Virus Genes最新文献

Newcastle disease (ND) is a serious poultry disease in Ethiopia. F gene sequences have shown that the velogenic Newcastle disease virus (NDV) sub-genotype VII.1.1 is prevalent in Ethiopia and other East African countries. However, the F gene sequence alone is not enough to fully understand the pathogenicity, antigenicity, and epidemiological characteristics of NDVs. Whole-genome characterizations of currently circulating virus strains are needed to understand the molecular basis of the pathogenicity and antigenicity differences between vaccine and field strains. In this study, we obtained the complete genome sequences of seven NDV sub-genotype VII.1.1 isolated from chicken farms in Ethiopia and compared them with closely related NDVs and vaccine strains. Whole-genome sequencing revealed that all isolates have genome length of 15,192 nucleotides and are composed of six genes in the order 3'-NP-P-M-F-HN-L-5'. Phylogenetic analysis of the whole genomes showed that sub-genotype VII.1.1 can be classified into three distinct lineages and that the Ethiopian isolates in this study clustered within lineage 1. Unique amino acid substitutions were identified in all six genes of the Ethiopian isolates when compared to closely related NDV strains and commonly used vaccine strains. Some of these substitutions have been linked to antigenic variation. Although sub-genotype VII.1.1 is widespread in Ethiopia and other horn of African countries, to the best of our knowledge, this is the first report describing its whole-genome characteristics in this region. The findings in this study are expected to support effective ND control strategies in the region.

Birds have historically served as key vectors for viruses causing significant diseases. Corvid birds, often living in close proximity to livestock, poultry, and humans, provide substantial opportunities for cross-species viral transmission. Such transmission can occur through their feces or via ectoparasites (such as ticks, mites, and fleas) on their bodies, thereby releasing viruses into the environment. Despite the development of viral metagenomics, an increasing number of RNA viruses are being characterized across different species. RNA viruses in birds' gut microbial communities remain poorly studied. Here we report an extensive analysis of an RNA virome in fecal samples from Large-billed crows (Corvus macrorhynchos) and Northern Ravens (Corvus corax), both of which are common Corvus species found in the high-altitude forest and grassland regions of the Qinghai-Tibetan Plateau. This study aims to assess the RNA viruses present in the intestines of these corvids and provides the first comprehensive characterization of the diversity of gut-colonizing viruses in these two crow species.

In this study, we report the discovery of a novel virus, Yunxiao leafhopper virus 1 (YXLeV1), found in the insect vector Recilia dorsalis, a significant pest of rice crop. The complete genome of YXLeV1, consisting of 14,115 bp, was sequenced and analyzed. The whole viral genome shares only 36.32% identity with the RNA-dependent RNA polymerase (RdRp) of Hubei diptera virus 11, belonging to genus Alasvirus. It contains four open reading frames encoding a nucleoprotein (N), a hypothetical protein (p78) of unknown function, a glycoprotein (G), and an RNA-dependent RdRp. The N, G, and RdRp proteins of YXLeV1 share 22.0%, 34.05%, and 36.32% amino acid sequence identity with the corresponding sequence of Hubei diptera virus 11. As per the genus demarcation criteria of the family Xinmoviridae, viruses sharing less than 60% amino acid identity in the RdRp sequence with known members are considered to belong to new genera, so the observed 36.32% identity between YXLeV1 and Hubei diptera virus 11 supports the classification of YXLeV1 as the first member of a novel genus, which we propose to name Recilivirus. Phylogenetic analysis further confirms that YXLeV1 is distantly related to Hubei diptera virus 11, the sole member of the genus Alasvirus, and forms a separate clade supporting its classification as a member of a new genus. Given the ecological significance of R. dorsalis as a vector, this discovery adds to the catalog of viruses associated with this species and contributes to our understanding of virus vector associations.

Hepatitis B Virus (HBV) infection is a global health concern. HBV genotypes differ in disease potential and geographical distribution. These genotypes impact the diagnostic and preventive strategies. Furthermore, limited data are available on Torque Teno Virus (TTV) co-infections with HBV. Hence, this study evaluated HBV infection prevalence, genotype distribution, and the presence of TTV among HBV-positive patients. During the study period, a total of 1820 serum samples were collected and tested for HBsAg using ELISA method. Of this, 43 (2.36%) were HBsAg positive. These HBsAg-positive samples were further subjected to conventional PCR followed by Sanger sequencing for HBV and TTV genotype detection. In this study, only HBV genotypes D (subgenotype D2) (97%) and A (subgenotype A1) (3%) were detected. 15% of HBV-infected patients were positive for TTV in which genotype 1A was detected in 66.67% of cases and 1B in 33.33% of cases. To the best of our knowledge, this study represents the first of its kind from Puducherry to document Torque Teno Virus (TTV) co-infection in HBV-positive cases from the non-renal transplant population. This study underscores the significance of HBV genotypes and TTV co-infection in HBV patients. Further studies and surveillance are needed to monitor circulating HBV genotypes and explore TTV's role in co-infection, particularly its pathogenesis and clinical implications.

The Polymycoviridae family is an expanding group of mycoviruses, generally characterized by atypical capsids and segmented double-stranded (ds) RNA genomes. Polymycoviruses have been associated with various changes in their hosts' traits, such as shifts in spore production, changes in pigmentation, and alterations in growth and virulence, either enhancing or reducing them. Here, we report the complete genome sequence of a polymycovirus identified in an entomopathogenic, fungicolous, and keratinophilic, filamentous ascomycete species Lecanicillium aphanocladii, isolated from a patient with foot dermatophytosis (Tinea pedis). The virus, denominated Lecanicillium aphanocladii polymycovirus 1 (LaPmV1), has six genomic dsRNA segments. Phylogenetic analysis of RNA-dependent RNA polymerase (RdRp) sequences revealed that LaPmV1 is closely related to the previously reported Beauveria bassiana polymycovirus 4. Virus-curing studies revealed that LaPmV1 regulates pigmentation and decreases sporulation in its host while not affecting mycelial growth in vitro. LaPmV1 has also been shown to slightly increase the host's susceptibility to certain common antifungals, including itraconazole, voriconazole, and posaconazole.

Viruses have long been known to infect various arthropod hosts, playing crucial roles in their ecology and evolution. While viral diversity has been well studied in insects, knowledge of viruses in arachnids remains limited. This study investigated the DNA virome of Androctonus mauritanicus (Moroccan black thick-tailed scorpion) to expand our understanding of viral diversity in non-insect arthropods and explore the evolutionary relationships of scorpion-associated viruses. Samples of Androctonus mauritanicus collected from the region of Marrakech, Morocco, were subjected to high-throughput DNA sequencing via the Illumina X Ten platform. After the assembly, a complete circular viral genome of 136,386 bp in size with a GC content of 31.75% was identified that bears protein homology to the Ascovirus and Toursvirus genes and was provisionally named Androctonus mauritanicus toursvirus (AmTV). AmTV genome annotation resulted in 144 predicted ORFs, including proteins involved in DNA replication, gene transcription, protein modification, virus assembly, lipid metabolism, and apoptosis. Phylogenetic analysis revealed that AmTV is basal to the Toursvirus genus of the Ascoviridae family and forms a sister clade with Dasineura jujubifolia toursvirus 2a (DjTV-2a) and Diadromus pulchellus ascovirus 1a (DpTV-1a). Comparative genomic analysis revealed that AmTV shares 97 genes with DjTV-2a (average amino acid identity: 43.72%) and 95 genes with DpTV-1a (average amino acid identity: 44.30%), but the genomic structure of AmTV differs significantly from that of both viruses, indicating that these viruses diverged early in their evolutionary history. These findings imply that toursviruses might infect a wider variety of hosts than previously understood, providing insights into the evolution of the Ascoviridae family. The discovery of the presence of viruses in scorpions, a group of arthropods often overlooked in viral studies, broadens our understanding of host-virus interactions and highlights the importance of expanding viral surveillance to new arthropod and arachnid species.

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.

Human parvovirus B19 (B19V) primarily targets erythroid progenitor cells and is associated with various hematological disorders. However, the detailed mechanisms underlying its life cycle, particularly the viral assembly process, remain largely unknown. In this study, we used in vitro engineered DNA-binding molecule-mediated chromatin immunoprecipitation (in vitro enChIP) to identify host proteins associated with the B19V genome in infected UT7/Epo-S1 cells. Using guide RNAs targeting the viral terminal hairpin region, we successfully enriched viral genomic DNA. Mass spectrometry analysis of the precipitated fractions revealed specific enrichment of desmosomal proteins, including desmoplakin (DSP), desmoglein-1, desmocollin-1, and junction plakoglobin, suggesting that the components of the entire desmosome complex may be associated with the B19V genome. Immunofluorescence microscopy showed that the viral VP2 protein was strongly localized to the extranuclear foci, where it colocalized with DSP. Pull-down assays further demonstrated that VP2, but not VP1, interacted with DSP, indicating that the VP1-unique N-terminal region (VP1u) may inhibit this interaction. Notably, B19V-infected cells displayed reduced cell-cell adhesion and diminished cellular aggregation, implying that these interactions may be involved in the disruption of cell adhesion during infection. These findings revealed a novel mechanism by which B19V exploits the host desmosomal machinery to facilitate viral propagation in infected cells.

In Saudi Arabia, where millions from different countries converge on the holy sites of Makkah and Madina, surveillance of respiratory viruses, especially influenza viruses, is of utmost importance. The influenza B virus (IBV) is constantly changing genetically, which affects vaccine effectiveness and immune evasion. While IBV epidemiology has been studied extensively around the world, little is known about its genetic dynamics in Saudi Arabia. The current study aims to investigate the genetic evolution, antigenic diversity, and potential vaccine mismatches of IBV in Riyadh throughout the 2020-2023 epidemic season. IBV-positive samples underwent whole-HA and NA gene sequencing and phylogenetic analysis. The HA and NA genes were examined for mutations, antigenic site amino acid substitutions, and glycosylation patterns. Divergence was assessed using a comparative examination of vaccination strains. During the three study seasons (winters 2020/21, 2021/22, and 2022/23), 5.26% of participants had confirmed IBV profiles, mostly female children aged 5-12 years. The HA gene contains 118 mutations, 46 of which are amino acid substitutions with significant antigenic site changes. In comparison to the B/Austria/1359417/2021 vaccination strain, 50 mutations were found, including a unique 9-nucleotide deletion. Increased O-glycosylation in Riyadh isolates indicates improved immune evasion. The phylogenetic analysis reveals that all Riyadh isolates (n = 20) belong to the B/Victoria lineage. The major lineage, B/Victoria V1A.3a.2, is consistent with worldwide circulation patterns. IBV in Riyadh shows high genetic drift and antigenic diversity, which may limit vaccine effectiveness. Continuous genomic surveillance is critical for detecting new mutations and directing vaccination updates.

We studied the fate of a gene called ORF8 in different coronaviruses species during their passage to humans. We showed that this gene harbored stop codons in many epidemic SARS-CoV-2 variants in humans and in up to 86% of SARS-CoV-2 circulating in 2023 and therefore could be a non-virulence gene whose disappearance helps the epidemics spread. We questioned whether this is a general phenomenon following coronavirus passage to humans from another species, most often bats. We studied SARS-CoV, SARS-CoV-2, MERS-CoV, and the four coronaviruses endemic in humans for several years or decades and observed gene degradation after species jumps from animals to humans. For SARS-CoV-2, we observed the progressive disappearance of its ORF8 with one or several stop codons and partial or even complete deletions, which is reminiscent of the 'Cheshire cat phenomenon' described in the L. Caroll's Alice's Adventures in Wonderland novel, where a cat gradually disappears to leave only a smile. In viruses that emerged earlier in humans and adapted to this host, only footprints of a few bases remain, but which are significantly associated with the original gene.