Search Results (83)

Long Terminal Repeat (LTR) retrotransposons (LTR-RTEs) comprise up to 90% of some plant genomes and drive genome diversification through their amplification. Novel insertions arise during the final stages of the LTR-RTE life cycle, which depends on both LTR-RTE-encoded proteins and host cellular factors. The LTR-RTE elements require host transcriptional machinery for RNA production, followed by nuclear processing/export, translation, virus-like particle assembly, reverse transcription, and genomic integration. This review addresses the following question: What host proteins promote LTR-RTE transposition in plants? Our analysis of recent literature on host factors and cellular compartments implicated in the retrotransposition cycle reveals the extensive integration of LTR-RTEs into host processes. Nonetheless, the precise mechanisms remain poorly resolved, especially in plants with their rich repertoire of LTR-RTEs. We propose integrating plant mobilomics with transposition reporters, genome editing, synthetic biology, and interactomics to elucidate plant-specific mechanisms. Full article

The continued diversification of the H9N2 avian influenza virus (AIV) into multiple antigenically and phylogenetically distinct lineages is promoting the emergence of strains with pandemic potential. Constant monitoring of the genetic evolution and changes in biological characteristics of the H9N2 viruses is therefore essential. In this study, we analyzed the genetic evolution of the H9N2 viruses isolated from poultry farms between 2022 and 2023 and evaluated their pathogenicity in chickens and mice. The HA genes of all ten isolates belonged to the h9.4.2.5 lineage, which is currently the predominant evolutionary lineage in China. Yet, their HA genes further divided into distinct subbranches within the h9.4.2.5 lineage. The NA genes of these viruses shared high homology with the prevalent H9N2 AIVs in recent years. However, these viruses were located in different evolutionary groups. Notably, the internal genes showed close relationships with those of recent H3, H6, and H9 subtype AIVs, suggesting active reassortment events among co-circulating viruses. Pathogenicity assessment in mice and chickens demonstrated divergent virulence between two representative isolates, FS22 and JM14, which clustered into different h9.4.2.5 subbranches. FS22 exhibited more efficient and prolonged replication in the lungs and turbinates of mice compared to JM14. Both viruses replicated efficiently in the lungs, kidneys, and trachea of chickens at 3 days post-infection (DPI), but differed in their horizontal transmission potential. Particularly, inoculated and contacted chickens all produced high antibody levels from the 5 DPI until the end of the experiment, and peak antibody titers for both viruses occurred at 7 DPI. These findings underscored the continuous evolution ofH9N2 AIV enhanced its genetic and phenotypic diversity, leading it to pose a threat to public health. Thus, continuous surveillance in poultry farms is necessary. Full article

Watermelon chlorotic stunt virus (WmCSV), a bipartite begomovirus, poses a severe and expanding threat to global cucurbit and watermelon production, driving an urgent need to unravel its genetic diversity indices and evolutionary complexities. To elucidate its evolutionary history, this study investigated the genetic diversity, evolutionary dynamics, and global dispersal of its genomic components, DNA-A (WmA) and DNA-B (WmB). The analyses uncovered striking contrasts between the components. WmB exhibited markedly greater genetic diversity (π = 0.0508 vs. 0.0119 for WmA), a slightly faster evolutionary rate (1.26 × 10⁻⁴ vs. 1.44 × 10⁻³ substitutions/site/year), and a far more complex recombination profile, with 34 events detected compared to only one in WmA. The abundance of recombination breakpoints in WmB underscores its central role in shaping genomic variability and adaptive potential. Phylogenetic analyses of both components unveil eight robustly supported clades per segment, predominantly shaped by geographical boundaries, hinting at localized evolutionary trajectories with constrained long-distance gene flow, with the exception of Oman. Bayesian time-scaled phylogenies and phylogeographic reconstructions further illuminate distinct dissemination pathways, suggesting an intriguing origin, with WmA likely emerging from the United States and WmB tracing back to Saudi Arabia, while the Middle East emerges as a dynamic epicenter for regional spread and subsequent incursions into the Americas. Together, these findings reveal contrasting evolutionary forces driving WmCSV diversification and provide critical insights into its origins and ongoing global emergence. Full article

Hantaviridae (order Bunyavirales) is a family of negative-sense, single-stranded RNA viruses. To date, several genetically distinct hantaviruses have been found in the same species of shrews and moles. In this report, we describe Biya River virus (BIRV), a novel hantavirus detected in the Eurasian water shrew (Neomys fodiens), the principal host of Boginia virus (BOGV). Genetic analysis of the complete L- and M-genomic segments and partial S-genomic segments showed that BIRV shared a common evolutionary origin with shrew-borne Altai (ALTV) and Lena (LENV) viruses, belonging to the Mobatvirus genus, and that BIRV was distantly related to BOGV and other shrew- and mole-borne orthohantaviruses. Ancient cross-species transmission of hantaviruses, with subsequent diversification within the Soricinae subfamily in Eurasia, might have shaped the evolutionary history of BIRV, ALTV, and LENV. Full article

The SARS-CoV-2 Omicron variant caused a global surge in COVID-19 cases following its emergence in November 2021, rapidly diversifying in the subsequent months. Although many studies have documented Omicron’s diversification, few have explored its impact on pediatric populations or the seasonality of other respiratory viruses in children. This study aims to investigate the diversity and circulation patterns of SARS-CoV-2 Omicron sublineages in pediatric patients in São Paulo, Brazil, and assess their co-circulation with other respiratory pathogens. Respiratory samples collected from patients under 18 years old across five hospitals between January 2022 and April 2023 were tested for different respiratory viruses using real-time RT-PCR. Whole-genome sequencing was performed on SARS-CoV-2-positive samples. Among the 7868 pediatric respiratory samples tested, 3902 were positive for viral pathogens. Respiratory Syncytial Virus accounted for the highest number of positive cases (n = 1248), exhibiting an atypical off-season peak in November 2022. SARS-CoV-2 was detected in 297 samples, of which 103 were sequenced. BA.1 and BA.5 sublineages had predominant genomic diversity and circulation time. These findings highlight the Omicron variant’s significant impact on the epidemiology and seasonal distribution of respiratory viruses in children, emphasizing the ongoing need for vaccination and robust surveillance efforts in pediatric populations. Full article

Bovine viral diarrhea virus (BVDV) is a pathogen of worldwide economic importance. In Uruguay, BVDV is endemic, with seroprevalence >80% at the farm level. This study analyzed 912 samples collected from January 2018 to October 2024 by reverse transcription PCR and sequencing, from calves with diarrhea, aborted fetuses, heifers with a history of abortions, and animals exhibiting symptoms of Mucosal Disease. This work summarizes ten years (2014–2024) of molecular epidemiology and evolution of BVDV. Analysis of the BVDV 5′UTR/N^pro genomic region revealed that the BVDV-1a, 1e, 1i, and 2b subtypes circulate in Uruguay. BVDV-1a remains the most prevalent subtype, followed by BVDV-2b, whose prevalence has been increasing. Our previous studies revealed that BVDV-1a showed geographical diversification in Uruguay. In this work, evolutionary studies conducted with N^pro genomic region showed that BVDV-2b is evolving at a substitution rate of 6.09 × 10⁻⁴ substitutions/site/year and has been introduced from Brazil in six separate events between 1870 and 1928, showing no geographical diversification. This work demonstrates that BVDV-1a and BVDV-2b are evolving differently in Uruguay. This evolutionary divergence is notable when comparing patterns observed in other countries where these subtypes circulate. Our findings provide crucial knowledge that should be considered for developing effective BVDV control measures in Uruguay. Full article

Psittacine Beak and Feather Disease (PBFD) is a highly contagious viral condition caused by Circovirus parrot—commonly known as Beak and Feather Disease Virus (BFDV)—a small, single-stranded DNA virus of the family Circoviridae. The disease primarily affects parrots (order Psittaciformes) and is characterized by progressive feather dystrophy, beak deformities, immunosuppression, and high mortality rates, particularly in juvenile birds. Although PBFD was initially documented in Australian psittacines, the virus has now attained global distribution, facilitated predominantly by the international trade in live parrots, both legal and illegal. This review provides a comprehensive synthesis of current knowledge on the virology, clinical presentation, molecular epidemiology, and phylogeographic spread of BFDV. Particular attention is given to the role of parrot trade in shaping transmission dynamics and genetic diversification. The review further evaluates existing biosecurity policies, diagnostic challenges, and disease management strategies within both captive and wild avian contexts. Given PBFD’s dual status as a veterinary concern and a growing conservation threat, strengthening international surveillance, regulating wildlife trade, and integrating molecular diagnostics into routine screening are critical priorities. Effective containment of BFDV requires a multidisciplinary approach involving veterinarians, aviculturists, conservation biologists, and policymakers to safeguard the health and genetic viability of endangered psittacine species globally. Full article

The Coronavirus disease 2019 (COVID-19) pandemic had a profound global impact, yet children exhibited distinct clinical and epidemiological patterns compared to adults. Pediatric cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were generally characterized by milder disease, lower hospitalization rates, and few long-term sequelae. However, a subset of children developed severe complications such as multisystem inflammatory syndrome in children (MIS-C), highlighting the heterogeneity in disease presentation. Differences in immune system maturity and comorbidities likely contribute to the age-dependent manifestation of SARS-CoV-2 and other respiratory viruses. Persistent SARS-CoV-2 infection, particularly in immunocompromised individuals, has been implicated in the emergence of new viral variants with immune escape characteristics due to ongoing viral replication in the presence of selective pressure. While SARS-CoV-2 evolution in persistently infected adults has been well-documented, it is less clear how the virus evolves during persistent infection in the pediatric population. To address this question, we performed viral whole genome sequencing of longitudinal specimens collected from immunocompetent and immunocompromised pediatric COVID-19 patients. Similarly to what has been observed in adult cohorts, mutations associated with enhanced viral fitness and immune escape arose intra-host over time. Intra-host diversity accumulated at similar rates in immunocompetent and immunocompromised children, though more mutations overall were observed in the immunocompromised cohort due to the longer infection time courses. Overall, we identified similar viral evolutionary trends over the course of infection despite clinical differences in pediatric COVID-19 manifestation and severity. This similarity suggests that persistent infection in children may be an additional, but not unique, source of ongoing viral diversification. Full article

Background: The TGACG-BINDING FACTORS (TGA) gene family, a key subgroup of bZIP transcription factors, mediates plant stress responses and developmental processes by binding to the as-1 cis-element in target gene promoters to regulate transcriptional activation or repression. Despite its functional significance, systematic characterization of TGA genes in cotton (Gossypium spp.) remains insufficient. Methods: In this study, we performed a comprehensive genome-wide identification and phylogenetic analysis of TGA members across 10 Gossypium species and verified the functions of candidate genes using VIGS technology. Results: A total of 74 TGA homologous genes with conserved DOG1 and bZIP domains were identified. Evolutionary analysis revealed that the cotton TGA gene family can be classified into five distinct branches, suggesting functional diversification. Functional prediction analyses indicated these genes in cotton growth regulation and stress adaptation, potentially through hormone-mediated signaling pathways. Expression profiling demonstrated both tissue-specific expression patterns and salt-stress responsiveness in Gossypium hirsutum TGA genes, and GhTGA2 exhibited the most significant up-regulated expression under salt stress. Virus-induced gene silencing (VIGS)-mediated GhTGA2 silencing significantly reduced the salt tolerance in cotton. Conclusions: The TGA gene family is involved in regulating cotton growth, development, and stress responses, and plays a critical role in mediating salt stress tolerance in cotton. Our results provide mechanistic insights into cotton stress adaptation and establish a valuable genetic resource for developing elite salt-tolerant cotton cultivars, with direct implications for sustainable cotton production. Full article

Background/Objectives: The TOPLESS (TPL) and TOPLESS-related (TPR) proteins represent a highly conserved class of transcriptional co-repressors in plants, playing pivotal roles in modulating growth, development, and stress responses through the repression of key transcriptional regulators. However, a comprehensive genome-wide analysis of the TPL/TPR gene family and its involvement in stress responses remains unexplored in cotton. Methods: In this study, 60 TPL/TPR genes were identified from the genomes of ten Gossypium species via bioinformatics approaches, and their protein physicochemical properties, gene structures, phylogenetic relationships, cis-regulatory elements, and expression profiles were characterized. Results: Chromosomal localization and collinearity analyses revealed that segmental duplication events have contributed to the expansion of the TPL/TPR gene family. Further examination of exon–intron architectures and conserved motifs highlighted strong evolutionary conservation within each TPL/TPR subgroup. Expression profiling demonstrated that TPL/TPR genes exhibit tissue-specific expression patterns, with particularly high transcript abundance in floral organs (e.g., petals and stigmas). Cis-element analysis suggested their potential involvement in multiple stress-responsive pathways. Notably, GhTPL3 showed high constitutive expression across various tissues and under stress conditions, with the most pronounced up-regulation under salt stress. Functional validation via Virus-Induced Gene Silencing (VIGS) confirmed that GhTPL3 silencing significantly impairs cotton salt stress tolerance, underscoring its critical role in abiotic stress adaptation. Conclusions: Our findings provide novel insights into the functional diversification and regulatory mechanisms of the TPL/TPR family in cotton, offering a valuable genetic resource for breeding stress-resilient cotton varieties. Full article

Potyviruses (family Potyviridae, genus Potyvirus), including emerging ones, pose a growing threat to cucurbit production. This study presents the first virome analysis of severely symptomatic cucurbits in continental Croatia, combining high-throughput sequencing (HTS) and RT-PCR diagnostics. Zucchini, cucumber, and butternut squash plants with severe virus-like symptoms sampled in 2021–2022 were found to consistently host a complex of potyviruses, including watermelon mosaic virus (WMV), zucchini yellow mosaic virus (ZYMV), and Moroccan watermelon mosaic virus (MWMV)—the latter being newly reported in Croatia and representing likely its northernmost detection in Europe. Phylogenetic analysis classified WMV isolates as emerging strains of subgroup EM3 and ZYMV as subgroup A1, consistent with European lineages. Croatian MWMV isolates formed a distinct subclade within the Mediterranean group, raising questions about its diversification trajectory. The findings highlight the expanding range of MWMV and underscore the value of HTS for early detection of emerging threats. These results have critical implications for cucurbit disease management, indicating the need to re-evaluate resistance claims in commercial cultivars and implement stricter phytosanitary surveillance in Croatia. The potential role of climate change in facilitating virus spread via aphid vectors is discussed, warranting further risk assessment and international monitoring efforts. Full article

African swine fever virus (ASFV), the causative agent of African swine fever (ASF), poses a catastrophic threat to global swine industries through its capacity for immune subversion and rapid evolution. Multigene family genes (MGFs)-encoded proteins serve as molecular hubs governing viral evolution, immune evasion, cell tropism, and disease pathogenesis. This review synthesizes structural and functional evidence demonstrating that MGFs-encoded proteins suppress both interferon signaling and inflammasome activation, while their genomic plasticity in variable terminal regions drives strain diversification and adaptation. Translationally, targeted deletion of immunomodulatory MGFs enables the rational design of live attenuated vaccines that improve protective efficacy while minimizing residual virulence. Moreover, hypervariable MGFs provide strain-specific signatures for PCR-based diagnostics and phylogeographic tracking, directly addressing outbreak surveillance challenges. By unifying virology with translational innovation, this review establishes MGFs as priority targets for next-generation ASF countermeasures. Full article

Porcine reproductive and respiratory syndrome virus (PRRSV) poses a significant economic challenge to Japan’s swine industry. This review synthesizes the epidemiological evolution of PRRSV in Japan by examining the available scientific literature from its initial Type 2 isolation in 1993 to recent events. Endemic Type 2 strains, initially dominated by Cluster III (Lineage 4), have diversified significantly. This diversification was marked by key events including the emergence of vaccine-associated Cluster II (Lineage 5) and incursions of virulent Cluster IV/Lineage 1F (MN184A-like) strains and Type 1 virus around 2008. By 2018–2020, Clusters II and IV predominated nationwide, a trend strongly linked to widespread modified live virus (MLV) vaccination. The recent detection of the globally significant NADC34-like (Lineage 1A) strain underscores ongoing foreign incursion risks. Current MLV vaccines face challenges, including safety concerns and limited cross-protection against diverse field strains. Consequently, effective control requires integrated strategies, comprising optimized vaccination, stringent biosecurity, advanced molecular surveillance, improved diagnostics, and coordinated regional control programs guided by systematic herd classification and stakeholder partnerships. The development of next-generation vaccines and sustained multi-stakeholder collaboration are critical for mitigating the impact of PRRSV in Japan. Full article

Porcine Epidemic Diarrhea Virus (PEDV) was introduced in the United States (U.S.) in 2013, spreading rapidly and leading to economic losses. Two strains, S-INDEL and non-S-INDEL, are present in the U.S. We analyzed 313 genomes and 556 Spike protein sequences generated since its introduction. PEDV case numbers were highest during the first two years after its introduction (epidemic phase), then declined and stabilized in the following years (endemic phase). Sequence surveillance was higher during the initial epidemic phase. Our results suggest the non-S-INDEL strain is the predominant strain in U.S. The non-S-INDEL sequences exhibit pairwise nucleotide identity percentages above 97.6%. Most non-S-INDEL sequences sampled after 2017 clustered into two sub-clades. No descendants derived from other clades present in the epidemic period were detected in the contemporary data, suggesting that these clades are no longer circulating in the U.S. The two clades currently circulating are restricted to two respective geographic regions and our results suggest limited inter-regional spread. This insight helps determine the risk of re-introduction of PEDV if it were regionally eliminated. Ongoing molecular surveillance is essential to confirming that some older clades no longer circulate anymore in the U.S., mapping the distribution and spread of recent clades, and understanding PEDV’s evolutionary diversification. Full article

The B3 transcription factor superfamily, crucial for plant growth and stress adaptation, remains poorly characterized in cucumber (Cucumis sativus), a globally important vegetable crop. Here, we conducted the first genome-wide identification of 52 B3 superfamily genes in cucumber, classifying them into LAV, ARF, RAV, and REM subfamilies through integrated phylogenetic and structural analyses. These genes exhibited conserved B3 domains with lineage-specific motif architectures and diverse exon–intron organizations, particularly within the structurally divergent REM subfamily. Collinearity analysis revealed segmental duplication as a key driver of family expansion, notably between syntenic REM clusters on chromosomes 2 (CsREM5-7) and 6 (CsREM18-20). Promoter cis-element profiling identified enrichment in hormone-responsive and stress adaptation motifs, suggesting functional diversification in signaling pathways. Furthermore, tissue-specific expression divergence was observed across 10 organs, with ARF members displaying broad regulatory roles and REM genes showing apical meristem enrichment. Strikingly, CsRAV8 exhibited glandular trichome-specific expression, a novel finding, given Arabidopsis RAVs’ lack of trichome-related functions. Spatial validation via in situ hybridization localized CsRAV8 transcripts to trichome glandular head cells. Functional investigation using virus-induced gene silencing (VIGS) demonstrated that CsRAV8 suppression caused significant glandular trichome shriveling, implicating its role in maintaining glandular cavity integrity. This study provides the first comprehensive genomic inventory of B3 transcription factors in cucumber, providing evolutionary insights and functional frameworks for future functional genomics studies. Full article