Search Results (69)

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

Background: Birnaviruses infect a wide range of aquatic and terrestrial hosts, including several economically important fish species. This study aimed to isolate and characterize a novel birnavirus strain from mandarin fish (Siniperca chuatsi), a high-value freshwater species in Chinese aquaculture. Methods: A novel strain, designated mandarin fish birnavirus (MFBV), was isolated from diseased fish and propagated in SCK cells. The complete genome was determined using high-throughput sequencing and RACE. Viral replication kinetics, tissue distribution, and pathogenicity were assessed through in vitro infection, RT-qPCR, histopathology, and experimental challenges. In addition, disinfectant sensitivity and environmental stability were evaluated. Results: The MFBV genome comprises two segments (A: 3539 bp; B: 2719 bp), and phylogenetic analysis revealed close relatedness to largemouth bass birnavirus (LBBV) and Lates calcarifer birnavirus (LCBV). MFBV displayed rapid replication in SCK cells, completing a replication cycle in 8–10 h. In juvenile and fry fish, an experimental infection caused acute disease with cumulative mortality ranging from 41.8% to 83.6%, with fry showing higher susceptibility. Viral RNA was detected in multiple tissues (7.9 × 10⁶–7.9 × 10⁷ copies/μg RNA), and histopathological lesions were observed in the intestine, spleen, and kidney. MFBV was highly sensitive to glutaraldehyde (20 ppm), while other disinfectants showed reduced efficacy. Viral half-life ranged from 36.5 to 144.5 h at room temperature. Conclusions: These findings demonstrate that MFBV can induce acute systemic infection in mandarin fish. The results offer new insights into the genomic and biological features of birnaviruses, contributing to improved disease management and viral taxonomy. Full article

Viruses exhibit significantly greater diversity than cellular organisms, posing a complex challenge to their taxonomic classification. While primary sequences may diverge considerably, protein functional domains can maintain conserved 3D structures throughout evolution. Consequently, structural homology of viral proteins can reveal deep taxonomic relationships, overcoming limitations inherent in sequence-based methods. In this work, we introduce MPACT (Multimetric Pairwise Comparison Tool), an integrated tool that utilizes both sequence- and structure-based metrics. The program incorporates five metrics: sequence identity, similarity, maximum likelihood distance, TM-score, and 3Di-character similarity. MPACT generates heatmaps and distance trees to visualize viral relationships across multiple levels, enabling users to substantiate viral taxa demarcation. Taxa delineation can be achieved by specifying appropriate score cutoffs for each metric, facilitating the definition of viral groups, and storing their corresponding sequence data. By analyzing diverse viral datasets spanning various levels of divergence, we demonstrate MPACT’s capability to reveal viral relationships, even among distantly related taxa. This tool provides a comprehensive approach to assist viral classification, exceeding the current methods by integrating multiple metrics and uncovering deeper evolutionary connections. Full article

Cetacean morbillivirus (CeMV) is a major threat to cetaceans worldwide, causing individual deaths and outbreaks of mass mortality. Based on partial sequences of the viral phosphoprotein, CeMV is subclassified into seven strains and two distinct lineages. To date, only CeMV-1 strains, including the dolphin morbillivirus (DMV), have been completely sequenced. The CeMV-2 lineage was first reported in Guiana dolphins (Sotalia guianensis) in Brazil and was associated with an unusual mortality event in 2017–2018. Here we provide the nearly complete Guiana dolphin morbillivirus (GDMV) genome sequence, representing the first within the CeMV-2 lineage. GDMV was isolated using Vero.DogSLAMtag cells, the viral RNA was extracted, and deep sequencing analysis was performed. Gaps in the viral genome were completed by Sanger sequencing. The final genome length was 15,607 nucleotides covering 99.3% of the DMV reference genome, including full sequences of the six structural proteins encoded by morbillivirus. The sequence similarity was 74–77.9% to other CeMV strains, with highest identity to the DMV. The complete L protein amino acid sequence comparison-based taxonomy indicates that GDMV is a distinct morbillivirus species; however, as GDMV and CeMV-1 strains infect a similar host spectrum, our findings support that GDMV represents a new CeMV-2 lineage. Full article

The COVID-19 pandemic, driven by the high transmissibility and immune evasion caused by SARS-CoV-2 and its variants (e.g., Alpha, Delta, Omicron), has led to massive casualties worldwide. As of November 2024, the International Committee on Taxonomy of Viruses (ICTV) has identified 14,690 viral species across 3522 genera. The increasing infectious and resistance to FDA and EMA-approved antivirals, such as 300-fold efficacy reduction in Nirmatrelvir against the SARS-CoV-2 3CLpro, highlight the need for mutation-stable antivirals, likewise targeting the essential host proteins like kinases, heat shock proteins, lipid metabolism proteins, immunological pathway proteins, etc. Unlike direct-acting antivirals, HDAs reduce the risk of resistance by targeting conserved host proteins essential for viral replication. The proposal for repurposing current FDA-approved drugs for host-directed antiviral (HDA) approach is not new, such as the Ouabain, a sodium-potassium ATPase inhibitor for herpes simplex virus (HSV) and Verapamil, a calcium channel blocker for influenza A virus (IAV), to name a few. Given the colossal potential of the mutation-stable HDA approach to exterminate the virus infection, it has been increasingly studied on SARS-CoV-2. This review aims to unravel the interaction between viruses and human hosts and their successfully proposed host-directed antiviral approach to provide insight into an alternative treatment to the rampant mutation in SARS-CoV-2. The benefits, limitations, and potential of host protein-targeted antiviral therapies and their prospects are also covered in this review. Full article

Whole transcriptome amplification (WTA2) and sequence-independent single primer amplification (SISPA) are two widely used methods for combined metagenomic sequencing of RNA and DNA viruses. However, information on the reproducibility and bias of these methods on diverse viruses in faecal samples is currently lacking. A mock community (MC) of diverse viruses was developed and used to spike faecal samples at different concentrations. Virus-like particles (VLPs) were extracted, nucleic acid isolated, reverse-transcribed, and PCR amplified using either WTA2 or SISPA and sequenced for metagenomic analysis. A bioinformatics pipeline measured the recovery of MC viruses in replicates of faecal samples from three human donors, analysing the consistency of viral abundance measures and taxonomy. Viruses had different recovery levels with VLP extraction introducing variability between replicates, while WTA2 and SISPA produced comparable results. In comparing WTA2- and SISPA-generated libraries, WTA2 gave more uniform coverage depth profiles and improved assembly quality and virus identification. SISPA produced more consistent abundance, with a 50% difference between replicates occurring in ~20% and ~10% of sequences for WTA2 and SISPA, respectively. In conclusion, a bioinformatics pipeline has been developed to assess the methodological variability and bias of WTA2 and SISPA, demonstrating higher sensitivity with WTA2 and higher consistency with SISPA. Full article

The history of religions during the nineteenth and early twentieth centuries has been closely tied to the classification of Indigenous religions. However, recent scholarship in the field of religion has increasingly drawn on the work of subaltern and postcolonial historiography as a way of disrupting the European canon and dislodging Indigenous and non-western ways of knowing and being from the tyranny of the classical taxonomies of religion. Recent approaches to religious diversity have been challenged for reproducing imperial hierarchies of religion—assuming an accommodationist approach to Indigenous religions while also rendering invisible the internal diversity, fluidity, and adaptive orientations within Indigenous religions. In this paper, I contend that in the postcolonial context, Indigenous religions uncouple themselves from traditional taxonomies of religion, and, in particular, I propose religious complexity as a suitable framework and approach for accounting, contending with, and reporting on religious change in postcolonial South Africa. I explore questions about how to account for, ‘classify’, or ‘measure’ change related to everyday African Indigenous religious efforts and practices in the aftermath of and in response to colonialism, where conventional ideas about religious authority and affinity are displaced by Indigenous practices that can variously be described as simultaneously vital, viral, or feral. Full article

A novel vibriophage vB_VpaM_XM1 (XM1) was described in the present study. Morphological analysis revealed that phage XM1 had Myovirus morphology, with an oblate icosahedral head and a long contractile tail. The genome size of XM1 is 46,056 bp, with a G + C content of 42.51%, encoding 69 open reading frames (ORFs). Moreover, XM1 showed a narrow host range, only lysing Vibrio xuii LMG 21346 (T) JL2919, Vibrio parahaemolyticus 1.1997, and V. parahaemolyticus MCCC 1H00029 among the tested bacteria. One-step growth curves showed that XM1 has a 20-min latent period and a burst size of 398 plaque-forming units (PFU)/cell. In addition, XM1 exhibited broad pH, thermal, and salinity stability, as well as strong lytic activity, even at a multiplicity of infection (MOI) of 0.001. Multiple genome comparisons and phylogenetic analyses showed that phage XM1 is grouped in a clade with three other phages, including Vibrio phages Rostov 7, X29, and phi 2, and is distinct from all known viral families that have ratified by the standard genomic analysis of the International Committee on Taxonomy of Viruses (ICTV). Therefore, the above four phages might represent a new viral family, tentatively named Weiviridae. The broad physiological adaptability of phage XM1 and its high lytic activity and host specificity indicated that this novel phage is a good candidate for being used as a therapeutic bioagent against infections caused by certain V. parahaemolyticus strains. Full article

Advances in sequencing technologies and bioinformatics have led to breakthroughs in the study of virus biodiversity. Millipedes (Diplopoda, Myriapoda, Arthropoda) include more than 12,000 extant species, yet data on virus diversity in Diplopoda are scarce. This study aimed to explore the virome of the millipedes collected in the Dong Nai Biosphere Reserve in Vietnam. We studied 14 species of millipedes and managed to assemble and annotate the complete coding genomes of 16 novel viruses, the partial coding genomes of 10 more viruses, and several fragmented viral sequences, which may indicate the presence of about 54 more viruses in the studied samples. Among the complete and partial genomes, 27% were putative members of the order Picornavirales. Most of the discovered viruses were very distant from the viruses currently present in the relevant databases. At least eight viruses meet the criteria to be recognized as a new species by the International Committee on Taxonomy of Viruses, and, for two of them, a higher taxonomic status (genus and even family) can be suggested. Full article

Jeju, the largest island in Korea, is the most economically important in terms of marine aquaculture. We investigated the marine viral composition adjacent to Jeju Island over four seasons in 2022 and sequenced DNA libraries extracted from samples in March, June, September, and December using Illumina HiSeq 2000. We obtained 212,402, 186,542, 235,441, and 224,513 contigs from the four-season samples, respectively. Among the identified metagenomes, bacteriophages were dominant in all the samples. Bacillus phage G was the dominant species in March and June, whereas Pelagibacter phage HTVC 008M was the dominant species in September and December. Additionally, the number of viruses that infected algal hosts was higher in December than in other seasons. Marine viruses appeared in all seasons and infected marine vertebrates such as fish. Functional analysis using MG-RAST revealed that cell wall- and capsule-related metabolism groups were activated in March and June, whereas virulence-, disease-, and defense-related metabolism groups were activated in September and December. Conclusively, this study revealed seasonal changes in marine viral communities in the sea adjacent to Jeju Island. Our data will be useful in identifying emerging marine viral pathogens and for further community studies on marine organisms. Full article

Virus taxonomy uses a Linnaean-like subsumption hierarchy to classify viruses into taxonomic units at species and higher rank levels. Virus species are considered monophyletic groups of mobile genetic elements (MGEs) often delimited by the phylogenetic analysis of aligned genomic or metagenomic sequences. Taxonomic units are assumed to be independent organizational, functional and evolutionary units that follow a ‘natural history’ rationale. Here, I use phylogenomic and other arguments to show that viruses are not self-standing genetically-driven systems acting as evolutionary units. Instead, they are crucial components of holobionts, which are units of biological organization that dynamically integrate the genetics, epigenetic, physiological and functional properties of their co-evolving members. Remarkably, phylogenomic analyses show that viruses share protein domains and loops with cells throughout history via massive processes of reticulate evolution, helping spread evolutionary innovations across a wider taxonomic spectrum. Thus, viruses are not merely MGEs or microbes. Instead, their genomes and proteomes conduct cellularly integrated processes akin to those cataloged by the GO Consortium. This prompts the generation of compositional hierarchies that replace the ‘is-a-kind-of’ by a ‘is-a-part-of’ logic to better describe the mereology of integrated cellular and viral makeup. My analysis demands a new paradigm that integrates virus taxonomy into a modern evolutionarily centered taxonomy of organisms. Full article

Viral integration within the host genome plays a pivotal role in carcinogenesis. Various disruptive mechanisms are involved, leading to genomic instability, mutations, and DNA damage. With next-generation sequencing (NGS), we can now precisely identify viral and host genomic breakpoints and chimeric sequences, which are useful for integration site analysis. In this study, we evaluated a commercial hybrid capture NGS panel specifically designed for detecting three key viruses: HPV, HBV, and HIV-1. We also tested workflows for Viral Hybrid Capture (VHC) and Viral Integration Site (VIS) analysis, leveraging customized viral databases in CLC Microbial Genomics. By analyzing sequenced data from virally infected cancer cell lines (including SiHa, HeLa, CaSki, C-33A, DoTc2, 2A3, SCC154 for HPV; 3B2, SNU-182 for HBV; and ACH-2 for HIV-1), we precisely pinpointed viral integration sites. The workflow also highlighted disrupted and neighboring human genes that may play a crucial role in tumor development. Our results included informative virus–host read mappings, genomic breakpoints, and integration circular plots. These visual representations enhance our understanding of the integration process. In conclusion, our seamless end-to-end workflow bridges the gap in understanding viral contributions to cancer development, paving the way for improved diagnostics and treatment strategies. Full article

Neutropenia refers to a decrease in the absolute neutrophil count according to age and race norms and poses a common concern in pediatric practice. Neutrophils serve as host defenders and act crucially in acute inflammation procedures. In this narrative review, we systematically present causes of neutropenia in childhood, mainly adopting the pathophysiological classification of Frater, thereby studying (1) neutropenia with reduced bone marrow reserve, (2) secondary neutropenia with reduced bone marrow reserve, and (3) neutropenia with normal bone marrow reserve. Different conditions in each category are thoroughly discussed and practically approached from the clinician’s point of view. Secondary mild to moderate neutropenia is usually benign due to childhood viral infections and is expected to resolve in 2–4 weeks. Bacterial and fungal agents are also associated with transient neutropenia, although fever with severe neutropenia constitutes a medical emergency. Drug-induced and immune neutropenias should be suspected following a careful history and a detailed clinical examination. Cytotoxic chemotherapies treating malignancies are responsible for severe neutropenia and neutropenic shock. Rare genetic neutropenias usually manifest with major infections early in life. Our review of taxonomies clinical findings and associates them to specific neutropenia disorders. We consequently propose a practical diagnostic algorithm for managing neutropenic children. Full article

Over the last few decades, several pestiviruses have been discovered in ruminants, pigs, and, more recently, in non-ungulate hosts. Consequently, the nomenclature and taxonomy of pestiviruses have been updated. The Tunisian sheep-like pestivirus (TSV, Pestivirus N) is an additional ovine pestivirus genetically closely related to classical swine fever virus (CSFV). In this study, during a survey of pestivirus infections in ovine farms in the Lombardy region of Northern Italy, we identified and isolated a pestivirus strain from a sheep that was found to belong to Pestivirus N species based on its genomic nucleotide identity. The sheep itself and its lamb were found to be persistently infected. We performed molecular characterization and phylogenetic analysis of three viral genomic regions (a fragment of 5′-UTR, partial N^pro, and the whole E2 region). In conclusion, these results confirmed circulating TSV in Northern Italy after notification in Sicily, Italy, and France. Correlation with Italian, Tunisian, and French strains showed that detection might have resulted from the trading of live animals between countries, which supports the need for health control measures. Full article