Virus Genes最新文献

The complete genome sequence of Orthotospovirus tomatozonae (tomato zonate spot virus, TZSV) isolated in Japan was determined and compared with that of Chinese isolates. The lengths of the S, M, and L segments of the RNA genomes of the Japanese isolate (TZSV-TZ1-3) were 3194, 4675, and 8916 nucleotides, respectively, which were similar to the Chinese isolates. Moreover, the eight motifs on the RNA-dependent RNA polymerase (RdRp) gene were conserved in both TZSV-TZ1-3 and Chinese TZSV isolates (TZSV-Bidens and TZSV-Tomato-YN). The nucleotide identity of the genes among the TZSV isolates was more than 94%, indicating low diversity among viruses. The phylogenetic analysis and the prediction of the cleavage sites in the glycoprotein showed that the TZSV-TZ1-3 isolate was closely related to TZSV-Tomato-YN isolated from China. However, there were unique frameshifts and deletions on the RdRp and glycoprotein genes of the TZSV-Tomato-YN isolate, suggesting that both isolates were genetically distinct. The findings of this study indicate that the TZSV-TZ1-3 isolate originated in China and show the sequence diversity among TZSV isolates.

Virome analysis was performed on 174 grape genetic resources from the National Agriculture and Food Research Organization, Japan. A total of 20 bulk samples was prepared by grouping the vines into batches of 6-10 plants. Each of the bulk samples was analyzed using high-throughput sequencing, which detected 27 viruses and 5 viroids, including six viruses and one viroid reported in Japan for the first time (grapevine viruses F, L, and T, grapevine Kizil Sapak virus, grapevine Syrah virus 1, grapevine satellite virus, and grapevine yellow speckle viroid 2). In addition, a novel vitivirus was detected with a maximum nucleotide sequence identity of only 58% to its closest relative, grapevine virus A (GVA). The genome of this novel virus was 7,461 nucleotides in length and encoded five open reading frames showing the typical genomic structure of vitiviruses. Phylogenetic trees of vitiviruses placed it in a distinct position nearest to GVA or grapevine virus F (GVF) in genomes and amino acids of deduced replication-associated protein (RAP) and coat protein (CP). The amino acid sequence identities of RAP and CP with GVA, GVF, and other vitiviruses were a maximum of 53% and 73%, respectively, which were significantly below the species demarcation threshold of 80% in the genus. The low identity and phylogenetic analyses indicate the discovery of a novel vitivirus species provisionally named grapevine virus P.

Dengue fever virus (DENV) poses a significant public health risk in tropical and subtropical regions across the world. Although the dengue fever virus (DENV) exhibits significant genetic diversity and has the potential to evolve, there is a lack of comprehensive research on the comparative genomics and evolutionary dynamics of the virus in Pakistan. Phylogenetic analysis demonstrated the circulation of all four dengue virus serotypes (DENV-1, - 2, - 3, and - 4) with prevalent genotypes III and V within DENV-1, cosmopolitan genotype within DENV-2, genotype III within DENV-3, and genotype I within DENV-4 during 2006-2014. Based on the complete envelope region, genome-wide residue signature and genetic diversity indicate that there is a high level of genetic diversity among DENV-1 strains, while DENV-3 strains exhibit the least genetic diversity. Comparative analysis of all four DENV serotypes revealed that certain codons in DENV-2 and -4 were subject to strong purifying selection, while a few codon sites in the envelope region showed evidence of positive selection. These findings provided valuable insights into the comparative genomics and evolutionary pattern of DENV strains reported from Pakistan. Whether those characteristics conferred a fitness advantage to DENV-1 genotypes within a specific geography and time interval warrants further investigations. The findings of the current study will contribute to tracking disease dynamics, understanding virus transmission and evolution, and formulating effective disease control strategies.

Black gram (Vigna mungo L.) plants showing yellow mosaic symptoms during 2019-2022 crop seasons were collected randomly from a Dayalbagh field, Agra Region of Uttar Pradesh, India. Total genomic DNA was isolated from the infected leaf samples by the Cetyltrimethylammonium bromide (CTAB) method and subjected to PCR. After viral confirmation, the viral genome was amplified by rolling circle amplification following the standard protocol. The DNA A and DNA B subgenomes were cloned individually as a PstI and BamHI fragment in the pUC18 vector. Positive clones were subjected to DNA sequencing. The results revealed that DNA A and DNA B show the closest nucleotide identity with "mungbean yellow mosaic India virus-[Mungbean], DNA-A, the complete sequence" (GeneBank Accession No AF416742.1) with 98.14% identity, and "mungbean yellow mosaic India virus isolate Mu1-Dholi segment DNA-B, the complete sequence" (GeneBank Accession No MW814723.1) with 97.94% identity, respectively. The new isolate of mungbean yellow mosaic India virus (MYMIV) shows sequence similarity with the coat protein gene of various strains of MYMIV. In the new isolate of MYMIV, a point mutation was observed at the 2036th nucleotide of DNA B, which disrupts the reading frame to introduce a stop codon and thus leading to a decrease in the size of the movement protein gene. In the present study we are reporting the whole genome sequence of the MYMIV Dayalbagh isolate for the first time.

Mycoviruses pervade the fungal kingdom, yet their diversity within various fungal families and genera remains largely unexplored. In this study, 10 publicly available fungal transcriptomes from Ceratocystidaceae were analyzed for the presence of mycoviruses. Despite mycovirus associations being known in only four members of this family, our investigation unveiled the discovery of six novel mycoviruses. The majority of these mycoviruses are composed of positive sense single stranded RNA and are putatively assigned to the viral family Mitoviridae (with tentative classification into the genera Unuamitovirus and Duamitovirus). The double stranded RNA viruses, however, were associated with the family Totiviridae (with tentative classification into the genus Victorivirus). This study also revealed the discovery of an identical unuamitovirus in the fungal species Thielaviopsis ethacetica and Thielaviopsis paradoxa. This discovery was notable as these fungal isolates originated from distinct geographical locations, highlighting potential implications for the transmission of this mitovirus. Moreover, this investigation significantly expands the known host range for mycoviruses in this family, marking the initial identification of mycoviruses within Ceratocystis platani, Thielaviopsis paradoxa, Thielaviopsis ethacetica, and Huntiella omanensis. Future research should focus on determining the effects that these mycoviruses might have on their fungal hosts.

Porcine epidemic diarrhea (PED) is a highly contagious disease caused by the porcine epidemic diarrhea virus (PEDV), which results in significant economic losses. PEDV infection causes severe damage to the midgut barrier in the small intestine. YBX3, an important protein in tight junctions, promotes epithelial cell proliferation. However, its role in the process of PEDV infection remains unclear. In this study, we observed a significant increase in mRNA expression of YBX3 following PEDV infection. Additionally, the protein expression of YBX3 showed an initial increase followed by a decrease over time. Furthermore, treatment with 2% DSS resulted in a significant down-regulation of YBX3 mRNA and protein expression. Furthermore, we successfully generated knockout and overexpression cell lines of YBX3. Preliminary assays indicated that elevated expression of YBX3 inhibited the PEDV replication, while knockout of YBX3 had the opposite effect. In conclusion, our study has preliminarily revealed the functional role of YBX3 during PEDV infection. This finding lays the foundation for further investigation into its mechanism in future and also provides new insights into the mechanism of PEDV-host interactions.

Atopic dermatitis (AD) is accompanied by changes in skin microbiota, in which abnormal colonization of Staphylococcus aureus is particularly common. The antibiotic treatment is prone to destroy the commensal bacterial community, further exacerbating the microbiome dysbiosis. Elimination of S. aureus through phage-targeted therapies presents a promising method in the treatment strategy of AD. In this study, we isolated a novel phage SAP71, which specifically lysed S. aureus. Genome sequencing showed that SAP71 contained no virulence, lysogenic, or antimicrobial resistance genes, making this lytic phage a potential agent for phage therapy. Moreover, we demonstrated that phage SAP71 was able to significantly improve the skin lesions, reduce the bacterial loads in the skin, and prevent the development of AD-like skin pathological changes in an AD model. In short, phage SAP71 was demonstrated to effectively treat S. aureus infection in AD, which provided a theoretical basis for the clinical phage therapy of AD.

Orf or contagious ecthyma is a highly contagious, zoonotic, and economically important global viral disease of small ruminants and is endemic in India. Vaccination of susceptible goats/sheep along with suitable recombinant protein-based serological assay will be useful in the control of the infection. In this study, the full-length and truncated versions of F1L encoding gene (ORF 059) of orf virus were cloned into pFasBac HT A vector, transformed in DH10Bac cells, and expressed in insect cells. The full-length and truncated recombinant F1L proteins were expressed as a 6 × histidine-tagged fusion protein for ease of purification by Ni-NTA affinity chromatography under denaturing conditions. A protein with ~ 40 kDa and ~ 35 kDa for full-length and truncated F1L protein, respectively, were expressed and confirmed by SDS-PAGE and western blot. The protein reactivity evaluated by western blot analysis and indirect ELISA using ORFV hyperimmune serum was also found to be reactive. The results of the present study showed that the purified recombinant F1L protein can be used as a diagnostic antigen in sero-surveillance of ORFV infection in small ruminants. To the best of authors' knowledge, this is the first report on the expression of ORFV F1L in insect cells using a baculovirus vector and its successful purification to use as the potential diagnostic antigen in ELISA.

Nigeria recorded one of the earliest outbreaks of the Highly Pathogenic Avian Influenza (HPAI) virus H5N1 in 2006, which spread to other African countries. In 2023, 18 countries reported outbreaks of H5N1 in poultry, with human cases documented in Egypt, Nigeria, and Djibouti. There is limited information on the molecular epidemiology of HPAI H5N1 in Nigeria. We determined the molecular epidemiology and genetic evolution of the virus from 2006 to 2021. We investigated the trend and geographical distribution across Nigeria. The evolutionary history of 61 full-length genomes was performed from 13 countries worldwide, and compared with sequences obtained from the early outbreaks in Nigeria up to 2021. MEGA 11 was used to determine the phylogenetic relationships of H5N1 strains, which revealed close ancestry between sequences in Nigeria and those from other African countries. Clade classification was performed using the subspecies classification tool for Bacterial and Viral Bioinformatics Research Center (BV-BRC) version 3.35.5. H5N1 Clade 2.2 was observed in 2006, with 2.3.2, 2.3.2.1f clades observed afterwards and 2.3.4.4b in 2021. Our findings underscore the need for genomics surveillance to track antigenic variation and clades switching to monitor the epidemiological of the virus and safeguard human and animal health.Impacts Specific variations in the hemagglutinin (HA) and neuraminidase (NA) genes of Avian influenza virus are consistent in different geographical regions. H5N1 Clade 2.2 was reported in 2006, with 2.3.2, 2.3.2.1f afterwards and 2.3.4.4b in 2021. Nigeria is an epicentre for avian influenza with three major migratory routes for wild birds transversing the country. It is plausible that the Avian influenza in Northern Nigeria may be linked to wild bird sanctuaries in the region.

Echinacea is an herbaceous plant originating from North America that is cultivated for gardening and landscaping because of its showy flowers. Using high-throughput sequencing, we identified two viral contigs from echinacea seeds that were related to the family Tombusviridae. These two viruses were similar to oat chlorotic stunt virus (OCSV) and other unassigned tombusviruses; therefore, we tentatively named them Echinacea-associated tombusviruses 1 and 2 (EaTV1 and EaTV2, respectively). The EaTVs represent putative readthrough sites and have no poly(A) tails, aligning with the common features of family Tombusviridae. The EaTVs are included in a monophyletic group of OCSV and several unassigned tombusviruses. Because OCSV is the only member of Avenavirus to date, EaTVs are tentative members of Avenavirus, or they are close sister species to OCSV with several unassigned tombusviruses. RNA-dependent RNA polymerases and coat proteins were well conserved among EaTVs and unassigned tombusviruses; however, their similarities were not correlated, implying divergent and complex evolution.