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Simple Summary: This study evaluated the molecular prevalence and genetic characterization of equine EHV-1/4 in equids populations in Morocco. Among 154 samples analyzed, 27% tested positive for EHV-4, while only 1.94% were positive for EHV-1. Virus isolation was unsuccessful in EHV-4-positive samples but EHV-1 was isolated from a positive donkey sample. Phylogenetic and molecular analyses reclassified the EHV-1 isolate from the donkey as EHV-8, while the EHV-1 isolate from aborted fetal tissue was identified as clade 1 EHV-1. This study confirms the active circulation of EHV-1 and EHV-4 in Moroccan equines, reports the first detection of EHV-8 in a donkey in Africa, and highlights EHV-4′s prevalence and its association with respiratory disorders, abortions, and neonatal deaths. This study aimed to investigate the molecular prevalence and genetic characterization of EHV-1 and EHV-4 in equid populations in Morocco. A total of 154 equids (114 horses, 9 donkeys, and 31 mules) were sampled, with nasal swabs and tissue samples subjected to multiplex real-time PCR for the detection of EHV-1 and EHV-4. Additionally, an isolate from the tissue of an aborted horse fetus was included in the analysis. A subset of EHV-positive samples underwent virus isolation followed by whole-genome sequencing. PCR assays revealed that 42 samples (27%) tested positive for EHV-4, while only 3 samples (1.94%) were positive for EHV-1. Attempts to isolate the virus from EHV-4-positive samples were unsuccessful. However, virus isolation was successful in an EHV-1-positive nasopharyngeal sample from a donkey. Phylogenetic and molecular characterization reclassified the EHV-1 isolated from the donkey as an EHV-8. Meanwhile, the EHV-1 isolated from the aborted fetal tissue was classified as a clade 1 EHV-1 virus. This study is the first to report the molecular prevalence and genetic characterization of EHV-1 and EHV-4 in equid populations in Morocco, providing valuable insights into the distribution and genetic diversity of these viruses in the region. [ABSTRACT FROM AUTHOR]

Viruses are the most abundant biological entities on Earth, and they play a critical role in the environment and biosphere where they regulate microbial populations and contribute to nutrient cycling. Environmental viruses have been the most studied in the ocean, but viral investigations have now spread to other environments. Here, viral communities were characterized in four cave pools in Carlsbad Caverns National Park to test the hypotheses that (i) viral abundance is ten-fold higher than prokaryotic cell abundance in cavern pools, (ii) cavern pools contain novel viral sequences, and (iii) viral communities in pools from developed portions of the cave are distinct from those of pools in undeveloped parts of the same cave. The relationship between viral and microbial abundance was determined through direct epifluorescence microscopy counts. Viral metagenomes were constructed to examine viral diversity among pools, identify novel viruses, and characterize auxiliary metabolic genes (AMGs). Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Epifluorescence microscopy showed that the ratio of viral-like particles (VLPs) to microorganisms was approximately 22:1 across all sites. Viral communities from pools with higher tourist traffic were more similar to each other than to those from less visited pools, although surprisingly, viruses did not follow the same pattern as bacterial communities, which reflected pool geochemistry. Bacterial hosts predicted from viral sequences using iPHoP showed overlap with both rare and abundant genera and families in the 16S rRNA gene dataset. Gene-sharing network analysis revealed high viral diversity compared to a reference viral database as well as to other aquatic environments. AMG presence showed variation in metabolic potential among the four pools. Overall, Carlsbad Cavern harbors novel viruses with substantial diversity among pools within the same system, indicating that caves are likely an important repository for unexplored viromes. [ABSTRACT FROM AUTHOR]

Dengue virus has four distinct serotypes and the genetic diversity within each of the four serotypes contribute to its complexity. An important aspect of dengue molecular evolutionary studies has been the dissection of the extent and structure of genetic variation among major genotypes within each serotype. It is important to understand the role of dengue genetic variability and its potential role and impact in the effectiveness of the dengue vaccine. Demographic data and blood were collected from patients seen at a tertiary hospital in the Philippines and clinically diagnosed with dengue from 2014–2019. Dengue virus (DENV) RT-PCR was used to confirm infection and positive samples underwent whole genome sequencing. Phylogenetic analysis was performed on 127 samples (25 DENV-1, 19 DENV-2, 70 DENV-3, and 13 DENV-4). We observed a serotype shift in 2014 and 2022. We detected the following genotypes per serotype for the wild-type (WT) DENV sequences: genotype IV (DENV-1), cosmopolitan (DENV-2), genotype I (DENV-3) and genotype IIa (DENV-4). WT DENV belonged to different genotypes versus the QDENGA strains and except for DENV-4, belonged to different genotypes versus the Dengvaxia strains. Comparing Dengvaxia vaccine sequences with WT DENV, we observed 23, 24, 34, and 9 positions with amino acid changes in the entire envelope protein, with 1, 5, 1, and 2 positions with amino acid changes identified among the important human monoclonal antibodies (mAbs) targeted epitope positions. We detected 24, 25, 36 and 12 positions with amino acid changes in the E protein with 0, 5, 1, and 2 positions with amino acid changes among the important mAbs targeted epitope positions for DENV-1, DENV-2, DENV-3, and DENV-4, respectively when comparing QDENGA vaccine sequences with the WT DENV. We showed low genotype complexity, genetically distinct clades and local evolution for DENV circulating in the Philippines. Author summary: Dengue virus has four distinct serotypes and each serotype is further divided into distinct genotypes. There are currently two licensed dengue vaccines, Dengvaxia and QDENGA and we compared the genotypes of the circulating wild type (WT) dengue viruses (DENV) versus the genotypes of the strains of the two dengue vaccines. We also analyzed whether there were any amino acid changes in selected locations which have been previously identified as targets by potent virus neutralizing human monoclonal antibodies (mAbs) which are considered important in vaccine development. We collected blood from patients diagnosed with dengue from 2014 to 2019 from the Philippines and sequenced the dengue RT-PCR positive samples. WT DENV all belonged to different genotypes versus the QDENGA vaccine and except for DENV-4, belonged to different genotypes versus the Dengvaxia strains. We detected several amino acid changes in the dengue envelope protein and in particular, among important mAbs targeted epitope positions among the 4 serotypes when we compared QDENGA and Dengvaxia vaccine sequences with WT DENV sequences. We observed that the DENV genotypes circulating in the Philippines from 2014–2019 had low complexity and the circulating clades were genetically distinct. [ABSTRACT FROM AUTHOR]

Over the last decade metagenomic sequencing has facilitated an increasing number of virome-scale studies, leading to an exponential expansion in understanding of virus diversity. This is partially driven by the decreasing costs of metagenomic sequencing, improvements in computational tools for revealing novel viruses, and an increased understanding of the key role that viruses play in human and animal health. A central concern associated with this remarkable increase in the number of virome-scale studies is the lack of broadly accepted "gold standards" for reporting the data and results generated. This is of particular importance for animal virome studies as there are a multitude of nuanced approaches for both data presentation and analysis, all of which impact the resulting outcomes. As such, the results of published studies can be difficult to contextualise and may be of reduced utility due to reporting deficiencies. Herein, we aim to address these reporting issues by outlining recommendations for the presentation of virome data, encouraging a transparent communication of findings that can be interpreted in evolutionary and ecological contexts. Virome-scale studies are changing our understanding of the virosphere, but deficiencies in reporting may limit the value of these studies. To increase the usefulness of virome-scale studies, 10 recommendations for the improvement of reporting are provided. [ABSTRACT FROM AUTHOR]

Background Nipah virus (NiV), a highly lethal virus in humans, circulates in Pteropus bats throughout South and Southeast Asia. Difficulty in obtaining viral genomes from bats means we have a poor understanding of NiV diversity. Methods We develop phylogenetic approaches applied to the most comprehensive collection of genomes to date (N = 257, 175 from bats, 73 from humans) from 6 countries over 22 years (1999–2020). We divide the 4 major NiV sublineages into 15 genetic clusters. Using Approximate Bayesian Computation fit to a spatial signature of viral diversity, we estimate the presence and the average size of genetic clusters per area. Results We find that, within any bat roost, there are an average of 2.4 co-circulating genetic clusters, rising to 5.5 clusters at areas of 1500–2000 km2. We estimate that each genetic cluster occupies an average area of 1.3 million km2 (95% confidence interval [CI],.6–2.3 million km2), with 14 clusters in an area of 100 000 km2 (95% CI, 6–24 km2). In the few sites in Bangladesh and Cambodia where genomic surveillance has been concentrated, we estimate that most clusters have been identified, but only approximately 15% of overall NiV diversity has been uncovered. Conclusions Our findings are consistent with entrenched co-circulation of distinct lineages, even within roosts, coupled with slow migration over larger spatial scales. [ABSTRACT FROM AUTHOR]

Simple Summary: Bats represent a vast number of species, and Chiroptera is the second most diverse order of mammals. Desmodus rotundus, or the common vampire bat, is the most studied haematophagous species, as it is the primary host of the rabies virus in Latin America. Through high-throughput sequencing, we identified and characterized three novel members and a potential new genus of the Papillomaviridae family, named DrPV-1, DrPV-2, and DrPV-3. Papillomaviruses are capable of infecting many vertebrates, including bats, and can occasionally cause cancer. These findings contribute to the characterization of papillomaviruses in understudied groups such as bats, particularly in D. rotundus, whose viral diversity is often biased toward rabies detection. To the best of the authors' knowledge, this is the first description of papillomaviruses in D. rotundus. Bats are mammals with high biodiversity and wide geographical range. In Brazil, three haematophagous bat species are found. Desmodus rotundus is the most documented due to its role as a primary host of rabies virus in Latin America. Bats are known to harbor various emerging viruses causing severe human diseases. Beyond zoonotic viruses, these animals also harbor a diversity of non-zoonotic viruses. Papillomaviruses are circular double-stranded deoxyribonucleic acid (dsDNA) viruses that infect the epithelial and mucosal cells of many vertebrates, occasionally causing malignant lesions. High-throughput sequencing has enabled papillomaviruses discovery in different bat species. Here, 22 D. rotundus samples were collected through the rabies eradication program in Rio Grande do Sul. The DNA extracted from pooled intestines was amplified by the rolling-circle amplification (RCA) method and sequenced using the Illumina® MiSeq platform (San Diego, CA, USA).Analysis revealed three contigs corresponding to the Papillomaviridae family, representing three novel viruses named DrPV-1, DrPV-2, and DrPV-3. Phylogenetic analysis suggests DrPV-1 may constitute a new species within the Dyophipapillomavirus genus, while DrPV-2 and DrPV-3 may represent different types within the same species from a novel genus. This is the first description of a papillomavirus in the D. rotundus species, contributing to the characterization of PVs in the Chiropteran order. [ABSTRACT FROM AUTHOR]

Grapevine rupestris stem pitting-associated virus (GRSPaV; Foveavirus rupestris, Betaflexiviridae) is the most widespread grapevine virus in most viticulture regions, and this virus has high genetic variability. Genetic diversity of GRSPaV in Algeria was examined, based on the complete capsid protein (CP) gene. Similarity proportions between the CP sequences varied from 76% to 99%. The complete coding sequence of Algerian GRSPaV isolate ALG99 (8,646 nt) was determined using highthroughput sequencing and bioinformatic analyses. Algerian GRSPaV isolates clustered into four groups, with most sequences in groups III and IV. This research is the first to determine the genetic variability of GRSPaV in Algeria. [ABSTRACT FROM AUTHOR]

The biting midges Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) is highly relevant to epidemiology and public health, as it includes species that are potential vectors of human and animal arboviruses. The aim of this study was to investigate the presence of RNA viruses in species of the genus Culicoides collected in the Carajás mining complex in the state of Pará. The biting midges were collected in the municipalities of Canaã dos Carajás, Curionópolis and Marabá and morphologically identified. A total of 1139 specimens of seven Culicoides species were grouped into eight pools and subjected to metagenomic analysis. Eight new insect-specific viruses (ISVs) were characterized and assigned to the order Tolivirales, the families Chuviridae, Nodaviridae, Iflaviridae, Mesoniviridae, and Flaviviridae, and the taxon Negevirus. All viruses identified were assigned to clades, families and taxa never reported in Culicoides in Brazil. This study demonstrated that biting midges harbor a significant diversity of RNA viruses, many of which are still unknown, highlighting the importance of studies aiming at virome of these insects. [ABSTRACT FROM AUTHOR]

Background: Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne disease caused by Bandavirus dabieense. Initially identified in China, this disease has spread throughout Asian countries via tick bites and animal-to-human transmission. However, reports of the prevalence of SFTS virus (SFTSV) in cattle in Korea are lacking. This study aimed to investigate SFTSV infections in grazing cattle in the Republic of Korea (ROK). Materials and Methods: In total, 845 grazing cattle serum samples were collected over 2 years (2019 and 2020) in the ROK, and viral RNA was extracted using a kit. One-step RT-nested PCR was performed to amplify the S-segment of SFTSV. Positive serum samples were used to isolate SFTSV in Vero E6 cells, and the full sequences were analyzed. A phylogenetic tree was constructed using the maximum-likelihood method with MEGA X. In addition, immunoglobulin G antibodies against SFTSV were investigated using an enzyme-linked immunosorbent assay. Results: Here, 4.0% of serum samples (34/845) were positive for SFTSV S-segments, and one virus isolate was cultured in Vero E6 cells. Phylogenetic analysis based on the partial S-segment classified 4 SFTSV isolates as the B-2 genotype, 9 as the B-3 genotype, 18 as an unclassified B genotype, and 3 as the D genotype. One cultured virus was classified as the B-2 genotype based on SFTSV L-, M-, and S-segments. Antibody detection results showed that 21.1% of serum samples (161/763) were positive for SFTSV. Conclusion: To the best of our knowledge, this is the first study performed to identify the prevalence of SFTSV in grazing cattle in the ROK. Our findings indicate the necessity for more intensive and continuous SFTSV monitoring, not only in cattle but also in other animals, to comprehend the genetic diversity of the virus and its potential eco-epidemiological impact on human health. [ABSTRACT FROM AUTHOR]

The purpose of this study was the research of the avian influenza virus diversity at Moscow waterbodies and comparison of the virology changing pattern to the mallard's migratory features and wintering capacities at Moscow waterbodies, as well as an attempt to explain shifting in the virus composition and diversity. Mallard droppings were collected in the autumn of 2008–2023 from shores of Moscow and Moscow oblast waterbodies. Avian influenza viruses were extracted from the feces using a standard extraction process with the virus breeding on the chicken embryos. After the breeding the extracted viruses were subtyped by PCR with specific primaries to give type A virus sequences. In 2008–2013 European strains of the virus were prevalent in the mallard samples, whereas in 2014–2019 the prevalence shifted to Asian strains. Correlation of these observations with the changes in mallard migration allowed the assumption that European strains were entered into the Moscow oblast mainly from the southern Europe. The Asian strains were entered from the Western Europe. During 2008–2019 in the mallard feces from the Moscow waterbodies we observed a reduction of the virus strains. The frequency and the diversity of the extracted viruses decreased sharply after 2014. There could be several causes for the decline in the strain diversity, in particular, changes in the ratio of ducks hunted during spring and autumn hunting, increased mallard numbers at winter grounds within the breeding range, as well as reduced numbers of black-headed gulls that are also carriers of the avian influenza viruses. [ABSTRACT FROM AUTHOR]

Global evolutionary dynamics of influenza A virus (IAV) are fundamentally driven by the extent of virus diversity generated, transmitted, and shaped in individual hosts. How vaccination affects the degree of IAV genetic diversity that can be transmitted and expanded in pigs is unknown. To evaluate the effect of vaccination on the transmission of genetically distinct IAV variants and their diversity after transmission in pigs, we examined the whole genome of IAV recovered from the nasal cavities of pigs vaccinated with different influenza immunization regimens after being infected simultaneously by H1N1 and H3N2 IAVs using a seeder pig model. We found that the seeder pigs harbored more diversified virus populations than the contact pigs. Among contact pigs, H3N2 and H1N1 viruses recovered from pigs vaccinated with a single dose of an unmatched modified live vaccine generally accumulated more extensive genetic mutations than non-vaccinated pigs. Furthermore, the non-sterilizing immunity elicited by the single-dose-modified live vaccine may have exerted positive selection on H1 antigenic regions as we detected significantly higher nonsynonymous but lower synonymous evolutionary rates in H1 antigenic regions than non-antigenic regions. In addition, we observed that the vaccinated pigs shared significantly less proportion of H3N2 variants with seeder pigs than unvaccinated pigs. These results indicated that vaccination might reduce the impact of transmitted influenza variants on the overall diversity of IAV populations harbored in recipient pigs and that within-host genetic selection of IAV is more likely to occur in pigs vaccinated with improperly matched vaccines. [ABSTRACT FROM AUTHOR]

West Nile Virus (WNV) is considered one of the most widely distributed arboviruses worldwide. In 2018, Serbia was among the European countries reporting the highest number of WNV cases. This study aimed to characterize WNV strains circulating in Serbia, and to estimate the pathways and dynamics of WNV‐2 spread in the Balkans and globally through the phylogenetic approach. Fifty newly generated NS5 Serbian sequences were found to belong to WNV lineage 2. Phylodynamic analyses of the Balkan clade indicated the potential for an increase in genetic diversity and structure of virus populations. Presented phylogeographic analyses implied four instances of long‐distance WNV‐2 migration from Africa to Europe, during the 1940s to 1950s, while further dissemination of WNV‐2 originated in Hungary in mid‐1970s and subsequently spread to Austria and Serbia. Extensive dispersion took place during the 1990s–2000s, as the virus spread from Austria to central and western Europe, and from Hungary to the Balkans. Continuous phylogeography analysis of the Balkans WNV‐2 clade implied the central role of Serbia for WNV dissemination across the Balkan peninsula. Furthermore, previously undocumented instance of intercontinental migration of WNV‐2 from Europe to Asia was implied. In‐depth phylogenetic investigation into the global distribution of WNV‐2 may provide valuable insights into the prediction and prevention of potential epidemics. [ABSTRACT FROM AUTHOR]

Background: Ticks are significant vectors of pathogens, including viruses, bacteria, and protozoa. With approximately 900 tick species worldwide, many are expanding their geographical range due to changing socioeconomic and climate factors. The Danube Delta, one of Europe's largest wetlands, is an ecosystem that, despite its ecological importance, remains understudied concerning the risk of introducing new tick-borne viruses. This region serves as a critical habitat for migratory birds, which can carry ticks over long distances, potentially introducing exotic tick species and their pathogens into the local ecosystem. Hyalomma marginatum ticks, the primary vector of Crimean-Congo hemorrhagic fever virus (CCHFV), are of particular concern due to their expanding presence in Europe and potential to spread other arboviruses. In addition to being the primary vector for CCHFV, Hyalomma sp. ticks are capable of transmitting other pathogens of medical and veterinary importance, including Dugbe virus, West Nile virus, African horse sickness virus, and Kyasanur forest disease virus. Therefore, it is essential to monitor the presence of Hyalomma sp. ticks while simultaneously surveilling arbovirus circulation in tick populations to mitigate the risk of arboviral outbreaks. Methods: In this work, we used an RNA sequencing technique to analyze the virome of H. marginatum ticks collected from the Danube Delta Biosphere Reserve, Romania, one of the major bird migration hubs from Africa to Europe. Results: Among the viral taxa detected in H. marginatum ticks, sequences belonging to Volzhskoe tick virus (VTV), Balambala tick virus (BMTV) and Bole tick virus 4 (BTV4) were identified. In addition, we report the first identification of a novel Rhabdoviridae-related virus, Hyalomma marginatum rhabdovirus (HMRV). No CCHFV or any CCHFV-related nairovirus were detected in this study. Conclusions: To summarize, detecting new viruses is essential for monitoring potential viral outbreaks. Our research expands the understanding of virus diversity in Eastern Europe, including the identification of novel viruses. This insight is crucial for monitoring viruses that may pose risks to both animal and human health, such as CCHFV. [ABSTRACT FROM AUTHOR]

Background: Predator‒prey interactions and their dynamic changes provide frequent opportunities for viruses to spread among organisms and thus affect their virus diversity. However, the connections between dietary diversity and virus diversity in predators have seldom been studied. The avivorous bats, Ia io, show a seasonal pattern of dietary diversity. Although most of them primarily prey on insects in summer, they mainly prey on nocturnally migrating birds in spring and autumn. Results: In this study, we characterized the RNA virome of three populations of I. io in Southwest China during summer and autumn using viral metatranscriptomic sequencing. We also investigated the relationships between dietary diversity and RNA virus diversity by integrating DNA metabarcoding and viral metatranscriptomic sequencing techniques at the population level of I. io. We found 55 known genera belonging to 35 known families of RNA viruses. Besides detecting mammal-related viruses, which are the usual concern, we also found a high abundance of insect-related viruses and some bird-related viruses. We found that insect-related viruses were more abundant in summer, while the bird-related viruses were predominantly detected in autumn, which might be caused by the seasonal differences in prey selection by I. io. Additionally, a significant positive correlation was identified between prey diversity and total virus diversity. The more similar the prey composition, the more similar the total virus composition and the higher the count of potential new viruses. We also found that the relative abundance of Picornaviridae increased with increasing prey diversity and body mass. Conclusions: In this study, significant links were found between RNA virus diversity and dietary diversity of I. io. The results implied that dynamic changes in predator–prey interactions may facilitate frequent opportunities for viruses to spread among organisms. -pQNSPFCJqqnkMh129yG7y Video Abstract [ABSTRACT FROM AUTHOR]

Porcine reproductive and respiratory syndrome virus (PRRSV) is a highly variable virus with genetic diversity. This study comparatively examines the pathogenicity and immunological impact of two emergent PRRSV strains, SD53 and HuN4, in piglets. Our results indicate that SD53 strain induces milder clinical syndromes and less severe tissue damage than HuN4, despite similar replication rates. Hematological tests showed less perturbations in peripheral blood cell profiles after SD53 infection, suggesting a less systemic impact. The neutrophil-to-lymphocyte ratio was notably lower in SD53-infected piglets, suggesting a less intense inflammatory reaction. Moreover, SD53 infection led to lower levels of pro-inflammatory cytokines, further supporting a less pronounced inflammatory profile. Both strains induced the production of PRRSV-specific antibodies. However, transcriptomic analysis of lung and lymph node tissues from infected piglets disclosed a more moderate up-regulation of core genes, including ISGs, in the SD53 group. Further analysis indicated that SD53 primarily enhanced immune-related signaling, particularly in T cell response modules, while HuN4 caused a more robust pro-inflammatory reaction and a dampening of T cell functionality. Flow cytometry analyses confirmed these findings, showing higher CD4/CD8 ratios and increased CD4+ T cell percentages in SD53-infected piglets, implying a more robust T cell response. Collectively, these findings broaden our comprehension of PRRSV pathogenesis and may inform the development of future therapeutic or prophylactic strategies for controlling PRRSV infections more effectively. IMPORTANCE The high mutation rate of porcine reproductive and respiratory syndrome virus (PRRSV) poses significant challenges to its accurate diagnosis and the implementation of effective control measures. This research explores the pathogenic profiles of two emerging PRRSV stains: the NADC30-like strain SD53 and the highly pathogenic strain HuN4. Our investigation reveals that SD53 initiates distinct immunopathological responses in vivo compared with those provoked by HuN4. By conducting a transcriptome analysis of differential gene expression in the lungs and lymph nodes of infected piglets, we unveil the intricate molecular mechanisms underlying the contrasting pathogenicity of these two strains. The comprehensive insights yielded by this study are instrumental in advancing our understanding of the dominant NADC30-like PRRSV strain, which has become increasingly prevalent in China's swine industry. [ABSTRACT FROM AUTHOR]

Chlamys farreri is primarily cultivated in Japan, China, and South Korea. Although mass mortality of scallops has been occurring recently, likely caused by high temperatures or infectious diseases, the underlying cause remains unclear. Little is known regarding the viral diseases affecting them. Therefore, we explored DNA virus diversity in the mid-gut gland of C. farreri and compared it with that of seawater. C. farreri was cultivated at depths below 5 m from the sea surface in the coastal waters of South Korea and sampled from May to August 2018. Different DNA viral communities were observed in both C. farreri and seawater. In C. farreri, prevalent groups included Mimiviridae (7%), Poxviridae (6%), and Phycodnaviridae (5%). Conversely, the dominant groups in seawater were Autographiviridae (20%), Kyanoviridae (12%), and Zobellviridae (10%). We identified C. farreri-specific viral communities and potentially infectious viruses, such as Ostreid herpesvirus 1 and Abalone herpesvirus Victoria/AUS/2009. Furthermore, C. farreri acts as a reservoir for various viruses, which impact microbial community dynamics and disease transmission in marine ecosystems. Understanding these viral communities is crucial to protecting and restoring coastal ecosystems by highlighting their role in the transmission of potential avian- and bivalve-specific viruses. [ABSTRACT FROM AUTHOR]

Bovine viral diarrhoea (BVD) is one of the most economically damaging livestock enzootic diseases in the world. BVD aetiological agents are three pestiviruses (BVDV-1, -2 and HoBi-like pestivirus), which exhibit high genetic diversity and complex transmission cycles. This considerably hampers the management of the disease, which is why eradication plans have been implemented in several countries. In France, a national plan has been in place since 2019. Our understanding of its impact on the distribution of BVDV genotypes is limited by the availability of French genetic data. Here, we conducted a molecular epidemiology study to refine our knowledge of BVDV genetic diversity in France, characterise its international relationships, and analyse national spatio-temporal genotypic distribution. We collated 1037 BVDV-positive samples throughout France between 2011 and 2023, with a greater sampling effort in two major cattle production areas. We developed a high-throughput sequencing protocol which we used to complete the 5'UTR genotyping of this collection. We show that two main BVDV-1 genotypes, 1e and 1b, account for 88% of genotyped sequences. We also identified seven other BVDV-1 genotypes occurring at low frequencies and three BVDV-2 samples (genotype 2c). Phylogenetic analyses indicate different worldwide distribution patterns between the two main BVDV-1 genotypes. Their relative frequencies present no major changes in France since the 1990s and few variations at the national scale. We also found some degree of local spatial structuring in western France. Overall, our results demonstrate the potential of large-scale sequence-based surveillance to monitor changes in the epidemiological situation of enzootic diseases. [ABSTRACT FROM AUTHOR]

Commercially cultivated Prunus species are commonly grown in adjacent or mixed orchards and can be infected with unique or commonly shared viruses. Apple (Malus domestica), another member of the Rosacea and distantly related to Prunus, can share the same growing regions and common pathogens. Pollen can be a major route for virus transmission, and analysis of the pollen virome in tree fruit orchards can provide insights into these virus pathogen complexes from mixed production sites. Commercial honey bee (Apis mellifera) pollination is essential for improved fruit sets and yields in tree fruit production systems. To better understand the pollen-associated virome in tree fruits, metagenomics-based detection of plant viruses was employed on bee and pollen samples collected at four time points during the peak bloom period of apricot, cherry, peach, and apple trees at one orchard site. Twenty-one unique viruses were detected in samples collected during tree fruit blooms, including prune dwarf virus (PDV) and prunus necrotic ringspot virus (PNRSV) (Genus Ilarvirus, family Bromoviridae), Secoviridae family members tomato ringspot virus (genus Nepovirus), tobacco ringspot virus (genus Nepovirus), prunus virus F (genus Fabavirus), and Betaflexiviridae family member cherry virus A (CVA; genus Capillovirus). Viruses were also identified in composite leaf and flower samples to compare the pollen virome with the virome associated with vegetative tissues. At all four time points, a greater diversity of viruses was detected in the bee and pollen samples. Finally, the nucleotide sequence diversity of the coat protein regions of CVA, PDV, and PNRSV was profiled from this site, demonstrating a wide range of sequence diversity in pollen samples from this site. These results demonstrate the benefits of area-wide monitoring through bee pollination activities and provide new insights into the diversity of viruses in tree fruit pollination ecosystems. [ABSTRACT FROM AUTHOR]

Paramyxoviridae is one of the most well known and largest virus families, including some animal and human pathogens, such as the Hendra, Nipah, and Rinderpest viruses, with a high potential for the emergence of human diseases. Based on recent phylogenetic analyses, two new genera (Narmovirus and Jeilongvirus) have been described. The newly recognized genus Jeilongvirus has rapidly increased in number and has grown to 15 species from 7 a few years ago. However, little is known about the diversity, host range, or evolution of Jeilongvirus. As a well-known host reservoir for many pathogens, rodents have always been the focus for characterizing their pathogenic potential. In this study, we isolated a Tailam virus strain (RN-JH-YN-2022-1) belonging to the genus Jeilongvirus from Rattus norvegicus in Yunnan Province, China. The virus presented a near-complete genome (19,046 nucleotides). Similar to other members of the genus Jeilongvirus, the genome of RN-JH-YN-2022-1 contains eight basic genes (3′-N-P/V/C-M-F-SH-TM-G-L-5′) with 88.88% sequence identity to Tailam virus (TL8K). Additionally, we discuss the pattern of genus Jeilongvirus diversity and the possible route of spread of the Tailam virus, which could provide new clues into the host range, virus diversity, and geographical distribution of the genus Jeilongvirus. [ABSTRACT FROM AUTHOR]

Viral haemorrhagic fevers encompass a diverse group of severe, often life-threatening illnesses caused by viruses from multiple families, including Arenaviridae, Filoviridae, Flaviviridae, Hantaviridae, Nairoviridae, Peribunyaviridae, and Phenuiviridae. Characterised by fever and haemorrhagic symptoms, these diseases challenge public health systems by overwhelming healthcare facilities, complicating diagnostic processes, and requiring extensive resources for containment and treatment, especially in resource-limited settings. This discussion explores the intricate relationships between VHFs and their transmission vectors—both animal and arthropod—and examines the impact of ecological and geographic factors on disease spread. The primary transmission of VHFs typically occurs through direct contact with infected animals or via bites from haematophagous arthropods, facilitating zoonotic and, at times, human-to-human transmission. With an emphasis on the role of diverse wildlife, domesticated animals, and vectors such as mosquitoes and ticks in the epidemiology of VHFs, there is a recognised need for robust surveillance and strategic public health responses to manage outbreaks. This review discusses the necessity of interdisciplinary approaches that integrate virology, ecology, and public health to enhance diagnostic capabilities, develop vaccines and antivirals, and improve outbreak interventions. Exploring the ecological and biological dynamics of VHFs will help bolster a deeper understanding of these emerging viruses and underpin preparation for future outbreaks. The importance of enhanced global cooperation, continuous research, and collaboration to mitigate the public health threats posed by these complex infections is a central theme, serving as a foundational strategy to reinforce worldwide preparedness and response efforts. Future directions include addressing gaps in vaccine development and tailoring public health strategies to the unique challenges of managing VHFs, such as the rapid mutation rates of viruses, the need for cold chain logistics for vaccine distribution, and socio-economic barriers to healthcare access, in order to ensure readiness for and effective response to emerging threats worldwide. [ABSTRACT FROM AUTHOR]

RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus–host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identify RNA viruses of all types, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks. [ABSTRACT FROM AUTHOR]

Porcine circoviruses, particularly porcine circovirus type 2 (PCV2) and porcine circovirus type 3 (PCV3), significantly impact the global pig industry due to their high prevalence and pathogenicity. Conversely, porcine circovirus type 1 (PCV1) and porcine circovirus type 4 (PCV4) currently have low positivity rates. This study aimed to characterize the distribution and epidemiology of porcine circoviruses in Xinjiang, while also analyzing the genetic diversity and evolution of PCV2 and PCV3, which pose the greatest threats to the industry. In this study, we collected blood and tissue samples from 453 deceased pigs across eight regions in Xinjiang Province from 2022 to 2024. We utilized real-time PCR to detect the presence of PCV1, PCV2, PCV3, and PCV4. The positive rates were 15%, 71%, 25%, and 17%, respectively. Genetic analysis showed 9 PCV2 sequences and 12 PCV3 sequences. The capsid protein of PCV2 showed significant variability. In contrast, the amino acid sequences of capsid in PCV3 were relatively stable. Moreover, we predicted antigenic epitopes for PCV3 capsid using IEDB and ElliPro. The findings from this study provide valuable epidemiological data on PCV coinfection in the Xinjiang region and enhance the understanding of virus diversity nationwide. This research may serve as an important reference for the development of strategies to prevent and control porcine circovirus infections. [ABSTRACT FROM AUTHOR]

Viruses of microbes are ubiquitous biological entities that reprogram their hosts' metabolisms during infection in order to produce viral progeny, impacting the ecology and evolution of microbiomes with broad implications for human and environmental health. Advances in genome sequencing have led to the discovery of millions of novel viruses and an appreciation for the great diversity of viruses on Earth. Yet, with knowledge of only "who is there?" we fall short in our ability to infer the impacts of viruses on microbes at population, community, and ecosystem-scales. To do this, we need a more explicit understanding "who do they infect?" Here, we developed a novel machine learning model (ML), Virus-Host Interaction Predictor (VHIP), to predict virus-host interactions (infection/non-infection) from input virus and host genomes. This ML model was trained and tested on a high-value manually curated set of 8849 virus-host pairs and their corresponding sequence data. The resulting dataset, 'Virus Host Range network' (VHRnet), is core to VHIP functionality. Each data point that underlies the VHIP training and testing represents a lab-tested virus-host pair in VHRnet, from which meaningful signals of viral adaptation to host were computed from genomic sequences. VHIP departs from existing virus-host prediction models in its ability to predict multiple interactions rather than predicting a single most likely host or host clade. As a result, VHIP is able to infer the complexity of virus-host networks in natural systems. VHIP has an 87.8% accuracy rate at predicting interactions between virus-host pairs at the species level and can be applied to novel viral and host population genomes reconstructed from metagenomic datasets. Author summary: The ecology and evolution of microbial communities are deeply influenced by viruses. Metagenomics analysis, the non-targeted sequencing of community genomes, has led to the discovery of millions of novel viruses. Yet, through the sequencing process, only DNA sequences are recovered, begging the question: which microbial hosts do those novel viruses infect? To address this question, we developed a computational tool to allow researchers to predict virus-host interactions from such sequence data. The power of this tool is its use of a high-value, manually curated set of 8849 lab-verified virus-host pairs and their corresponding sequence data. For each pair, we computed signals of coevolution to use as the predictive features in a machine learning model designed to predict interactions between viruses and hosts. The resulting model, Virus-Host Interaction Predictor (VHIP), has an accuracy of 87.8% and can be applied to novel viral and host genomes reconstructed from metagenomic datasets. Because the model considers all possible virus-host pairs, it can resolve complete virus-host interaction networks and supports a new avenue to apply network thinking to viral ecology. [ABSTRACT FROM AUTHOR]

DNA Stable Isotope Probing is emerging as a potent methodology for investigating host–virus interactions, based on the essential reliance of viruses on host organisms for the production of virions. Despite the anticipated link between host isotopic compositions and the generated virions, the application of stable isotope probing to viral DNA has never been evaluated on simple biological models. In this study, we assessed the efficacy of this method on the bacteriophage T4 and its host, Escherichia coli. Through the cultivation of E. coli cells on a 13C-enriched substrate and subsequent propagation of T4 bacteriophage, we examine the degree of isotopic enrichment in viral DNA. Our investigation reveals a strong correlation between the proportion of 13C6-d-glucose in the growth substrate and the buoyant density in CsCl gradient of T4 DNA, confirming the validity of DNA SIP in viral ecology. These findings underscore the potential of DNA SIP as a robust tool for characterizing the diversity of viruses infecting hosts with specific metabolic activities and provide then a foundation for further exploration in viral ecology research. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

ABSTRACT Archaea play a significant role in natural ecosystems and the human body. Archaeal viruses exert a considerable influence on the structure and composition of archaeal communities and their associated ecological environments. The present study revealed the complete genomes of 38 archaeal head-tailed proviruses through comprehensive data mining. The hosts of these proviruses were identified as belonging to the following four dominant phyla: Halobacteriota, Thermoplasmatota, Thermoproteota, and Nanoarchaeota. In addition to the 14 proviruses of halophilic archaea related to the Graaviviridae family, the remaining proviruses exhibited limited genetic similarities to known (pro)viruses, suggesting the existence of 14 potential novel families. Of the 38 archaeal proviruses, 30 have the potential to lyse host cells. Eleven proviruses contain genes linked to antiviral defense mechanisms, including those involved in restriction modification (RM), clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR–Cas) nucleases, defense island system associated with restriction-modification (DISARM), and DNA degradation (Dnd). Moreover, auxiliary metabolic genes were identified in the proviruses of Bathyarchaeia and Halobacteriota archaea, including those involved in carbohydrate and amino acid metabolism. Our findings indicate the diversity of archaeal viruses, their interactions with archaeal hosts, and their roles in the adaptation of the host.IMPORTANCEThe field of archaeal virology has seen a rapid expansion through the use of metagenomics, yet the diversity of these viruses remains largely uncharted. In this study, the complete genomes of 38 novel archaeal proviruses were identified for the following four dominant phyla: Halobacteriota, Thermoplasmatota, Thermoproteota, and Nanoarchaeota. Two families and six genera of Archaea were the first to be identified as hosts for viruses. The proviruses were found to contain diverse genes that were involved in distinct adaptation strategies of viruses to hosts. Our findings contribute to the expansion of the lineages of archaeal viruses and highlight their intricate interactions and essential roles in enabling host survival and adaptation to diverse environmental conditions.

Dothistroma septosporum and Dothistroma pini are severe foliar pathogens of conifers. They infect a broad spectrum of hosts (mainly Pinus spp.), causing chlorosis, defoliation of needles, and eventually the death of pine trees in extreme cases. Mycoviruses represent a novel and innovative avenue for controlling pathogens. To search for possible viruses hosted by Dothistroma spp. we screened a subset of isolates (20 strains of D. septosporum and one D. pini) originating from the Czech Republic, Slovenia, Italy, Austria and Ireland for viral dsRNA segments. Only five of them showed the presence of dsRNA segments. A total of 21 fungal isolates were prepared for total RNA extractions. RNA samples were pooled, and two separate RNA libraries were constructed for stranded total RNA sequencing. RNA-Seq data processing, pairwise sequence comparisons (PASC) and phylogenetic analyses revealed the presence of thirteen novel putative viruses with varying genome types: seven negative-sense single-stranded RNA viruses, including six bunya-like viruses and one new member of the order Mononegavirales; three positive-sense single-stranded RNA viruses, two of which are similar to those of the family Narnaviridae, while the genome of the third correspond to those of the family Gammaflexiviridae; and three double-stranded RNA viruses, comprising two novel members of the family Chrysoviridae and a potentially new species of gammapartitivirus. The results were confirmed with RT-PCR screening that the fungal pathogens hosted all the viruses and showed that particular fungal strains harbour multiple virus infections and that they are transmitted vertically. In this study, we described the narnavirus infecting D. pini. To our knowledge, this is the first virus discovered in D. pini.

Background and Purpose: There is a need for effective anti‐COVID‐19 treatments, mainly for individuals at risk of severe disease such as the elderly and the immunosuppressed. Drug repositioning has proved effective in identifying drugs that can find a new application for the control of coronavirus disease, in particular COVID‐19. The purpose of the present study was to find synergistic antiviral combinations for COVID‐19 based on lethal mutagenesis. Experimental Approach: The effect of combinations of remdesivir and ribavirin on the infectivity of SARS‐CoV‐2 in cell culture has been tested. Viral populations were monitored by ultra‐deep sequencing, and the decrease of infectivity as a result of the treatment was measured. Key Results: Remdesivir and ribavirin exerted a synergistic inhibitory activity against SARS‐CoV‐2, quantified both by CompuSyn (Chou‐Talalay method) and Synergy Finder (ZIP‐score model). In serial passage experiments, virus extinction was readily achieved with remdesivir‐ribavirin combinations at concentrations well below their cytotoxic 50 value, but not with the drugs used individually. Deep sequencing of treated viral populations showed that remdesivir, ribavirin, and their combinations evoked significant increases of the number of viral mutations and haplotypes, as well as modification of diversity indices that characterize viral quasi‐species. Conclusion and Implications: SARS‐CoV‐2 extinction can be achieved by synergistic combination treatments based on lethal mutagenesis. In addition, the results offer prospects of triple drug treatments for effective SARS‐CoV‐2 suppression. [ABSTRACT FROM AUTHOR]

Amplicon sequencing is an effective and increasingly applied method for studying viral communities in the environment. Here, we present vAMPirus, a user‐friendly, comprehensive, and versatile DNA and RNA virus amplicon sequence analysis program, designed to support investigators in exploring virus amplicon sequencing data and running informed, reproducible analyses. vAMPirus intakes raw virus amplicon libraries and, by default, performs nucleotide‐ and amino acid‐based analyses to produce results such as sequence abundance information, taxonomic classifications, phylogenies and community diversity metrics. The vAMPirus analytical framework leverages 16 different opensource tools and provides optional approaches that can increase the ratio of biological signal‐to‐noise and thereby reveal patterns that would have otherwise been masked. Here, we validate the vAMPirus analytical framework and illustrate its implementation as a general virus amplicon sequencing workflow by recapitulating findings from two previously published double‐stranded DNA virus datasets. As a case study, we also apply the program to explore the diversity and distribution of a coral reef‐associated RNA virus. vAMPirus is streamlined within Nextflow, offering straightforward scalability, standardization and communication of virus lineage‐specific analyses. The vAMPirus framework is designed to be adaptable; community‐driven analytical standards will continue to be incorporated as the field advances. vAMPirus supports researchers in revealing patterns of virus diversity and population dynamics in nature, while promoting study reproducibility and comparability. [ABSTRACT FROM AUTHOR]

Endogenous viral elements (EVEs) have been reported to exist widely in the genomes of eukaryotic organisms, and they are closely associated with the growth, development, genetics, adaptation, and evolution of their hosts. In this study, two methods—homologous sequence search and genome alignment—were used to explore the endogenous viral sequences in the genomes of Fragaria species. Results revealed abundant endogenous pararetroviruses (EPRVs) in the genomes of Fragaria species, including 786 sequences belonging to five known taxa such as Caulimovirus and other unclassified taxa. Differences were observed in the detected EPRVs between the two methods, with the homologous sequence search having a greater number of EPRVs. On the contrary, genome alignment identified various types and sources of virus-like sequences. Furthermore, through genome alignment, a 267-bp sequence with 95% similarity to the gene encoding the aphid-transmitted protein of Strawberry vein banding virus (Caulimovirus venafragariae) was discovered in the F. chiloensis genome, which was likely a recent insertion. In addition, the statistical analysis of the genome alignment results indicated a remarkably higher abundance of virus-like sequences in the genomes of polyploid strawberries compared with diploid ones. Moreover, the differences in virus-like sequences were observed between the genomes of Fragaria species and those of their close relatives. This study enriched the diversity of viruses that infect strawberries, and laid a theoretical foundation for further research on the origin of endogenous viruses in the strawberry genome, host–virus interactions, adaptation, evolution, and their functions. [ABSTRACT FROM AUTHOR]

The potato leafhopper (Empoasca fabae, PLH) is a serious pest that feeds on a wide range of agricultural crops and is found throughout the United States but is not known to be a vector for plant-infecting viruses. We probed the diversity of virus sequences in field populations of PLH collected from four Midwestern states: Illinois, Indiana, Iowa, and Minnesota. High-throughput sequencing data from total RNAs extracted from PLH were used to assemble sequences of fifteen positive-stranded RNA viruses, two negative-stranded RNA viruses, and one DNA virus. These sequences included ten previously described plant viruses and eight putative insect-infecting viruses. All but one of the insect-specific viruses were novel and included three solemoviruses, one iflavirus, one phenuivirus, one lispivirus, and one ambidensovirus. Detailed analyses of the novel genome sequences and their evolutionary relationships with related family members were conducted. Our study revealed a diverse group of plant viruses circulating in the PLH population and discovered novel insect viruses, expanding knowledge on the untapped virus diversity in economically important crop pests. Our findings also highlight the importance of monitoring the emergence and circulation of plant-infecting viruses in agriculturally important arthropod pests. [ABSTRACT FROM AUTHOR]

Plant diseases are mostly multicausal with several factors influencing the health status of affected hosts. Common ash (Fraxinus excelsior), a significant tree species of European forests, is currently mostly endangered by ash dieback, caused by the invasive fungus Hymenoscyphus fraxineus. However, contributing factors, including pathogenic viruses, are poorly understood. Here, we report the results of a virus screening conducted on selected special stands of F. excelsior. Over three consecutive years, ash trees from different origins were tested, including leaf material from mature seed trees, young trees and ash seedlings from the natural regeneration. Using RT-PCR, we screened for five viruses, including the generalist species ArMV (Nepovirus arabis) and CLRV (Nepovirus avii), as well as newly discovered viruses in ash, including the emaravirus ASaV (Emaravirus fraxini), the idaeovirus PrLBaV (Idaeovirus ligustri), and cytorhabdoviruses. The results revealed a high virus diversity in common ash. An association of ASaV detection with specific leaf symptoms, including shoestring, chlorotic ringspots, and vein yellowing, was documented. An analyses of relevant gene products of cytorhabdoviruses obtained from ashes of different sites revealed sequence diversities and two distinct phylogenetic groups present in ash populations. Signatures of novel viruses from different families have been identified by high-throughput sequencing. Together, our results provide insights into the virus diversity and distribution of viruses in ash and expand our knowledge about the virome of this endangered tree species. [ABSTRACT FROM AUTHOR]

Background: Symbioses between primary producers and bacteria are crucial for nutrient exchange that fosters host growth and niche adaptation. Yet, how viruses that infect bacteria (phages) influence these bacteria-eukaryote interactions is still largely unknown. Here, we investigate the role of viruses on the genomic diversity and functional adaptations of bacteria associated with pelagic sargassum. This brown alga has dramatically increased its distribution range in the Atlantic in the past decade and is predicted to continue expanding, imposing severe impacts on coastal ecosystems, economies, and human health. Results: We reconstructed 73 bacterial and 3963 viral metagenome-assembled genomes (bMAGs and vMAGs, respectively) from coastal Sargassum natans VIII and surrounding seawater. S. natans VIII bMAGs were enriched in prophages compared to seawater (28% and 0.02%, respectively). Rhodobacterales and Synechococcus bMAGs, abundant members of the S. natans VIII microbiome, were shared between the algae and seawater but were associated with distinct phages in each environment. Genes related to biofilm formation and quorum sensing were enriched in S. natans VIII phages, indicating their potential to influence algal association in their bacterial hosts. In-vitro assays with a bacterial community harvested from sargassum surface biofilms and depleted of free viruses demonstrated that these bacteria are protected from lytic infection by seawater viruses but contain intact and inducible prophages. These bacteria form thicker biofilms when growing on sargassum-supplemented seawater compared to seawater controls, and phage induction using mitomycin C was associated with a significant decrease in biofilm formation. The induced metagenomes were enriched in genomic sequences classified as temperate viruses compared to uninduced controls. Conclusions: Our data shows that prophages contribute to the flexible genomes of S. natans VIII-associated bacteria. These prophages encode genes with symbiotic functions, and their induction decreases biofilm formation, an essential capacity for flexible symbioses between bacteria and the alga. These results indicate that prophage acquisition and induction contribute to genomic and functional diversification during sargassum-bacteria symbioses, with potential implications for algae growth. 1vVC6YGWLCm_DZc419o4RC Video Abstract [ABSTRACT FROM AUTHOR]

Mumps is a vaccine-preventable disease with high contagious capability. Its incidence declined rapidly since one dose of mumps vaccine was introduced into Expanded Program of Immunization (EPI) in 2008 in China. Nonetheless, the outbreaks of mumps remain frequent in China. Here we aim to assess herd immunity level followed by one-dose mumps ingredient vaccine and to elucidate the genetic characteristics of mumps viruses circulating in the post vaccine era in Jiangsu province of China. The complete sequences of mumps virus small hydrophobic(SH) gene were amplified and sequenced; coalescent-based Bayesian method was used to perform phylogenetic analysis with BEAST 1.84 software. Commercially available indirect enzyme-linked immune-sorbent IgG assay was used for the quantitative detection of IgG antibody against mumps virus. Our results show that genotype F was the predominant mumps viruses and belonged to indigenous spread, and most of Jiangsu sequences clustered together and formed a monophyly. The prevalence of mumps reached a peak in 2012 and subsequently declined, which presented an obvious different trajectory with virus circulating in other regions of China. The gene diversity of viruses circulating in Jiangsu province was far less than those in China. The antibody prevalence reached 70.42% in the general population during 2018 to 2020. The rising trend of antibody level was also observed. Although mumps antibody prevalence does not reach expected level, mumps virus faces higher pressure in Jiangsu province than the whole of China. To reduce further the prevalence of mumps viruses, two doses of mumps vaccine should be involved into EPI. [ABSTRACT FROM AUTHOR]

Background: Viral gastrointestinal infections remain a major public health concern in developing countries. In Burkina Faso, there are very limited updated data on the circulating viruses and their genetic diversity. Objectives: This study investigates the detection rates and characteristics of rotavirus A (RVA), norovirus (NoV), sapovirus (SaV) and human astrovirus (HAstV) in patients of all ages with acute gastrointestinal infection in urban and rural areas. Study design & Methods: From 2018 to 2021, stool samples from 1,295 patients with acute gastroenteritis were collected and screened for RVA, NoV, SaV and HAstV. Genotyping and phylogenetic analyses were performed on a subset of samples. Results: At least one virus was detected in 34.1% of samples. NoV and SaV were predominant with detection rates of respectively 10.5 and 8.8%. We identified rare genotypes of NoV GII, RVA and HAstV, recombinant HAstV strains and a potential zoonotic RVA transmission event. Conclusions: We give an up-to-date epidemiological picture of enteric viruses in Burkina Faso, showing a decrease in prevalence but a high diversity of circulating strains. However, viral gastroenteritis remains a public health burden, particularly in pediatric settings. Our data advocate for the implementation of routine viral surveillance and updated management algorithms for diarrheal disease. Author summary: Diseases of the gastrointestinal tract can be caused by a variety of pathogens, such as bacteria, viruses, fungi or parasites. Viruses play a particularly important role, especially in low-income countries, where viral gastroenteritis leads to high morbidity and mortality, particularly among children and the elderly. As part of the African Network for Improved Diagnostics, Epidemiology and Management of Common Infectious Agents (ANDEMIA), patients of all ages from four African countries with symptoms of acute gastroenteritis were tested for the most common viral, bacterial and parasitic pathogens. Samples from Burkina Faso that tested positive for noroviruses, rotaviruses, sapoviruses or astroviruses were further genotyped and characterized in the present study. In this study we described for the first time the detection of rare rotavirus and astrovirus strains circulating in Burkinabe patients. The knowledge about the circulating virus variants is essential to develop suitable vaccines and adequate pharmaceuticals. [ABSTRACT FROM AUTHOR]

Fig mosaic disease (FMD) poses a significant threat to fig (Ficus carica) trees globally. Fig mosaic virus (Emaravirus fici, Family Fimoviridae) is one of the main causes involved in FMD. E. fici has been reported in many countries, including Iran. This research investigated the genetic diversity and distribution of this virus in Kermanshah Province, the third fig‐producing region in Iran. In 2021 and 2022, 128 samples, mainly displaying FMD symptoms, were collected from fig trees across nine counties. Using DAS‐ELISA with polyclonal antibodies, 86 samples tested positive for fig mosaic virus. The 2‐year‐old healthy fig saplings grafted with scions from infected trees exhibited mosaic symptoms and tested positive for the virus in DAS‐ELISA. Reverse transcription‐polymerase chain reaction (RT‐PCR) by RdRp‐specific primers (E5‐s and E5‐a) also amplified a DNA fragment with the expected size of about 302 bp from the ELISA‐positive samples. Five of the 12 symptomless samples showed positive results in both DAS‐ELISA and RT‐PCR. This indicates that the absence of symptoms in propagation sources does not imply that they are virus‐free. Nucleotide sequences of RT‐PCR products confirmed the fig mosaic virus infection. BLAST analysis of 20 samples (GenBank accession numbers OQ552535 to OQ552554) revealed that 19 sequences show high nucleotide identity (93.4%–96.8%) with an isolate from Lorestan Province, Iran (GenBank accession number KT732024). Notably, isolate FM203 showed distinct genetic divergence (86.6%–90.2% nucleotide identity) and shared similarities with some other Iranian isolates, including those from Kermanshah and Mazandaran provinces. Phylogenetic analysis grouped most isolates with the Lorestan isolate, while FM203 was placed in a separate cluster. This study highlighted the widespread presence of fig mosaic virus in Kermanshah Province, emphasizing varying infection rates across different counties, with Dalahoo County (Rijab) showing the highest prevalence. [ABSTRACT FROM AUTHOR]

A virus discovery investigation using high‐throughput sequencing in sugarcane samples from Ethiopia revealed the presence of sugarcane mild mosaic virus (SCMMV, genus Ampelovirus) and sugarcane umbra‐like virus (SULV, genus Umbravirus). The genome sequences of two isolates of SCMMV and one SULV were determined. The sequences of the two SCMMV isolates were 13,005 nucleotides in length and showed ~73.5% nucleotide identity along the genome and ~90.2, 96.8, and 90.4% amino acid sequence identity among each other in the RdRp, CP, and HSP70h, respectively. Isolate SCMMV ET2 showed a close relationship to group A isolates from Colombia, the USA, and the Philippines, with amino acid sequence identity of the predicted virus proteins in the range of 94–98.9%. Conversely, SCMMV ET1 shared a closer relationship with group B isolates from Colombia, Ivory Coast, and Argentina, exhibiting a 93–99% amino acid sequence identity. The complete genome sequence of SULV, comprising 3041 nucleotides, exhibited the highest identity with its counterpart from South Africa (MN868593). These findings contribute to expanding our understanding of the viral diversity within the sugarcane crop in Ethiopia. [ABSTRACT FROM AUTHOR]

Cassava Mosaic Disease (CMD) is a dreadful disease of cassava (Manihot esculenta Crantz) production systems in sub-Saharan Africa. The objective of this study was to establish the viruses associated with CMD and their spatio-temporal distribution in the South Kivu Province of the Democratic Republic of Congo. A total of 590 cassava leaf samples were collected during November in 2020 and March 2022 and analysed for laboratory analysis using molecular methods. Results showed that various virus strains (African Cassava Mosaic Virus (ACMV), East African Cassava Mosaic Virus (EACMV), ACMV+EACMV-UG, EACMCV and unspecified strains) were widely distributed in South Kivu. Strain EACMV-UG was widespread in all territories of South Kivu Province; while the Cameroonian strain (EACMCV) was only found in the Kalehe Territory (2%). There was a mixed infection (ACMV+EACMVUG), though at low levels, rising from 2.3% in 2020 to 3% in 2022. All the territories surveyed had wide diversity of viruses, with the exception of that of Uvira, which only had the EACMV-UG. The ACMV viruses were the most abundant; followed by EACMV-UG, in the study region. A sharp increase in virus diversity occurred during 2020 and 2022, with rates rising from 33.07 to 57.5%. [ABSTRACT FROM AUTHOR]

Arms race dynamics are a common outcome of host–parasite coevolution. While they can theoretically be maintained indefinitely, realistic arms races are expected to be finite. Once an arms race has ended, for example due to the evolution of a generalist-resistant host, the system may transition into coevolutionary dynamics that favour long-term diversity. In microbial experiments, host–parasite arms races often transition into a stable coexistence of generalist-resistant hosts, (semi-)susceptible hosts, and parasites. While long-term host diversity is implicit in these cases, parasite diversity is usually overlooked. In this study, we examined parasite diversity after the end of an experimental arms race between a unicellular alga (Chlorella variabilis) and its lytic virus (PBCV-1). First, we isolated virus genotypes from multiple time points from two replicate microcosms. A time-shift experiment confirmed that the virus isolates had escalating host ranges, i.e., that arms races had occurred. We then examined the phenotypic and genetic diversity of virus isolates from the post-arms race phase. Post-arms race virus isolates had diverse host ranges, survival probabilities, and growth rates; they also clustered into distinct genetic groups. Importantly, host range diversity was maintained throughout the post-arms race phase, and the frequency of host range phenotypes fluctuated over time. We hypothesize that this dynamic polymorphism was maintained by a combination of fluctuating selection and demographic stochasticity. Together with previous work in prokaryotic systems, our results link experimental observations of arms races to natural observations of long-term host and parasite diversity. Graphical Abstract [ABSTRACT FROM AUTHOR]

We conducted an integrative analysis to elucidate the spatial epidemiological patterns of the Vesicular Stomatitis New Jersey virus (VSNJV) during the 2014–15 epizootic cycle in the United States (US). Using georeferenced VSNJV genomics data, confirmed vesicular stomatitis (VS) disease cases from surveillance, and a suite of environmental factors, our study assessed environmental and phylogenetic similarity to compare VS cases reported in 2014 and 2015. Despite uncertainties from incomplete virus sampling and cross-scale spatial processes, patterns suggested multiple independent re-invasion events concurrent with potential viral overwintering between sequential seasons. Our findings pointed to a geographically defined southern virus pool at the US–Mexico interface as the source of VSNJV invasions and overwintering sites. Phylodynamic analysis demonstrated an increase in virus diversity before a rise in case numbers and a pronounced reduction in virus diversity during the winter season, indicative of a genetic bottleneck and a significant narrowing of virus variation between the summer outbreak seasons. Environment–vector interactions underscored the central role of meta-population dynamics in driving disease spread. These insights emphasize the necessity for location- and time-specific management practices, including rapid response, movement restrictions, vector control, and other targeted interventions. [ABSTRACT FROM AUTHOR]

Dengue virus (DENV) is the causative agent of dengue. Although most infected individuals are asymptomatic or present with only mild symptoms, severe manifestations could potentially devastate human populations in tropical and subtropical regions. In hyperendemic regions such as South Asia and Southeast Asia (SEA), all four DENV serotypes (DENV-1, DENV-2, DENV-3, and DENV-4) have been prevalent for several decades. Each DENV serotype is further divided into multiple genotypes, reflecting the extensive diversity of DENV. Historically, specific DENV genotypes were associated with particular geographical distributions within endemic regions. However, this epidemiological pattern has changed due to urbanization, globalization, and climate change. This review comprehensively traces the historical and recent genetic epidemiology of DENV in Asia from the first time DENV was identified in the 1950s to the present. We analyzed envelope sequences from a database covering 16 endemic countries across three distinct geographic regions in Asia. These countries included Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan, and Sri Lanka from South Asia; Cambodia, Laos, Myanmar, Thailand, and Vietnam from Mainland SEA; and Indonesia, the Philippines, Malaysia, and Singapore from Maritime SEA. Additionally, we describe the phylogenetic relationships among DENV genotypes within each serotype, along with their geographic distribution, to enhance the understanding of DENV dynamics. [ABSTRACT FROM AUTHOR]

The viromes of freshwater bodies are underexplored. The Picornavirales order, with 371 acknowledged species, is one of the most expansive and diverse groups of eukaryotic RNA viruses. In this study, we add 513 picorna-like viruses to the assemblage of more than 2000 unassigned picorna-like viruses. Our set of the aquatic Picornavirales virome of the Teltow Canal in Berlin, Germany, consists of 239 complete and 274 partial genomes. This urban freshwater body is characterized by the predominance of marna-like viruses (30.8%) and dicistro-like viruses (19.1%), whereas picornaviruses, iflaviruses, solinvi-like viruses, polycipi-like viruses, and nora-like viruses are considerably less prevalent. Caliciviruses and secoviruses were absent in our sample. Although presenting characteristic domains of Picornavirales, more than 100 viruses (20.8%) could not be assigned to any of the 9 Picornavirales families. Thirty-three viruses of the Marnaviridae—mostly locarna-like viruses—exhibit a monocistronic genome layout. Besides a wealth of novel virus sequences, viruses with peculiar features are reported. Among these is a clade of untypeable marna-like viruses with dicistronic genomes, but with the capsid protein-encoding open reading frame located at the 5′ part of their RNA. A virus with a similar genome layout but clustering with dicistroviruses was also observed. We further detected monocistronic viruses with a polymerase gene related to aparaviruses. The detection of Aichi virus and five novel posa-like viruses indicates a slight burden in municipal wastewater. [ABSTRACT FROM AUTHOR]

Background: Porcine reproductive and respiratory syndrome virus (PRRSV) is a prevalent swine pathogen, which has caused adverse impact on the global swine industry for almost 30 years. However, due to the immune suppression caused by the virus and the genetic diversity in PRRSV, no virus-targeting broad neutralizing strategy has been successfully developed yet. Antiviral peptide and nanobody have attracted extensive attention with the ease in production and the efficacy in practice. In this study, four new fusion proteins named nanobody peptide conjugates (NPCs) were developed by combining PRRSV specific non-neutralizing nanobodies with CD163-derived peptides targeting the receptor binding domain (RBD) of PRRSV proteins. Results: Four NPCs were successfully constructed using two nanobodies against PRRSV N and nsp9 individually, recombining with two antiviral peptides 4H7 or 8H2 from porcine CD163 respectively. All four NPCs demonstrated specific capability of binding to PRRSV and broad inhibitory effect against various lineages of PRRSV in a dose-dependent manner. NPCs interfere with the binding of the RBD of PRRSV proteins to CD163 in the PRRSV pre-attachment stage by CD163 epitope peptides in the assistance of Nb components. NPCs also suppress viral replication during the stage of post-attachment, and the inhibitory effects depend on the antiviral functions of Nb parts in NPCs, including the interference in long viral RNA synthesis, NF-κB and IFN-β activation. Moreover, an interaction was predicted between aa K31 and T32 sites of neutralizing domain 4H7 of NPC-N/nsp9-4H7 and the motif 171NLRLTG176 of PRRSV GP2a. The motif 28SSS30 of neutralizing domain 8H2 of NPC-N/nsp9-8H2 could also form hydrogens to bind with the motif 152NAFLP156 of PRRSV GP3. The study provides valuable insights into the structural characteristics and potential functional implications of the RBD of PRRSV proteins. Finally, as indicated in a mouse model, NPC intranasally inoculated in vivo for 12–24 h sustains the significant neutralizing activity against PRRSV. These findings inspire the potential of NPC as a preventive measure to reduce the transmission risk in the host population against respiratory infectious agents like PRRSV. Conclusion: The aim of the current study was to develop a peptide based bioactive compound to neutralize various PRRSV strains. The new antiviral NPC (nanobody peptide conjugate) consists of a specific nanobody targeting the viral protein and a neutralizing CD163 epitope peptide for virus blocking and provides significant antiviral activity. The study will greatly promote the antiviral drug R&D against PRRSV and enlighten a new strategy against other viral diseases. [ABSTRACT FROM AUTHOR]

Currently, the analyses of and prediction using COVID-19-related data extracted from patient information repositories compiled by hospitals and health organizations are of paramount importance. These efforts significantly contribute to vaccine development and the formulation of contingency techniques, providing essential tools to prevent resurgence and to effectively manage the spread of the disease. In this context, the present research focuses on analyzing the biological information of the SARS-CoV-2 viral gene sequences and the clinical data of COVID-19-affected patients using publicly accessible data from Ecuador. This involves considering variables such as age, gender, and geographical location to understand the evolution of mutations and their distributions across Ecuadorian provinces. The Cross-Industry Standard Process for Data Mining (CRISP-DM) methodology is applied for data analysis. Various data preprocessing and statistical analysis techniques are employed, including Pearson correlation, the chi-square test, and analysis of variance (ANOVA). Statistical diagrams and charts are used to facilitate a better visualization of the results. The results illuminate the genetic diversity of the virus and its correlation with clinical variables, offering a comprehensive understanding of the dynamics of COVID-19 spread in Ecuador. Critical variables influencing population vulnerability are highlighted, and the findings underscore the significance of mutation monitoring and indicate a need for global expansion of the research area. [ABSTRACT FROM AUTHOR]

Dengue, a mosquito‐borne viral disease, poses a significant public health challenge in Pakistan, with a significant outbreak in 2023, prompting our investigation into the serotype and genomic diversity of the dengue virus (DENV). NS‐1 positive blood samples from 153 patients were referred to the National Institute of Health, Pakistan, between July and October 2023. Among these, 98 (64.1%) tested positive using multiplex real‐time PCR, with higher prevalence among males (65.8%) and individuals aged 31‐40. Serotyping revealed DENV‐1 as the predominant serotype (84.7%), followed by DENV‐2 (15.3%). Whole‐genome sequencing of 18 samples (DENV‐1 = 17, DENV‐2 = 01) showed that DENV‐1 (genotype III) samples were closely related (>99%) to Pakistan outbreak samples (2022), and approx. > 98% with USA (2022), Singapore and China (2016), Bangladesh (2017), and Pakistan (2019). The DENV‐2 sequence (cosmopolitan genotype; clade IVA) shared genetic similarity with Pakistan outbreak sequences (2022), approx. > 99% with China and Singapore (2018−2019) and showed divergence from Pakistan sequences (2008−2013). No coinfection with dengue serotypes or other viruses were observed. Comparisons with previous DENV‐1 sequences highlighted genetic variations affecting viral replication efficiency (NS2B:K55R) and infectivity (E:M272T). These findings contribute to dengue epidemiology understanding and underscore the importance of ongoing genomic surveillance for future outbreak responses in Pakistan. [ABSTRACT FROM AUTHOR]

Simple Summary: Viruses present a significant challenge to the sustainable growth of the aquaculture sector. Perinereis, a valuable live-feed source in aquaculture, carries the risk of harboring unknown viruses, potentially jeopardizing the biosecurity of aquatic organisms. Despite this risk, there is a notable absence of research investigating novel viruses in Perinereis using meta-transcriptomic sequencing techniques. Therefore, it becomes imperative to explore the viral diversity within Perinereis. In this report, 12 previously unidentified viruses was documented in two distinct Perinereis species through meta-transcriptomic sequencing. These newly identified viruses were classified into four major viral families, shedding light on the intricate viral landscape within Perinereis. By unveiling these novel viruses, this research contributes to a broader knowledge base of the viral ecology in Perinereis, offering valuable insights into the potential risks and impacts associated with Perinereis in aquaculture settings. Such findings also highlight the need for enhancing biosecurity measures and disease management strategies within the aquaculture industry. Perinereis species are essential benthonic animals in coastal ecosystems and have significant roles as live feed in aquaculture, owing to their high-protein and low-fat nutritional profile. Despite their ecological importance, the viral communities associated with these organisms need to be better understood. In this study, we generated 2.6 × 108 reads using meta-transcriptomic sequencing and de novo assembled 5.3 × 103 virus-associated contigs. We identified 12 novel RNA viruses from two species, Perinereis aibuhitensis and P. wilsoni, which were classified into four major viral groups: Picobirnaviridae, Marnaviridae, unclassified Picornavirales, and unclassified Bunyavirales. Our findings revealed the hidden diversity of viruses and genome structures in Perinereis, enriching the RNA virosphere and expanding the host range of Picobirnaviridae, Marnaviridae, and Bunyavirales. This study also highlighted the potential biosecurity risk of the novel viruses carried by Perinereis to aquaculture. [ABSTRACT FROM AUTHOR]

Background: Dengue is a major public health concern in Reunion Island, marked by recurrent epidemics, including successive outbreaks of dengue virus serotypes 1 and 2 (DENV1 and DENV2) with over 70,000 cases confirmed since 2017. Methodology/Principal findings: In this study, we used Oxford Nanopore NGS technology for sequencing virologically-confirmed samples and clinical isolates collected between 2012 and 2022 to investigate the molecular epidemiology and evolution of DENV in Reunion Island. Here, we generated and analyzed a total of 499 DENV1, 360 DENV2, and 18 DENV3 sequences. By phylogenetic analysis, we show that different genotypes and variants of DENV have circulated in the past decade that likely originated from Seychelles, Mayotte and Southeast Asia and highly affected areas in Asia and Africa. Conclusions/Significance: DENV sequences from Reunion Island exhibit a high genetic diversity which suggests regular introductions of new viral lineages from various Indian Ocean islands. The insights from our phylogenetic analysis may inform local health authorities about the endemicity of DENV variants circulating in Reunion Island and may improve dengue management and surveillance. This work emphasizes the importance of strong local coordination and collaboration to inform public health stakeholders in Reunion Island, neighboring areas, and mainland France. Author summary: This study, conducted from 2012 to 2022, aimed at understanding the dynamics and genetic diversity of dengue virus on Reunion Island, a French overseas department located in the southwestern Indian Ocean, which is regularly affected by dengue epidemics. Several thousand clinical isolates and patient samples were collected from across the island and sequenced, resulting in 877 new genetic sequences of dengue virus. Our results show significant genetic diversity among dengue virus variants that circulated on the island over the past decade. This diversity indicates the simultaneous presence of multiple lineages and closely related viruses, which may have resulted from regular introductions of new variants. Our phylogenetic analyses show that the sequences detected in Reunion Island may have originated from other Indian Ocean islands, such as Seychelles and Mayotte, as well as from Asian regions where dengue virus circulates. [ABSTRACT FROM AUTHOR]