Viruses

23 pages, 2193 KiB

Open AccessArticle

A Virome Scanning of Saffron (Crocus sativus L.) at the National Scale in Iran Using High-Throughput Sequencing Technologies

by Hajar Valouzi, Akbar Dizadji, Alireza Golnaraghi, Seyed Alireza Salami, Nuria Fontdevila Pareta, Serkan Önder, Ilhem Selmi, Johan Rollin, Chadi Berhal, Lucie Tamisier, François Maclot, Long Wang, Rui Zhang, Habibullah Bahlolzada, Pierre Lefeuvre and Sébastien Massart

Viruses 2025, 17(8), 1079; https://doi.org/10.3390/v17081079 - 4 Aug 2025

Abstract

Saffron (Crocus sativus L.) is a vegetatively propagated crop of high economic and cultural value, potentially affected by viral infections that may impact its productivity. Despite Iran’s dominance in global saffron production, knowledge of its virome remains limited. In this study, we [...] Read more.

Saffron (Crocus sativus L.) is a vegetatively propagated crop of high economic and cultural value, potentially affected by viral infections that may impact its productivity. Despite Iran’s dominance in global saffron production, knowledge of its virome remains limited. In this study, we conducted the first nationwide virome survey of saffron in Iran employing a high-throughput sequencing (HTS) approach on pooled samples obtained from eleven provinces in Iran and one location in Afghanistan. Members of three virus families were detected—Potyviridae (Potyvirus), Solemoviridae (Polerovirus), and Geminiviridae (Mastrevirus)—as well as one satellite from the family Alphasatellitidae (Clecrusatellite). A novel Potyvirus, tentatively named saffron Iran virus (SaIRV) and detected in three provinces, shares less than 68% nucleotide identity with known Potyvirus species, thus meeting the ICTV criteria for designation as a new species. Genetic diversity analyses revealed substantial intrapopulation SNP variation but no clear geographical clustering. Among the two wild Crocus species sampled, only Crocus speciosus harbored turnip mosaic virus. Virome network and phylogenetic analyses confirmed widespread viral circulation likely driven by corm-mediated propagation. Our findings highlight the need for targeted certification programs and biological characterization of key viruses to mitigate potential impacts on saffron yield and quality. Full article

(This article belongs to the Special Issue Emerging and Reemerging Plant Viruses in a Changing World)

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21 pages, 1330 KiB

Open AccessArticle

Global Circulation Dynamics and Its Determinants of Dengue Virus: A Network Evolution and Model Study from 1990 to 2019

by Haoyu Long, Jinfeng Zeng, Yilin Chen, Kang Tang, Chi Zhang, Qianru Sun, Lei Gao, Yuhui Lin, Junting He, Chunhui Yang, Xiaoying Lin, Wenzhe Su, Kuibiao Li, Biao Di, Min Kang, Chongguang Yang and Xiangjun Du

Viruses 2025, 17(8), 1078; https://doi.org/10.3390/v17081078 - 4 Aug 2025

Abstract

As dengue is an increasing global health threat, a better understanding of the global circulation dynamics and its determinants would be helpful for precise prevention and control of dengue. The dynamics of global circulation of the four dengue virus serotypes were explored utilizing [...] Read more.

As dengue is an increasing global health threat, a better understanding of the global circulation dynamics and its determinants would be helpful for precise prevention and control of dengue. The dynamics of global circulation of the four dengue virus serotypes were explored utilizing genetic sequences through a network-based method. Four new circulation indicators, including local intensity, betweenness centrality, tip frequency, and persistence time, were defined. Three circulation roles, including source, hub, and destination, were proposed on the basis of new indicators. Spatial and temporal changes of the three circulation roles, along with the persistence time, were explored. Important determinants were also evaluated by machine learning models. Thailand, Indonesia, and Vietnam in Asia and Venezuela and Colombia in Americas were the sources for all four serotypes in different decades. Destinations were observed mostly in island regions. Over the decades, the number of regions with different circulation roles and persistence of DENV-1 increased significantly. Climate and airline factors were involved in the important determinants to circulation roles and persistence of dengue. The roles identified in the global circulation of dengue and important determinants, including climate and airline factors, provide new insights into global dynamics and are beneficial for controlling dengue. Full article

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

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26 pages, 3619 KiB

Open AccessReview

Baculovirus-Based Biocontrol: Synergistic and Antagonistic Interactions of PxGV, PxNPV, SeMNPV, and SfMNPV in Integrative Pest Management

by Alberto Margarito García-Munguía, Carlos Alberto García-Munguía, Paloma Lucía Guerra-Ávila, Estefany Alejandra Sánchez-Mendoza, Fabián Alejandro Rubalcava-Castillo, Argelia García-Munguía, María Reyna Robles-López, Luis Fernando Cisneros-Guzmán, María Guadalupe Martínez-Alba, Ernesto Olvera-Gonzalez, Raúl René Robles-de la Torre and Otilio García-Munguía

Viruses 2025, 17(8), 1077; https://doi.org/10.3390/v17081077 - 2 Aug 2025

Abstract

The use of chemical pesticides in agriculture has led to the development of resistant pest populations, posing a challenge to long-term pest management. This review aims to evaluate the scientific literature on the individual and combined use of baculoviruses with conventional chemical and [...] Read more.

The use of chemical pesticides in agriculture has led to the development of resistant pest populations, posing a challenge to long-term pest management. This review aims to evaluate the scientific literature on the individual and combined use of baculoviruses with conventional chemical and biological insecticides to combat Plutella xylostella, Spodoptera exigua, and Spodoptera frugiperda in broccoli, tomato, and maize crops. Notable findings include that both individual Plutella xylostella nucleopolyhedrovirus (PxNPV) and the combination of Plutella xylostella granulovirus (PxGV) and azadirachtin at a low dose effectively control Plutella xylostella; both combinations of Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) with emamectin benzoate and chlorfenapyr reduced resistance in Spodoptera exigua and increased the efficacy of the insecticides; and the combination of Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV) and spinetoram is effective against Spodoptera frugiperda. Integrating baculoviruses into pest management strategies offers a promising approach to mitigate the adverse effects of chemical pesticides, such as resistance development, health risks, and environmental damage. However, there remains a broad spectrum of research opportunities regarding the use of baculoviruses in agriculture. Full article

(This article belongs to the Special Issue Applications of Baculoviruses: Expression Factories, Vaccines and VLPs, Gene Delivery Vectors, and Virus Genetics Models)

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16 pages, 2285 KiB

Open AccessArticle

Pegiviruses and Coronavirus: Biomolecular Prevalence and Phylogenetic Analysis of Strains Detected in Italian Horse Populations

by Ida Ricci, Francesca Rosone, Giulia Pacchiarotti, Giuseppe Manna, Antonella Cersini, Andrea Carvelli, Davide La Rocca, Elisa Cammalleri, Roberta Giordani, Silvia Tofani, Raffaella Conti, Pasquale Rombolà, Roberto Nardini, Carlo Alberto Minniti, Reno Caforio, Boris Linardi and Maria Teresa Scicluna

Viruses 2025, 17(8), 1076; https://doi.org/10.3390/v17081076 - 2 Aug 2025

Abstract

Equestrian sports play a significant economic role in the horse industry. In recent years, numerous equine viruses have emerged, among which are equine Pegiviruses and the re-emerging Equine coronavirus (ECoV). These viruses are distributed globally and primarily cause subclinical infections with unknown morbidity, [...] Read more.

Equestrian sports play a significant economic role in the horse industry. In recent years, numerous equine viruses have emerged, among which are equine Pegiviruses and the re-emerging Equine coronavirus (ECoV). These viruses are distributed globally and primarily cause subclinical infections with unknown morbidity, even if ECoV can occasionally induce febrile and diarrheic episodes. To broaden the data on the Italian equine population, a study was conducted to assess their prevalence in two distinct horse populations belonging to the Carabinieri Corps (CC) and the Italian Army (IA) of the Italian Armed Forces (IAF). Samples consisted of blood serum and rectal swabs of 436 horses collected within the national surveillance program for equine infectious anemia and gastrointestinal parasite monitoring and analyzed for Pegivirus (caballi and equi) and ECoV by Real-Time RT PCR. The prevalence detected were 6.56% and 3.53%, respectively, for Pegivirus caballi and equi for the IA, while for the CC, they were 10.13% and 0.84%. Only one sample tested positive for ECoV belonging to a horse of the CC. Phylogenetic analyses were carried out on the PCR-positive samples that were sequenced using Sanger protocols. Understanding the epidemiology of these viruses is essential for evaluating the implementation of effective prevention strategies. Full article

(This article belongs to the Section Animal Viruses)

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23 pages, 2284 KiB

Open AccessArticle

The Replication Function of Rabies Virus P Protein Is Regulated by a Novel Phosphorylation Site in the N-Terminal N Protein-Binding Region

by Ericka Tudhope, Camilla M. Donnelly, Ashish Sethi, Cassandra David, Nicholas Williamson, Murray Stewart, Jade K. Forwood, Paul R. Gooley and Gregory W. Moseley

Viruses 2025, 17(8), 1075; https://doi.org/10.3390/v17081075 - 1 Aug 2025

Abstract

The rabies virus (RABV) phosphoprotein (P protein) has multiple functions, including acting as the essential non-catalytic cofactor of the viral polymerase (L protein) for genome replication and transcription; the principal viral antagonist of the interferon (IFN)-mediated innate immune response; and the chaperone for [...] Read more.

The rabies virus (RABV) phosphoprotein (P protein) has multiple functions, including acting as the essential non-catalytic cofactor of the viral polymerase (L protein) for genome replication and transcription; the principal viral antagonist of the interferon (IFN)-mediated innate immune response; and the chaperone for the viral nucleoprotein (N protein). Although P protein is known to undergo phosphorylation by cellular kinases, the location and functions of the phosphorylation sites remains poorly defined. Here, we report the identification by mass-spectrometry (MS) of residues of P protein that are modified by phosphorylation in mammalian cells, including several novel sites. Analysis of P protein with phospho-mimetic and phospho-inhibitory mutations of three novel residues/clusters that were commonly identified by MS (Ser48, Ser183/187, Ser217/219/220) indicate that phosphorylation at each of these sites does not have a major influence on nuclear trafficking or antagonistic functions toward IFN signalling pathways. However, phosphorylation of Ser48 in the N-terminus of P protein impaired function in transcription/replication and in the formation of replication structures that contain complexes of P and N proteins, suggestive of altered interactions of these proteins. The crystal structure of P protein containing the S48E phospho-mimetic mutation indicates that Ser48 phosphorylation facilitates the binding of residues 41–52 of P protein into the RNA-binding groove of non-RNA-bound N protein (N⁰), primarily through the formation of a salt bridge with Arg434 of N protein. These data indicate that Ser48 modification regulates the cycling of P-N⁰ chaperone complexes that deliver N protein to RNA to enable transcription/replication, such that enhanced interaction due to S48E phospho-mimetic mutation reduces N protein delivery to the RNA, inhibiting subsequent transcription/replication processes. These data are, to our knowledge, the first to implicate phosphorylation of RABV P protein in conserved replication functions of the P gene. Full article

(This article belongs to the Section Animal Viruses)

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13 pages, 1085 KiB

Open AccessArticle

Comparative Endosymbiont Community Structures of Nonviruliferous and Rice Stripe Virus-Viruliferous Laodelphax striatellus (Hemiptera: Delphacidae) in Korea

by Jiho Jeon, Minhyeok Kwon, Bong Choon Lee and Eui-Joon Kil

Viruses 2025, 17(8), 1074; https://doi.org/10.3390/v17081074 - 1 Aug 2025

Abstract

Insects and their bacterial endosymbionts form intricate ecological relationships, yet their role in host–pathogen interactions are not fully elucidated. The small brown planthopper (Laodelphax striatellus), a polyphagous pest of cereal crops, acts as a key vector for rice stripe virus (RSV), [...] Read more.

Insects and their bacterial endosymbionts form intricate ecological relationships, yet their role in host–pathogen interactions are not fully elucidated. The small brown planthopper (Laodelphax striatellus), a polyphagous pest of cereal crops, acts as a key vector for rice stripe virus (RSV), a significant threat to rice production. This study aimed to compare the endosymbiont community structures of nonviruliferous and RSV-viruliferous L. striatellus populations using 16S rRNA gene sequencing with high-throughput sequencing technology. Wolbachia was highly dominant in both groups; however, the prevalence of other endosymbionts, specifically Rickettsia and Burkholderia, differed markedly depending on RSV infection. Comprehensive microbial diversity and composition analyses revealed distinct community structures between nonviruliferous and RSV-viruliferous populations, highlighting potential interactions and implications for vector competence and virus transmission dynamics. These findings contribute to understanding virus-insect-endosymbiont dynamics and could inform strategies to mitigate viral spread by targeting symbiotic bacteria. Full article

(This article belongs to the Special Issue Plant Viruses and Their Vectors: Epidemiology and Control)

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19 pages, 633 KiB

Open AccessReview

Predictive Factors and Clinical Markers of Recurrent Wheezing and Asthma After RSV Infection

by Luca Buttarelli, Elisa Caselli, Sofia Gerevini, Pietro Leuratti, Antonella Gambadauro, Sara Manti and Susanna Esposito

Viruses 2025, 17(8), 1073; https://doi.org/10.3390/v17081073 - 31 Jul 2025

Abstract

Respiratory syncytial virus (RSV) is a major cause of acute lower respiratory infections (ALRIs) in young children, especially bronchiolitis, with significant global health and economic impact. Increasing evidence links early-life RSV infection to long-term respiratory complications, notably recurrent wheezing and asthma. This narrative [...] Read more.

Respiratory syncytial virus (RSV) is a major cause of acute lower respiratory infections (ALRIs) in young children, especially bronchiolitis, with significant global health and economic impact. Increasing evidence links early-life RSV infection to long-term respiratory complications, notably recurrent wheezing and asthma. This narrative review examines these associations, emphasizing predictive factors and emerging biomarkers for risk stratification. Early RSV infection can trigger persistent airway inflammation and immune dysregulation, increasing the likelihood of chronic respiratory outcomes. Risk factors include severity of the initial infection, age at exposure, genetic susceptibility, prematurity, air pollution, and tobacco smoke. Biomarkers such as cytokines and chemokines are showing promise in identifying children at higher risk, potentially guiding early interventions. RSV-related bronchiolitis may also induce airway remodeling and promote Th2/Th17-skewed immune responses, mechanisms closely linked to asthma development. Advances in molecular profiling are shedding light on these pathways, suggesting novel targets for early therapeutic strategies. Furthermore, passive immunization and maternal vaccination offer promising approaches to reducing both acute and long-term RSV-related morbidity. A deeper understanding of RSV’s prolonged impact is essential to develop targeted prevention, enhance risk prediction, and improve long-term respiratory health in children. Future studies should aim to validate biomarkers and refine immunoprophylactic strategies. Full article

(This article belongs to the Special Issue RSV Epidemiological Surveillance: 2nd Edition)

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16 pages, 1622 KiB

Open AccessArticle

Simian Foamy Virus Prevalence and Evolutionary Relationships in Two Free-Living Lion Tamarin Populations from Rio de Janeiro, Brazil

by Déa Luiza Girardi, Thamiris Santos Miranda, Matheus Augusto Calvano Cosentino, Caroline Carvalho de Sá, Talitha Mayumi Francisco, Bianca Cardozo Afonso, Flávio Landim Soffiati, Suelen Sanches Ferreira, Silvia Bahadian Moreira, Alcides Pissinatti, Carlos Ramon Ruiz-Miranda, Valéria Romano, Marcelo Alves Soares, Mirela D’arc and André Felipe Santos

Viruses 2025, 17(8), 1072; https://doi.org/10.3390/v17081072 - 31 Jul 2025

Abstract

Simian foamy virus (SFV) is a retrovirus that infects primates. However, epidemiological studies of SFV are often limited to captive populations. The southeastern Brazilian Atlantic Forest is home to both an endemic, endangered species, Leontopithecus rosalia, and an introduced species, Leontopithecus chrysomelas [...] Read more.

Simian foamy virus (SFV) is a retrovirus that infects primates. However, epidemiological studies of SFV are often limited to captive populations. The southeastern Brazilian Atlantic Forest is home to both an endemic, endangered species, Leontopithecus rosalia, and an introduced species, Leontopithecus chrysomelas, to which no data on SFV exist. In this study, we assessed the molecular prevalence of SFV, their viral load, and their phylogenetic relationship in these two species of primates. Genomic DNA was extracted from 48 oral swab samples of L. chrysomelas and 102 of L. rosalia. Quantitative PCR (qPCR) was performed to diagnose SFV infection and quantify viral load. SFV prevalence was found to be 23% in L. chrysomelas and 33% in L. rosalia. No age-related differences in prevalence were observed; however, L. rosalia showed a higher mean viral load (3.27 log10/10⁶ cells) compared to L. chrysomelas (3.03 log10/10⁶ cells). The polymerase gene sequence (213 pb) of L. rosalia (SFVlro) was clustered within a distinct SFV lineage found in L. chrysomelas. The estimated origin of SFVlro dated back approximately 0.0836 million years ago. Our study provides the first molecular prevalence data for SFV in free-living Leontopithecus populations while offering insights into the complex evolutionary history of SFV in American primates. Full article

(This article belongs to the Special Issue Spumaretroviruses: Research and Applications)

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10 pages, 1037 KiB

Open AccessConference Report

Thirteenth International Foamy Virus Conference—Meeting Report

by Arifa S. Khan, Martin Löchelt, Florence Buseyne, Ottmar Herchenröder, Dirk Lindemann, William M. Switzer, André F. A. Santos and Marcelo A. Soares

Viruses 2025, 17(8), 1071; https://doi.org/10.3390/v17081071 - 31 Jul 2025

Abstract

The 13th International Foamy Virus (FV) Conference was held from 8 to 10 November 2023 at the BioParque/Zoological Garden in Rio de Janeiro, Brazil. This was the first conference on spumaretroviruses to be held in the Southern Hemisphere and in the unique environment [...] Read more.

The 13th International Foamy Virus (FV) Conference was held from 8 to 10 November 2023 at the BioParque/Zoological Garden in Rio de Janeiro, Brazil. This was the first conference on spumaretroviruses to be held in the Southern Hemisphere and in the unique environment of the rainforest. New developments and current perspectives in FV research were presented. Highlights of the conference included the structural biology of the envelope protein (Env) and insights into its function and evolution, epidemiologic identification of Amazonian indigenous people with a high prevalence of simian FV (SFV) infections, investigations of virus biology and genomics using synthetic FV DNAs, studies of humoral immune response, and development and applications of SFV vectors. The last day of the meeting was a special tour of the Centro de Primatologia do Rio de Janeiro, located northeast of Rio de Janeiro amidst the protected rainforest, where New World primate hosts of spumaretroviruses are rescued and studied. Our report summarizes the meeting highlights and outcomes for future discussions. Full article

(This article belongs to the Special Issue Spumaretroviruses: Research and Applications)

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19 pages, 8583 KiB

Open AccessArticle

Development and Immunogenic Evaluation of a Recombinant Vesicular Stomatitis Virus Expressing Nipah Virus F and G Glycoproteins

by Huijuan Guo, Renqiang Liu, Dan Pan, Yijing Dang, Shuhuai Meng, Dan Shan, Xijun Wang, Jinying Ge, Zhigao Bu and Zhiyuan Wen

Viruses 2025, 17(8), 1070; https://doi.org/10.3390/v17081070 - 31 Jul 2025

Abstract

Nipah virus (NiV) is a highly pathogenic bat-borne zoonotic pathogen that poses a significant threat to human and animal health, with fatality rates exceeding 70% in some outbreaks. Despite its significant public health impact, there are currently no licensed vaccines or specific therapeutics [...] Read more.

Nipah virus (NiV) is a highly pathogenic bat-borne zoonotic pathogen that poses a significant threat to human and animal health, with fatality rates exceeding 70% in some outbreaks. Despite its significant public health impact, there are currently no licensed vaccines or specific therapeutics available. Various virological tools—such as reverse genetics systems, replicon particles, VSV-based pseudoviruses, and recombinant Cedar virus chimeras—have been widely used to study the molecular mechanisms of NiV and to support vaccine development. Building upon these platforms, we developed a replication-competent recombinant vesicular stomatitis virus (rVSVΔG-eGFP-NiV_BD F/G) expressing NiV attachment (G) and fusion (F) glycoproteins. This recombinant virus serves as a valuable tool for investigating NiV entry mechanisms, cellular tropism, and immunogenicity. The virus was generated by replacing the VSV G protein with NiV F/G through reverse genetics, and protein incorporation was confirmed via immunofluorescence and electron microscopy. In vitro, the virus exhibited robust replication, characteristic cell tropism, and high viral titers in multiple cell lines. Neutralization assays showed that monoclonal antibodies HENV-26 and HENV-32 effectively neutralized the recombinant virus. Furthermore, immunization of golden hamsters with inactivated rVSVΔG-eGFP-NiV_BD F/G induced potent neutralizing antibody responses, demonstrating its robust immunogenicity. These findings highlight rVSVΔG-eGFP-NiV_BD F/G as an effective platform for NiV research and vaccine development. Full article

(This article belongs to the Section Animal Viruses)

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31 pages, 1537 KiB

Open AccessReview

Hepatitis C Virus: Epidemiological Challenges and Global Strategies for Elimination

by Daniela Toma, Lucreția Anghel, Diana Patraș and Anamaria Ciubară

Viruses 2025, 17(8), 1069; https://doi.org/10.3390/v17081069 - 31 Jul 2025

Abstract

The global elimination of hepatitis C virus (HCV) has been prioritized by the World Health Organization (WHO) as a key public health target, with a deadline set for 2030. This initiative aims to significantly reduce both new infection rates and HCV-associated mortality. A [...] Read more.

The global elimination of hepatitis C virus (HCV) has been prioritized by the World Health Organization (WHO) as a key public health target, with a deadline set for 2030. This initiative aims to significantly reduce both new infection rates and HCV-associated mortality. A major breakthrough in achieving this goal has been the development of direct-acting antiviral agents (DAAs), which offer cure rates exceeding 95%, along with excellent safety and tolerability. Nevertheless, transmission via parenteral routes continues to be the dominant pathway, particularly among high-risk groups, such as individuals who inject drugs, incarcerated populations, those exposed to unsafe medical practices, and healthcare professionals. Identifying, monitoring, and delivering tailored interventions to these groups is crucial to interrupt ongoing transmission and to reduce the burden of chronic liver disease. On a global scale, several nations have demonstrated measurable progress toward HCV elimination, with some nearing the targets set by WHO. These achievements have largely resulted from context-adapted policies that enhanced diagnostic and therapeutic access while emphasizing outreach to vulnerable communities. This review synthesizes current advancements in HCV prevention and control and proposes strategic frameworks to expedite global elimination efforts. Full article

(This article belongs to the Special Issue Advancing Hepatitis Elimination: HBV, HDV, and HCV)

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20 pages, 2586 KiB

Open AccessArticle

Virome Survey of Banana Plantations and Surrounding Plants in Malawi

by Johnny Isaac Gregorio Masangwa, Coline Temple, Johan Rollin, François Maclot, Serkan Önder, Jamestone Kamwendo, Elizabeth Mwafongo, Philemon Moses, Isaac Fandika and Sebastien Massart

Viruses 2025, 17(8), 1068; https://doi.org/10.3390/v17081068 - 31 Jul 2025

Abstract

A virome survey of banana plantations and their surrounding plants was carried out at nation-wide level in Malawi using virion associated nucleic acids (VANA) high throughput sequencing (HTS) on pooled samples and appropriate alien controls. In total, 366 plants were sequenced, and 23 [...] Read more.

A virome survey of banana plantations and their surrounding plants was carried out at nation-wide level in Malawi using virion associated nucleic acids (VANA) high throughput sequencing (HTS) on pooled samples and appropriate alien controls. In total, 366 plants were sequenced, and 23 plant virus species were detected, three species on banana (275 plants) and 20 species in surrounding plants (91 plants). Two putative novel virus species; ginger tymo-like virus and pepper derived totivirus were detected and confirmed by RT-PCR on ginger and pepper. Nine known virus species and detected a host plant was identified for two of them. No viral exchange between banana and surrounding plants was observed. Results from the VANA protocol, applied to pooled banana samples, were compared with previous targeted PCR results obtained from individual banana samples. HTS test detected better BanMMV than IC-(RT)-PCR on individual samples (better inclusivity) but detected with much lower sensitivity BBTV and BSV species, often with less than 10 reads per sample. Detection of novel and known viruses and new host plants calls for strengthened sanitory and phytosanitory measures within and beyond banana production systems. Our research confirms that HTS sensitivity depends on sampling, pooling protocol and targeted virus species. Full article

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

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Graphical abstract

18 pages, 4051 KiB

Open AccessArticle

Chimeric Vesicular Stomatitis Virus Bearing Western Equine Encephalitis Virus Envelope Proteins E2-E1 Is a Suitable Surrogate for Western Equine Encephalitis Virus in a Plaque Reduction Neutralization Test

by Kerri L. Miazgowicz, Bailey E. Maloney, Melinda A. Brindley, Mattie Cassaday, Raegan J. Petch, Paul Bates, Aaron C. Brault and Amanda E. Calvert

Viruses 2025, 17(8), 1067; https://doi.org/10.3390/v17081067 - 31 Jul 2025

Abstract

In December 2023, infections of western equine encephalitis virus (WEEV) within Argentina were reported to the World Health Organization (WHO). By April 2024, more than 250 human infections, 12 of which were fatal, and 2500 equine infections were identified in South America. Laboratory [...] Read more.

In December 2023, infections of western equine encephalitis virus (WEEV) within Argentina were reported to the World Health Organization (WHO). By April 2024, more than 250 human infections, 12 of which were fatal, and 2500 equine infections were identified in South America. Laboratory diagnosis and surveillance in affected countries were hindered by a lack of facilities equipped with BSL-3 laboratories, as confirmatory serodiagnosis for WEEV requires live virus in the plaque reduction neutralization test (PRNT). To expand serodiagnosis for WEEV in the Americas, we developed a virus chimera composed of vesicular stomatitis virus (VSV) engineered to display the E2-E1 glycoproteins of WEEV (VSV/WEEV) in place of the VSV glycoprotein (G). PRNT₉₀ and IC₉₀ values of parental WEEV and VSV/WEEV were analogous using sera collected from mice, horses, and chickens. VSV/WEEV rapidly formed plaques with clear borders and reduced the assay readout time by approximately 8 h compared to the parental virus. Overall, we demonstrate that chimeric VSV/WEEV is a suitable surrogate for WEEV in a diagnostic PRNT. Use of chimeric VSV/WEEV in place of authentic WEEV will dramatically expand testing capacity by enabling PRNTs to be performed at BSL-2 containment, while simultaneously decreasing the health risk to testing personnel. Full article

(This article belongs to the Special Issue Mosquito-Borne Encephalitis Viruses)

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20 pages, 1573 KiB

Open AccessArticle

Polyvalent Mannuronic Acid-Coated Gold Nanoparticles for Probing Multivalent Lectin–Glycan Interaction and Blocking Virus Infection

by Rahman Basaran, Darshita Budhadev, Eleni Dimitriou, Hannah S. Wootton, Gavin J. Miller, Amy Kempf, Inga Nehlmeier, Stefan Pöhlmann, Yuan Guo and Dejian Zhou

Viruses 2025, 17(8), 1066; https://doi.org/10.3390/v17081066 - 30 Jul 2025

Abstract

Multivalent lectin–glycan interactions (MLGIs) are vital for viral infection, cell-cell communication and regulation of immune responses. Their structural and biophysical data are thus important, not only for providing insights into their underlying mechanisms but also for designing potent glycoconjugate therapeutics against target MLGIs. [...] Read more.

Multivalent lectin–glycan interactions (MLGIs) are vital for viral infection, cell-cell communication and regulation of immune responses. Their structural and biophysical data are thus important, not only for providing insights into their underlying mechanisms but also for designing potent glycoconjugate therapeutics against target MLGIs. However, such information remains to be limited for some important MLGIs, significantly restricting the research progress. We have recently demonstrated that functional nanoparticles, including ∼4 nm quantum dots and varying sized gold nanoparticles (GNPs), densely glycosylated with various natural mono- and oligo- saccharides, are powerful biophysical probes for MLGIs. Using two important viral receptors, DC-SIGN and DC-SIGNR (together denoted as DC-SIGN/R hereafter), as model multimeric lectins, we have shown that α-mannose and α-manno-α-1,2-biose (abbreviated as Man and DiMan, respectively) coated GNPs not only can provide sensitive measurement of MLGI affinities but also reveal critical structural information (e.g., binding site orientation and mode) which are important for MLGI targeting. In this study, we produced mannuronic acid (ManA) coated GNPs (GNP-ManA) of two different sizes to probe the effect of glycan modification on their MLGI affinity and antiviral property. Using our recently developed GNP fluorescence quenching assay, we find that GNP-ManA binds effectively to both DC-SIGN/R and increasing the size of GNP significantly enhances their MLGI affinity. Consistent with this, increasing the GNP size also significantly enhances their ability to block DC-SIGN/R-augmented virus entry into host cells. Particularly, ManA coated 13 nm GNP potently block Ebola virus glycoprotein-driven entry into DC-SIGN/R-expressing cells with sub-nM levels of EC₅₀. Our findings suggest that GNP-ManA probes can act as a useful tool to quantify the characteristics of MLGIs, where increasing the GNP scaffold size substantially enhances their MLGI affinity and antiviral potency. Full article

(This article belongs to the Special Issue Role of Lectins in Viral Infections and Antiviral Intervention)

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19 pages, 4270 KiB

Open AccessArticle

Viral Inactivation by Light-Emitting Diodes: Action Spectra Reveal Genomic Damage as the Primary Mechanism

by Kazuaki Mawatari, Yasuko Kadomura-Ishikawa, Takahiro Emoto, Yushi Onoda, Kai Ishida, Sae Toda, Takashi Uebanso, Toshihiko Aizawa, Shigeharu Yamauchi, Yasuo Fujikawa, Tomotake Tanaka, Xing Li, Eduardo Suarez-Lopez, Richard J. Kuhn, Ernest R. Blatchley III III and Akira Takahashi

Viruses 2025, 17(8), 1065; https://doi.org/10.3390/v17081065 - 30 Jul 2025

Abstract

Irradiation with ultraviolet light-emitting diodes (UV-LEDs) represents a promising method for viral inactivation, but a detailed understanding of the wavelength-dependent action spectra remains limited, particularly across different viral components. In this study, we established standardized UV action spectra for infectivity reduction in pathogenic [...] Read more.

Irradiation with ultraviolet light-emitting diodes (UV-LEDs) represents a promising method for viral inactivation, but a detailed understanding of the wavelength-dependent action spectra remains limited, particularly across different viral components. In this study, we established standardized UV action spectra for infectivity reduction in pathogenic viruses using a system equipped with interchangeable LEDs at 13 different peak wavelengths (250–365 nm). The reduction in viral infectivity induced by UV-LED exposure was strongly related to viral genome damage, whereas no significant degradation of viral structural proteins was detected. Peak virucidal efficiency was observed at 267–270 nm across all tested viruses, representing a slight shift from the traditionally expected 260 nm nucleic acid absorption peak. Enveloped RNA viruses, including influenza A virus, respiratory syncytial virus, and coronavirus, exhibited greater UV sensitivity than nonenveloped viruses such as feline calicivirus and adenovirus. These observations indicate that structural characteristics, such as the presence of an envelope and genome organization, influence UV susceptibility. The wavelength-specific action spectra established in this study provide critical data for optimizing UV-LED disinfection systems to achieve efficient viral inactivation while minimizing energy consumption in healthcare, food safety, and environmental sanitation. Full article

(This article belongs to the Special Issue Influenza and Other Respiratory Viruses: Prevention, Diagnosis, Treatment: 2nd Edition)

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24 pages, 1024 KiB

Open AccessReview

SARS-CoV-2 Infection and Antiviral Strategies: Advances and Limitations

by Vinicius Cardoso Soares, Isabela Batista Gonçalves Moreira and Suelen Silva Gomes Dias

Viruses 2025, 17(8), 1064; https://doi.org/10.3390/v17081064 - 30 Jul 2025

Abstract

Since the onset of the COVID-19 pandemic, remarkable progress has been made in the development of antiviral therapies for SARS-CoV-2. Several direct-acting antivirals, such as remdesivir, molnupiravir, and nirmatrelvir/ritonavir, offer clinical benefits. These agents have significantly contributed to reducing the viral loads and [...] Read more.

Since the onset of the COVID-19 pandemic, remarkable progress has been made in the development of antiviral therapies for SARS-CoV-2. Several direct-acting antivirals, such as remdesivir, molnupiravir, and nirmatrelvir/ritonavir, offer clinical benefits. These agents have significantly contributed to reducing the viral loads and duration of the illness, as well as the disease’s severity and mortality. However, despite these advances, important limitations remain. The continued emergence of resistant SARS-CoV-2 variants highlights the urgent need for adaptable and durable therapeutic strategies. Therefore, this review aims to provide an updated overview of the main antiviral strategies that are used and the discovery of new drugs against SARS-CoV-2, as well as the therapeutic limitations that have shaped clinical management in recent years. The major challenges include resistance associated with viral mutations, limited treatment windows, and unequal access to treatment. Moreover, there is an ongoing need to identify novel compounds with broad-spectrum activity, improved pharmacokinetics, and suitable safety profiles. Combination treatment regimens represent a promising strategy to increase the efficacy of treating COVID-19 while minimizing the potential for resistance. Ideally, these interventions should be safe, affordable, and easy to administer, which would ensure broad global access and equitable treatment and enable control of COVID-19 cases and preparedness for future threats. Full article

(This article belongs to the Special Issue Natural, Semisynthetic, and Synthetic Antiviral Drugs Targeting HIV and SARS-CoV-2)

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19 pages, 4764 KiB

Open AccessArticle

Evolutionary Diversity of Bat Rabies Virus in São Paulo State, Brazil

by Luzia H. Queiroz, Angélica C. A. Campos, Marissol C. Lopes, Elenice M. S. Cunha, Avelino Albas, Cristiano de Carvalho, Wagner A. Pedro, Eduardo C. Silva, Monique S. Lot, Sandra V. Inácio, Danielle B. Araújo, Marielton P. Cunha, Edison L. Durigon, Luiz Gustavo B. Góes and Silvana R. Favoretto

Viruses 2025, 17(8), 1063; https://doi.org/10.3390/v17081063 - 30 Jul 2025

Abstract

The history of the rabies virus dates back four millennia, with the virus being considered by many to be the first known transmitted between animals and humans. In Brazil, rabies virus variants associated with terrestrial wild animals, marmosets, and different bat species have [...] Read more.

The history of the rabies virus dates back four millennia, with the virus being considered by many to be the first known transmitted between animals and humans. In Brazil, rabies virus variants associated with terrestrial wild animals, marmosets, and different bat species have been identified. In this study, bat samples from different regions of São Paulo State, in Southeast Brazil, were analyzed to identify their genetic variability and patterns. A total of 51 samples were collected over ten years (1999–2009) and submitted to the immunofluorescent technique using monoclonal antibodies for antigenic profile detection (the diagnostic routine used in Latin American countries) and genetic evolution analysis through maximum likelihood approaches. Three antigenic profiles were detected: one related to the rabies virus maintained by hematophagous bat populations (AgV3), part of the monoclonal antibody panel used, and two other profiles not included in the panel (called NC1 and NC2). These antigenic profiles were genetically distributed in five groups. Group I was related to hematophagous bats (AgV3), Groups II and III were related to insectivorous bats (NC1) and Groups IV and V were also related to insectivorous bats (NC2). The results presented herein show that genetic lineages previously restricted to the northwest region of São Paulo State are now found in other state regions, highlighting the need for a comprehensive genetic study of bat rabies covering geographic and temporal space, through expanded genomic analysis using a standard genomic fragment. Full article

(This article belongs to the Special Issue Advances in Rabies Research 2024)

20 pages, 3054 KiB

Open AccessArticle

Development of COVID-19 Vaccine Candidates Using Attenuated Recombinant Vesicular Stomatitis Virus Vectors with M Protein Mutations

by Mengqi Chang, Hui Huang, Mingxi Yue, Yuetong Jiang, Siping Yan, Yiyi Chen, Wenrong Wu, Yibing Gao, Mujin Fang, Quan Yuan, Hualong Xiong and Tianying Zhang

Viruses 2025, 17(8), 1062; https://doi.org/10.3390/v17081062 - 30 Jul 2025

Abstract

Recombinant vesicular stomatitis virus (rVSV) is a promising viral vaccine vector for addressing the COVID-19 pandemic. Inducing mucosal immunity via the intranasal route is an ideal strategy for rVSV-based vaccines, but it requires extremely stringent safety standards. In this study, we constructed two [...] Read more.

Recombinant vesicular stomatitis virus (rVSV) is a promising viral vaccine vector for addressing the COVID-19 pandemic. Inducing mucosal immunity via the intranasal route is an ideal strategy for rVSV-based vaccines, but it requires extremely stringent safety standards. In this study, we constructed two rVSV variants with amino acid mutations in their M protein: rVSV-M2 with M33A/M51R mutations and rVSV-M4 with M33A/M51R/V221F/S226R mutations, and developed COVID-19 vaccines based on these attenuated vectors. By comparing viral replication capacity, intranasal immunization, intracranial injection, and blood cell counts, we demonstrated that the M protein mutation variants exhibit significant attenuation effects both in vitro and in vivo. Moreover, preliminary investigations into the mechanisms of virus attenuation revealed that these attenuated viruses can induce a stronger type I interferon response while reducing inflammation compared to the wild-type rVSV. We developed three candidate vaccines against SARS-CoV-2 using the wildtype VSV backbone with either wild-type M (rVSV-JN.1) and two M mutant variants (rVSV-M2-JN.1 and rVSV-M4-JN.1). Our results confirmed that rVSV-M2-JN.1 and rVSV-M4-JN.1 retain strong immunogenicity while enhancing safety in hamsters. In summary, the rVSV variants with M protein mutations represent promising candidate vectors for mucosal vaccines and warrant further investigation. Full article

(This article belongs to the Special Issue Structure-Based Antiviral Drugs and Vaccine Design)

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21 pages, 2233 KiB

Open AccessArticle

In the Absence of Type-1 IFN, HSV-1 LAT Increases γ34.5 Expression and Enhances Mortality in Infected Mice

by Jay J. Oh, Ujjaldeep Jaggi, Deepak Arya, Shaohui Wang and Homayon Ghiasi

Viruses 2025, 17(8), 1061; https://doi.org/10.3390/v17081061 - 29 Jul 2025

Abstract

Type-I Interferon (IFN) is essential for antiviral immunity in both mice and humans; thus, we investigated whether LAT affects HSV-1 infectivity in the absence of IFN by infecting IFNαβR^−/− and wild-type control mice with HSV-1 McKrae (LAT-plus) and dLAT2903 (LAT-minus) viruses. IFNαβR [...] Read more.

Type-I Interferon (IFN) is essential for antiviral immunity in both mice and humans; thus, we investigated whether LAT affects HSV-1 infectivity in the absence of IFN by infecting IFNαβR^−/− and wild-type control mice with HSV-1 McKrae (LAT-plus) and dLAT2903 (LAT-minus) viruses. IFNαβR^−/− mice survived ocular infection with the LAT-plus virus, while no infected mice survived infection with the LAT-minus virus. Increased death in infected mice correlated with a higher expression in the neurovirulence γ34.5 gene but not with gB expression. To determine the region of LAT that contributed to higher mortality, IFNαβR^−/− mice were infected with recombinant viruses expressing the first 1.5 kb or the first 811bp region of 1.5 kb LAT. Similar to LAT-plus infected mice, IFNαβR^−/− mice infected with LAT1.5kb were protected from death, while infection with the LAT811bp virus was similar to that of LAT-minus, suggesting that increased pathogenicity in the absence of LAT depends on the second half of 1.5 kb LAT. To confirm the in vivo upregulation of γ34.5 expression in the absence of LAT, rabbit skin and Neuro2A cells were infected with LAT-plus, LAT-minus, LAT1.5kb, or LAT811bp viruses. γ34.5 expression was significantly higher in LAT-minus- and LAT811bp-infected rabbit skin cells and Neuro2A cells than in LAT-plus- and LAT1.5kb-infected cells, suggesting that sequences after the 811bp of LAT contribute to γ34.5 upregulation. However, except for γ34.5 expression, ICP0, ICP4, and gB expression were not affected by the absence of LAT or truncated forms of LAT. To confirm that higher γ34.5 expression contributes to higher mortality in the absence of LAT, we infected IFNαβR^−/− mice with a recombinant virus lacking LAT and γ34.5 expression, and, in contrast to LAT-minus, all infected mice survived. Our results suggest that LAT controls γ34.5 expression and that higher γ34.5 expression and mortality in infected mice are associated with the second half of 1.5 kb LAT. Full article

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

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