent wastewater samples and was nearly undetectable two weeks later. These findings represent the first reported detection of MRV in U.S. wastewater and demonstrate the utility of pan-viral wastewater surveillance for identifying uncommon viruses with potential public health relevance. Continued genomic and epidemiologic surveillance will improve understanding of MRV circulation and zoonotic transmission in North America. Full article

(This article belongs to the Special Issue Controlling Zoonotic Viral Diseases from One Health Perspective 2026)

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30 pages, 1267 KB

Open AccessReview

Integrated Diagnosis of Hepatitis B, C, and D Viruses and HIV in Populations Evaluated for Sexually Transmitted Infections: A Narrative Review and Operational Framework

by Joaquín Cabezas, Ezequiel Ridruejo, José Antonio Velarde-Ruiz Velasco, Graciela Castro-Narro, Lorena Cayón-González, Carolina Jiménez, Hugo Cheinquer, Fernando Contreras, Nelia Hernández, Christie Perelló, José Luis Calleja and Javier Crespo

Viruses 2026, 18(8), 861; https://doi.org/10.3390/v18080861 - 6 Aug 2026

Abstract

Hepatitis B virus (HBV), hepatitis C virus (HCV), and hepatitis D virus (HDV), together with HIV and bacterial sexually transmitted infections (STIs), account for a rising toll of more than one million deaths annually and overlap within shared behavioral and social networks, yet [...] Read more.

Hepatitis B virus (HBV), hepatitis C virus (HCV), and hepatitis D virus (HDV), together with HIV and bacterial sexually transmitted infections (STIs), account for a rising toll of more than one million deaths annually and overlap within shared behavioral and social networks, yet are still diagnosed through separate, pathogen-specific pathways. This narrative review synthesizes contemporary evidence on the convergence between viral hepatitis, HIV, and high-risk STI groups—men who have sex with men, pre-exposure prophylaxis (PrEP) users, people practicing chemsex, people who inject drugs, incarcerated populations, and migrants from endemic regions—and characterizes the diagnostic technologies and linkage-to-care models available to address it. Despite effective antivirals, the diagnostic cascade remains the principal bottleneck: most people with chronic HCV are undiagnosed, and HDV—with a pooled anti-HDV seroprevalence of approximately 4.5% among HBsAg-positive individuals—is its clearest expression, as most carriers are never tested. Reflex algorithms, multiplex panels, point-of-care assays, dried blood spots, and electronic health record alerts are validated but unevenly implemented. We argue that, alongside persistent resource, political, and equity-related constraints, a substantial share of the remaining barriers is operational rather than purely technological, and propose a practical, STI-clinic-centered framework integrating reflex testing, population-specific periodicity, and explicit linkage pathways toward the WHO 2030 elimination targets. Full article

(This article belongs to the Special Issue 2nd Edition: How to Adjust the Action Steps for Achieving the Global Hepatitis Virus (HBV/HCV/HDV) Elimination Targets?)

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25 pages, 11199 KB

Open AccessArticle

Bat-Associated Parvoviruses: High Genetic Diversity and Novel Viruses in Gia Lai and Dong Nai Provinces, Vietnam

by Vasilina K. Lapshina, Alina A. Gorbacheva, Polina A. Nikolaeva, Diana A. Grigoryan, Ivan F. Stetsenko, Mo T. Luong, Truong V. Tran, Alexander P. Yuzefovich, Ilia O. Prikhodko, Alexander Yu. Alekseev, Sergey M. Yudin, German A. Shipulin, Alina D. Matsvay and Veronika I. Skvortsova

Viruses 2026, 18(8), 860; https://doi.org/10.3390/v18080860 - 6 Aug 2026

Abstract

Bats are recognized as key reservoirs for diverse viruses, including members of the Parvoviridae family. Vietnam hosts an exceptionally wide variety of bat species, yet the diversity of parvoviruses in these populations remains largely unexplored. This study provides the first survey of parvoviruses [...] Read more.

Bats are recognized as key reservoirs for diverse viruses, including members of the Parvoviridae family. Vietnam hosts an exceptionally wide variety of bat species, yet the diversity of parvoviruses in these populations remains largely unexplored. This study provides the first survey of parvoviruses in bats from Gia Lai and Dong Nai provinces, screening 150 samples from 26 bat species and detecting parvoviruses in 38 (25%). A total of 45 viral operational taxonomic units (OTUs) were identified, encompassing four parvoviral subfamilies: Parvovirinae, Densovirinae, Penbrevirinae, and Hamavirinae. However, only two of these OTUs were attributed to ICTV-accepted species. Twenty-six OTUs were assigned to recognized genera but exhibited insufficient sequence similarity to established species, suggesting they may represent novel species within these genera. The remaining 25 OTUs could not be assigned to any ICTV-accepted genus, including 14 that remained unclassified even at the subfamily level, indicating the presence of novel parvovirus lineages at the genus rank or above. Overall, 95% of detected viral variants were classified as potentially novel, revealing a substantial reservoir of Parvoviridae diversity in the region. Phylogenetic analysis of vertebrate-infecting parvoviruses showed that the detected dependoparvoviruses were most closely related to viruses from primates and pinnipeds, while the chaphamavirus sequences formed a clade associated with carnivore viruses, and the embehamavirus sequences showed high homology to a virus previously detected in human plasma from a neuroinfection case. These results underscore the importance of comprehensive bat virome surveillance and enhance our understanding of the viral diversity and potential zoonotic threats posed by parvoviruses. Full article

(This article belongs to the Section Animal Viruses)

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17 pages, 2423 KB

Open AccessArticle

Establishment and Application of a Duplex TaqMan Real-Time PCR Assay for Simultaneous Detection of Chicken Anemia Virus (CAV) and Gyrovirus Galga 1 (GyVg1)

by Kai-Xuan Gu, Zhi-Hao Ren, Xiao-Long Sun, Yang Li, Tao Sun, Wen-Ping Cui, Shuang Chang, Peng Zhao, Yu-Long Gao and Yi-Xin Wang

Viruses 2026, 18(8), 859; https://doi.org/10.3390/v18080859 - 6 Aug 2026

Abstract

Both Chicken anemia virus (CAV) and Gyrovirus galga 1 (GyVg1) belong to the family Anelloviridae and genus Gyrovirus. They are non-enveloped, single-stranded circular DNA viruses that can infect chicken populations, leading to similar clinical symptoms such as growth retardation and immunosuppression, making [...] Read more.

Both Chicken anemia virus (CAV) and Gyrovirus galga 1 (GyVg1) belong to the family Anelloviridae and genus Gyrovirus. They are non-enveloped, single-stranded circular DNA viruses that can infect chicken populations, leading to similar clinical symptoms such as growth retardation and immunosuppression, making clinical differentiation challenging. This study established a duplex TaqMan real-time PCR assay to simultaneously detect CAV and GyVg1. Specific primers and probes were developed to target the VP3 gene of CAV (labeled with VIC) and the VP1 gene of GyVg1 (labeled with FAM). The optimization process involved fine-tuning reaction conditions, such as primer/probe concentrations and annealing temperature, through a systematic matrix approach. The assay demonstrated remarkable linearity under optimized conditions (0.4 μmol/L primers, 0.2 μmol/L probes, and an annealing temperature of 52 °C), yielding high R² values of 0.9973 for CAV and 0.9981 for GyVg1. The method exhibited high specificity, showing no cross-reactivity with other common avian pathogens. The limits of detection were 1.0 × 10⁰ copies/μL for CAV and 1.0 × 10¹ copies/μL for GyVg1, making it 10-fold more sensitive than conventional PCR. Intra-assay and inter-assay coefficients of variation were below 1.5% and 2.5%, respectively, indicating excellent reproducibility. When tested on 411 clinical samples from Shandong Province, CAV showed a positivity rate of 48.66% (200/411), GyVg1 18.73% (77/411), and a co-detection rate of 17.52% (72/411). Moreover, 25 complete genome sequences of GyVg1 (2376 bp each) were acquired from positive samples. These sequences exhibited a nucleotide identity ranging from 93.6% to 99.3% among the isolates and 92.2% to 99.6% with reference strains. The phylogenetic analysis, which was based on whole-genome sequences, categorized the Shandong isolates into four clusters (I–IV). Notably, the strains were dispersed across these clusters and were intertwined with references from various regions and hosts. This observation suggests the absence of distinct geographic clustering and implies frequent cross-regional and cross-species transmission. In summary, this duplex real-time PCR assay offers a sensitive, specific, and dependable method for concurrently detecting and distinguishing CAV and GyVg1. The study’s findings reveal a significant co-infection rate and genetic variation in GyVg1, underscoring the importance of increased surveillance and deeper exploration of its pathogenicity and transmission patterns. Full article

(This article belongs to the Special Issue Avian Viruses and Antiviral Immunity)

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23 pages, 1590 KB

Open AccessReview

The Rectal Mucosal Myeloid Niche in HIV-1 Persistence: Reservoir Support, Viral Sequestration, and Therapeutic Opportunities

by Hanyi Zhang, Peiming Huang, Xu Zhang and Ting Pan

Viruses 2026, 18(8), 858; https://doi.org/10.3390/v18080858 - 5 Aug 2026

Abstract

Persistent HIV-1 reservoirs remain a major barrier to a durable functional cure despite long-term suppressive antiretroviral therapy. Although resting memory CD4⁺ T cells constitute the best-characterized cellular reservoir, tissue microenvironments shape viral persistence and immune clearance. The rectal mucosa represents a specialized [...] Read more.

Persistent HIV-1 reservoirs remain a major barrier to a durable functional cure despite long-term suppressive antiretroviral therapy. Although resting memory CD4⁺ T cells constitute the best-characterized cellular reservoir, tissue microenvironments shape viral persistence and immune clearance. The rectal mucosa represents a specialized tissue niche containing HIV-susceptible target cells, antigen-presenting cells, microbial products, inflammatory cues, and local metabolic signals. Within this setting, myeloid-lineage cells, particularly tissue-resident macrophages and dendritic cells, may contribute to HIV-1 persistence through mechanisms distinct from classical T-cell latency. Here, we review how rectal mucosal macrophages may support HIV-1 persistence through longevity, resistance to apoptosis, metabolic adaptation, epigenetic regulation, and sequestration of virions within virus-containing compartments. We also discuss the dual role of mucosal dendritic cells as sentinels that capture and transfer HIV-1 to CD4⁺ T cells, while considering the limited evidence for inducible proviral persistence in selected anatomical and cellular contexts. Importantly, we further distinguish bona fide reservoir-bearing cells from reservoir-supportive mechanisms, including viral capture, trans-infection, immune suppression, and niche-mediated protection. We also highlight how mucosal dysbiosis, barrier disruption, microbial metabolites, chronic interferon signaling, and immunoregulatory myeloid programs may stabilize HIV-1 persistence in rectal tissues. Integrating intact proviral assays, functional measurements, single-cell profiling, multiplex imaging, and spatial transcriptomics will be critical for defining myeloid-associated persistence and guiding tissue-targeted HIV-1 cure strategies. Full article

(This article belongs to the Special Issue HIV Reservoir Establishment in Myeloid Cells, Restriction Mechanisms and Therapeutic Strategies)

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21 pages, 2949 KB

Open AccessReview

Is PPR Epidemiological Research Addressing Global Eradication Priorities? A Scoping Review (2015–2025)

by Gezahegn Alemayehu and Theodore Knight-Jones

Viruses 2026, 18(8), 857; https://doi.org/10.3390/v18080857 - 5 Aug 2026

Abstract

The PPR Global Research and Expertise Network (GREN) plays a central role in identifying research priorities supporting the Global Peste des Petits Ruminants (PPR) Eradication Programme (GEP). A scoping review of PPR epidemiological research published between 2015 and 2025 was conducted to assess [...] Read more.

The PPR Global Research and Expertise Network (GREN) plays a central role in identifying research priorities supporting the Global Peste des Petits Ruminants (PPR) Eradication Programme (GEP). A scoping review of PPR epidemiological research published between 2015 and 2025 was conducted to assess progress and remaining gaps across research domains relevant to GREN priorities. A total of 670 PPR-related publications were retrieved. Epidemiological research constituted 46.9% of the PPR literature, pathogenesis (19.1%), and diagnostics (15.6%), followed by vaccinology (9.5%) and immunology (7.9%). From the 273 epidemiological studies, most originated from Africa (53.1%) and Asia (37.7%). The epidemiological studies were categorized into seven domains. Molecular epidemiology and virus strain characterization represented the largest proportion of published studies (40.0%), followed by surveillance and disease monitoring (23.8%), transmission dynamics and risk modelling (12.5%), vaccination epidemiology (10.6%), analytical and risk factor epidemiology (8.4%), control strategy evaluation (2.9%), and socioeconomic research (1.8%). Progress towards GREN research priorities was variable. Molecular epidemiology and surveillance demonstrated the greatest methodological advancement, supported by widespread application of phylogenetics, serological surveillance, and expanding sequencing capacity across endemic settings. Transmission dynamics and risk modelling also showed increasing analytical sophistication through spatial modelling, network analysis, ecological suitability modelling, and dynamic simulation approaches, although applications remained geographically concentrated and only partially integrated into operational decision-support systems. In contrast, vaccination epidemiology, comparative evaluation of control strategies, and socioeconomic research remained limited in volume and operational integration. Across domains, important gaps persisted in implementation-focused evaluation, integrated surveillance systems, and translation of research evidence into adaptive eradication planning and policy development. Overall, the findings demonstrate substantial growth in the global PPR epidemiological evidence base over the past decade but also reveal a persistent imbalance across research domains and geographies. While major advances have been achieved in molecular characterization and descriptive surveillance, greater integration of epidemiological, operational, modelling, and socioeconomic evidence is needed to strengthen adaptive eradication planning and improve alignment between research priorities and policy implementation. Research and policy need to be better integrated, with policy needs driving research focus and research findings then informing policy. Experience from rinderpest eradication demonstrates that strong research–policy interfaces are essential to ensure that scientific evidence is translated into effective eradication strategies and decision-making. Full article

(This article belongs to the Special Issue Peste Des Petits Ruminants (PPR): Progress and Efforts Toward 2030 Eradication)

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17 pages, 10042 KB

Open AccessArticle

Cross-Border Circulation and Molecular Surveillance of HIV-1 in the Azov and Donbas Regions: A Study of Genetic Diversity and Drug Resistance

by Anastasiia Antonova, Anatolii Vinokurov, Daria Kustova, Andrei Pochtovyi, Daria Ogarkova, Ruslan Adgamov, Anna Kuznetsova, Elena Tsyganova, Inna Kulikova, Andrei Plutnitskii, Vladimir Gushchin, Aleksandr Gintsburg, Denis Logunov and Aleksei Mazus

Viruses 2026, 18(8), 856; https://doi.org/10.3390/v18080856 - 5 Aug 2026

Abstract

As critical geopolitical and migratory hubs in Eastern Europe, the Azov and Donbas regions represent an epidemiological melting pot for HIV-1 trafficking, exacerbating the global trend of rising dolutegravir (DTG) resistance through the cross-border dissemination of drug-resistant strains. This study presents a comprehensive [...] Read more.

As critical geopolitical and migratory hubs in Eastern Europe, the Azov and Donbas regions represent an epidemiological melting pot for HIV-1 trafficking, exacerbating the global trend of rising dolutegravir (DTG) resistance through the cross-border dissemination of drug-resistant strains. This study presents a comprehensive molecular epidemiological analysis of HIV-1 in these regions in 2025 (N = 1666), focusing on drug resistance and cross-border transmission networks using phylogenetic and molecular network approaches. The study cohort was predominantly female (53.33%) and had heterosexual transmission (78.77%). Most patients (87.64%) received antiretroviral therapy (ART). Sub-subtype A6 predominated, with the radiation’s origin traced to September 1994. Molecular network analysis identified the study area as a significant node, demonstrating viral exports towards the Russian Federation and Belarus, alongside multiple imports from Ukraine, Poland, and Russia. The overall resistance prevalence was 4.49% to integrase strand transfer inhibitors (INSTIs), 2.49% to protease inhibitors (PIs), 12.19% to nucleoside reverse transcriptase inhibitors (NRTIs), and 16.07% to non-nucleoside reverse transcriptase inhibitors (NNRTIs). Surveillance drug resistance mutations in treatment-naive individuals stood at 0.89% (INSTIs), 4.90% (PIs), 4.90% (NRTIs), and 8.82% (NNRTIs). Crucially, intermediate or high-level DTG resistance and key mutations (G118R, R263K, and Y143R) were detected in individuals without prior DTG exposure. This 4.49% integrase inhibitor resistance cannot be considered low; combined with intense cross-border viral dissemination, it may indicate the formation of a stable pool of resistant variants, potentially posing a risk of dolutegravir-based regimen failure and highlighting the need for enhanced regional molecular surveillance. Full article

(This article belongs to the Special Issue Molecular Epidemiology of HIV: Genotypic Diversity, Evolution, and Drug Resistance)

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9 pages, 4359 KB

Open AccessBrief Report

Preferential Exhaustion and Loss of Predominant Reservoir in Gut-Associated Lymph Nodes of a SIVmac239-Infected Rhesus Macaque with Terminal AIDS

by Cong-Jiao Bai, Yu Zhang, Zhang-Ran Du, Yu-Qiu Wang, Meng-Xue Sun, Liu-Meng Yang, Yong-Tang Zheng and Tian-Zhang Song

Viruses 2026, 18(8), 855; https://doi.org/10.3390/v18080855 - 4 Aug 2026

Abstract

Gut-associated lymph nodes (GALNs) constitute an important anatomical reservoir during early and chronic human immunodeficiency virus (HIV)/simian immunodeficiency virus (SIV) infection, but the fate of this compartment during terminal AIDS remains unclear. This study investigated viral persistence and lymph node injury in a [...] Read more.

Gut-associated lymph nodes (GALNs) constitute an important anatomical reservoir during early and chronic human immunodeficiency virus (HIV)/simian immunodeficiency virus (SIV) infection, but the fate of this compartment during terminal AIDS remains unclear. This study investigated viral persistence and lymph node injury in a rhesus macaque with long-term SIVmac239 infection and end-stage AIDS, characterized by profound CD4+ T cell depletion (30 cells/μL) and persistent viremia (1192 copies/mL). At necropsy, GALNs, including mesenteric, paracolic, and ileocecal lymph nodes, and non-gut-associated lymph nodes (NGALNs), including hepatic hilar, common iliac, and inguinal lymph nodes, were collected for viral RNA/DNA quantification, histopathology, immunofluorescence, and transcriptomics. SIV DNA was markedly lower in GALNs than in NGALNs, whereas SIV RNA was detectable only in NGALNs. GALNs exhibited extensive fibrotic remodeling, paracortical collapse, severe CD4+ T cell loss across B cell and paracortical regions, and pronounced CD8+ T cell accumulation within B cell zones. Transcriptomic profiling further revealed an exhaustion signature in GALNs, with reduced DNA replication and repair, impaired cell-cycle activity, and suppressed RNA processing, accompanied by activation of innate immune programs and attenuation of adaptive immune responses. These findings indicate that, during terminal AIDS, GALNs no longer serve as the predominant viral reservoir but instead undergo preferential and severe structural and functional exhaustion. This case highlights marked anatomical heterogeneity in lymph node vulnerability during advanced disease and supports a model in which collapse of the gut-associated immune barrier contributes to disease progression toward terminal AIDS. Full article

(This article belongs to the Special Issue HIV-1 Infection and Immunometabolism: Relevance to HIV Pathogenesis and Persistence 3.0)

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22 pages, 371 KB

Open AccessReview

Direct-Acting Antivirals in Patients with Comorbidities for the Simplified Management of HCV Infection: An Expert Review with a Focus on Sofosbuvir–Velpatasvir

by Alessio Aghemo, Alessia Ciancio, Ernesto Claar, Nicola Coppola, Alessandra Mangia, Marco Riglietta and Massimo Puoti

Viruses 2026, 18(8), 854; https://doi.org/10.3390/v18080854 - 4 Aug 2026

Abstract

Introduction: Hepatitis C virus (HCV) infection often coexists with comorbidities, increasing vulnerability, complications, and adverse events. Direct-acting antivirals (DAAs) have dramatically improved HCV management, but they differ in drug–drug interaction (DDI) profiles. Sofosbuvir/velpatasvir (SOF/VEL) is associated with minimal clinically relevant interactions. Areas covered: [...] Read more.

Introduction: Hepatitis C virus (HCV) infection often coexists with comorbidities, increasing vulnerability, complications, and adverse events. Direct-acting antivirals (DAAs) have dramatically improved HCV management, but they differ in drug–drug interaction (DDI) profiles. Sofosbuvir/velpatasvir (SOF/VEL) is associated with minimal clinically relevant interactions. Areas covered: A narrative review of the literature was conducted by searching PubMed and major international guidelines, focusing on studies published in the DAA era addressing HCV patients with major comorbidities, focusing on diabetes, metabolic syndrome, and cardiovascular disease; neuropsychiatric disorders; cancer; transplants; and use of substances or treatment with opioid agonists; and patients requiring hormone therapy including transgender patients. Expert opinion: Based on the literature and real-world data, managing polypharmacy in HCV patients with comorbidities is effective and well-tolerated, provided thorough drug review, potential DDI analysis, proactive monitoring, and coordinated multidisciplinary care are ensured. DAAs have dramatically improved the management of HCV patients; however, they have different DDI profiles that should be carefully checked. SOF/VEL has been shown to be associated with minimal clinically relevant interactions and offers a simple dosing regimen. DAA treatment is strongly advised in HCV comorbid patients not only to cure HCV but also to improve the course of comorbidities, provided that DDIs are no longer considered mere minor details. Full article

(This article belongs to the Section Human Virology and Viral Diseases)

22 pages, 22383 KB

Open AccessArticle

Non-Polio Enterovirus A71 and D68 Infection of Human Neuromuscular Organoids Reveals Distinct Mechanisms of Neuromuscular Impairment

by Amber J. Schotting, Inés García-Rodríguez, Eline Freeze, Anoop T. Ambikan, Michael Wagner, Mira Mioch, Aymeric P. Y. L. Moffelein, William Jackson, Dasja Pajkrt, Katja C. Wolthers, Renata Vieira de Sá and Adithya Sridhar

Viruses 2026, 18(8), 853; https://doi.org/10.3390/v18080853 - 4 Aug 2026

Abstract

Enterovirus A71 (EV-A71) and enterovirus D68 (EV-D68) are recognised as causative agents of severe neurological complications, including acute flaccid myelitis (AFM). However, the molecular mechanisms underlying the neurovirulence and effects on neuromuscular integrity remain poorly understood. Here, we employed human induced pluripotent stem [...] Read more.

Enterovirus A71 (EV-A71) and enterovirus D68 (EV-D68) are recognised as causative agents of severe neurological complications, including acute flaccid myelitis (AFM). However, the molecular mechanisms underlying the neurovirulence and effects on neuromuscular integrity remain poorly understood. Here, we employed human induced pluripotent stem cell-derived neuromuscular organoids (NMOs) to investigate the cellular tropism and pathogenic effects of EV-A71 and EV-D68 in a human-relevant context. Both viruses infected neuronal populations within NMOs, with EV-A71 exhibiting higher levels of viral replication than EV-D68. Transcriptomic analysis revealed downregulation of neuronal and muscular gene networks following infection. EV-A71 preferentially suppressed neuronal pathways, while both viruses exerted comparable effects on muscle-associated gene expression. These transcriptional changes highlighted alterations in pathways governing neuronal and muscle function and communication, prompting examination of synaptic vesicle machinery components. At the protein level, both viruses were associated with sporadic cleavage of the neuronal SNARE protein synaptosomal-associated protein 25 (SNAP25). In addition, infection with either virus increased cleaved caspase-3 levels, consistent with activation of apoptotic signalling. Together, these findings indicate virus-specific downstream effects and establish NMOs as a robust platform for dissecting enterovirus–host interactions relevant to AFM. Full article

(This article belongs to the Special Issue Viruses 2026—New Horizons in Virology)

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12 pages, 1305 KB

Open AccessArticle

Equine Ulcerative Genital Lesions Associated with Parapoxvirus

by Ann Cullinane, Marie Garvey, Donald Collins, Rachel Lyons, Maura Nelly and Adam Grimes

Viruses 2026, 18(8), 852; https://doi.org/10.3390/v18080852 - 4 Aug 2026

Abstract

In 2026, a widespread outbreak of ulcerative dermatitis of unknown aetiology occurred in breeding horses in Ireland. The lesions resembled those associated with equine herpesvirus 3 (EHV3) infection, i.e., papules, vesicles, and ulcers on the penis of stallions and on the vulval and [...] Read more.

In 2026, a widespread outbreak of ulcerative dermatitis of unknown aetiology occurred in breeding horses in Ireland. The lesions resembled those associated with equine herpesvirus 3 (EHV3) infection, i.e., papules, vesicles, and ulcers on the penis of stallions and on the vulval and anal areas of mares. This study aimed to identify the probable causative agent. The methods applied included metagenomic sequencing of DNA, phylogenetic analysis, and real-time PCR. Metagenomic analysis directly from a penile sample confirmed the presence of equine parapoxvirus (EqPPV) DNA. Phylogenetic analysis indicated that it clustered closely with EqPPV first identified in Finland in 2013 from a horse with proliferative dermatitis, and associated with outbreaks of pastern dermatitis in trotting racehorses in 2021/2022. Comparison of the amino acid sequences of the DNA polymerase gene showed that the EqPPVs from Finland and Ireland share 99% identity in contrast to 76–80% with other members of the parapoxvirus genus. A specific PCR test for EqPPV, adapted from that developed in Finland, successfully identified viral DNA in samples from 22 of 25 suspect cases that tested negative for EHV3. In conclusion, this study is the first documented outbreak of genital lesions in breeding horses associated with EqPPV. Full article

(This article belongs to the Special Issue Advances in Parapoxvirus Research: From Veterinary Infections to Public Health Implications)

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15 pages, 9069 KB

Open AccessArticle

Genetic Diversity and Phylogeny of Chilli Veinal Mottle Virus in Yunnan Tobacco-Planting Regions Based on the CP Gene

by Ning Jiang, Haonan Fang, Zhongyue Mai, Xiaotong Gai, Zhenyuan Xia, Caixiu Ya, Zuqing Hu and Dehui Xi

Viruses 2026, 18(8), 851; https://doi.org/10.3390/v18080851 - 4 Aug 2026

Abstract

Chilli veinal mottle virus (ChiVMV, Potyvirus capsivenamaculae) can infect various Solanaceae crops, causing a decrease in yield and quality. In recent years, ChiVMV has become one of the most prevalent viruses affecting tobacco production, but its diversity and genetic structure are still [...] Read more.

Chilli veinal mottle virus (ChiVMV, Potyvirus capsivenamaculae) can infect various Solanaceae crops, causing a decrease in yield and quality. In recent years, ChiVMV has become one of the most prevalent viruses affecting tobacco production, but its diversity and genetic structure are still elusive. In this study, 202 ChiVMV isolates were obtained from 13 tobacco-producing areas in Yunnan Province between 2021 and 2025. Analysis of the coat protein (CP) genes of the 202 isolates showed that there exist 193 haplotypes and abundant genetic diversity. The highest variation was observed at the N-terminus of ChiVMV CP. Further analysis displayed three high-confidence recombination events in the CP gene of ChiVMV Yunnan isolates, with isolate 25DLYP-7 from the Dali region playing a putative parental isolate for these recombinations. The results of neutral and selection pressure analyses indicated that the CP gene of ChiVMV Yunnan isolates exhibits purifying selection. Distribution analysis of these ChiVMV Yunnan isolates showed that geographical isolation is closely related to the genetic diversity of ChiVMV, and field weeds may serve as important initial sources of infection. Phylogenetic analysis demonstrated that ChiVMV Yunnan populations display close association with isolates from southwestern China, as well as isolates from South Asia and Europe. Full article

(This article belongs to the Special Issue Plant Virus Research and Biotechnology-Based Resistance Strategies—In Honor of Professor Andrew Otis Jackson)

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13 pages, 1121 KB

Open AccessArticle

Development of Cell Culture-Derived Hemagglutination Antigens for Japanese Encephalitis Virus Genotypes 1 and 3

by Seong-In Lim, Dong-Kun Yang, Gyeong Hui Kwon, Hyobi Kim, Yoon-Gi Baek, Eun-Jung Kim, Eun Mee Park, Soo Hyun Moon, Min Ji Kim and Jae-Myung Kim

Viruses 2026, 18(8), 850; https://doi.org/10.3390/v18080850 - 3 Aug 2026

Abstract

Conventional Japanese encephalitis virus (JEV) hemagglutination inhibition (HI) antigens are contingent on sucking mouse brain (SMB), and present ethical and standardization challenges. In this study, we established an alternative cell culture platform using LFBK cells to produce JEV genotype I (GI) and III [...] Read more.

Conventional Japanese encephalitis virus (JEV) hemagglutination inhibition (HI) antigens are contingent on sucking mouse brain (SMB), and present ethical and standardization challenges. In this study, we established an alternative cell culture platform using LFBK cells to produce JEV genotype I (GI) and III (GIII) antigens. Viral replication and hemagglutination (HA) activity were evaluated in six cell lines. Although raw supernatants exhibited limited HA activity, 100-fold polyethylene glycol (PEG) 8000 concentration and binary ethylenimine (BEI) inactivation of LFBK cultures successfully resulted in high-titer antigens for the K95 (GI, 256 HAU), K87 (GIII, 64 HAU), and Nakayama (GIII, 1024 HAU) strains. Diagnostic validation with swine sera showed 100% concordance between the cell-derived Nakayama antigen and commercial SMB standard. Notably, cell-concentrated GI antigens (K95 and K87) demonstrated significantly higher sensitivity (p < 0.05) for several positive samples. These results indicate that the LFBK cell platform can effectively replace traditional SMB methods and provide an ethically sustainable and highly sensitive tool for genotype-specific JEV serosurveillance. Full article

(This article belongs to the Section Animal Viruses)

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22 pages, 5754 KB

Open AccessArticle

Sheeppox and Goatpox: Molecular Epidemiology, Phylogeny and Transmission Patterns

by Alexander Sprygin, Fedor Korennoy, Rajabmurod Atovullozoda, Shawn Babiuk, Oksana Vernygora, Oliver Lung, Mohammad Abed Alhussen, Sulaimon Nazrullozoda, Natalia Yarygina, Nikita Tenitilov, Olga Byadovskaya and Ilya Chvala

Viruses 2026, 18(8), 849; https://doi.org/10.3390/v18080849 - 3 Aug 2026

Abstract

Sheep- and goatpox are highly contagious, transboundary viral diseases caused by capripoxviruses (CaPV), severely impacting small ruminant production and resulting in significant economic losses. Our study aimed to analyze the spatiotemporal SGP distribution using the available genome sequence data and to evaluate the [...] Read more.

Sheep- and goatpox are highly contagious, transboundary viral diseases caused by capripoxviruses (CaPV), severely impacting small ruminant production and resulting in significant economic losses. Our study aimed to analyze the spatiotemporal SGP distribution using the available genome sequence data and to evaluate the recombination occurrence. For this, the WAHIS, WOAH and FAO databases were utilized for the epidemiological analysis of SGP outbreaks. The cross-correlation was calculated to assess the impact of massive animal movements associated with the Islamic holiday of Eid al-Adha on the SGP epizootic situation, and phylodynamic and phylogeographic analysis, as well as a recombination analysis were performed. A total of 1629 SGP outbreaks were reported to WAHIS during 2010–2024, with the majority occurring in Mongolia, the Balkan countries, Russia and the Middle East. Over 60% of all SGP outbreaks were associated with croplands or grasslands, with the highest proportion corresponding to animal densities of 10–50 head/km². Statistically significant positive cross-correlation (p < 0.05) was identified between the month of the Eid al-Adha celebration and the number of SGP outbreaks in Russia, Mongolia, Bulgaria and Tajikistan, while in Greece and China no significant correlation was found. The inferred goat pox virus (GTPV) transmission pathways from China to Vietnam and from India to Bangladesh; for the sheeppox virus SPPV, the routes between Kazakhstan and Russia, Kazakhstan and India, as well as between Russia and China, had the strongest Bayes factor support. Intra-specific recombination events were not detected for the SSPV and GTPV datasets. However, inter-specific CaPV recombination analysis identified a single recombination event in GTPV. Therefore, the use of molecular epidemiological tools, along with the time-calibrated phylodynamic and phylogeographic analyses, has significant applications in the local and international surveillance of the occurrence of SGP outbreaks and for identification of potential recombination events. Full article

(This article belongs to the Section Animal Viruses)

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15 pages, 3896 KB

Open AccessArticle

Phylogenetic Analysis of Foot-and-Mouth Disease Virus from Cattle in Nigeria, 2017–2020

by Aliyu Sada, Jibril Adamu, Haruna M. Kazeem, Junaidu Kabir, Hussaini G. Ularamu, Yiltawe Wungak, Kabiru H. Ahmad, Bala N. Umar, Bridget Fomenky, Kate Hole, Sean Yeo, Shawn Babiuk, Oliver Lung and Charles Nfon

Viruses 2026, 18(8), 848; https://doi.org/10.3390/v18080848 - 2 Aug 2026

Abstract

The aim of this study was to detect and characterize foot-and-mouth disease virus (FMDV) serotypes circulating in cattle from Nigeria and to determine the genetic relationship with FMDV from previous studies in Nigeria. A cross-sectional study was undertaken between 2017 and 2020, during [...] Read more.

The aim of this study was to detect and characterize foot-and-mouth disease virus (FMDV) serotypes circulating in cattle from Nigeria and to determine the genetic relationship with FMDV from previous studies in Nigeria. A cross-sectional study was undertaken between 2017 and 2020, during which a total of 234 epithelial tissue samples were collected from reported outbreaks in nine states across Nigeria over a four-year period. Serotypes O/EA-3 and SAT2/VII were identified in samples from 2017 and 2018, serotypes A/Africa/G-IV and SAT2/VII in 2019, and all three serotypes including O/EA-3 and O/WA were identified in samples from 2020. This study identified the presence of three FMDV serotypes (O/EA-3 and O/WA, A/Africa/G-IV and SAT2/VII) circulating in Nigeria. The three serotypes detected in this study can be recommended for production of the appropriate vaccines to control FMDV in Nigeria. Full article

(This article belongs to the Section Animal Viruses)

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