Archives of Virology最新文献

{"title":"2024 taxonomic update for the families Naryaviridae, Nenyaviridae, and Vilyaviridae","authors":"Arvind Varsani,&nbsp;Andrew Hopkins,&nbsp;Michael C Lund,&nbsp;Mart Krupovic","doi":"10.1007/s00705-024-06186-1","DOIUrl":"10.1007/s00705-024-06186-1","url":null,"abstract":"<div><p>The families <i>Naryaviridae</i> (order <i>Rivendellvirales</i>), <i>Nenyaviridae</i> (order <i>Rohanvirales</i>), and <i>Vilyaviridae</i> (order <i>Cirlivirales</i>), all within the class <i>Arfiviricetes</i> of the phylum <i>Cressdnaviricota</i>, include single-stranded DNA viruses associated with protozoan parasites of the genera <i>Entamoeba</i> and <i>Giardia</i> as well as viruses found in various environmental samples, also likely infecting protozoans. Here, we provide a taxonomic update for these three families, which were recently expanded with multiple new members. In particular, we established seven new genera and nine new species in the family <i>Naryaviridae</i>, one new genus with one new species in the family <i>Nenyaviridae</i>, and three new genera and nine new species in the family <i>Vilyaviridae.</i> We also summarize the genomic properties and protein characteristics, including conserved motifs of the rolling-circle replication initiation proteins, of the viruses in the three families. Notably, the high GC content of vilyavirids (51–61%) and considerably lower GC content of naryavirids and nenyavirids (33–44%) appear to represent an adaptation to their hosts, <i>Giardia</i> and <i>Entamoeba</i> species<i>,</i> respectively.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142817093","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":"Evidence of natural lumpy skin disease virus (LSDV) infection and genetic characterization of LSDV strains from water buffaloes (Bubalus bubalis) in India","authors":"Shashi Bhushan Sudhakar,&nbsp;Niranjan Mishra,&nbsp;Semmannan Kalaiyarasu,&nbsp;Rangnath Puri,&nbsp;Pravinkumar Ghule,&nbsp;Falguni Agarwal,&nbsp;Ajay Mustare,&nbsp;Sanjay J. Pawar,&nbsp;Yahaya Khan Pathan,&nbsp;Aniket Sanyal","doi":"10.1007/s00705-024-06193-2","DOIUrl":"10.1007/s00705-024-06193-2","url":null,"abstract":"<div><p>Lumpy skin disease (LSD) has emerged as a threat to cattle production in Asia, and India has been facing LSD epidemics since 2019. Although water buffalo (<i>Bubalus bubalis</i>) is susceptible to natural LSDV infection, there have been no confirmed reports of LSDV infection in water buffalo in India. In this study, we investigated suspected cases of LSD in water buffaloes from 12 Indian states and one union territory during 2020–2023. Buffaloes showed mild to moderate clinical disease with fever and nodular skin lesions, but most remained asymptomatic. Eighteen of 177 (10.18%) buffaloes in 12 districts in three states tested positive for LSDV by real-time PCR, while 22 of 57 (38.59%) from nine districts in six states tested positive for LSDV-neutralizing antibodies, demonstrating the prevalence of LSDV infection in buffaloes over a wider geographic area. Successful virus isolation and nucleotide sequencing confirmed natural LSDV infection in buffaloes. Phylogenetic analysis of complete GPCR, RPO30, and EEV gene sequences revealed the presence of wild-type strains of two divergent LSDV lineages (1.2.1 and 1.2.2) in buffaloes. The 1.2.2 strains were closely related to the dominant LSDV strain (subcluster 1.2.2, KSGP-like) circulating in India, while the 1.2.1 strains clustered with strains from the Middle East, Europe, and the Balkans, confirming that there have been multiple introductions of LSDV into India. The detection of viruses with identical sequences in buffaloes and local cattle implied that the LSDV strain found in buffaloes is probably of cattle origin. We also found evidence of cocirculation of LSDV 1.2.1 and 1.2.2 wild-type strains in the same area, highlighting the importance of LSDV surveillance and genetic analysis. This is the first confirmed report of natural LSDV infection in water buffaloes in India. Further investigations are needed to assess the impact of LSDV infection in buffalo production and the role of buffalo in LSD epidemiology.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142810824","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 analysis of a novel nepovirus isolated from Jasminum polyanthum in Yunnan, China","authors":"Xiyan zhao,&nbsp;Rex Frimpong Anane,&nbsp;Jianwei Guo,&nbsp;Shaomei Zi,&nbsp;Bifan Chu,&nbsp;Zefen Yang,&nbsp;Kai Yan,&nbsp;Kaifei Ji,&nbsp;Shangyun Li,&nbsp;Zeli Chen,&nbsp;Mingfu Zhao","doi":"10.1007/s00705-024-06196-z","DOIUrl":"10.1007/s00705-024-06196-z","url":null,"abstract":"<div><p>Here, we report the complete genome sequence of Jasminum polyanthum nepovirus 1 (JPV1), a novel virus associated with foliar ringspot symptoms in <i>Jasminum polyanthum</i> (Oleaceae). The genome of JPV1 consists of RNA1 and RNA2, both of which are monocistronic and are 7081 nt and 4212 nt in length, respectively. RNA1 encodes six functional proteins, including the X1 protein, X2 protein, NTP-binding protein (NTB), VPg protein, protease cofactor (Pro), and RNA-dependent RNA polymerase (RdRp), while RNA2 encodes three functional proteins: the 2A protein, movement protein (MP), and capsid protein (CP). Pairwise sequence comparisons showed that the JPV1 protease-polymerase (Pro-Pol) and CP proteins each shared less than 40% aa sequence identity with those of other nepoviruses. Phylogenetic analysis indicated that JPV1 is a putative member of the genus <i>Nepovirus</i>. Based on these results, we propose that JPV1 is a member of subgroup B of the genus <i>Nepovirus</i>.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142810825","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 a new member of the genus Badnavirus infecting nettle (Urtica dioica)","authors":"Elena Motsar,&nbsp;Anna Sheveleva,&nbsp;Svetlana Tsygankova,&nbsp;Fedor Sharko,&nbsp;Kristina Petrova,&nbsp;Irina Mitrofanova,&nbsp;Sergei Chirkov","doi":"10.1007/s00705-024-06197-y","DOIUrl":"10.1007/s00705-024-06197-y","url":null,"abstract":"<div><p>A new badnavirus was discovered in nettle plants (<i>Urtica dioica</i> L., family Urticaceae) with vein banding symptoms using high-throughput sequencing. This virus was provisionally named \"nettle badnavirus 1\" (NBV 1). The complete NBV 1 genome consists of 7598 bp and contains three overlapping open reading frames. NBV 1 found to be was most closely related to green Sichuan pepper vein clearing-associated badnavirus, sharing 73.9% nucleotide sequence identity in the whole genome. These two viruses showed 76.3% nucleotide sequence identity in the region of the genome encoding RT-RNase H. This is lower than the species demarcation cutoff (80%) for the genus <i>Badnavirus</i> of the family <i>Caulimoviridae</i>, suggesting that NBV 1 is a new member of this genus. Phylogenetic analysis based on full-length badnavirus genome sequences showed that NBV 1 belongs to the same clade as a badnavirus whose genome was found to be integrated into chromosome 6 of the nettle genome, sharing 78% identity. Using PCR, NBV 1 was detected in a symptomless nettle plant growing next to symptomatic ones. It is therefore likely that the observed vein banding was due to an idaeovirus or a partitivirus, which were shown to be coinfecting the symptomatic plant. These findings expand the list of viruses infecting nettle.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142810827","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":"Circulatory microRNAs as potential biomarkers for different aspects of COVID-19","authors":"Mahsan Zali,&nbsp;Mona Sadat Larijani,&nbsp;Anahita Bavand,&nbsp;Ladan Moradi,&nbsp;Fatemeh Ashrafian,&nbsp;Amitis Ramezani","doi":"10.1007/s00705-024-06184-3","DOIUrl":"10.1007/s00705-024-06184-3","url":null,"abstract":"<div><p>The coronavirus disease of 2019 (COVID-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can alter the expression levels of host microRNAs (miRNAs). Increasing evidence suggests that circulating miRNAs can potentially play an important role in the diagnosis and prognosis of respiratory infectious diseases, especially COVID-19, and might serve as sensitive indicators of disease before the emergence of clinical symptoms. Here, we review the potential of circulatory microRNAs as novel biomarkers for different aspects of COVID-19. Recent studies have suggested that they can be useful not only for COVID‐19 prognosis but also for prediction of disease severity and mortality among intensive care unit (ICU) and ward patients. Moreover, extracellular vesicle (EV) miRNAs can be associated with antibody titer after COVID-19 vaccination. This review provides an overview of miRNA‐based biomarkers.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142810826","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":"Characterization and complete genome sequence of a novel zetapatitivirus from Penicillium exsudans isolate RCEF7900","authors":"Yanjie Zhao,&nbsp;Ping Wang,&nbsp;Lili He,&nbsp;Guogen Yang,&nbsp;Bo Huang","doi":"10.1007/s00705-024-06205-1","DOIUrl":"10.1007/s00705-024-06205-1","url":null,"abstract":"<div><p><i>Penicillium exsudans</i> strain RCEF7900, obtained from leaf litter, was found to harbor two double-stranded RNA (dsRNA) elements, designated as dsRNA1 and dsRNA2, with lengths of 1,816 bp and 1,625 bp, respectively. dsRNA1 encodes a 572-amino-acid RNA-dependent RNA polymerase (RdRp) protein (65.29 kDa), while dsRNA2 encodes a 503-amino-acid coat protein (CP) (56.73 kDa). A BLASTp search indicated that dsRNA1 and dsRNA 2 together constitute the genome of a novel partitivirus, which we have named \"Penicillium exsudans partitivirus 1\" (PePV1). Phylogenetic analysis based on RdRp amino acid sequences revealed that these genome segments belong to a member of a new species within the proposed genus “<i>Zetapatitivirus</i>” of the family <i>Partitiviridae</i>, with the RdRp showing the most sequence similarity (79.72% identity) to that of Sonifin virus. This is the first report of a zetapatitivirus from <i>P. exsudans</i>, expanding our understanding of mycoviral diversity in this fungal species.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811298","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 novel victorivirus isolated from Stagonosporopsis citrulli","authors":"Xiaofang Ma,&nbsp;Xing Zhang,&nbsp;Lifeng Zhai,&nbsp;Yingchun Jiang,&nbsp;Peter Moffett,&nbsp;Yu Zhang,&nbsp;Fang Song,&nbsp;Xin Song,&nbsp;Zhijing Wang,&nbsp;Ligang He,&nbsp;Shengmei Ji,&nbsp;Liming Wu","doi":"10.1007/s00705-024-06185-2","DOIUrl":"10.1007/s00705-024-06185-2","url":null,"abstract":"<div><p>Members of the fungal genus <i>Stagonosporopsis</i> are important plant pathogens that can cause severe disease on a wide range of economically important plants and crops. Here, a novel victorivirus, tentatively named \"Stagonosporopsis citrulli victorivirus 1\" (SciVV1), was isolated from <i>S. citrulli</i> isolate HS2-8. The SciVV1 genome is 5,163 nucleotides in length, with a predicted GC content of 63.85%, and contains two open reading frames (ORF1 and ORF2), which overlap at an AUGA sequence. ORF1 and ORF2 are predicted to encode a coat protein (CP) and an RNA-dependent RNA polymerase (RdRp). A phylogenetic tree based on RdRp amino acid (aa) sequences showed that SciVV1 clustered together with members of the genus <i>Victorivirus</i> in the family <i>Pseudototiviridae</i>. Our results indicate that SciVV1 is a novel victorivirus. This is the first report of the complete genome sequence of SciVV1 infecting <i>S. citrulli</i>.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811108","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":"Direct TaqMan assay for the detection and genotyping of bovine viral diarrhea virus types 1 and 2","authors":"Shakir Ullah,&nbsp;Kosuke Notsu,&nbsp;Akatsuki Saito,&nbsp;Tamaki Okabayashi,&nbsp;Hirohisa Mekata,&nbsp;Norikazu Isoda,&nbsp;Satoshi Sekiguchi","doi":"10.1007/s00705-024-06207-z","DOIUrl":"10.1007/s00705-024-06207-z","url":null,"abstract":"<div><p>Bovine viral diarrhea (BVD), caused by bovine viral diarrhea virus (BVDV), has a significant economic impact on affected farms worldwide. For effective disease control, it is crucial to select an appropriate vaccine based on the specific genotype of BVDV. Therefore, developing a rapid and reliable assay to detect and genotype BVDV is imperative for controlling the spread of disease. In this study, we developed a TaqMan assay to detect and genotype BVDV types 1 and 2 directly in bovine serum without extraction of RNA. The direct BVDV TaqMan assay effectively detected both BVDV1 and BVDV2 with confirmed specificity and showed no cross-reactivity with any of the other viruses tested, including bovine respiratory syncytial virus, bovine coronavirus, Akabane virus, bovine herpesvirus 1, bovine parainfluenza virus 3, bovine immunodeficiency virus, and bovine leukemia virus. The assay could detect the virus in serum samples with a titer as low as 10² TCID₅₀/mL in two out of three trials for BVDV1 and all three trials for BVDV2, indicating that its sensitivity is equivalent to that of virus isolation. Our findings represent a significant advancement in BVDV detection and typing directly from bovine serum.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00705-024-06207-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811107","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":"Characterisation of the genetic diversity of citrus viroid VII using amplicon sequencing","authors":"Grant A. Chambers,&nbsp;Andrew D.W. Geering,&nbsp;Daniel R. Bogema,&nbsp;Paul Holford,&nbsp;Georgios Vidalakis,&nbsp;Nerida J. Donovan","doi":"10.1007/s00705-024-06191-4","DOIUrl":"10.1007/s00705-024-06191-4","url":null,"abstract":"<div><p>Viroids occur in plants as swarms of sequence variants clustered around a dominant variant, leading to adoption of the term ‘quasispecies’ to describe the viroid population in an individual host. The composition of the quasispecies can potentially change according to the age of the infection, the position of the leaf or branch in the canopy, and the host species. The primary aim of this study was to investigate the quasispecies concept for citrus viroid VII (CVd-VII), a recently discovered member of the family <i>Pospiviroidae</i>. Three experiments were conducted to determine factors affecting viroid variability (i) within different tissues of a lemon plant, (ii) among different plants of the same species (citron), and (iii) among different species and hybrids of citrus. Using two primer sets to produce amplicons for high-throughput sequencing, viroid population profiles were generated for each sample. The number of variants that were identified with both primer sets ranged from 2 to 13 per sample, and each sample comprised 1 to 4 major (&gt; 10% sample) variants. The composition of variants differed in samples from different plants and among tissue types of a single plant. Single-nucleotide polymorphisms (SNPs), mostly in the form of substitutions, were the primary source of variation; in this study, SNPs were observed in approximately 10% of the viroid genome. The results of the three experiments indicate that CVd-VII follows the quasispecies model as reported for other viroids and that variability occurs in viroid populations in different tissue types and host species.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00705-024-06191-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811109","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":"Complete genome sequence of a novel bipartite begomovirus infecting butterfly pea (Clitoria ternatea L.) in India","authors":"Mohammad Akram,&nbsp;Deepender Kumar,&nbsp;Naimuddin Kamaal","doi":"10.1007/s00705-024-06203-3","DOIUrl":"10.1007/s00705-024-06203-3","url":null,"abstract":"<div><p>In India, plants from the non-cultivated, horticultural, and agricultural categories are commonly infected with various begomoviruses, most of which produce yellow mosaic, bright yellow mosaic, or curling symptoms on leaves. In this study, the complete genome of a new bipartite begomovirus causing yellow mosaic disease (YMD) in butterfly pea (<i>Clitoria ternatea</i> L.) was characterized using rolling-circle amplification followed by restriction digestion, cloning, and sequencing to obtain the full-length DNA-A (2727 nt) and DNA-B (2648 nt) sequences. The DNA-A and DNA-B components have a genome organization that is typical of the Old World bipartite begomoviruses, and the common regions (95 nt) of DNA-A and DNA-B share 91% nucleotide sequence identity, which is well above the threshold (&gt;85%) for them to be considered cognate components. Both DNA molecules contain a begomovirus nonanucleotide motif, conserved iterons, and a putative stem-loop structure. The DNA-A of this virus was found to be most similar to that of Cajanus scarabaeoides yellow mosaic virus (CsYMV), with 82.61% nucleotide sequence identity, which is far below the species demarcation threshold (&lt; 91%) for begomoviruses, whereas the DNA-B sequence showed the most similarity (77.16% identity) to that of Rhynchosia yellow mosaic virus (RhYMV). In phylogenetic analysis, both DNA-A and DNA-B were formed a clade with the corresponding genome segments of other YMD-causing begomoviruses. Based on these characteristics, this virus, for which the name “butterfly pea yellow mosaic virus” (BpYMV) is proposed, should be considered a member of a new species in the genus <i>Begomovirus</i>.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"170 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805983","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}