Irkut virus (IRKV) is a member of genus Lyssavirus, which leads to fatal encephalitis in humans and is primarily found in bats and dogs that transmit the virus to humans via bites/saliva. Most cases have been reported in Russia and in Siberia and recently in China. Whole genome sequencing has shown a number of codon changes in antigenic sites common to the Rabies vaccine reducing cross-protection, which makes IRKV a serious public health threat because of its high fatality. In this study, a multi-epitope vaccine against the IRKV glycoprotein was designed via reverse vaccinology approach. Seven B-cell, seven MHC-I, and seven MHC-II epitopes were selected. These epitopes have predicted HLA binding affinity and are non-allergen, and 12 out of 21 epitopes were fully conserved across the three circulating IRKV strains, whereas remaining nine carried out one or two substitutions. The chosen epitopes covered 99.57
Getah virus (GETV) is a mosquito-borne alphavirus (family Togaviridae) that poses a significant threat to the swine industry by causing reproductive disorders in sows and neurological symptoms in piglets. In this study, a GETV strain, designated HN-2025, was isolated from a commercial pig farm in Hunan Province, China, during a clinical outbreak. The isolate induced typical cytopathic effects (CPE) in BHK-21 cells, including cell rounding, shrinkage, and detachment. The complete genome of HN-2025 was determined to be 11,689 nucleotides (nt) in length and exhibited the canonical genomic organization of GETV: 5’ untranslated region (UTR), nonstructural proteins (nsP1-nsP4), structural proteins (C, E3, E2, 6 K, E1), and 3’ UTR. Sequence homology analysis revealed that HN-2025 shared the highest nucleotide identity (98.6
Zucchini yellow mosaic virus (ZYMV) is a major pathogen that negatively affects cucurbit crops. To elucidate the molecular characteristics and evolutionary dynamics of ZYMV in China, ZYMV was isolated from Cucurbita and Luffa samples collected from plants exhibiting typical yellow mosaic symptoms in Tai’an, Shandong Province, and its complete genome sequence was determined. Using reverse transcription PCR combined with rapid amplification of cDNA ends, the full-length genome sequences of two isolates obtained from Luffa and Cucurbita (ZYMV-sg, GenBank accession no. PV007922; ZYMV-ng, GenBank accession no. PV007923) were determined. Both genomes were 9,592 nt in length (excluding the poly(A) tail). The genomes encoded a polyprotein of 3,080 amino acids and exhibited a genomic organization typical of members of the family Potyviridae. Phylogenetic analysis revealed that both isolates were most closely related to Chinese isolates and formed a distinct subclade within the major group B-I. Recombination analysis identified specific recombination events in ZYMV-ng, indicating that genetic recombination contributed to the molecular evolution of ZYMV. Further analyses suggested that purifying selection played a dominant role in shaping ZYMV evolution. These findings provide important molecular insights into the genomic structure, phylogenetic relationships, and sequence evolution of ZYMV isolates from Cucurbita and Luffa in China and provide a basis for further research on virus–host interactions and the development of targeted disease control strategies.
Begomoviruses are one of the most genetically diverse plant-infecting DNA viruses. They significantly limit chilli (Capsicum annuum L.) production in tropical and sub-tropical areas. Their evolution is largely influenced by recombination and mixed infections. However, the relationship between genetic diversity and selection pressure in natural populations of chilli-infecting begomoviruses remains poorly understood. We collected chilli plants showing leaf curl disease symptoms from Bargarh district, Odisha, India, and tested them for begomovirus presence. Molecular analysis showed the presence of chilli leaf curl Ahmedabad virus (ChiLCAV), tomato leaf curl Joydebpur virus (ToLCJoV), and an associated betasatellite, tomato leaf curl Joydebpur betasatellite (ToLCJoB). Recombination analysis revealed multiple statistically significant recombination events in both begomovirus genomes and the betasatellite. To assess broader patterns of genetic diversity and selection, the newly generated sequences were analysed alongside publicly available sequences retrieved from the NCBI virus database. These comparative analyses revealed high haplotype diversity and a high number of segregating sites, whilst most coding regions showed strong purifying selection, with only a small number of sites showing evidence of episodic diversifying selection. These findings indicate that mixed infections can provide opportunities for recombination and the generation of genetic variation, whereas strong purifying selection constrains changes in functionally important coding regions. The combined action of recombination and selection, therefore, appears to shape the genetic diversity and evolutionary stability of chilli-infecting begomoviruses. To the best of our knowledge, this is the first report of a mixed infection involving ChiLCAV, ToLCJoV, and ToLCJoB associated with chilli leaf curl disease in India, providing new insights into the evolutionary dynamics of begomovirus complexes infecting chilli.
Bovine leukemia virus (BLV) is an oncogenic deltaretrovirus that establishes lifelong infection in cattle and may progress from asymptomatic carriage to persistent lymphocytosis (PL) and lymphoma. Although adaptive immune alterations have been widely studied, the stage-specific transcriptional landscape of innate immunity in BLV infection remains incompletely defined. In this study, we performed a targeted innate immune transcriptomic analysis using RNA-seq data derived from 18 Holstein dairy cows selected from a screened population of 130 animals in Querétaro, Mexico. Animals were classified into three groups based on serology, proviral load, and hematological criteria: BLV-seronegative controls (n = 5), asymptomatic BLV-infected cattle (AL), and BLV-infected cattle with PL. Total peripheral blood leukocytes were subjected to RNA extraction and sequencing on the Illumina NovaSeq platform. Differential gene expression analysis was conducted using DESeq2 with significance defined as adjusted P-value (padj) < 0.05 and |log2 fold change|≥ 1. A curated panel of innate immune-related genes encompassing pattern recognition receptors, interferon signaling, inflammatory mediators, inflammasome components, and cytotoxic effectors was analyzed. Comparison between Control and Asymptomatic cattle identified 8 genes that were significantly altered (padj < 0.05). Asymptomatic animals demonstrated upregulation of antiviral and immune-regulatory genes, including EIF2AK2 (log2FC = 1.10, padj = 0.011), KLRK1 (log2FC = 0.98, padj = 0.009), and IL18 (log2FC = 0.77, padj = 0.015), indicating activation of interferon-associated and inflammatory pathways. Marked upregulation of TNFRSF13C (log2FC = 3.25, padj = 0.046) and TNFAIP3 (log2FC = 2.03, padj = 0.049) suggests modulation of B-cell survival signaling and NF-κB regulatory control. In contrast, NCR1 (log2FC = − 1.04, padj = 0.044), LMX1B (log2FC = − 0.80, padj = 0.030), and TNFSF12 (log2FC = − 0.78, padj = 0.044) were downregulated, reflecting selective adjustment of cytotoxic and TNF superfamily pathways. PL animals exhibited broader innate immune transcriptional alterations consistent with sustained inflammatory activation. These findings demonstrate that asymptomatic BLV infection is characterized by controlled activation of antiviral and regulatory innate immune pathways, whereas disease progression toward PL is associated with expanded inflammatory reprogramming. Stage-specific innate immune signatures may therefore contribute to viral persistence and clinical outcome in BLV-infected cattle.
