Virus Genes最新文献

A novel lytic phage with a broad host range was isolated from pig faeces and the complete genome was subsequently sequenced. The phage was found to lyse Staphylococcus hyicus, S. pseudintermedius, S. schleiferi and S. warneri, generating approximately 27 PFU per infected S. hyicus cell. The phage has an isometric head of 42 ± 2 nm in diameter and a noncontractile tail of 114 ± 9 nm long. The genome is 53,660 bp in size and consists of 79 predicted ORFs and one tRNA^Arg gene. The phage has been classified within the Caudoviricetes, specifically the Chaseviridae family. Its broad host range and absence of harmful genes make it suitable for use in phage therapy. In addition, a novel temperate phage was discovered that was spontaneously released from a S. hyicus isolate Pel11 from a pig with exudative epidermitis. This novel temperate phage differs from the known temperate phages in S. hyicus strains NCTC10350, MM2101 or 83/7-1B, representing a novel pathogenicity element in the S. hyicus genome.

Norovirus is the primary cause of acute gastroenteritis outbreaks, considerably impacting children under 5 years, followed by older adults and immunocompromised individuals. As an RNA virus, norovirus exhibits high genetic variability, driven by recombination events at the ORF1-ORF2 junction. This study reports the first detection of the rare norovirus GI.5 [P4] variant in Northeastern Mexico, identified in a single positive isolate (MTY0115; GenBank: PQ369661) from a sample group of 386 individuals, with a prevalence of 0.25%. Notably, norovirus GII was not detected. Phylogenetic analysis of the partial RdRp/VP1 region revealed clustering with global GI.5 [P4] sequences, revealing evolutionary relationships with isolates from Asia, Europe, and America. A recombination event was identified at position 5307 (breakpoint based on reference sequences of GI.5 [P5] and GI.4 [P4]) within ORF1, with genetic inheritance from a GI.5 [P5] isolate from Moscow, Russia, and a GI.4 [P4] isolate from France. Typing classification through sequencing of overlapping ORF1 and ORF2 regions is valuable for understanding genomic variations and their epidemiological impact on at-risk and non-risk populations.

Proteomics plays a pivotal role in clinical diagnostics and monitoring. We conducted proteome-wide Mendelian randomization (MR) study to estimate the causal association between plasma proteins and Herpes simplex virus (HSV) infection. Data for 2,923 plasma protein levels were obtained from a large-scale protein quantitative trait loci study involving 54,219 individuals, conducted by the UK Biobank Pharma Proteomics Project. HSV-associated SNPs were derived from the FinnGen study, which included a total of 400,098 subjects infected with HSV. MR analysis was performed to assess the links between protein levels and the risk of HSV infection. Furthermore, a Phenome-wide MR analysis was utilized to explore potential alternative indications or predict adverse drug events. Finally, we evaluated the impact of 1,949 plasma proteins on HSV infection, identifying 48 proteins that were negatively associated with HSV infection and 54 proteins that were positively associated. Genetically higher HLA-E levels were significantly associated with increased HSV infection risk (OR = 1.39, 95% CI: 1.17-1.65, P = 2.13 × 10^-4, while ULBP2 showed a significant negative association with HSV infection risk (OR = 0.81, 95% CI: 0.73-0.90, P = 6.25 × 10^-5) in the primary analysis. No significant heterogeneity or pleiotropy was observed in any of the results. Additionally, we found a suggestive association of Lymphotoxin-beta, SMOC1, MICB_MICA, ASGR1, and ANXA10 with HSV infection risk (P < 0.003). In Phenome-wide MR analysis, HLA-E was associated with 214 phenotypes (P_FDR < 0.10) while ULBP2 did not show significant associations with any diseases after FDR adjustment. The comprehensive MR analysis established a causal link between multiple plasma proteins and HSV infection, emphasizing the roles of HLA-E and ULBP2. These results provide new insights into the biological mechanisms of HSV and support the potential for early intervention and treatment strategies, although further research is needed to validate these plasma protein biomarkers.

Human Papillomavirus Type 59 (HPV-59) is a high-risk subtype linked to cervical and other cancers. However, its codon usage patterns remain underexplored despite their importance in understanding viral behavior and vaccine optimization. This study reveals a mild codon usage bias in HPV-59, with a notable preference for A/T-ending codons and 29 favored codons, primarily ending in A or T. Additionally, CpG dinucleotides were significantly underrepresented, potentially aiding immune evasion. Analyses using the Parity Rule 2, Effective Number of Codons plot, and neutrality plot indicate that both mutational pressure and natural selection shape codon usage, with natural selection playing a dominant role. The virus's codon usage moderately aligns with human translational machinery, as shown by the Isoacceptor tRNA pool, Codon Adaptation Index, and Relative Codon Deoptimization Index, reflecting an evolutionary balance between protein synthesis efficiency and host compatibility. These findings provide valuable insights into HPV-59 biology, offering guidance for developing optimized vaccines.

Nudiviruses (family Nudiviridae) are a diverse group of enveloped, rod-shaped viruses with double-stranded DNA genomes that infect a wide range of insects and crustaceans. These viruses are of significance both as biological control agents in agriculture and as agents of disease in aquaculture and insect rearing. In this work, we found four segments of a novel and divergent nudivirus identified through RNA-seq data from the two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae). The sequences of this virus were detected only in a subset of mite transcriptomes. The assembled segments covered a total of 100,780 bp, with 122 annotated ORFs, including all the 28 conserved nudiviral core genes. Phylogenetic analysis based on the predicted amino acid sequences of 17 selected nudiviral core genes placed the virus within the Alphanudivirus genus, in a clade containing nudiviruses identified from flea transcriptomes. This placement was confirmed by phylogenies of segment-specific concatenated core gene alignments. Indeed, the virus was designated as Tetranychus urticae alphanudivirus (TuNV). Transcriptional profiling revealed variable levels of transcriptional activity among genomic segments and viral genes. Arthropod gene homologs were found interspersed among nudiviral genes across all segments along with several unique genes. This genomic and phylogenetic characterization enhances our understanding of nudivirus diversity and evolution within arthropod hosts.

Recently, mpox has spread in some parts of Africa, such as Congo (DRC), Burundi, Rwanda, Uganda, and Kenya, worsening the situation in DRC and Burundi compared to the other parts of Africa due to the spread of the Clade Ib, with several confirmed and lethal cases. The study aims to analyze the broader molecular phylogenetics using greater complete genome sequences and molecular phylogenetics of Clade I (Clade Ia and Clade Ib), nucleotide diversity of the genome of Clade I, NGA/TCN context of G- > A/C- > T mutations, and epidemiology of the recent spread of mpox in the African countries. Overall molecular phylogenetics of mpox inform the divergence was noted between 0.00220 and 0.00265 and found Clade IIb has further subdivided into 37 sublineages. From our phylogenetic analysis and the tracking of recent mpox variants, we report the spread of Clade I (Clade Ib) of mpox, a virulent mpox, in the African continent, Thailand, Sweden, and USA. Furthermore, two Clades, Clade Ia and Clade Ib, have originated from Clade I. Recently, Clade Ib has expanded its region within African continent. We reported the mutation pattern in the genome. Epidemiological analysis indicates the most affected country is the Democratic Republic of the Congo (DRC). This work shows that mpox is steadily adapting as geographic area increases and can help the health authorities develop policies such as vaccinations, and travel restrictions to contain the spread of mpox.

The first complete genome of spiranthes mosaic virus 3 (SpiMV3, genus Potyvirus, Potyviridae) was determined using high-throughput sequencing (GenBank PQ374234). The virus was detected from a Phlox paniculata plant, displaying severe foliar mosaic, in the Botanical Garden of Lomonosov Moscow State University, Moscow, Russia. The complete SpiMV3 genome comprised 9544 nucleotides (nt), excluding the 3'-terminal poly(A) tail. The large open-reading frame 9258 nt long encoded a polyprotein of 3085 amino acid residues, in which nine putative cleavage sites were identified. BLASTn showed that the complete SpiMV3 genome had the highest identity (66.4%) to Colombian datura potyvirus. Eight more SpiMV3 isolates were found on different phlox cultivars in the Tsitsin Main Botanical Garden, Moscow, by RT-PCR using primers designed based on the complete genome of the Russian SpiMV3 isolate. The coat protein (CP) gene phylogeny showed that known SpiMV3 isolates formed two distinct clusters and were grouped irrespective of their host plant species or geographical origin. The Russian isolates were assigned to one of the clusters. The CP genes of the Russian SpiMV3 isolates shared 94.4-98.1% nucleotide identity to each other, 92.2-96.9% to the rest of the isolates from this group, and 72.7-75.6% to the isolates from another cluster. This is the first report of SpiMV3 from Russia expanding the information on the geographical distribution and genetic diversity of the virus. The complete genome of this virus was sequenced and characterized for the first time.

Infectious bronchitis (IB) is a highly contagious disease caused by the avian infectious bronchitis virus (IBV). This disease mainly causes damage to the respiratory system and has brought serious harm to the poultry industry in China. At present, QX-like IBV is the most prevalent strain in China, which is highly pathogenic and causes severe nephritis. Based on the construction of the H120 infectious clone, this study successfully constructed and rescued the recombinant virus H120-S1/LMH by using RED/ET recombination engineering technology combined with ccdB reverse selection to replace the S1 gene of the H120 infectious clone with the S1 gene of the prevalent IBV LMH strain. The recombinant virus showed good genetic stability and propagation in 15 continuous generations on chick kidney cells (CK cells). To evaluate the protection of this candidate vaccine strain, we conducted a vaccination challenge test. The specific-pathogen-free (SPF) chicks were immunized at 3 days of age and challenged with the QX-like IBV virulent strain LMH after 14 days. The results showed that the recombinant virus could provide 90% protection against the virulent IBV LMH strain, and mortality was significantly reduced, indicating the potential of H120-S1/LMH as a candidate vaccine. This study provides a strategy for precisely and rapidly generating IBV vaccine candidates by reverse genetics and lays a foundation for the further development of a new IBV vaccine against prevalent strains.

Zika virus (ZIKV) infection has emerged as a significant public health concern due to its association with fetal microcephaly and Guillain-Barre syndrome (GBS). Unfortunately, its detailed pathogenesis remains unclear. To better understand how ZIKV evades host antiviral immunity, we analyzed the microarray dataset (GSE98889) of ZIKV-infected primary human brain microvascular endothelial cells (hBMECs) retrieved from the gene expression omnibus (GEO). 160, 1423, 969, 829, and 600 differentially expressed genes (DEGs) were identified at 12, 24, 48, 72, and 216 hours post-ZIKV infection in hBMECs, respectively. Subsequently, 31 common DEGs across all time-points were selected for further analysis. Gene ontology (GO) functional analysis showed these 31 DEGs were mainly involved in the host antiviral innate immune responses. Protein-protein interaction (PPI) network analysis identified 10 hub genes (MX1, OAS1, OAS2, IFI44, IFI44L, IFIT1, IFIT2, IFIT3, IFIH1, and XAF1), which were all interferon-stimulated genes (ISGs) and upregulated. qRT-PCR was used to validate the expression patterns of these 10 hub genes in different ZIKV-infected cell lines. Finally, miRNA-mRNA regulatory network analysis revealed that hsa-miR-129-2-3p, hsa-miR-138-5p, hsa-miR-21-3p, hsa-miR-27a-5p, hsa-miR-449a, and hsa-miR449b-5p were key miRNAs regulating these hub genes. Our study showed that ZIKV infection activated the host innate immune response to restrict ZIKV infection. The common pathways, hub genes, and their regulatory miRNA network offer new insights into virus-host interactions, enhancing our understanding of ZIKV pathogenesis.

This study aimed to determine sub-subtypes and circulating recombinant forms (CRFs) in Pakistan using the pol gene, identification of amino acid substitutions, structural changes, and drug resistance evaluation in the p66 region of reverse transcriptase. A total of 50 HIV-positive blood samples were collected from Lahore Pakistan, confirmed by Real Time-Polymerase Chain Reaction. The samples were further processed for pol gene amplification followed by nucleotide sequencing through the Sanger method. Out of 50 samples, 26 samples were amplified, and 14 sequences were obtained. The sequences were aligned with reference sequences to determine subtyping and phylogenetic analysis. Moreover, amino acid substitutions and drug resistance patterns were also determined in the RTp66 region. Phylogenetic analysis showed that 8 sequences of our isolates were closely related to circulating recombinant form (CRF43_02 G), and 3 sequences were of CRF30_026 (CRF02_AG) subtypes while the remaining 3 sequences were related to CRF35_A1D, CRF95_02B (CRF02_AG) and Subtype G of HIV-1. Several amino acid substitutions were identified in our isolates which show no impact on the structure of protein. Furthermore, the isolate QAU-AZ2 (OR086936) proposes variable degree of resistance to nevirapine (NVP), etravirine (ETR), rilpivirine (RPV), efavirenz (EFV), Doravirine (DOR); while no resistance against NNTRI and NTRI was observed in the remaining isolates. Further studies are required to (i) examine the function of identified amino acid substitutions through molecular docking, and (ii) sequence the complete pol gene of the viral isolates from Pakistani patients to determine possible drug resistance associated with amino acid substitutions.