Archives of Virology最新文献

{"title":"Complete genome analysis and biological characterization of phage vB_Bsu_hmny2 infecting Bacillus subtilis","authors":"Qihong Liu,&nbsp;Guanhua Xuan,&nbsp;Yinfeng Wang,&nbsp;Hong Lin,&nbsp;Jingxue Wang","doi":"10.1007/s00705-025-06243-3","DOIUrl":"10.1007/s00705-025-06243-3","url":null,"abstract":"<div><p><i>Bacillus subtilis</i>, a key microorganism in food fermentation, is frequently compromised by phage contamination, which can result in fermentation failures. Therefore, understanding and controlling <i>B. subtilis</i>-infecting phages is critical for enhancing fermentation stability. In this study, we characterized a novel lytic <i>B. subtilis</i> phage, vB_Bsu_hmny2, isolated from sewage collected at a seafood market in Qingdao, China. This phage has a linear double-stranded DNA genome of 18,762 bp with 25 open reading frames (ORFs), the functions of 17 of which were predicted. Transmission electron microscopy examination revealed that the phage exhibits podovirus morphology, with a head measuring 40 ± 10 nm in diameter and a short tail measuring 20 ± 6 nm in length. vB_Bsu_hmny2 exhibited stability across a range of temperatures and pH levels and was found to belong to the species <i>Beecentumtrevirus Nf</i> in the family <i>Salasmaviridae</i>. vB_Bsu_hmny2 is the first phage of the genus <i>Beecentumtrevirus</i> to undergo physiological characterization. This research addresses a gap in the functional analysis of phages, providing valuable insights for phage control in industrial fermentation processes.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143602282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete genome sequence of fig leaf mottle-associated virus 2","authors":"Rachelle Bester,&nbsp;Shannon Goodchild,&nbsp;Hans J. Maree","doi":"10.1007/s00705-025-06262-0","DOIUrl":"10.1007/s00705-025-06262-0","url":null,"abstract":"<div><p>The complete genome sequence of fig leaf mottle-associated virus 2 (FLMaV2), a positive-sense single-stranded RNA virus with a genome length of 16,925 nucleotides, was determined via RT-PCR and rapid amplification of cDNA ends (RACE). Its genome organization resembles those of little cherry virus 2 (LChV2) and yam asymptomatic virus 1 (YaV1), both of which are currently classified as members of the genus <i>Ampelovirus</i> but differ from typical ampeloviruses. Phylogenetic analysis based on amino acid sequences of the RNA-dependent RNA polymerase and coat protein of members of the family <i>Closteroviridae</i> showed that FLMaV2 clustered with LChV2 and YaV1. Because of their unusual genome organization, FLMaV2, LChV2, and YaV1 might represent a distinct genus within the family <i>Closteroviridae</i>.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00705-025-06262-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143594710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diagnostic challenges due to hepatitis B virus surface antigen mutations outside the major hydrophilic region","authors":"Ruchi Supekar,&nbsp;Jit Sarkar,&nbsp;Partha Chakrabarti,&nbsp;Subhajit Biswas","doi":"10.1007/s00705-025-06256-y","DOIUrl":"10.1007/s00705-025-06256-y","url":null,"abstract":"<div><p>The number of observed cases of occult hepatitis B virus infection (OBI) in eastern India has been increasing. Here, S gene mutations were identified in apparently healthy individuals with OBI, and the S protein variants from these patients were characterized <i>in vitro</i>. Plasma samples from 217 healthy blood donors were collected from three different regions in eastern India and screened for hepatitis B virus (HBV) infection using a nucleic acid amplification test and immunoassays for serological markers. S protein variants found in positive plasma samples were characterized using a liver cell line. Twenty-nine of the 217 plasma samples tested, were positive for HBV DNA and were negative for hepatitis B surface antigen (HBsAg) and antibody to HBV core antigen (anti-HBc). Sequencing of the HBV S gene revealed a novel S protein mutation (L173H) in an area outside the major hydrophilic region. Known OBI-associated mutations (S34L, P178R), a mutation resulting in a stop codon at position 196, associated with lamivudine-resistance, the substitution I81T, and a dual mutation (G145A and Q101H) were also identified. S proteins containing these mutations, produced by transfection of human hepatoma (Huh7) cells with recombinant plasmids, were undetectable or gave significantly weaker signals than the wild-type control, despite similar levels of S mRNA production for the mutant and wild-type plasmids. The OBI cases in this study were unexpectedly seronegative. <i>In vitro</i> analysis revealed that the mutations identified here caused the virus to evade immunodetection using commercial immunoassays, thereby rendering a large portion of the population “silently” infected with HBV.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00705-025-06256-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143581242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular characterization of a novel non-segmented double-stranded RNA mycovirus isolated from the phytopathogenic fungus Lasiodiplodia pseudotheobromae","authors":"Zhengzhe Guan,&nbsp;Mengjiao Wang,&nbsp;Jiayi Ma,&nbsp;Mengyuan Mu,&nbsp;Xinyu Li,&nbsp;Peimeng Sun,&nbsp;Mengyuan Zhang,&nbsp;Yuanyuan Zhang,&nbsp;Luyang Song,&nbsp;Caiyi Wen,&nbsp;Ying Zhao","doi":"10.1007/s00705-025-06263-z","DOIUrl":"10.1007/s00705-025-06263-z","url":null,"abstract":"<div><p>In this study, we isolated a novel mycovirus from <i>Lasiodiplodia pseudotheobromae</i> strain YY-1, which we named “Lasiodiplodia pseudotheobromae mycovirus 1” (LpMyV1). The complete genome of LpMyV1 is 2877 bp in length and contains two non-overlapping open reading frames (ORF1 and ORF2). ORF1 encodes a putative protein of 316 amino acids with a molecular weight of 34.1 kDa that shares similarity with the coat proteins of several mycoviruses. ORF2 encodes a protein of 561 amino acids with a molecular weight of 63.2 kDa that contains a conserved RNA-dependent RNA polymerase (RdRp) domain. BLASTp results showed that the RdRp of LpMyV1 shares the highest similarity with those of non-segmented dsRNA viruses. A multiple sequence alignment and phylogenetic analysis indicated that LpMyV1 is a new member of the proposed genus “<i>Unirnavirus</i>”. This is the first report of a mycovirus from <i>L. pseudotheobromae</i>.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00705-025-06263-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143581216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacteriophage-derived depolymerase: a review on prospective antibacterial agents to combat Klebsiella pneumoniae","authors":"Xin Jiao,&nbsp;Menglu Wang,&nbsp;Yanxia Liu,&nbsp;Shuqi Yang,&nbsp;Qianhui Yu,&nbsp;Jinjuan Qiao","doi":"10.1007/s00705-025-06257-x","DOIUrl":"10.1007/s00705-025-06257-x","url":null,"abstract":"<div><p><i>Klebsiella pneumoniae</i> is a Gram-negative bacterium that colonizes mucosal surfaces and is a common cause of nosocomial infections. The emergence of antimicrobial resistance in <i>K. pneumoniae</i>, particularly carbapenem-resistant strains, poses a significant threat to human health, with high mortality rates and healthcare costs. Another major problem is that hypervirulent <i>K. pneumoniae</i> tends to form biofilms. Bacteriophage-derived depolymerases, a class of enzymes that degrade diverse bacterial surface carbohydrates, have been exploited as antibiofilm and antimicrobial adjuvants because of their high stability, specificity, strong antimicrobial activity, and low incidence of bacterial resistance. This review presents a summary of the structure and properties of depolymerase, as well as an overview of both <i>in vitro</i> and <i>in vivo</i> studies of depolymerase therapy for multidrug-resistant or biofilm-forming <i>K. pneumoniae</i> infections. These studies employed a range of approaches, including utilizing a single depolymerase or combinations of depolymerase and phages or antibiotics. Furthermore, this review outlines the current challenges facing depolymerase therapy and potential future approaches for treating <i>K. pneumoniae</i> infections.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00705-025-06257-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143581215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic characterization of lumpy skin disease virus (LSDV) isolates from an outbreak on Great Nicobar Island, India, in 2022 reveals the involvement of a cluster 2.5 recombinant LSDV strain (East/Southeast Asian lineage)","authors":"Shashi Bhushan Sudhakar,&nbsp;Niranjan Mishra,&nbsp;Semmannan Kalaiyarasu,&nbsp;Falguni Agrawal,&nbsp;Aniket Sanyal","doi":"10.1007/s00705-025-06252-2","DOIUrl":"10.1007/s00705-025-06252-2","url":null,"abstract":"<div><p>Lumpy skin disease (LSD) has emerged as a global threat to cattle health and production. Although India has been encountering regular episodes of LSD epidemics on the mainland since 2019, the Andaman and Nicobar Islands remained free of LSD until 2021. In this study, we investigated the first LSD outbreak on Great Nicobar Island in 2022 and examined the genetic characteristics of the LSDV strain associated with this outbreak. The morbidity and mortality rates in cattle were 38.29% and 1.89%, respectively. We screened 123 samples (whole blood, nasal swab, or skin tissue) from 111 cattle by LSDV real-time PCR and sera from 86 cattle by LSDV antibody ELISA, and the results confirmed LSDV infection. Subsequent nucleotide sequencing and phylogenetic analysis of five selected marker genes (GPCR, RPO30, P32, EEV, and B22R) revealed that the LSDV strain from Great Nicobar Island resembled cluster 2.5 LSDV recombinant strains from East and Southeast Asia but was distinct from wild-type LSDV strains (1.2.1, 1.2.2) circulating in mainland India, indicating an exotic source of introduction. Phylogenetic analysis using a concatenated sequence (GPCR-RPO30-P32-EEV-B22R) showed that both the wild-type and recombinant LSDV strains formed well-supported clusters, indicating that this type of analysis may be used as an alternative to whole-genome sequence analysis. We also found that determination of the nucleotide sequence of the C-terminal 717 bp of the B22R gene may be sufficient for reliable assignment of circulating LSDV isolates to a particular cluster. This is the first report of the detection of a recombinant LSDV strain in India, demonstrating the spread of cluster 2.5 recombinant LSDV further into South Asia. Our findings highlight the value of LSDV surveillance and genetic analysis for LSDV epidemiology, which may be helpful for developing effective control strategies.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In vitro inhibitory activity of indole alkaloid derivatives against porcine epidemic diarrhea virus","authors":"Yaoying Jian,&nbsp;Siqi Dong,&nbsp;Qianyi Zhang,&nbsp;Jiali Pan,&nbsp;Ruiming Hu,&nbsp;Zhen Ding,&nbsp;Huansheng Wu,&nbsp;Shaoyong Ke,&nbsp;Zheng Chen","doi":"10.1007/s00705-025-06251-3","DOIUrl":"10.1007/s00705-025-06251-3","url":null,"abstract":"<div><p>Porcine epidemic diarrhea virus (PEDV) is an enteric coronavirus that can cause acute diarrhea, vomiting, dehydration, and high mortality of newborn piglets, leading to huge economic losses to the world pig industry. Given the limited efficacy of current PEDV vaccines, there is an urgent need for the development of antiviral drugs. In this study, the antiviral effects of 17 synthesized indole alkaloid derivatives against PEDV were investigated. It was observed that indole alkaloid derivative no. 14 exhibited significant inhibition of PEDV replication in a dose-dependent manner. Furthermore, time-of-addition assays and quantitative real-time PCR (QPCR) showed that delayed administration of this compound resulted in a weaker inhibitory effect on PEDV compared to early treatment. Mechanistic analysis revealed that this compound exerts its inhibitory effects during the entry stage of the PEDV life cycle. This study demonstrates the anti-PEDV effects of indole alkaloid derivative no. 14, suggesting its potential as a candidate drug for treating PEDV infections.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular characterization of a polymycovirus in Leptosphaeria biglobosa","authors":"Nesma M. Samir,&nbsp;Jacob Locke-Gotel,&nbsp;Syun-Ichi Urayama,&nbsp;Adel A. El-Morsi,&nbsp;Ghada A. El-Sherbeny,&nbsp;Yongju Huang,&nbsp;Bruce D. L. Fitt,&nbsp;Hiromitsu Moriyama,&nbsp;Robert H. A. Coutts,&nbsp;Ioly Kotta-Loizou","doi":"10.1007/s00705-025-06253-1","DOIUrl":"10.1007/s00705-025-06253-1","url":null,"abstract":"<div><p><i>Leptosphaeria biglobosa</i> is a phytopathogenic ascomycete of <i>Brassica napus</i> that causes phoma stem canker/blackleg. A new double-stranded RNA (dsRNA) mycovirus from this fungus has been fully characterized. The virus genome has five dsRNA segments, ranging in length from 1,180 bp to 2,402 bp. Each dsRNA has a single open reading frame flanked by 5′ and 3′ untranslated regions. The proteins encoded by dsRNAs 1 and 3, an RNA-dependent RNA polymerase (RdRP) and a methyltransferase, respectively, have significant similarity to those of Plasmopara viticola lesion associated polymycovirus 1. The proline-alanine-serine-rich protein encoded by dsRNA 5 is similar to that of Erysiphe necator associated polymycovirus 1. The proteins encoded by dsRNAs 2 and 4 have significant similarity to those of a mycovirus identified in <i>Alternaria</i> sp. FA0703. Phylogenetic analysis based on RdRP sequences showed that this virus clusters with members of the family <i>Polymycoviridae</i>. Based on these observations, this virus, which we have named \"Leptosphaeria biglobosa polymycovirus 1\", should be classified as a member of the family <i>Polymycoviridae</i>. This is the first report of a polymycovirus in<i> L. biglobosa.</i></p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00705-025-06253-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome sequence of a new densovirus infecting the leaf-curl plum aphid brachycaudus helichrysi","authors":"Yuxiang Li,&nbsp;Yixiang Ma,&nbsp;Xinrong Liu,&nbsp;Ya Guo,&nbsp;Ning Ji,&nbsp;Zhaofei Li","doi":"10.1007/s00705-025-06266-w","DOIUrl":"10.1007/s00705-025-06266-w","url":null,"abstract":"<div><p>Using degenerate primers and an overlap PCR approach, we identified a new densovirus (family <i>Parvoviridae</i>, subfamily <i>Densovirinae</i>) in an asexual clone of the leaf-curl plum aphid, <i>Brachycaudus helichrysi</i>, collected in Baoji, China, in June 2021. A nearly complete genome sequence of 5,551 nucleotides (nt) was obtained. The virus, with the proposed name “Brachycaudus helichrysi densovirus” (BhDV), has an ambisense genome organization with two ORFs in the sense strand encoding the nonstructural proteins NS1 and NS2 and one ORF at the antisense strand encoding the virion capsid protein VP. These proteins share 37–70% and 10–33% amino acid sequence identity with homologs of the other aphid densoviruses and non-aphid densoviruses, respectively. Phylogenetic analysis suggested that this virus is a member of a new species in the genus <i>Hemiambidensovirus</i>.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 4","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143554063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of nucleotide pair frequency and synonymous codon usage in the evolution of bovine viral diarrhea virus","authors":"Xili Feng,&nbsp;Zeyu Liu,&nbsp;Yongli Mo,&nbsp;Shubin Zhang,&nbsp;Xiao-Xia Ma","doi":"10.1007/s00705-025-06250-4","DOIUrl":"10.1007/s00705-025-06250-4","url":null,"abstract":"<div><p>Synonymous codon usage plays an important role in the adaptation of viruses to their hosts. Bovine viral diarrhea virus (BVDV) relies on a high mutation rate in its genome to achieve the necessary fitness in a particular host. However, the question of which selective forces influence nucleotide pair and synonymous codon usage patterns in different BVDV genotypes remains unresolved. Here, 169 BVDV strains isolated at different times in various countries were analyzed to compare their dinucleotide frequency and synonymous codon usage. Examination of the nucleotide usage pattern in the open reading frame (ORF) of BVDV revealed a significantly higher frequency of purine than pyrimidine, with the highest extent of nucleotide usage bias observed in the first codon position. Moreover, a nucleotide pair bias, especially favoring CpG dinucleotides, was observed in all of the genotypes. Together, the nucleotide composition constraints and nucleotide pair bias appear to have influenced the overall codon usage pattern. Nucleotide pair and synonymous codon usage biases were associated with individual genotypes to different degrees. Of particular note, BVDV-1 exhibited more variation in its nucleotide pair and synonymous codon usage than BVDV-2 and BVDV-3, suggesting that these patterns are shaped both by selection of mutations in the viral genome and translational selection in the host.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 3","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143496880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}