Search Results (82)

The geographic range and outbreak intensity of vector-borne viral infections are increasing as climate, land use, urbanization, and human mobility reshape vector ecology and human exposure. Despite their growing importance to public health, effective antiviral and preventive options remain limited for many emerging and reemerging vector-borne viruses due to viral genetic diversity, rapid evolutionary capacity, sporadic outbreak patterns, and economic constraints. While these viruses differ in taxonomy, genome organization, vector specificity, tissue tropism, and clinical manifestations, they exploit a shared vulnerability in host antiviral defense, particularly the timing of innate antiviral immunity to support viral replication, immune evasion, inflammatory dysregulation, and disease progression. Rather than simply suppressing antiviral defense, vector-borne viruses can delay early viral nucleic acid sensing, attenuate interferon induction or responsiveness, and extend the initial phase for viral replication. As viral burden increases and infected tissues undergo stress or damage, delayed immune activation can shift toward excessive inflammatory amplification, contributing to disease-specific pathology. In this study, we examine this temporal rewiring of innate antiviral immunity in representative vector-borne viruses such as dengue virus, chikungunya virus, and severe fever with thrombocytopenia syndrome virus and propose that understanding these conserved host dependencies may lead to broader, stage-specific, adaptable antiviral strategies that complement conventional virus-directed approaches. Full article

Soybean diseases caused by fungal, bacterial, and viral pathogens represent a major constraint to global agricultural productivity. Although molecular phylogenetic analyses have advanced the understanding of pathogen evolution, the extent to which disease phenotypes reflect evolutionary relationships remains poorly understood. In this study, we developed an integrative framework combining deep learning-based phenotypic analysis with phylogenetic inference to investigate the relationship between soybean disease symptoms and pathogen evolution. An EfficientNet-B0 convolutional neural network (CNN) was trained to classify 10 soybean disease classes comprising 703 leaf images and achieved a mean cross-validation accuracy of 98.72 ± 1.17%, a weighted F1-score of 98.74 ± 1.16%, and a macro F1-score of 98.47 ± 1.74%. Evaluation on a held-out test set generated through image-level partitioning yielded an accuracy of 96.19%, a weighted F1-score of 96.28%, and a macro F1-score of 95.86%. Latent feature embeddings revealed a structured phenotypic space with clear separation among most disease classes and enabled quantitative analyses of phenotypic similarity. To provide biological context, taxonomy-derived distance matrices and sequence-based phylogenetic analyses of the fungal subset using 28S rRNA sequences were compared with CNN-derived phenotypic representations. A Mantel test identified a moderate and statistically significant association between phenotypic and phylogenetic distances (Spearman r = 0.3393, p = 0.0050), indicating that pathogen evolutionary history contributes to disease phenotype while explaining only part of the observed phenotypic variation. Overall, the results demonstrate that deep learning effectively captures biologically meaningful phenotypic information while highlighting that disease symptoms arise from the combined influence of pathogen evolution, host responses, and environmental conditions. This study provides an integrative framework for combining image-based phenotyping with phylogenetic analysis to support biologically informed interpretation of plant disease phenotypes. Full article

Vesicular stomatitis virus (VSV) causes clinical disease in livestock that mimics Foot-and-Mouth Disease, necessitating its status as a reportable pathogen to the World Organization for Animal Health. Given the importance of accurate classification for epidemiological surveillance, this study aims to update VSV taxonomic organization using whole-genome sequence criteria to better monitor disease dynamics. Using phylogenetic analysis and the Species Demarcation Tool (SDT), we analyzed pairwise identity across publicly available sequences, constructing a rooted maximum likelihood tree to cluster strains based on robust genetic identity scores. The results demonstrate that nucleotide divergences exceeding 30% define distinct species within the Vesiculovirus genus. Within a species, divergences between 10% and 30% successfully delineate genotypes, while differences between 6% and 10% identify specific subtypes. These quantitative benchmarks provide a precise framework for viral classification, significantly enhancing genomic surveillance and the ability to track the evolution and transmission of VSV genotypes and subtypes across diverse geographic regions. Full article

Phlebotomine sand flies are dipterans that transmit leishmaniasis, bartonellosis, and arboviruses of public health importance. Colombia is a tropical country with high annual incidences of arboviruses, such as dengue and, more recently, yellow fever, all of which have similar symptoms. This study characterized the viruses circulating in phlebotomine sand flies in two departments in the Colombian Caribbean. Between August 2023 and December 2024, a descriptive study was conducted in the Departments of Córdoba and Cesar in Colombia. Four municipalities were selected per department, and four insect captures were performed using CDC light traps. Specimens were taxonomically identified and organized into groups according to species and study area, and total RNA was extracted for NGS analysis. Short sequences were quality-assessed, assembled using MEGAHIT to obtain contigs, and classified using DIAMOND-MEGAN6 to select viral genomic sequences for phylogenetic analysis. Thirteen viral families were identified, including a virus from the family Rhabdoviridae in Pi. evansi in the department of Cesar and another from the family Dicistroviridae in Lutzomyia gomezi in both departments. Two genome segments of the family Phenuiviridae were found in Lutzomyia gomezi in the department of Córdoba, Colombia. Sand flies harbor a diverse range of viral families, some of which are previously undescribed, and can be studied to determine their taxonomy and assess their potential to infect vertebrate cells or their interactions with medically important pathogens such as Leishmania spp. Full article

Angelica dahurica (A. dahurica) is an important medicinal plant in China; however, its production is affected by viral infections, leading to reduced yields and quality. In this study, we identified a novel carlavirus, tentatively named Angelica carlavirus virus (AnCV), in the leaves of A. dahurica exhibiting mosaic and leaf crinkling symptoms. Notably, the complete genome of AnCV was 8562 nt long and contained six open reading frames, with a genomic organization typical of the genus Carlavirus. AnCV exhibited 44.5–57.8% nucleotide identity at the whole-genome level with known members of the genus Carlavirus. In the polymerase gene and coat protein regions, the highest nucleotide and amino acid identities were 59.4–60.0% and 46.5–55.8%, respectively, which were below the species demarcation criteria established by the International Committee on Taxonomy of Viruses for the genus Carlavirus. Importantly, 10 AnCV isolates clustered within subgroup I of the genus Carlavirus, forming a relatively distinct branch. Moreover, 119 of the 280 A. dahurica samples were positive for AnCV (detection rate of 42.58%). Our study revealed that AnCV is a novel member of the genus Carlavirus that infects A. dahurica, providing a theoretical basis for the monitoring and control of viral diseases in A. dahurica. Full article

Variegated squirrel bornavirus 1 (VSBV-1) is a recently identified zoonotic virus associated with fatal encephalitis in humans. A literature search in electronic databases such as PubMed, Web of Science, Scopus, and Google Scholar was performed using the following search terms: “VSBV-1”, “orthobornavirus”, “squirrel”, “zoonotic encephalitis”, and “mammalian bornavirus”, to identify peer-reviewed literature relevant to the veterinary and zoonotic aspects of VSBV-1. This narrative review summarizes the current knowledge on VSBV-1 with emphasis on veterinary aspects, including taxonomy, epidemiology, clinical presentation, diagnostics, hypothetical transmission routes, surveillance strategies, and proposed biosecurity measures. However, evidence regarding virus shedding, natural reservoirs, distribution, and transmission pathways is presently absent. VSBV-1 may persist undetected in infected squirrels due to the absence of clinical signs and limited surveillance efforts. Large-scale epidemiological studies have not yet been performed. Given the limited understanding of viral epidemiology and the severe course of zoonotic infection, a precautionary approach is warranted. Structured surveillance, control of animal movements, and occupational protection are essential to limit both viral spread and the risk of zoonotic infection. Future research should focus on identifying natural reservoirs, virus distribution in captive squirrel populations, transmission pathways, and improving diagnostic tools. Full article

Bovine adenovirus (BAdV) is associated with respiratory and enteric diseases in cattle. In this study, the complete genomic sequence of a novel BAdV strain (named BAdV/LN/CHN/2023) was sequenced and annotated using the next-generation sequencing (NGS) technology. The viral genome comprises 32,391 base pairs with a GC content of 44.93%, encoding 33 predicted open reading frames (ORFs), consistent with the genomic organization of mastadenoviruses. Comparative genomic analysis confirmed that BAdV/LN/CHN/2023 contains conserved structural and functional motifs characteristic of the genus Mastadenovirus. Phylogenetic analysis revealed that BAdV/LN/CHN/2023 shares low similarity with all currently recognized bovine mastadenoviruses classified by the International Committee on Taxonomy of Viruses (ICTV). In addition, an open reading frame (ORF) encoding the 146R protein was annotated in this strain; this feature has not been identified in any previously recognized bovine mastadenoviruses. This study presents the first full-length genomic sequence of a putative BAdV-11 strain, and based on ICTV criteria, we propose that this strain represents a novel mastadenovirus species, supported by phylogenetic distance and genomic divergence. Our findings expand the known genetic diversity of BAdVs and contribute to a better understanding of their evolutionary relationships. Full article

Viruses are key regulators of marine microbial communities, yet their temporal dynamics in tropical intertidal sediments remain poorly characterized. We conducted a year-long metagenomic survey of sandy intertidal sediments in Sanya Bay (60 monthly samples from five sites) to examine viral taxonomy, community structure, lytic proteins, and auxiliary metabolic genes (AMGs). Within the classifiable fraction, the assemblages were consistently dominated by Assiduviridae. However, NMDS analysis revealed a significant overall seasonal shift, with October–December samples separating from the rest of the year. Co-occurrence network analysis identified five co-occurrence modules with distinct temporal patterns, alongside a concurrent decline in module abundance and lytic proteins in October. Functional annotation showed that cysteine and methionine metabolism, primarily driven by DNA methyltransferases, was identified as a highly represented AMG category among the annotated functions, while other pathways displayed seasonal variability. Collectively, these findings suggest that although characterized by a classifiable fraction dominated by Assiduviridae, the highly complex tropical intertidal viral communities undergo substantial seasonal reorganization in structure and functional potential. Full article

Bovine viral diarrhea (BVD) is a major cause of economic losses in the global cattle industry, particularly in countries characterized by intensive livestock production systems. Pestivirus tauri, formerly known as Bovine viral diarrhea virus type 2 (BVDV-2), is the current taxonomic designation according to the International Committee on Taxonomy of Viruses (ICTV). Between 2005 and 2018, Pestivirus tauri was detected in cattle herds in mainland Italy, particularly in the Lombardy region. Four viral strains were successfully isolated in cell cultures and subjected to whole-genome sequencing. Phylogenetic reconstruction placed all Italian isolates within the Pestivirus tauri subgenotype c, a lineage encompassing strains reported in Asia, Europe and the United States. Consistently, comparative sequence identity analyses indicated the highest similarity with the Parker strain (USA, 1991) and the Potsdam 1600 strain (Germany, 2000). These results contribute to a more detailed understanding of Pestivirus tauri genomic architecture and evolutionary dynamics, providing a valuable resource for comparative genomic studies. Such data are crucial for exploring viral diversity and evolution, optimizing the design of diagnostic primers and probes, and advancing insights into the molecular epidemiology of Pestivirus. Full article

Human adenoviruses (HAdVs) remain prominent global human pathogens, particularly in dense, crowded populations. The advent of genomic and bioinformatic tools allows for high-resolution means to identify, characterize, and understand these pathogens. These tools also provide the basis for the standardization of names, as well as an accessible archive of all genotypes (“Human Adenovirus Working Group”). This overview and perspective of all the genotypes in one setting provides a better understanding of the mechanisms of their molecular evolution: genome recombination plays a major role in the emergence of novel adenoviral pathogens. In the context of the fidelity of their DNA polymerase replication machinery, this strategy provides entry into immune-naïve host populations through the acquisition of genome sequences that may include antigenic epitopes that have not circulated commonly, widely, or recently, as well as sequences encoding host cell entry proteins. Using the “chess” metaphor for describing the rapid evolution of RNA viruses, we propose a similar but diametrically opposed “White King Reigns in the Family of Human Adenoviruses”. Full article

The Coronaviridae family represents a broad group of RNA-containing viruses that infect humans and animals. This family belongs to the order Nidovirales and is divided into four main genera: α-CoV, β-CoV, γ-CoV and δ-CoV. It is particularly noteworthy that representatives of β-CoV have caused serious epidemics in humans, such as the outbreaks of SARS-CoV, MERS-CoV, and COVID-19 caused by SARS-CoV-2. Although the clinical manifestations of CoVs can range from mild cold-like symptoms to severe respiratory diseases, they share common features in their structure, modes of transmission, and natural reservoirs. Identifying natural reservoirs, as well as establishing intermediate hosts, is crucial for understanding the mechanisms of interspecies transmission of CoVs. These processes are often mediated by molecular interactions between viral spike (S) proteins and cellular receptors of different species, which contribute to zoonotic outbreaks. Thus, the interaction of various species and the study of these processes of viral spread, cross-species transmission, and pathogen evolution play a key role in ensuring global biological safety. Therefore, we conducted this review to summarize the data from existing studies focused on the taxonomy of CoVs, their main types, natural reservoirs, intermediate hosts, pathways of interspecies transmission, and the significance of the One Health concept as an interdisciplinary approach to monitoring, prevention and control of CoV infections at the intersection of human, animal, and environmental health. We examined databases such as PubMed, Science Direct, Web of Science, and Google Scholar to identify relevant scientific articles in English available for such a review. The aim of this work is to study the taxonomy and classification of coronaviruses, as well as to identify their natural reservoirs, intermediate hosts, and applicable control measures. A review of human and animal coronaviruses has revealed their evolutionary diversity, their main natural reservoirs, their intermediate hosts, and their interactions with cellular receptors. This information allows for a better understanding of the mechanisms by which the viruses are transmitted from animals to humans. The concept of One Health demonstrated the interconnections between human, animal and environmental factors. Full article

The COVID-19 pandemic initially focused clinical efforts on hospitalized patients. However, as the pandemic progressed, attention shifted to outpatients who often experience milder symptoms yet still contribute to viral transmission. This scoping review aimed to document and evaluate the clinical outcomes assessed in randomized controlled trials (RCTs) involving outpatients with COVID-19, identifying gaps and areas for improvement in trial design. This review followed the PRISMA-ScR guidelines. A comprehensive search of four electronic databases (PubMed, Scopus, Cochrane CENTRAL, and Web of Science) was conducted for RCTs published between December 2019 and December 2023. Studies were included if they involved outpatients with confirmed COVID-19 and reported clinical outcomes. Data were extracted from eligible studies, and outcomes were categorized using the COMET taxonomy. A total of 91 studies were included, representing a wide geographical distribution, with the USA, Iran, and Brazil contributing the most studies. The most frequently investigated treatments included hydroxychloroquine, fluvoxamine, convalescent plasma, and ivermectin. Key outcomes focused on hospitalization rates, symptom resolution, and disease progression. Mortality, although less common in outpatients, was reported in 65 studies, underscoring the importance of outpatient interventions. This review highlights the need for standardized outcome measures in outpatient COVID-19 trials. Full article

The increasing resistance of pathogens to conventional antibiotics has necessitated the search for novel antimicrobial agents from medicinal plants. Nelsonia canescens—a plant traditionally used in Africa and Asia for the management of health issues, such as viral infections, cardiovascular diseases, and inflammation—has been reported to demonstrate antimicrobial activity and has been investigated for its bioactive constituents. The whole plant was collected, air-dried, and extracted using 70% methanol. The crude methanol extract was partitioned into hexane, chloroform, ethyl acetate, and butanol fractions. The ethyl acetate fraction was subjected to column chromatography and gel filtration, leading to the isolation of a compound coded A₁. The structure of compound A₁ was established through UV, FTIR, NMR (¹H, ¹³C, DEPT, COSY, HMQC, and HMBC), and chemical tests. Compound A₁ was identified as a 2*-hydroxy-4*-phenyl-(2**-hydroxy-ethyl)-3′-(4′′′→1′′) glucose-rhamnose-3-hydroxy phenyl ester, a flavonoid derivative. A spectral analysis confirmed its structure, with key signals including olefinic protons (δ 6.30 and 7.62) in the trans-configuration, aromatic protons, and sugar moieties. The compound exhibited a melting point of 105–107 °C and was partially soluble in chloroform but fully soluble in methanol, suggesting that the compound is highly polar in nature. This is the first report on the isolation of the 2*-hydroxy-4*-phenyl-(2**-hydroxy-ethyl)-3′-(4′′′→1′′) glucose-rhamnose-3-hydroxy phenyl ester from Nelsonia canescens, contributing to the taxonomy of the plant. The compound’s structural features suggest potential bioactive properties, warranting further investigation into its pharmacological applications through in vitro and molecular docking studies. Full article

Henipaviruses are emerging zoonotic viruses that have caused deadly outbreaks in humans and livestock across several regions of the world. The fusion (F) protein of henipaviruses plays a critical role in viral entry into host cells and represents a key determinant of viral pathogenicity. This review provides a comprehensive analysis of current knowledge regarding trafficking, activation, as well as the role in particle assembly, of henipavirus F proteins. We discuss the unique characteristics of henipavirus F proteins compared to other paramyxovirus fusion proteins, with particular emphasis on their distinctive trafficking and activation mechanisms. Attention is also given to novel henipaviruses that have been detected in hosts other than bats, namely rodents and shrews. These viruses are sufficiently different that the International Committee on Taxonomy of Viruses has proposed a new genus for them, the Parahenipaviruses. We discuss how variations in F protein characteristics between Henipaviruses, Parahenipaviruses, and yet-unclassified henipa-like viruses might influence their trafficking and activation. Understanding these molecular mechanisms is crucial for developing effective therapeutic strategies against henipavirus infections and for predicting the emergence of novel henipavirus strains with pandemic potential. Full article

Rodents represent the most diverse order of mammals, comprising over 2200 species and nearly 42% of global mammalian biodiversity. They are major reservoirs of zoonotic pathogens, including viruses, bacteria, protozoa, and fungi, and are particularly effective at transmitting diseases, especially synanthropic species that live in close proximity to humans. As of April 2025, approximately 15,205 rodent-associated viruses have been identified across 32 viral families. Among these, key zoonotic agents belong to the Arenaviridae, Hantaviridae, Picornaviridae, Coronaviridae, and Poxviridae families. Due to their adaptability to both urban and rural environments, rodents serve as efficient vectors across diverse ecological landscapes. Environmental and anthropogenic factors, such as climate change, urbanization, deforestation, and emerging pathogens, are increasingly linked to rising outbreaks of rodent-borne diseases. This review synthesizes current knowledge on rodent-borne viral zoonoses, focusing on their taxonomy, biology, host associations, transmission dynamics, clinical impact, and public health significance. It underscores the critical need for early detection, effective surveillance, and integrated control strategies. A multidisciplinary approach, including enhanced vector control, improved environmental sanitation, and targeted public education, is essential for mitigating the growing threat of rodent-borne zoonoses to global health. Full article