Chili leaf curl virus (ChiLCV) is a Begomovirus chillicapsici that is one of the most devastating viruses impacted on the production of chili in the world, especially in South Asia. In the present study, we combined high-throughput computational genomics with experimental analysis of global diversity. A workflow was created using automated Python scripts to download, curate and process ChiLCV genomes from public database. About 410 complete ChiLCV genomes download from public databases. Using a phylogenetic approach, these isolates were subdivided into 34 strains, belonging to 10 major clades, showing significant genetic diversity. Geographic analysis revealed that Pakistan (207 isolates) and India (148 isolates) were the main sources of ChiLCV diversity and the remainder of the isolates were from Oman, Bangladesh, Iran, Saudi Arabia and Sri Lanka. Recombination was observed as a major evolutionary force as more than twenty recombination events were detected. Analysis of cis-regulatory elements showed a complex structure of the viral promoter, including multiple binding sites for transcription factors, hormone-response elements, light-responsive elements, and stress-responsive elements, indicating a high number of interactions between viral regulatory elements and host signaling pathways. Pangenome analysis showed the presence of a highly dynamic open pangenome made up of strain-specific orthologous groups (species-specific orthogroups). Experimental inoculation of chili plants was also carried out to assess the biological effects of infection, along with phytochemical, FTIR, HPLC, and qPCR analyses.
High-throughput sequencing revealed a new emaravirus named clerodendrum yellow blotch virus (ClYBV), infecting Clerodendrum thomsoniae plants in São Paulo State, Brazil. Four genomic RNA segments (RNA1, RNA3, RNA4, and RNA5) were recovered, whereas RNA2 remained undetected. Phylogenetic analysis and pairwise comparisons based on amino acid sequences showed ClYBV is most closely related to redbud yellow ringspot-associated virus (RYRaV, Emaravirus cercidis). No ClYBV particles were observed by transmission electron microscopy in leaf tissues from infected plants. These results support the identification of ClYBV as a new Emaravirus member, though the undetectable RNA2 suggests the isolate may be defective, lacking this segment and unable to produce virus particles. The binomial species name “Emaravirus clerodendri” is proposed.
Tick-borne viruses represent a significant and growing public health concern in Europe. This study investigated the minimum infection rates (MIRs) of tick-borne encephalitis virus (TBEV) and Tribeč virus (TRBV) in Ixodes ricinus ticks collected in Slovakia during 2016–2017 and 2023–2024. A total of 3,686 ticks (3,262 nymphs in 359 pools and 424 adults in 99 pools) from 13 sampling sites were screened for viral RNA. The overall MIRs were 0.38
Adenoviruses (Adenoviridae) and their associated replication-deficient dependoparvoviruses (Parvoviridae) are recognized as significant components of the avian virome. While well-studied in domestic birds, these viruses remain underexplored in wild Antarctic birds. Information is limited on viruses circulating in penguins, particularly outside of the Antarctic Peninsula Region. Here we leverage a fecal sample collected for diet analyses to identify an aviadenovirus (37,731 nt) and two distinct dependoparvoviruses. The Adélie penguin (Pygoscelis adeliae) feces-derived adenovirus exhibits a genome organization consistent with members of the genus Aviadenovirus but shares only 64
In this study, a taxonomically novel avian calicivirus detected and characterized by next generation sequencing, RT-PCR and Sanger sequencing methods in faecal specimen collected from black-headed gull (Chroicocephalus ridibundus) in Hungary. The complete genome length of the calicivirus strain gull/HA15097/HUN/2018 (PZ810127) is remarkably long, 8,845 nucleotides, which had type IV internal ribosomal entry site (IRES) at the 5’, and a stem-loop-II-like (s2m) sequence motif at the 3’ untranslated regions. The VP1 capsid protein had less than 26
We report the complete genome sequence of a novel partitivirus identified from Trichoderma harzianum NFCF092 strain, designated Trichoderma harzianum partitivirus 4 (ThPV4). Unlike canonical members of the family Partitiviridae, which possess a bipartite genome consisting of two double-stranded RNA (dsRNA) segments encoding an RNA-dependent RNA polymerase (RdRP) and a capsid protein (CP), ThPV4 harbors a third dsRNA segment encoding a protein of unknown function. The complete genome consists of dsRNA1 (1,950 bp; encoding the RdRP), dsRNA2 (1,772 bp; encoding the CP), and dsRNA3 (1,629 bp; encoding a protein with unknown function). Sequence analysis shows that each segment possesses a single open reading frame (ORF). The deduced amino acid sequence of the RdRP shows the highest similarity (90.5
The 5′ untranslated region (5′UTR) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains highly conserved stem-loop structures that regulate viral gene expression. This study investigated the functional contributions of selected 5′UTR stem-loop elements to reporter gene expression using a plasmid-based mammalian expression system. Five constructs were tested using a non-integrating plasmid: the wild-type (WT) 5′UTR fused to GFP under the CMV promoter, and four deletion variants (ΔB, ΔC, ΔD, and ΔE) corresponding to deletions of stem-loop 4 (SL4), SL4.5, SL5, and SL5a, respectively. Following transfection into HEK293 cells, GFP fluorescence was quantified using a fluorescence microplate reader, and relative GFP transcript abundance was assessed by RT-qPCR. Deletion of SL4 (ΔB) resulted in marked reduction in both fluorescence and relative transcript abundance compared to WT construct, indicating substantially reduced reporter gene expression. In contrast, deletion of SL4.5, SL5, or SL5a did not produce the pronounced reduction observed for ΔB, although descriptive RT-qPCR analysis indicated differences in relative transcript abundance among these variants. Statistical analysis of fluorescence data demonstrated significant differences among constructs (one-way ANOVA, p < 0.05). Because the reporter assay was based on plasmid expression, the observed differences likely reflect combined contributions from transcription, transcript abundance, RNA stability, and translation rather than translation alone. These findings demonstrate that the SL4 region contributes substantially to reporter gene expression in this experimental system, whereas the remaining stem-loop regions examined exert comparatively modest effects. This study provides additional insight into the functional organization of the SARS-CoV-2 5′UTR and establishes a framework for future investigations aimed at distinguished the transcriptional, post-transcriptional, and translational contributions of individual RNA structural elements.
This study aimed to estimate the prevalence and distribution of HPV in a cohort of vaccinated French women undergoing cervical cancer screening (CCS). Women vaccinated against HPV (either by the bivalent HPV16/18, the quadrivalent HPV6/11/16/18 or the nonavalent HPV6/11/16/18/31/33/45/52/58 vaccine) and for whom a cervical specimen had been collected were included. Detection and genotyping of 32 alpha-HPV genotypes (HPV6/11/16/18/26/31/33/35/39/40/42/43/44/45/51/52/53/54/56/58/59/61/62/66/67/68/70/73/81/82/83/89) was systematically performed (INNO-LIPA, Fujirebio). In a sub-study, high-risk HPV (hrHPV) was detected using two different HPV screening tests, according to the study period. 464 vaccinated women were included. Cytology was normal for 80.6
Clarireedia jacksonii is a phytopathogenic fungus responsible for dollar spot disease in turfgrass worldwide. In this study, we characterized the complete genome sequences of three novel mycoviruses isolated from C. jacksonii isolate MBCT-836 using next-generation sequencing and the fragmented and primer-ligated dsRNA sequencing (FLDS) method. Two of these viruses, designated Clarireedia jacksonii mitovirus 1 (CjMV1) and Clarireedia jacksonii mitovirus 2 (CjMV2), possess positive-sense single-stranded RNA genomes of 2,575 bp and 2,856 bp, respectively. Both viruses contain a single open reading frame that utilizes the mitochondrial genetic code and encodes an RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis placed CjMV1 and CjMV2 within the genera Unuamitovirus and Duamitovirus, respectively, in the family Mitoviridae. The third virus, Clarireedia jacksonii negative-stranded RNA virus 1 (CjNSV1), features a bisegmented negative-sense RNA genome consisting of a large segment (7,961 nt) encoding an RdRp with a conserved Bunya_RdRp domain, and a small segment (1,444 nt) encoding a protein showing homology to bunyavirus nucleocapsid proteins. Phylogenetic analysis revealed that CjNSV1 clusters with members of the proposed family Sclerobunyaviridae within the order Bunyavirales. To our knowledge, this study provides the first report of complete genome sequences of mycoviruses infecting C. jacksonii, expanding our understanding of the mycovirosphere in economically significant turfgrass pathogens.
In recent years, bovine enterovirus (BEV) has been increasingly associated with diarrhea in cattle in China, posing new challenges for disease control in the cattle industry. However, the mechanisms underlying BEV pathogenesis and virulence remain poorly understood. Infectious cDNA clones provide a powerful tool for dissecting viral replication and pathogenic mechanisms. In this study, we generated a full-length infectious cDNA clone of the BEV-F isolate HB19-1. Three overlapping fragments spanning the complete viral genome were amplified by RT-PCR and assembled downstream of a cytomegalovirus (CMV) promoter placed immediately upstream of the 5' untranslated region (5'UTR). To establish a reporter virus system, the green fluorescent protein (GFP) gene was inserted between the 5'UTR and the N terminus of VP4, followed by a 2A cleavage sequence (IKTAG) at the C terminus of GFP. The recombinant rHB19-GFP virus was successfully rescued. Growth curve analysis demonstrated that rHB19-GFP exhibited slower replication kinetics at early time points relative to the parental HB19-1 virus, with no significant difference in their peak viral titers. This GFP-expressing reporter virus enables convenient monitoring of BEV replication and provides a useful platform for antiviral screening. Using this system, we found that 5-(N-Ethyl-N-isopropyl)amiloride (EIPA) inhibited BEV replication, suggesting its potential as an antiviral candidate. Overall, the rHB19-GFP infectious clone developed here offers a practical tool for studying BEV biology and for identifying antiviral compounds against BEV.
The association between Human Pegivirus 1 (HPgV-1, Pegivirus hominis, family Hepaciviridae) with disease etiology remains unclear, yet this virus is widely distributed among people exposed to contaminated blood. This study aimed to identify the prevalence and characterize HPgV-1 genomes obtained from acute febrile patients (n = 92 from 2019) and from blood donors (n = 633 from 2022) sampled in Mato Grosso, Brazil. The serum samples were tested by RT-qPCR for a conserved 5’ UTR region of HPgV-1. Nucleic acid of 28 positive samples was converted to ds-cDNA, purified and sequenced with an Illumina NextSeq platform. The prevalence of HPgV-1 among acute febrile patients was 4.35
Chikungunya virus (CHIKV) is an arthropod-borne virus responsible for an acute febrile illness characterized by severe polyarthralgia, predominantly affecting peripheral joints. In a substantial proportion of patients, these symptoms may progress to chronic manifestations that significantly impair quality of life. Animal models are therefore critical for the development of effective therapeutic and preventive strategies, including antiviral agents and vaccines. In this context, the aim of this study was to establish an experimental model of CHIKV infection using immunocompetent C57BL/6 mice. Animals were infected with CHIKV and subsequently monitored for clinical signs, viremia, viral dissemination across tissues, total leukocyte counts, and susceptibility to reinfection. Results revealed no deaths among the animals during the experimental period, and infected animals exhibited significant viremia as well as detectable viral loads in the popliteal lymph node, femoral bone marrow, and muscle, demonstrating CHIKV capacity to disseminate and reach multiple target tissues. In addition, a global reduction in leukocyte counts was observed in infected mice. Notably, animals previously infected with CHIKV were resistant to reinfection, indicating the establishment of a protective immune response, as evidenced by the presence of neutralizing antibodies. In conclusion, the murine model established in this study recapitulates key features of CHIKV infection and provides a robust platform for investigating viral pathogenesis, as well as for evaluating novel antiviral strategies and vaccine candidates.
Psittacine beak and feather disease virus (PBFDV), currently classified within the species Circovirus parrot, is an infectious agent in avian species, particularly psittacine birds. PBFDV is the causative agent of psittacine beak and feather disease (PBFD), leading to feather loss, deformed beaks and nails, immunosuppression, and high mortality. However, there is limited information on PBFDV in Vietnam, particularly in domesticated parrots. This study aims to detect and molecularly characterize PBFDV in psittacine birds in Northern Vietnam. Among the 193 psittacine birds tested by conventional PCR, 48 were PBFDV-positive, corresponding to a positivity rate of 24.87
Rabies lyssavirus, the causative agent of rabies (acute progressive encephalomyelitis) requires specific receptors on host cell to mediate neurotropism. Typically, cell lines used for rabies vaccine production are devoid of these receptors. In this study, we developed and optimized a protocol for adapting a locally isolated wild type rabies virus belonging to the Arctic-like lineage A1a, to a vaccine producing cell line, quantified its infectious titer using peroxidase-based immunostaining and virus neutralization was assessed using sera obtained from Abhayrab®-vaccinated individuals. The virus was initially propagated in mouse neuroblastoma cell line and gradually adapted to replicate in Vero E6 by serial passages. The adaptation was confirmed by cytopathic effect and the viral titer rose to as high as 1.72 × 107 FFU/mL. This is the first study to provide a detailed documentation of significant and typical cytopathic effect induced by an Arctic-like A1a lineage RABV in Vero E6 cells.
Tilapia lake virus (TiLV) has emerged as an important pathogen that negatively impacts tilapia farming globally. Using RNA sequencing technology, this study investigated the liver transcriptomic profile of apparently healthy and TiLV-infected Oreochromis niloticus from wild. RNA sequence libraries generated 3,356 differentially expressed genes (DEGs), with 1,726 genes that were upregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 680 different pathways with differential regulation of the metabolic and immune-related pathways indicating that TiLV may interfere in host metabolism and replicate to establish the infection. This study provides transcriptomic insights into the liver responses of naturally TiLV-infected wild O. niloticus and highlights key immune and metabolic pathways associated with viral infection.
Atractylodes lancea is an important medicinal crop, but viral diseases have become increasingly severe in recent years. Viruses in the genus Carlavirus are common plant pathogens that are primarily transmitted by aphids and can cause stunted growth and reduced yields in their host plants. In this study, a novel carlavirus, tentatively named Atractylodes virus A (AVA), was identified from A. lancea plants exhibiting virus-like symptoms. The full-length genome of AVA is 8,817 nt in length and contains six open reading frames, displaying the typical genomic organization of the genus Carlavirus. The replicase and CP exhibit 53.43
Alphaviruses, including Mayaro virus (MAYV) and Chikungunya virus (CHIKV), pose a growing public health threat, with increasing reports worldwide and no licensed antiviral treatments available. This study evaluated the antiviral activity of pyridine-3-carbohydrazide (P-3-C) against MAYV (strains BeAr and TRVL) and CHIKV (strain La Reunion, LR). Vero E6 or U-2OS cells were infected and treated with P-3-C for 24 h, and cell viability and replication levels were assessed. The 50
Bacterial wilt caused by Ralstonia solanacearum species complex (RSSC) is a significant threat to agriculture due to the pathogen’s broad host range and persistence in soil. Bacteriophages (phages) are being explored as biocontrol agents, and such strategies are gaining interest. In this study, we isolated and characterized vB_RsoP_HXg1W, a novel phage propagated on R. pseudosolanacearum GMI1000. The phage has a linear double-stranded DNA genome of 40,184 bp with a GC content of 62.3
We report the first complete nucleotide sequence of an isolate of iris yellow spot virus (IYSV; Orthotospovirus iridimaculaflavi) from Brazil. Isolate Br-25 was collected in 2025 in Imbuia, Santa Catarina, from symptomatic onion scapes. The genome of IYSV-Br-25 consisted of L, M and S genomic RNAs of 8879, 4866 and 3223 nt, respectively. Comparison of the L segment nucleotide (nt) sequence showed identities 96
Yams (Dioscorea spp.) are an important vegetatively propagated food security crop grown for their starchy tubers. Yams are susceptible to several viruses, and their genomes harbor a diverse array of endogenous pararetroviral sequences (EPRVs), which complicate diagnostics and germplasm exchange because of their similarity to episomal viruses. To better characterize EPRV diversity, we analyzed 86 publicly available whole-genome sequences from five Dioscorea species (D. rotundata, D. alata, D. praehensilis, D. abyssinica, and D. dumetorum). Assembled genomes were screened for endogenous pararetrovirus sequences (EPRVs) using the CAULIFINDER pipeline, targeting conserved RT/RNase H domains of the Caulimoviridae family. Our analyses revealed four major EPRV groups in D. rotundata: Yendovirus, Badnavirus, Yam Endovirus 1, and a Dioscovirus-like lineage. While most insertions were fragmented, we found full-length putative viral genomes corresponding to the Yam Badnavirus and Dioscovirus-like clades. These findings expand knowledge of yam EPRV diversity, contribute to the development of improved diagnostic tools to differentiate endogenous and episomal forms, and promote a science-based, risk-proportionate approach to yam phytosanitation that facilitates global germplasm exchange while maintaining biosecurity.
