Virus Genes最新文献

The complete genomic characterization of two Seoul virus (SEOV) strains of Rattus norvegicus captured in Buenos Aires City in 1983 and 2001 is reported for the first time. The nucleotide and amino acid identities observed between the Argentinian SEOV strains for the coding regions of the S, M, and L segments and their deduced amino acid sequences were similar to those observed between Argentinian SEOV strains and those from other parts of the world. Phylogenetic analyses using the maximum-likelihood method show that the two Argentinian SEOV strains grouped with other strains from Asia, Europe, and the US in two different clades, indicating possible independent introductions in Argentina and more studies are needed to understand the evolution and migratory movements of the SEOV. Human cases of disease have not yet been reported in Argentina, and further eco-epidemiological studies are required in order to analyze the pathogenic potential of the SEOV strains circulating in our country.

Genomic surveillance of respiratory viruses is an expanding field. As of 2024, only 110 (near-) complete genomes of human parainfluenza virus type 2 (HPIV2) were available in GenBank, none being from France. Here we aimed to obtain and analyze HPIV2 genomes from residues of HPIV2 RNA-positive respiratory samples from patients diagnosed in university hospitals of Marseille, Southern France, between 2017 and 2022. Prior to next-generation sequencing (NGS), an in-house PCR-based enrichment strategy was implemented with primers chosen with PrimalScheme. NGS used Illumina technology on a NovaSeq 6000 instrument. HPIV2 genomes were generated from NGS reads by mapping and de novo assembly using CLC Genomics. Mutations were identified by NextClade, and phylogeny was performed by MEGA and NextClade. Seventy-seven near-complete (≥ 90% coverage) genomes and 239 genomes with ≥ 70% coverage were recovered from 318 HPIV2 RNA-positive samples. Two major genotypes, G1a (n = 129 genomes) and G3 (110), were identified, and five subgenotypes, namely G1a.5 (n = 23 genomes), G1a.8 (68), G3.4 (4), G3.5 (7), and G3.7 (23), were newly proposed. Genotype-specific mutations were in the L gene (encoding RNA polymerase) for G1a (T14612A/T11981A/T12374C) and the hemagglutinin-neuraminidase-encoding gene for G3 (G8171A/A14057G/10367G). Subgenotype G3 was only detected in 2019. Subgenotype G1a was absent during the 2021-2022 winter, before becoming majority again during autumn 2022. Although preliminary, this work increased by 70% the number of HPIV2 genomes available worldwide and produced the first genomes from France. It shows an evolution of genotypes, with significant genetic diversity, and of their distribution. It justifies the genomic surveillance of this virus.

Hepatitis B virus (HBV) infection remains a leading cause of chronic liver disease and liver failure worldwide. Although miR-148a-3p has been implicated in liver pathophysiology, its specific role in HBV replication through autophagy-related signaling pathways is not fully understood. This study aimed to investigate the effects of miR-148a-3p on HBV transcription and replication, focusing on its regulation of AMPK/mTOR-dependent autophagy. HepG2.2.15 cells were transfected with miR-148a-3p mimics or inhibitors, with or without the AMPK agonist AICAR. HBV replication markers (pgRNA, HBsAg, HBeAg), autophagy-related proteins (LC3, p62, Beclin-1), and AMPK/mTOR/S6 pathway components were analyzed by Western blotting, ELISA, qRT-PCR, and immunofluorescence. Cell viability was measured using the MTT assay at 12-72-h post-transfection. Overexpression of miR-148a-3p increased pgRNA, HBsAg, and HBeAg production (P < 0.01), enhanced autophagy as indicated by elevated Beclin-1 and LC3-II with reduced p62 (P < 0.01), activated AMPK, and inhibited mTOR and S6 phosphorylation (P < 0.01). In contrast, miR-148a-3p knockdown reduced HBV replication and autophagy, effects that were partially reversed by AICAR treatment (P < 0.01). miR-148a-3p promotes HBV transcription and replication by inducing autophagy via AMPK activation and mTOR/S6 suppression. These findings provide mechanistic insight into HBV pathogenesis and identify miR-148a-3p as a potential therapeutic target for regulating HBV replication and autophagy.

This study was conducted to ascertain the positive incidence, genogrouping, and amino acid variations in the VP1 gene of chicken infectious anaemia virus (CIAV) among layer flocks in Gujarat, India. A single pooled sample was collected from each of the 32 farms visited, all of which had a history and post-mortem lesions suggestive of chicken infectious anaemia (CIA) across five districts of the state. Samples were processed, and CIAV was confirmed by PCR targeting the VP3 gene and genogrouped. In histopathological examination, generalised lymphoid atrophy with prominent lymphocyte depletion was observed in both the cortex and medulla of the thymus and bursa of Fabricius. Out of the total 32 pooled tissue samples, 21 (65.63%) tested positive for the presence of CIAV. The effect of vaccination on disease prevention was found to be nonsignificant, as all five vaccinated flocks (100%) tested positive. Upon phylogenetic analysis, these isolates were found to be virulent and of genogroup IIIb (sub-clade G-II-b of clade G-II), but distant to strains of genogroup IIIa and II. The notable amino acid difference of C149M/E was similar to the change reported from South India in 2022. Amino acids were different from IIIa strains at V75I, L125I, K139Q, S287A, and G370S positions, Cux-1 vaccine at V157M, S287T, and G370S, and group I strains at L125I positions. The possession of virulence-determining amino acids, variations from vaccine strains and IIIa field strains, and divergence from other Indian strains might be the cause of escape from vaccinal immunity.

In the present study, the full-genome sequence of a novel potyvirus, provisionally named "Sauropus androgynus potyvirus 1" (SAPV1), was determined using a combination of high-throughput sequencing (HTS) contig assembly, reverse transcription polymerase chain reaction (RT-PCR), and rapid amplification of cDNA ends (RACE) PCR. The full-genome sequencing of SAPV1, excluding the 3' poly(A) tail, was 10,365 nucleotides long and encoded a large polyprotein comprising 3,315 amino acids. Maximum likelihood phylogenetic analysis based on the multiple sequence alignment of the polyprotein sequence revealed that SAPV1 clustered with the genus Potyvirus as a monophyletic clade, with its closest evolutionary relative being the Plum pox virus (PPV). BLAST searches revealed that the polyprotein sequence of SAPV1 shares the highest amino acid sequence identity of 45.6% with known viruses, with the highest being PPV. According to the species demarcation criteria of the family Potyviridae and the phylogenetic analysis, we propose that SAPV1 represents a novel member of the genus Potyvirus, infecting Sauropus androgynus, a plant widely used in medicine and the food industry.

The complete genome sequence of a baculovirus isolated from larvae of the Virginia pine sawfly, Neodiprion pratti pratti, was determined from sequence data generated from two isolates of this virus obtained from virus-killed larvae harvested during a N. pratti pratti outbreak in Maryland, Virginia, and North Carolina, USA, during the 1950s. Sequence assembly and analysis of this virus, Neodiprion pratti pratti nucleopolyhedrovirus (NeppNPV), revealed a circular genome of 81,658 bp. BLASTp queries with the 89 ORFs annotated for NeppNPV indicated a close relationship with Neodiprion lecontei nucleopolyhedrovirus (NeleNPV). Pairwise nucleotide distances and phylogeny determined from alignments of baculovirus core gene homologs indicated that NeppNPV and NeleNPV are both members of species Gammabaculovirus nelecontei. NeppNPV and NeleNPV were distinguishable by differences in ORF content and indels suggestive of intramolecular recombination. Overlapping geographic ranges and shared host plants for N. pratti pratti and N. lecontei suggest the potential for cross-infections of larvae of these two sawfly species with NeppNPV and NeleNPV.

Celavirus is a genus within the family Potyviridae, currently comprising a single recognized species, Celavirus apii, represented by celery latent virus (CeLV), and one additional potential member, Striga-associated poty-like virus 2 (SaPlV2). The Celavirus genome is highly divergent from those of other potyvirids, and its polyprotein architecture remains incompletely resolved. In this study, we conducted systematic mining of publicly available transcriptome datasets and identified eight novel celavirus-like viral genome contigs from five distinct sources, including Chrysanthemum × morifolium, Leucadendron linifolium, L. muirii, Dalzellia ubonensis, and mycorrhizal protocorms formed by Serapias vomeracea and Tulasnella calospora. Based on sequence comparisons and species demarcation criteria, these genome contigs likely represent four novel viral species. Phylogenetic analysis placed all novel viruses in a monophyletic clade with CeLV and SaPlV2, distinct from all other approved genera in the family Potyviridae. Conserved functional domains typical of potyvirid polyproteins, including CI, NIa-Pro, and NIb, were identified, whereas other canonical domains such as P1, HC-Pro, and CP were not detected, likely due to high sequence divergence. These findings expand the known diversity of Celavirus and offer new insights into its genome organization, host associations, and evolutionary position within the Potyviridae.

This study investigates the potential pathogens associated with joint swelling, yellow exudates, and scab formation near the joints and eyelids in adult white racing pigeons.Pooled samples of scab and swab were collected and subjected to molecular, microbiological, and histopathological analyses. Initial screening focused on the detection of poxvirus using polymerase chain reaction (PCR). Subsequently, next-generation sequencing (metagenomic sequencing) using the Illumina MiSeq platform was performed, followed by virus isolation in embryonated specific pathogen-free chicken eggs and Vero cells, along with histopathological examination.Polymerase chain reaction (PCR) analysis for pigeon pox virus did not produce the expected amplicons, indicating a negative result for this virus. However, metagenomic sequencing identified the complete genome of Pigeon Torque Teno Virus (PTTV), with a genome size of 1574 nucleotides. Comparative sequence analysis revealed a nucleotide sequence similarity of 96.47%-97.7%, with the highest identity to a Canadian PTTV genome previously detected in the Bursa of Fabricius of a dead pigeon. Genome annotation identified two open reading frames (ORFs): encoding replication-associated protein and viral capsid protein. The presence of PTTV was further confirmed through real-time PCR and virus isolation in embryonated SPF chicken eggs and Vero cell cultures.The present study marks the first identification of PTTV in white racing pigeons with joint, ocular, and pock-like lesions. Although pigeon pox virus (PPV) was not detected, the findings suggest that PTTV could be an emerging avian pathogen necessitating further investigation into its pathogenicity, transmission dynamics, and clinical significance in pigeons.

Orbiviruses are emerging pathogens of public and veterinary health concern. This study reports the discovery and genomic characterization of a novel orbivirus in adult ticks collected from African savanna elephants (Loxodonta africana) in Kafue National Park, Zambia. Six ticks were identified through genetic analyses; one Rhipicephalus maculatus and five Amblyomma tholloni. Salivary gland and blood meal samples were dissected for virus characterization. Total nucleic acids were extracted and reverse-transcribed, and libraries were prepared for deep sequencing. De novo assembly of trimmed sequences recovered four novel viruses designated "zaloxo" to indicate their association with Zambian elephants (genus Loxodonta), abbreviated ZXLV-1 to ZXLV-4. ZXLV-1, a member of the genus Orbivirus, belongs to the same subclade of dsRNA orbiviruses as bluetongue virus, epizootic hemorrhagic disease virus, and African horse sickness virus. ZXLV-2 and ZXLV-3 are most closely related to dsRNA Totiviridae and ssDNA Circoviridae viruses, respectively. ZXLV-4 belongs to the genus Alphapolyomavirus, dsDNA viruses which are ubiquitous in mammals but have unclear associations with disease. While the pathogenicity of these viruses remains unclear, these results suggest that a hidden diversity of viruses likely exists in elephant ectoparasites, warranting attention from the perspective of both health and conservation.

Papillomaviruses (PVs) are small, non-enveloped viruses with double-stranded circular DNA genomes that infect a wide range of hosts, including mammals, birds, reptiles, and fish. While human papillomaviruses are extensively studied, recent advancements in high-throughput sequencing techniques have increased the detection and genetic characterization of PVs from various animal species. Here, we describe the identification and whole-genome characterization of a divergent equine papillomavirus (EcPV) detected through a viral metagenomic investigation of a horse in Denmark exhibiting neurological signs. Using Nanopore sequencing and Sanger sequencing, we assembled a complete viral genome of 7767 nucleotides. Phylogenetic analysis, based on concatenated E1, E2, L2, and L1 gene sequences, showed that the identified virus clustered within the same clade as EcPV3 (genus Dyoiotapapillomavirus) and EcPV6 (genus Dyorhopapillomavirus) but was situated on a distinct separate branch. Comparative genome analysis revealed approximately 52% nucleotide sequence similarity to EcPV3 and EcPV6, which share 66% similarity with each other. The L1 gene, commonly used for papillomavirus classification, exhibited a sequence identity to EcPV3 (58.4%) and EcPV6 (60.0%). The other viral genes displayed a 39-62% identity to the respective genes from EcPV3 and 6 further supporting the divergence of this newly identified PV. The combination of the phylogenetic analysis and the genetic divergence suggests that this newly identified papillomavirus may constitute a novel species or genus within the Papillomaviridae family. Our findings expand the known diversity of equine papillomaviruses and contribute valuable insights into their evolutionary relationships.