The viral coat protein (CP) is a major antigenic determinant and represents a key genomic region for classification and comparative analysis. Accordingly, CP-based detection and comparative studies are widely used. While genetic variation in the CP coding region of satsuma dwarf virus (SDV) has been investigated, sequence substitutions in isolates obtained after graft transmission and propagation in a new host plant were not characterized. In this study, SDV isolates derived from Citrus reticulata ‘Ohta Ponkan’ (SDV-Oh) and Citrus unshiu ‘Aoshima unshiu’ (SDV-Ao) were used as virus donors and transmitted to multiple citrus cultivars via double grafting using new shoots and seedlings. Sequences of the CP coding region were characterized and compared with those of the donor viruses. All isolates exhibited sequence differences from the donor viruses, including both synonymous and nonsynonymous substitutions. Notably, identical nucleotide substitutions at the same genomic positions were consistently observed across all isolates, whereas no host cultivar-dependent substitutions were detected. Nucleotide diversity was comparable to that reported for other citrus viruses and members of the family Secoviridae. To assess the potential effects of these substitutions, structural and epitope analyses were conducted. Most substitutions were located in structurally flexible regions, and no substantial changes in the overall CP structure were predicted. Moreover, predicted epitope regions were conserved, and none of the amino acid substitutions occurred within these regions. These results indicate frequent site-specific substitutions in the SDV CP coding region irrespective of host cultivar following graft transmission, while structural and antigenic features remain conserved.
Dengue, chikungunya and Zika (DCZ) viruses co-circulate necessitating the need for development of multiplex real-time RT-PCR assays to enable simultaneous early differential diagnosis. In the present study, we developed a multiplex real-time RT-PCR assay for detection of DCZ viruses using β-actin gene as an internal control for verification of RNA extraction efficiency and assess PCR inhibition. Limit of detection (LOD) was tested using virus stocks with known plaque-forming units (PFU/ml). Cross reactivity was tested using related viruses. The assay was validated using both DCZ virus-positive and -negative clinical samples (DENV, n = 257; CHIKV, n = 113; ZIKV, n = 4; negative, n = 220) and Quality Control for Molecular Diagnostics (QCMD) proficiency panels covering the years 2022 to 2025. Sequence conservation in the primer- and probe-binding regions was assessed using in silico inclusivity analysis. No cross reactivity was observed with related flaviviruses, respiratory viruses, bacterial and protozoan pathogens that cause acute febrile illness. The 95
Rotavirus (RV) type A is a leading cause of severe infantile gastroenteritis globally. Studies show that prostaglandin E2 (PGE2) levels increase during RV infection, enhancing viral attachment and internalisation. However, the underlying mechanism for the increased PGE2 levels remains unclear. Using a plasmid-based reverse genetics system, we engineered a recombinant RV carrying mutations in the viroporin domain of NSP4 that decreased cytoplasmic calcium (Ca2+) conductivity. This resulted in decreased cytoplasmic phospholipase A2 (cPLA2) activity, the rate-limiting enzyme in PGE2 biosynthesis, and subsequently reduced PGE2 levels and viral yield. These findings are consistent with RV-induced PGE2 production occurring in a NSP4-cyto[Ca²⁺]-cPLA2-dependent manner.
Rhabdoviruses are highly diverse RNA viruses that cause substantial economic losses in both wild and farmed fish populations. In this study, we determined the complete genome sequence of the snakehead rhabdovirus - Indian strain (SHRV-In), originally isolated from diseased snakehead fish with clinical symptoms of surface ulceration and high mortality. The viral genome is 11,550 nucleotides (11.55 kb) in length and contains 69 putative open reading frames (ORFs). Among these, six major ORFs are predicted to encode functional proteins, including RNA-dependent RNA polymerase (L), matrix protein (M), glycoprotein (G), non-virion protein (NV), phosphoprotein (P), and nucleoprotein (N), which are arranged in the conserved order of 3′–N–P–M–G–NV–L–5′. Comparative genomic analyses, including multiple sequence alignment, phylogenetic reconstruction, mutation identification, analysis of transcription signals, identification of conserved domains and comparative analysis of Untranslated regions (UTRs) revealed that SHRV-In shares significant homology with related fish rhabdoviruses but exhibits distinct genetic divergence from other snakehead rhabdovirus isolates. The whole genome exhibits a 96.11
The nearly complete genomes of a new paramyxovirus (Piscisplanusvirus hippoglossi, PpH) and a new rhabdovirus (Rhombovirus hippoglossi, RoH) were obtained from Atlantic halibut fry suffering mortalities during start feeding and weaning to dry feed. The genome of the paramyxovirus is 15,159 nucleotides in length and consists of eight putative genes coding for nucleoprotein (N), putative unknown protein (U1), phospho-protein (P), cysteine-rich protein (V), matrix protein (M), fusion protein (F), hemagglutinin-neuraminidase protein (HV), and large polymerase protein (L). The gene junctions have conserved transcription start and stop signal sequences and intergenic regions. Comparisons of the amino acid sequences and phylogenetic analyses using the L protein sequence show that PpH represents a putative new genus within sub-family Feraresvirinae. The genome of the rhabdovirus is 11,140 nucleotides long and consists of the canonical N-P-M-G-L proteins found in other rhabdovirus, in addition to a putative ORF encoding an unknown protein (U1). The transcription termination and the start sequences are conserved in the genome and separated by four nucleotide intergenic sequences. Based on analyses of amino acid sequences RoH belongs within Alpharhabdovirinae constituting a putative new genus, Rhombovirus. This is the first description of a paramyxovirus and a rhabdovirus obtained from Atlantic halibut (Hippoglossus hippoglossus). The rhabdovirus (RoH) is associated with liver pathology while it has not been possible to identify any pathology associated with the paramyxovirus. Both viruses are present in start-feeding larvae and larvae during weaning to dry feed in tanks with mortalities.
