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  • Recommendations for the nomenclature of enteroviruses and rhinoviruses
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-25
    P. Simmonds, A. E. Gorbalenya, H. Harvala, T. Hovi, N. J. Knowles, A. M. Lindberg, M. S. Oberste, A. C. Palmenberg, G. Reuter, T. Skern, C. Tapparel, K. C. Wolthers, P. C. Y. Woo, R. Zell

    Abstract Enteroviruses (EVs) and rhinoviruses (RVs) are significant pathogens of humans and are the subject of intensive clinical and epidemiological research and public health measures, notably in the eradication of poliovirus and in the investigation and control of emerging pathogenic EV types worldwide. EVs and RVs are highly diverse in their antigenic properties, tissue tropism, disease associations and evolutionary relationships, but the latter often conflict with previously developed biologically defined terms, such as “coxsackieviruses”, “polioviruses” and “echoviruses”, which were used before their genetic interrelationships were understood. This has created widespread formatting problems and inconsistencies in the nomenclature for EV and RV types and species in the literature and public databases. As members of the International Committee for Taxonomy of Viruses (ICTV) Picornaviridae Study Group, we describe the correct use of taxon names for these viruses and have produced a series of recommendations for the nomenclature of EV and RV types and their abbreviations. We believe their adoption will promote greater clarity and consistency in the terminology used in the scientific and medical literature. The recommendations will additionally provide a useful reference guide for journals, other publications and public databases seeking to use standardised terms for the growing multitude of enteroviruses and rhinoviruses described worldwide.

    更新日期:2020-01-26
  • A recombinant infectious bronchitis virus from a chicken with a spike gene closely related to that of a turkey coronavirus
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-25
    Yan Wang, Xuejiao Cui, Xu Chen, Shixing Yang, Yu Ling, Qianben Song, Su Zhu, Luying Sun, Chuang Li, Yu Li, Xutao Deng, Eric Delwart, Wen Zhang

    Abstract Using viral metagenomics, the complete genome sequence of an infectious bronchitis virus (IBV) strain (named ahysx-1) from a fecal sample from a healthy chicken in Anhui province, China, was determined. The genome sequence of ahysx-1 was found to be very similar to that of IBV strain ck/CH/LLN/131040 (KX252787), except for the spike gene region, which is similar to that of a turkey coronavirus strain (EU022526), suggesting that ahysx-1 is a recombinant. Recombination analysis and phylogenetic analysis based on the genomic sequences of ahysx-1 and other related strains confirmed that ahysx-1 appears to be a recombinant resulting from a recombination event that occurred between a chicken coronavirus and a turkey coronavirus. Further studies need to be performed to determine whether this recombinant IBV strain is pathogenic and whether it is transmitted between chickens and turkeys.

    更新日期:2020-01-26
  • Identification and genomic characterization of a novel tobamovirus from prickly pear cactus
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-24
    Héctor Salgado-Ortíz, Rodolfo De La Torre-Almaraz, Jesús Ángel Sánchez-Navarro, Vicente Pallás

    Abstract In this work, we describe the complete sequence and genome organization of a novel tobamovirus detected in a prickly pear plant (Opuntia sp.) by high-throughput sequencing, tentatively named “opuntia virus 2”. The full genome of opuntia virus 2 is 6,453 nucleotides in length and contains four open reading frames (ORFs) coding for the two subunits of the RNA polymerase, the movement protein, and the coat protein, respectively. Phylogenetic analysis using the complete nucleotide sequence revealed that the virus belongs to the genus Tobamovirus (family Virgaviridae), showing the highest nucleotide sequence identity (49.8%) with cactus mild mottle virus (CMMoV), being indicating that it belongs in the Cactaceae subgroup of tobamoviruses.

    更新日期:2020-01-24
  • Characterization of the first bovine gammaherpesvirus 4 strain isolated from an aborted bovine fetus in Argentina
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-24
    Romeo Florencia, Manrique Julieta, Perez Sandra, Louge Uriarte Enrique, Marín Maia, Cantón German, Maria R. Leunda, González Altamiranda Erika, Pereyra Susana, Spetter Maximiliano, Odeón Anselmo, Jones Leandro, Andrea E. Verna

    Abstract Bovine herpesvirus 4 (BoHV-4) is increasingly believed to be responsible for several disorders of the bovine reproductive tract. The first characterization of BoHV-4 in Argentina was from samples from an aborted fetus. Argentinean isolates are highly diverse and are phylogenetically grouped in three genotypes. In this study, we describe the isolation of BoHV-4 from a bovine fetus with a gestational age of 8 months and without macroscopic lesions. Genetic analyses revealed that the isolated strain belongs to genotype 2. This is the first report on the presence of infectious BoHV-4 in tissues from an aborted bovine fetus.

    更新日期:2020-01-24
  • Molecular characterization of a novel botoulivirus from the phytopathogenic fungus Sclerotinia minor
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-24
    Na Liang, Dan Yang, Mingde Wu, Jing Zhang, Guoqing Li, Long Yang

    Abstract In this study, the complete genomic sequence of a novel botoulivirus (Sclerotinia minor botoulivirus 1, SmBV1) from the phytopathogenic fungus Sclerotinia minor strain LC45 was determined. The genome of SmBV1 is 2,882 nucleotides in length and contains a single large open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis showed that SmBV1 clustered with the botoulivirus clade within the family Botourmiaviridae. This is the first report of a botoulivirus in S. minor.

    更新日期:2020-01-24
  • Development of a cross-priming isothermal amplification assay based on the glycoprotein B gene for instant and rapid detection of feline herpesvirus type 1
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-24
    Yuxin Tan, Guoying Dong, Hefeng Xu, Jiangting Niu, Wei Lu, Kai Wang, Hao Dong, Shuang Zhang, Hailong Huang, Guixue Hu

    Abstract A cross-priming isothermal amplification (CPA) assay was developed for detection of feline herpesvirus type 1 (FHV-1). In this assay, the target fragment of the FHV-1 glycoprotein B gene is amplified rapidly by Bst DNA polymerase at a constant temperature (63 °C, 45 min), using a simple thermostat. The assay had no cross-reactions with four types of feline viruses, and the detection limit was 100 copies/μl. The positive rate of clinical samples from CPA was 100% consistent with qPCR but higher than ordinary PCR, indicating its superiority to ordinary PCR. Visualization was achieved using SYBR Green I dye.

    更新日期:2020-01-24
  • Complete genome sequence of MMP7, a novel Meiothermus bacteriophage of the family Myoviridae isolated from a hot spring
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-21
    Feng Wang, Yao Xiao, Yan Xiong, Yunjian Jiao, Qilin Zhang, Lianbing Lin

    Abstract The genome sequence of a novel Meiothermus bacteriophage, named MMP7, which was isolated from Tengchong hot spring in Yunnan Province of China and belongs to the family Myoviridae, was sequenced in this study. To the best of our knowledge, this is the first reported genome sequence of a Meiothermus phage, which has a circular DNA genome of 32,864 bp and a GC content of 64%. The MMP7 genome contains 53 putative protein-encoding genes but no rRNA or tRNA genes, and it exhibits low overall sequence similarity and no significant homology to phage genomes whose sequences are publicly available, suggesting that MMP7 is a novel phage. Consistent with current taxonomic results, whole-genome-based phylogenetic analysis revealed that Meiothermus phage MMP7 has close evolutionary relationship to Thermus phages. Together, our results could be helpful for discovering new thermostable antimicrobial agents and understanding the evolution and genetic diversity of Meiothermus phages in extreme environments.

    更新日期:2020-01-22
  • High prevalence and viremia of human pegivirus 2 in the HIV-infected population in Honghe Prefecture, Yunnan Province
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-21
    Tianyi Li, Shixing Tang, Yingying Su, Zuoyi Bao, Xiaolin Wang, Yongjian Liu, Hanping Li, Jingwan Han, Zhichao Pei, Zhengwei Wan, Hang Fan, Yigang Tong, Lin Li, Ning Wang, Jingyun Li

    Abstract Human pegivirus 2 (HPgV-2) is a recently recognized pegivirus of the family Flaviviridae. To investigate the epidemic features of HPgV-2 circulating in the human immunodeficiency virus (HIV)-infected population, we tested for antibodies and viral RNA of HPgV-2 and hepatitis C virus (HCV) with retrospective plasma samples collected from 771 HIV infections with multiple risk behaviors in Honghe Prefecture of Yunnan Province. A total of 195 subjects (25.29%) were seroreactive to HPgV-2, and 41 (5.32%) were RNA positive. Although the positive rate of HPgV-2 antibodies in HIV/HCV-coinfected individuals (27.69%) was significantly higher than that of HIV monoinfections (20.82%) (p = 0.036), this is the first report of HPgV-2 viremia in HIV-infected individuals without HCV infection and the presence of two HPgV-2 lineages in China. Our data indicate that HPgV-2 can also be transmitted sexually, which might be facilitated when combined with HCV infection, injecting drug use, and risky sexual behavior, which appear to have a synergistic effect on HPgV-2 infection. Phylogenetic analysis of 26 near-full-length genome sequences showed that the HPgV-2 strains in China are divided into two clusters.

    更新日期:2020-01-22
  • Design of a novel rapid immunoassay for simultaneous detection of hepatitis C virus core antigen and antibodies
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-21
    Jayendrakumar Patel, Preeti Sharma

    Abstract HCV is a potential cause of viral hepatitis, which leads to blood-borne chronic hepatitis, liver cirrhosis and hepatocellular carcinoma. Anti-HCV antibody detection assays detect HCV infection after approximately 70 days. HCV core antigen can be detected much earlier than anti-HCV antibodies. However, it disappears soon after the appearance of anti-HCV antibodies. Thus, there is a need for a rapid assay for simultaneous detection of HCV core antigen and anti-HCV antibodies for early diagnosis of HCV infection. A rapid diagnostic assay (HCV Ag-Ab Combo) for simultaneous detection of HCV core antigen and anti-HCV antibodies for early diagnosis of HCV infection was developed. HCV Ag-Ab Combo was evaluated in order to determine its potential for detection of HCV infection earlier than anti-HCV antibody detection assays. We compared the sensitivity of the newly developed assay with anti-HCV antibody detection assays (ELISA [HCV Ab ELISA] and rapid test [HCV Ab Rapid]) and HCV core antigen/anti-HCV antibody detection ELISA (HCV Ag-Ab ELISA). This study included 11 samples that were found positive in HCV RNA detection and HCV Ag-Ab ELISA but negative in HCV antibody detection assays (HCV Ab ELISA and rapid), 10 samples that were found positive in HCV Ag-Ab ELISA and HCV Ab ELISA but negative in HCV Ab Rapid, 69 samples that were found positive in HCV Ag-Ab ELISA, HCV Ab ELISA, and HCV Ab Rapid, and 509 samples that were found negative in HCV Ag-Ab ELISA, HCV Ab ELISA, and HCV Ab Rapid. Three seroconversion panels, PHV 913, PHV 911 (M) and PHV904-00-1.0, and a HCV RNA genotype qualification panel (2400-0182) acquired from Seracare Life Sciences (USA) were also tested. HCV Ag-Ab Combo showed a combined sensitivity and specificity of 100% when tested with 90 samples that were positive for HCV by HCV Ag-Ab ELISA and 509 HCV-negative samples. Its positive predictive value (PPV) and negative predictive value (NPV) were found to be 100%. It detected HCV infection approximately 7 to 12 days earlier than the HCV Ab detection assays, and its performance was not affected when testing different genotypes of HCV. HCV Ag-Ab Combo did not detect HCV infection as early as HCV RNA or HCV Ag-Ab ELISA. HCV Ag-Ab Combo provided a significant improvement for the early detection of HCV infection during the preseroconversion phase when compared with anti-HCV antibody detection assays. It could be a useful screening assay, and an alternative to HCV RNA detection or HCV Ag-Ab ELISA when nucleic acid technologies cannot be implemented.

    更新日期:2020-01-22
  • A novel circular Rep-encoding single-stranded DNA virus detected in Agrotis ipsilon (Lepidoptera: Noctuidae) in China
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-20
    Fan Yang, Xianming Yang, Kongming Wu

    Abstract Long-distance migratory insects carry microorganisms that can potentially play a crucial role in the life cycles of their hosts. Here, we used Illumina and Sanger sequencing to determine the complete genome sequence of a novel circular Rep-encoding single-stranded (ss) DNA virus from an important migratory pest, Agrotis ipsilon (Hufnagel). The full genome of this new virus is about 2, 242 nt in length and shares 55-75% genome-wide pairwise sequence identity with members of the family Genomoviridae but 91% nucleotide sequence identity with finch-associated genomovirus 3 isolate S30P_D, which is tentatively abbreviated “FaGmV-3”. Viral infection rates in A. ipsilon from Yantai, Langfang and Xinxiang were 4.5% (n = 88), 11.8% (n = 85) and 0% (n = 35), respectively. Phylogenetic analysis based on the deduced amino acid sequence of Rep indicated that the Agrotis ipsilon-associated virus is closely related to members of the genus Gemykibivirus, and we propose it to be a new member of this genus. Hence, it is tentatively named “Agrotis ipsilon-associated genomovirus” (AiGmV).

    更新日期:2020-01-21
  • The small molecule AZD6244 inhibits dengue virus replication in vitro and protects against lethal challenge in a mouse model
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-16
    Leonardo C. de Oliveira, Aryádina M. Ribeiro, Jonas D. Albarnaz, Alice A. Torres, Luís F. Z. Guimarães, Amelia K. Pinto, Scott Parker, Konstantin Doronin, James D. Brien, Mark R. Buller, Cláudio A. Bonjardim

    Dengue virus (DENV) is the most common mosquito-borne viral disease. The World Health Organization estimates that 400 million new cases of dengue fever occur every year. Approximately 500,000 individuals develop severe and life-threatening complications from dengue fever, such as dengue shock syndrome (DSS) and dengue hemorrhagic fever (DHF), which cause 22,000 deaths yearly. Currently, there are no specific licensed therapeutics to treat DENV illness. We have previously shown that the MEK/ERK inhibitor U0126 inhibits the replication of the flavivirus yellow fever virus. In this study, we demonstrate that the MEK/ERK inhibitor AZD6244 has potent antiviral efficacy in vitro against DENV-2, DENV-3, and Saint Louis encephalitis virus (SLEV). We also show that it is able to protect AG129 mice from a lethal challenge with DENV-2 (D2S20). The molecule is currently undergoing phase III clinical trials for the treatment of non-small-cell lung cancer. The effect of AZD6244 on the DENV life cycle was attributed to a blockade of morphogenesis. Treatment of AG129 mice twice daily with oral doses of AZD6244 (100 mg/kg/day) prevented the animals from contracting dengue hemorrhagic fever (DHF)-like lethal disease upon intravenous infection with 1 × 105 PFU of D2S20. The effectiveness of AZD6244 was observed even when the treatment of infected animals was initiated 1-2 days postinfection. This was also followed by a reduction in viral copy number in both the serum and the spleen. There was also an increase in IL-1β and TNF-α levels in mice that were infected with D2S20 and treated with AZD6244 in comparison to infected mice that were treated with the vehicle only. These data demonstrate the potential of AZD6244 as a new therapeutic agent to treat DENV infection and possibly other flavivirus diseases.

    更新日期:2020-01-16
  • Recombinant adenovirus carrying a core neutralizing epitope of porcine epidemic diarrhea virus and heat-labile enterotoxin B of Escherichia coli as a mucosal vaccine
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-16
    Van Tan Do, Jisung Jang, Jeongho Park, Hoai Thu Dao, Kiju Kim, Tae-Wook Hahn

    Abstract Porcine epidemic diarrhea virus (PEDV) targets the intestinal mucosa in pigs. To protect against PEDV invasion, a mucosal vaccine is utilized effectively. In this study, we generated a recombinant adenovirus vaccine encoding the heat-labile enterotoxin B (LTB) and the core neutralizing epitope (COE) of PEDV (rAd-LTB-COE). The fusion protein LTB-COE was successfully expressed by the recombinant adenovirus in HEK293 cells, and the immunogenicity of the vaccine candidate was assessed in BALB/c mice and piglets. Three intramuscular or oral vaccinations with rAd-LTB-COE at two-week intervals induced robust humoral and mucosal immune responses. Moreover, a cell-mediated immune response was promoted in immunized mice, and the neutralizing antibody inhibited both the vaccine strain and the emerging PEDV isolate. Immunization experiments in piglets revealed that rAd-LTB-COE was immunogenic and induced good immune responses in piglets. Further studies are required to evaluate the efficacy of rAd-LTB-COE against a highly virulent PEDV challenge.

    更新日期:2020-01-16
  • Molecular characterization and genetic diversity of the infectious laryngotracheitis virus strains circulating in Egypt during the outbreaks of 2018 and 2019
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-14
    Mahmoud Bayoumi, Mohamed El-Saied, Haitham Amer, Mostafa Bastami, Ezz Eldein Sakr, Magdy El-Mahdy

    Abstract Infectious laryngotracheitis (ILT) is a respiratory disease that causes significant economic losses in the poultry industry worldwide. In this study, ILT outbreaks were reported on 30 farms located in eight Egyptian governorates between January 2018 and May 2019. Gross examination of diseased chickens revealed congestion and hemorrhage of laryngeal and tracheal mucosa with fibrinohemorrhagic casts and/or caseous material in the lumens. Histopathological examination showed epithelial sloughing, syncytium formation, heterophilic exudation, and development of eosinophilic intranuclear inclusion bodies. Infectious laryngotracheitis virus (ILTV) antigen was detected in the tracheal epithelium, infiltrated inflammatory cells, and syncytial cells, using immunohistochemistry. PCR targeting a portion of the thymidine kinase gene was further utilized to confirm the presence of ILTV DNA. The complete coding sequences of three envelope glycoprotein genes, gG, gD, and gJ, and a partial sequence of the infected cell polypeptide 4 (ICP4) gene from samples representing all of the farms and disease outbreaks were determined. Five prototype strains with unique sequences were chosen for detailed molecular characterization. Sequence comparisons and phylogenetic analysis of the partial ICP4 gene revealed that two strains were chicken embryo origin (CEO)-vaccine-like strains, and three were tissue culture origin (TCO)-vaccine-like strains. Analysis of the gJ gene sequence indicated that all of the strains were CEO vaccine-like strains. It was predicted that the latter three strains were recombinants of CEO- and TCO-vaccine-like strains. In conclusion, immunohistochemistry coupled with multi-genomic PCR sequencing proved to be efficient for identification and typing of ILTV strains during disease outbreaks. Both CEO-vaccine-like and recombinant virus strains were circulating in Egypt during the 2018 and 2019 outbreaks.

    更新日期:2020-01-15
  • The pattern of antiviral protein expression induced by interferon λ1 in peripheral blood mononuclear cells of patients with chronic hepatitis C virus infection
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-11
    Hamzeh Choobin, Taravat Bamdad, Mehdi Shekarabi

    Abstract Interferon lambda was discovered in recent years to be an antiviral agent, and research on different aspects of this antiviral factor in viral infection and investigations of its effectiveness are also progressing. The immunological effects of interferon lambda on different cell populations is not precisely known, which may be due to its use of a heterodimeric receptor consisting of IL-10R2 and IFN-λR1, which are not broadly expressed in all types of cells. In the present study, signaling by interferon lambda and its effect on the expression of hepatitis C virus (HCV) proteins were measured, and the expression pattern of some antiviral proteins and IL-10 levels were investigated in peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from 50 patients with chronic genotype 1a HCV infection and 10 healthy individuals as controls. The PBMCs were treated with various doses of interferon lambda at different times of cultivation. Real-time PCR was used for relative quantification of Mxa, PKR, OAS, ISG15 and HCV core mRNAs. Expression of the NS5A protein was measured by flow cytometry, and IL-10 production was assessed by ELISA. A significant increase in the expression of mRNA encoding antiviral proteins and a decrease in the expression of mRNAs encoding the HCV core protein were observed when cells were treated with interferon lambda in an intermittent manner. The expression of HCV NS5A protein and interleukin 10 levels were also lower than in the control group. It was shown that the maximum antiviral effect of interferon lambda in PBMCs is dependent on the dose and treatment time.

    更新日期:2020-01-13
  • Retraction Note to: Mitochondrial bioenergy alterations in avian HD11 macrophages infected with infectious bronchitis virus.
    Arch. Virol. (IF 2.261) Pub Date : null
    Sergio E L da Silva,Helena L Ferreira,Andrea F Garcia,Felipe E S Silva,Roberto Gameiro,Carolina U F Fabri,Dielson S Vieira,Tereza C Cardoso

    The Editor-in-Chief has retracted this article [1]. Figures 1A, 1D and 2B (bottom right) are identical with Figures 1A, 1H and 1B respectively in another article [2] which reports a study in a different species. In addition, Table 1 contains data presented in a third article [3], which also reports a study in a different species. The Editor-in-Chief therefore no longer has confidence in the validity of the data and the conclusions drawn. Tereza C. Cardoso disagrees with this retraction. Helena L. Ferreira agrees with this retraction. Sergio E. L. da Silva, Andrea F. Garcia, Felipe E. S. Silva, Roberto Gameiro, Carolina U. F. Fabri and Dielson S. Vieira have not responded to any correspondence about this retraction.

    更新日期:2020-01-13
  • Correction to: First report of fowl aviadenovirus serotypes FAdV-8b and FAdV-11 associated with inclusion body hepatitis in commercial broiler and broiler-breeder flocks in Turkey.
    Arch. Virol. (IF 2.261) Pub Date : null
    İsmail Şahindokuyucu,Fethiye Çöven,Hamza Kılıç,Özge Yılmaz,Mustafa Kars,Öznur Yazıcıoğlu,Ercüment Ertunç,Zafer Yazıcı

    The co-author names were found missed in the original publication of this article and the complete lists of authors were updated here. The original article has been corrected.

    更新日期:2020-01-13
  • Coding-complete genome sequencing suggests that Newcastle disease virus challenge strain Herts'33 (IVMP) may represent a distinct genotype.
    Arch. Virol. (IF 2.261) Pub Date : null
    Enikő Fehér,Ádám Bálint,Szilvia Marton,Krisztina Bali,Sándor Belák,Krisztián Bányai

    We determined the genomic sequence of a Newcastle disease virus (NDV) line obtained directly from the first NDV isolate, named Herts'33. This strain shared ≤ 90% nucleotide sequence identity with the NDV sequences available in the GenBank database, and formed a distinct branch in a phylogenetic tree. This branch may be considered to represent a separate NDV genotype. Our study indicates that investigation of the genomic sequences of old NDV strains that originated from the early outbreaks of Newcastle disease may alter the phylogenetic grouping of the NDV strains and provide data on the evolution of viral genomes over time.

    更新日期:2020-01-13
  • Complete genome sequence of rose virus A, the first carlavirus identified in rose.
    Arch. Virol. (IF 2.261) Pub Date : null
    Alfredo Diaz-Lara,Dimitre Mollov,Deborah Golino,Maher Al Rwahnih

    A novel virus was discovered in a Rosa wichuraiana Crep. by high-throughput sequencing and tentatively named "rose virus A" (RVA). Based on sequence identity and phylogenetic analysis, RVA represents a new member of the genus Carlavirus (family Betaflexiviridae). The genome of RVA is 8,849 nucleotides long excluding the poly(A) tail and contains six open reading frames (ORFs). The predicted ORFs code for a replicase, triple gene block (TGB), coat protein, and nucleic acid binding protein, as in a typical carlavirus. RVA is the first carlavirus identified in rose and has the highest nucleotide sequence similarity to poplar mosaic virus. Reverse transcription-PCR-based assays were developed to confirm the presence of RVA in the original source and to screen additional rose plants.

    更新日期:2020-01-13
  • Complete nucleotide sequence of loquat virus A, a member of the family Betaflexiviridae with a novel genome organization.
    Arch. Virol. (IF 2.261) Pub Date : null
    Qiyan Liu,Liu Yang,Zhiyou Xuan,Jiaxing Wu,Yuanjian Qiu,Song Zhang,Di Wu,Changyong Zhou,Mengji Cao

    Analysis of a loquat tree with leaf curl symptoms by deep sequencing revealed a novel virus with a single-stranded RNA genome, for which the name "loquat virus A" (LoVA) was proposed. The complete genome sequence comprised 7553 nucleotides (nt) and an additional poly(A) tail at the 3' terminus. Sequence comparisons of LoVA showed moderate similarity to cherry virus A (CVA), currant virus A (CuVA), and mume virus A (MuVA), which are members of the genus Capillovirus in the family Betaflexiviridae. Phylogenetic analysis of the full-genome nt sequence and replicase-like protein supported the placement of LoVA within the genus Capillovirus. However, it has a distinct genome organization, differing from recognized capilloviruses, as it contains three open reading frames (ORFs), with the coat protein (CP) expressed separately from the replication-associated protein (RP) rather than being encoded in the same ORF. This indicates that LoVA is a novel member of the genus Capillovirus in the family Betaflexiviridae with a distinct genomic organization.

    更新日期:2020-01-13
  • Complete sequence of a new bipartite begomovirus infecting Sida sp. in Northeastern Brazil.
    Arch. Virol. (IF 2.261) Pub Date : null
    M A Macedo,C M Rêgo-Machado,M L Maliano,M R Rojas,A K Inoue-Nagata,R L Gilbertson

    In Brazil, non-cultivated plants, especially weeds, are infected with a diversity of begomoviruses and often show striking golden mosaic symptoms. In the present study, leaves showing these symptoms were collected from Sida sp. plants in Guadalupe, Piaui State, Northeastern Brazil, in 2015 and 2016. PCR tests with degenerate primers revealed the presence of begomovirus DNA-A and DNA-B components. Restriction enzyme digestion of rolling circle-amplified DNA revealed fragments totaling ~5.2 kb, indicating infection by a bipartite begomovirus. The DNA-A and DNA-B components have a genome organization typical of New World (NW) bipartite begomoviruses and a common region of 220 nucleotides (nt) with 96% identity, indicating these are cognate components. Comparisons performed with the DNA-A sequence revealed the highest nt sequence identity (84%) with that of sida angular mosaic virus (SiAMV), whereas those performed with the DNA-B sequence revealed highest identity (77%) with that of sida chlorotic vein virus (SiCVV). In phylogenetic analyses, the DNA-A sequence was placed in a strongly supported clade with SiAMV and SiCVV from Piaui, whereas the DNA-B sequence was placed in a clade with SiCVV and corchorus mottle virus. Based on the current ICTV criteria for the demarcation of begomovirus species (<91% nt sequence identity for the DNA-A component), this is a member of a new species for which the name "Sida yellow golden mosaic virus" is proposed.

    更新日期:2020-01-13
  • Genomic characterization of bacteriophage pEt-SU, a novel phiKZ-related virus infecting Edwardsiella tarda.
    Arch. Virol. (IF 2.261) Pub Date : 2019-10-21
    Sang Guen Kim,Sib Sankar Giri,Saekil Yun,Hyoun Joong Kim,Sang Wha Kim,Jung Woo Kang,Se Jin Han,Jun Kwon,Jin Woo Jun,Woo Taek Oh,Se Chang Park

    A bacteriophage infecting Edwardsiella tarda (named pEt-SU) was isolated from freshwater collected in Chung-ju, South Korea. The whole genome of pEt-SU was 276,734 bp in length, representing the first giant phage infecting Edwardsiella reported to date. A total of 284 putative open reading frames were predicted and annotated. Morphology and genome analyses verified that pEt-SU may be distantly related to the phiKZ-like phages, a well-known giant myovirus. The findings in this study provide new insights into the phages infecting E. tarda ads well as fundamental data for the study of giant phages.

    更新日期:2020-01-13
  • Complete genomic sequence of Pseudomonas lactis bacteriophage HU1 isolated from raw cow's milk.
    Arch. Virol. (IF 2.261) Pub Date : null
    Chikage Tanaka,Takahiro Nakayama,Takahiro Toba,Akiko Kashiwagi

    The lytic cold-active phage HU1, a member of the family Podoviridae, infects Pseudomonas lactis and was first isolated from raw cow's milk. In this study, we used deep sequencing to determine and analyze the DNA genome sequence of HU1. We identified a 42,551-base-pair genome comprising double-stranded DNA, with 69 predicted open reading frames and a GC content of 56.4%. A whole-genome comparison did not identify HU1 as a member of any previously reported cluster of Pseudomonas phages. By contrast, HU1 was most similar to AF, which infects P. putida, with nucleotide sequence alignment coverage of 24%. These results suggest that HU1 is a novel Pseudomonas phage.

    更新日期:2020-01-13
  • Complete genome sequence of aglaonema bacilliform virus (ABV).
    Arch. Virol. (IF 2.261) Pub Date : null
    R A Alvarez-Quinto,B E L Lockhart,J M Moreno-Martinez,N E Olszewski

    Aglaonema bacilliform virus (ABV), a member of the genus Badnavirus in the family Caulimoviridae, is associated with leaf deformation and chlorosis in Aglaonema modestum. The complete genome sequence of a Minnesota isolate of ABV was determined. The ABV genome is 7,178 bp in length and similar in size and organization to those of the members of the genus Badnavirus, containing three open reading frames (ORFs) with the potential to encode three proteins of 14.92, 13.33 and 207.95 kDa, respectively. The last ORF (ORF3) encodes a putative polyprotein with conserved domains, including zinc finger, aspartic protease, reverse transcriptase (RT) and RNase H domains, in that order. Phylogenetic analysis using the amino acid sequence of the ORF3 polyprotein showed that ABV clusters with several isolates of taro bacilliform CH virus (TaBCHV). Pairwise alignment using the highly conserved RT/RNase H region reveals that ABV has the highest level of identity (71%) at the nucleotide level to a Hawaiian isolate of TaBCHV.

    更新日期:2020-01-13
  • Complete genome sequence of a novel capillovirus infecting Hevea brasiliensis in China.
    Arch. Virol. (IF 2.261) Pub Date : null
    Zhaotong Li,Hongxing Wang,Ruibai Zhao,Ze Zhang,Zhihui Xia,Jinling Zhai,Xi Huang

    Tapping panel dryness (TPD) is a complex disorder that causes partial or complete cessation of latex drainage upon tapping of rubber trees (Hevea brasiliensis). In this work, we determined the complete genome sequences of a novel virus identified in a rubber tree with TPD syndrome in China. The genome of the virus consists of 6811 nt and possesses two overlapping open reading frames (ORF1 and ORF2), encoding a polyprotein and a movement protein, respectively. The polyprotein shares 37% amino acid sequence identity with cherry virus A (CVA, ARQ83874.1) over 99% coverage. The genome architecture is similar to that of members of the genus Capillovirus (family Betaflexiviridae). Phylogenetic analysis of the replicase proteins showed that the virus clustered together with members of the genus Capillovirus. The new virus is tentatively called "rubber tree virus 1" (RTV1). RTV1 is the first virus reported to infect rubber trees. This work lays a foundation for research into finding the potential causal agent of TPD in Hevea brasiliensis.

    更新日期:2020-01-13
  • Complete genomic sequence of tea-oil camellia deltapartitivirus 1, a novel virus from Camellia oleifera.
    Arch. Virol. (IF 2.261) Pub Date : null
    L-P Wu,Y-M Du,H Xiao,L Peng,R Li

    Three viral contig sequences, which represented complete genome of a novel virus with three dsRNAs of 1,712 nucleotides (nt) (dsRNA1), 1,504 nt (dsRNA2) and 1,353 nt (dsRNA3), were found in tea-oil camellia plants by high-throughput sequencing analysis. The three dsRNAs were re-sequenced by RT-PCR cloning. The largest dsRNA, dsRNA1, had a single open reading frame (ORF) that encoded a putative 52.7-kDa protein of a putative viral RNA-dependent RNA polymerase (RdRp). DsRNA2 and dsRNA3 were predicted to encode putative capsid proteins (CPs) of 40.47 kDa and 40.59 kDa, respectively. The virus, which is provisionally named "tea-oil camellia deltapartitivirus 1", shared amino acid sequence itentities of 36.09-69.18% with members of the genus Deltapartitivirus on RdRp. Phylogenetic analysis based on RdRp also placed the new virus and other deltapartitiviruses together in a group, suggesting that this virus should be considered a new member of the genus Deltapartitivirus.

    更新日期:2020-01-13
  • Transition in genetic constellations of H3N8 and H4N6 low-pathogenic avian influenza viruses isolated from an overwintering site in Japan throughout different winter seasons
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-10
    Ahmed Magdy Khalil, Natsuko Nishi, Isshu Kojima, Wataru Fukunaga, Masakazu Kuwahara, Tatsunori Masatani, Tsutomu Matsui, Makoto Ozawa

    The Izumi plain in Kagoshima Prefecture, Japan, is an overwintering site for migratory ducks and endangered cranes. We have surveyed avian influenza viruses (AIVs) in this area since 2012 and isolated low-pathogenic AIVs (LPAIVs) of various subtypes every winter season. H3N8 LPAIVs were isolated during the 2012/13 and 2016/17 seasons, and H4N6 LPAIVs were isolated during the 2012/13 and 2013/14 seasons. In the 2017/18 season, one H3N8 and two H4N6 LPAIV strains were isolated from environmental water samples. Genetic and phylogenetic analysis for each gene segment from these H3N8 and H4N6 LPAIVs suggested that our isolates were genetic reassortants generated by intermixing between AIVs circulating not only in Eurasia but also in Africa and/or North America. Comparison of the genetic constellations of our three isolates with their counterparts isolated during previous seasons from the Izumi plain revealed a drastic transition in the genetic constellations of both subtypes. These findings emphasize the importance of continuous surveillance of AIVs on the Izumi plain.

    更新日期:2020-01-11
  • Molecular characterization of two previously undescribed begomovirus-associated alphasatellite molecules infecting malvaceous species in Cameroon
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-09
    W. N. Leke, A. Kvarnheden, S. Avelar, J. K. Brown

    Abstract Two begomovirus-associated alphasatellites were isolated from okra and a malvastrum plant (Malvaceae) in Cameroon. The complete nucleotide sequences of the okra- and malvastrum-infecting alphasatellites were 1375 and 1416–1418 nucleotides, respectively, and both exhibited features characteristic of other alphasatellites. Based on pairwise sequence comparisons, these previously undescribed alphasatellites are members of distinct species in the genera Colecusatellite and Gosmusatellite and have been tentatively named “pepper yellow vein Mali alphasatellite” and “cotton leaf curl Gezira alphasatellite3”, respectively. Taken together with previous studies, alphasatellites endemic to Cameroon appear to be more diverse and infect plants of many more species and families than currently recognized.

    更新日期:2020-01-11
  • Prevalence and genotype distribution of human papillomavirus in Zhengzhou, China, in 2016
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-06
    Jinjin Liu, Shuhuan Ma, Chuan Qin, Suiling Zheng, Zhaoyun Chen, Yi Huang, Junli Xiong, Yuqi Huo

    Abstract In this study, the prevalence and genotype distribution of human papillomavirus (HPV) in 49,793 women aged 25–64 years were determined by fluorescent real-time polymerase chain reaction (PCR) assay. HPV was detected in 6,020 women, giving a prevalence of 12.09% (6020/49,793). Single and multiple infections accounted for 71.81% (4323/6020) and 28.19% (1697/6020) of total infections, respectively. The most commonly found genotypes were HPV52 (19.90%, 1198/6020) and HPV16 (19.17%, 1154/6020), followed by HPV58 (13.11%, 789/6020), HPV81 (10.10%, 608/6020) and HPV56 (9.00%, 542/6020). The prevalence of HPV increased with age and was highest in the 54- to 64-year-old age group. The genotypes covered by the nonavalent HPV vaccine accounted for 39.32% (2367/6020) and 22.81% (1373/6020) of the total monoinfections and polyinfections, respectively. This study indicates a high HPV infection rate in women in the city of Zhengzhou and a large percentage of women are infected with single or multiple high-risk HPV genotypes that cannot be prevented using the current nonavalent HPV vaccine. Vaccines incorporating more HPV genotypes and extended age coverage for the current nonavalent vaccine might be necessary to better prevent HPV-related cervical cancer.

    更新日期:2020-01-06
  • Characterization of sixteen Achromobacter xylosoxidans phages from Abidjan, Côte d’Ivoire, isolated on a single clinical strain
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-02
    Christiane Essoh, Jean-Philippe Vernadet, Gilles Vergnaud, Adama Coulibaly, Adèle Kakou-N’Douba, Assavo S.-P. N’Guetta, Thimotée Ouassa, Christine Pourcel

    Abstract Sixteen bacteriophages of Achromobacter xylosoxidans distributed into four genera have been isolated from sewage water in Abidjan, Côte d’Ivoire, using a single clinical strain, and their genomes have been sequenced. Three podoviruses belonged to the genus Phikmvvirus, and these represent the first A. xylosoxidans phages of this genus. Seven podoviruses, distributed into three groups, belonged to the genus Jwalphavirus. Among the siphoviruses, three revealed similarities to Pseudomonas phage 73 and members of the genus Septimatrevirus, and three were YuA-like phages. The virulence of these phages toward a panel of 10 genetically diverse strains was tested, with the phiKMV-like phages showing the broadest host range.

    更新日期:2020-01-04
  • Molecular characterization of a new partitivirus, MbPV1, isolated from the entomopathogenic fungus Metarhizium brunneum in China
    Arch. Virol. (IF 2.261) Pub Date : 2020-01-01
    Ping Wang, Guogen Yang, Najie Shi, Bo Huang

    Abstract Mycoviruses from Metarhizium anisopliae have been extensively studied, but their sequences have yet to be deposited in the NCBI database. In the present study, we characterized a new partitivirus obtained from the entomogenous fungus Metarhizium brunneum, named “Metarhizium brunneum partitivirus 1” (MbPV1). The complete genome of MbPV1, determined by metagenomic sequencing, RT-PCR, and RACE, comprised two dsRNA segments of 1,829 bp and 1,720 bp, respectively. Both dsRNAs contained a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp) and a coat protein (CP), respectively. The sequences of the RdRp and CP showed the highest similarity (61.4% and 44.4% identity, respectively) to those of Colletotrichum eremochloae partitivirus 1 (CePV1), which were obtained from the NCBI database. A phylogenetic tree based on the RdRp sequence showed that MbPV1 clustered with members of the proposed genus “Epsilonpartitivirus”, belonging to family Partitiviridae. Here, we propose that MbPV1 is a member of a new species of the proposed genus “Epsilonpartitivirus”. This is the first sequence data report of a new mycovirus from a member of the genus Metarhizium.

    更新日期:2020-01-04
  • Isolation and characterization of the novel Virgibacillus -infecting bacteriophage Mimir87
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-24
    Nikita Zrelovs, Elina Cernooka, Andris Dislers, Andris Kazaks

    The novel bacterial virus Mimir87, infecting the salt-tolerant bacterium Virgibacillus halotolerans, was isolated from worker honey bees. Mimir87 has an elongated head and a long non-contractile tail consistent with members of the Siphoviridae phage family. The phage genome comprises 48,016 base pairs and encodes 68 predicted proteins, to 34 of which a function could be assigned from homology analysis. The phage encodes two metabolism-related transporter proteins previously not observed in bacteriophage genomes. Mimir87 displays some relatedness to several Bacillus and Paenibacillus viruses; however, the overall sequence dissimilarity suggests Mimir87 to be a representative of a new phage genus.

    更新日期:2020-01-04
  • Co-contamination of food products from family farms in an environmental disaster area in Southeast Brazil with pathogenic bacteria and enteric viruses
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-23
    Sergio Vinicius de Castro Carvalho, Paula Rogovski, Rafael Dorighello Cadamuro, Aline Viancelli, William Michelon, Deyse Almeida dos Reis, Igor Aparecido Santana das Chagas, Regiana Assenço, Maria Célia da Silva Lanna, Helen Treichel, Gislaine Fongaro

    Abstract In the present study, we evaluated the degree of contamination of fresh vegetables, cheeses and jellies from disaster area in Brazil with bacteria and enteric viruses. Food samples (n = 350) were tested for Escherichia coli, Salmonella spp., Listeria monocytogenes, Staphylococcus spp., and enteric viruses (rotavirus A (RVA), human adenovirus (HAdV), hepatitis A virus (HAV), and human norovirus (HNoV). E. coli was present in 56% of the samples, Salmonella spp. was present in 14% of the samples, L. monocytogenes and Staphylococcus spp. (coagulase-positive) were present in 36% of the samples. The enteric viruses RVA and HAdV were detected in cheeses and vegetables.

    更新日期:2020-01-04
  • Development and application of an indirect ELISA for the serological detection of duck Tembusu virus infection based on the NS1 protein antigen
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-23
    Qi Zhou, Zhuangli Bi, Dongdong Yin, Xiangxue Gu, Zejun Xu, Rong Huang, Xue Xing, Kezong Qi, Guijun Wang

    Abstract Duck Tembusu virus (DTMUV) has caused significant economic losses in China since 2010. However, there is still a lack of effective methods to diagnose the disease caused by this virus, and especially to differentiate infection from vaccination. In this study, we established a novel indirect enzyme-linked immunosorbent assay (iELISA) and performed a retrospective serological survey for DTMUV in Anhui province, China. Our results show that the iELISA displayed high specificity sensitivity, and with no serological cross-reaction with other duck pathogens. These findings indicate that the newly developed iELISA could be a useful screening tool for large-scale monitoring of the epidemiology of DTMUV infection in ducks.

    更新日期:2020-01-04
  • A new polycipivirus identified in Colobopsis shohki
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-21
    Fumika Fukasawa, Miho Hirai, Yoshihiro Takaki, Ysuhiro Shimane, Cathleen E. Thomas, Syun-ichi Urayama, Takuro Nunoura, Satoshi Koyama

    Abstract A new polycipivirus was identified in the arboreal ant Colobopsis shohki. The viral RNA was 11,855 nt in length with five 5’-proximal open reading frames (ORFs) encoding structural proteins and a long 3’ ORF encoding the replication polyprotein. The protein sequences of these ORFs had significant similarity to those of the polycipiviruses Lasius niger virus 1 and Solenopsis invicta virus 2. The results of phylogenetic analysis and its genome organization suggested that this virus belongs to the genus Sopolycivirus in the family Polycipiviridae. The name “Colobopsis shohki virus 1” (CshV1) is proposed for the new virus.

    更新日期:2020-01-04
  • Genome characterization of novel lytic Myoviridae bacteriophage ϕVP-1 enhances its applicability against MDR-biofilm-forming Vibrio parahaemolyticus
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-21
    Nandita Matamp, Sarita G. Bhat

    A pathogen of significance in the aquaculture sector, the Gram-negative marine bacterium Vibrio parahaemolyticus causes gastroenteritis associated with consumption of improperly prepared seafood. This bacterium can be controlled using lytic bacteriophages as an alternative to antibiotics. ϕVP-1 is a lytic phage of V. parahaemolyticus that was isolated from an aquafarm water sample with the aim of assessing its potential as a bio-control agent and determining its physicochemical properties and genomic sequence. Morphological analysis by transmission electron microscopy and phylogenetic analysis based on the large terminase subunit gene showed that this phage belongs to the family Myoviridae. It could infect multiple-drug-resistant (MDR) V. parahaemolyticus and V. alginolyticus strains of mangrove and seafood origin. With a maximum adsorption time of 30 min, ϕVP-1 has a short latent period of 10 min with burst size of 44 particles/cell. Whole-genome sequencing was done using the Illumina platform, and annotation was done using GeneMarkS and Prodigal. The 150,764bp genome with an overall G+C content of 41.84% had 203 putative protein-encoding open reading frames, one tRNA gene, and 66 predicted promoters. A number of putative DNA replication and regulation, DNA packaging and structure, and host lysis genes were identified. Comparison of the ϕVP-1 genome sequence to those of known Vibrio phages indicated little discernible DNA sequence similarity, suggesting that ϕVP-1 is a novel Vibrio phage. Sequence analysis revealed the presence of 64 potential ORFs with a T4-like genomic organization. In silico analysis suggested an obligate lytic life cycle and showed the absence of lysogeny or virulence genes. The complete sequence of ϕVP-1 was annotated and deposited in the GenBank database (accession no. MH363700). The genetic features of this novel phage suggest that it might be applicable for phage therapy against pathogenic strains of V. parahaemolyticus.

    更新日期:2020-01-04
  • Phage vB_BmeM-Goe8 infecting Bacillus megaterium DSM319
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-20
    Lina Paola Baena Lozada, Michael Hoppert, Robert Hertel

    Abstract vB_BmeM-Goe8 is a phage preying on Bacillus megaterium. Its genome has a GC content of 38.9%, is 161,583 bp in size, and has defined ends consisting of 7436-bp-long terminal repeats. It harbours 11 genes encoding tRNAs and 246 coding DNA sequences, 66 of which were annotated. The particle reveals Myoviridae morphology, and the formation of a double baseplate upon tail sheath contraction indicates morphological relatedness to the group of SPO1-like phages. BLASTn comparison against the NCBI non-redundant nucleotide database revealed that Bacillus phage Mater is the closest relative of vB_BmeM-Goe8.

    更新日期:2020-01-04
  • First report of a pseudorabies-virus-infected wolf ( Canis lupus ) in China
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-20
    Kaiqi Lian, Mingliang Zhang, Lingling Zhou, Yuwei Song, Guodong Wang, Shuangshan Wang

    We provide the first report of a wolf infected with pseudorabies virus (PRV) in China. We observed the clinical symptoms and also dissected tissue samples from the wolf. The samples were ground under sterile conditions and injected subcutaneously into the necks of rabbits, which subsequently developed intense pruritus symptoms and died. The PRV strain from the wolf was isolated in porcine kidney (PK)-15 cells and was specifically recognized by pig PRV antibody-positive serum, as shown by indirect immunofluorescence. Tissues from the dead wolf and rabbits were examined by polymerase chain reaction (PCR), and the PCR-amplified partial glycoprotein E gene was sequenced, which confirmed that the wolf had died as a result of PRV infection.

    更新日期:2020-01-04
  • Genetic variability of pig and human rotavirus group A isolates from Slovakia
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-20
    S. Salamunova, A. Jackova, T. Csank, R. Mandelik, J. Novotny, Z. Beckova, L. Helmova, S. Vilcek

    The aim of this work was the genetic typing of RVA isolates originating from pigs and human patients in Slovakia. Seventy-eight rectal swabs from domestic pigs and 30 stool samples from humans were collected. The whole VP7 (G genotypes), VP6 (I genotypes) and partial VP4 (P genotypes) ORFs were amplified by RT-PCR. Genetic variability was higher amongst porcine sequences, where four G genotypes (G3, G4, G5, G11), two P genotypes (P[6], P[13]) and one I5 genotype were detected. Human RVA strains were represented by two G genotypes (G1, G3), two I genotypes (I1, I2), and one P genotype (P[8]). Genetic analysis did not show a relationship between Slovakian porcine and human RVA strains, but phylogenetic grouping of some Slovakian porcine sequences with Hungarian human sequences in both G and P genotypes was observed.

    更新日期:2020-01-04
  • Complete genome sequencing and genetic analysis of a Japanese porcine torovirus strain detected in swine feces
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-20
    Yuki Fujii, Yuki Kashima, Fujiko Sunaga, Hiroshi Aoki, Ryo Imai, Kaori Sano, Yukie Katayama, Tsutomu Omatsu, Mami Oba, Tetsuya Furuya, Satoko Tsuzuku, Yoshinao Ouchi, Junsuke Shirai, Tetsuya Mizutani, Tomoichiro Oka, Makoto Nagai

    We sequenced the complete genome of a porcine torovirus (PToV) strain from Japan for the first time. Whole-genome analysis revealed that this strain (Iba/2018) has a mosaic sequence composed of at least three genome backgrounds, related to US, Chinese and German PToV strains. Clear recombination breakpoints were detected in the M and HE coding regions. A similarity plot and structural analysis demonstrated that the HE coding region exhibits the highest diversity, and the most sequence variation was found in the lectin domain. PToVs were divided into two lineages in the HE region, whereas clear lineages were not found in other regions.

    更新日期:2020-01-04
  • Establishment of an enzyme-linked immunosorbent assay for Getah virus infection in horses using a 20-mer synthetic peptide for the E2 glycoprotein as an antigen
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-18
    Hiroshi Bannai, Manabu Nemoto, Koji Tsujimura, Minoru Ohta

    Abstract An enzyme-linked immunosorbent assay (ELISA) using a synthetic peptide for the E2 glycoprotein was developed for the serodiagnosis of Getah virus infection in horses. To identify an immunogenic epitope, a series of 20-mer peptides (n = 22) for the E2 protein was screened with pooled sera from horses infected with Getah virus. Peptide P11 (PTEEEIDMHTPPDIPDITLL) showed the strongest reaction. ELISA using P11 (E2-P11-ELISA) detected increased antibody levels in all seven experimentally infected horses and in five out of nine vaccinated horses. Out of 28 naturally infected horses, 25 were seronegative in their acute sera but turned seropositive in their convalescent sera. For the remaining three horses whose acute sera were seropositive, an endpoint method with serial dilutions detected a ≥ 4-fold increase in titer between paired sera. The concordance between E2-P11-ELISA and a virus-neutralization test in terms of seropositivity was assessed using a series of 220 horse sera, resulting in almost perfect agreement, with a kappa coefficient value of 0.865. E2-P11-ELISA had a sensitivity of 93.3% (95% CI 86.6–97.1%) and a specificity of 95.0% (95% CI 92.5–96.4%). This highly sensitive and specific E2-P11-ELISA should be useful for serodiagnosis of Getah virus infection in horses.

    更新日期:2020-01-04
  • Proposed revision of the family Secoviridae taxonomy to create three subgenera, “ Satsumavirus ”, “ Stramovirus ” and “ Cholivirus ”, in the genus Sadwavirus
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-17
    Hélène Sanfaçon, Indranil Dasgupta, Marc Fuchs, Alexander V. Karasev, Karel Petrzik, Jeremy R. Thompson, Ioannis Tzanetakis, René van der Vlugt, Thierry Wetzel, Nobuyuki Yoshikawa

    We present a taxonomic proposal for revision of the family Secoviridae, a taxon of plant viruses in the order Picornavirales. We propose the reorganization of the genus Sadwavirus to create three new subgenera and to update the classification of five existing species. The proposed subgenera are “Satsumavirus” (one species: Satsuma dwarf virus), “Stramovirus” (two species: Strawberry mottle virus and Black raspberry necrosis virus) and “Cholivirus” (two species: Chocolate lily virus A and Dioscorea mosaic associated virus).

    更新日期:2020-01-04
  • A potyvirus isolated from Mirabilis jalapa in China represents a new species
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-16
    Pengyuan Zhang, Xiaoqin Li, Longhui Ren, Suiyun Chen, Jianguang Wang

    We previously reported a possible potyvirus isolated from Mirabilis jalapa that exhibited a high degree of sequence similarity to Basella rugose mosaic virus (BaRMV) in the region encoding the coat protein (CP). Here, we present the complete genome sequence of this isolate, comprising a 9666-nucleotide-long monopartite ssRNA (excluding the poly(A) tail) encoding a 3080-amino-acid polyprotein. The CP region showed a high degree of nucleotide sequence similarity to three BaRMV isolates (75.2–77.3% identity), while other regions showed nucleotide sequence identity values (48.8–73.7%) below the species demarcation threshold proposed by the ICTV. Therefore, we propose that this isolate be considered a new member of the genus Potyvirus, tentatively named “mirabilis crinkle mosaic virus” (MiCMV).

    更新日期:2020-01-04
  • Status of the current vitivirus taxonomy
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-16
    H. J. Maree, A. G. Blouin, A. Diaz-Lara, I. Mostert, M. Al Rwahnih, T. Candresse

    Since the establishment of the genus Vitivirus, several additional viruses have been sequenced and proposed to represent new species of this genus. Currently, the International Committee on Taxonomy of Viruses recognizes 15 vitivirus species. The report of new vitiviruses that fail to completely adhere to the species demarcation criteria, the incorporation of non-vitivirus grapevine viruses in the unofficial “naming system”, and the existence of non-grapevine vitiviruses lead to inconsistencies in classification. In this report, we give a brief overview of vitiviruses and use currently available information to clarify the present status of the vitivirus taxonomy.

    更新日期:2020-01-04
  • Characterization of an infectious clone of pepper ringspot virus and its use as a viral vector
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-16
    Moana Lima Tavares-Esashika, Ravi Narayan Souza Campos, Rosana Blawid, Leonardo Lopes da Luz, Alice Kazuko Inoue-Nagata, Tatsuya Nagata

    Abstract The genus Tobravirus comprises three species: Tobacco rattle virus, Pea early-browning virus and Pepper ringspot virus. The genomes of tobraviruses consist of two positive-sense single-stranded RNA segments (RNA1 and RNA2). Infectious clones of TRV are extensively used as virus-induced gene-silencing (VIGS) vectors for studies of virus-host interactions and functions of plant genes. Complete infectious clones of pepper ringspot virus (PepRSV), the only tobravirus present in Brazil, however, have not yet been reported. Infectious clones will help to identify unique features of PepRSV RNA2 and provide another option for development of VIGS vectors. We constructed infectious clones based on two PepRSV isolates, CAM (RNA1 and RNA2) and LAV (RNA2). The cDNA constructs for both homologous (RNA1 and RNA2 of the CAM isolate) and heterologous (RNA1/CAM and RNA2/LAV) combinations were infectious in Nicotiana benthamiana plants. VIGS vector constructs with green fluorescent protein or phytoene desaturase genes inserted in RNA2 silenced the target genes. The systemic translocation of the PepRSV RNA1 construct alone (nonmultiple infection) was also confirmed in an N. benthamiana plant. These results are similar to those reported for tobacco rattle virus.

    更新日期:2020-01-04
  • A novel picornavirus identified in wild Macaca mulatta in China
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-16
    Yuanyun Ao, Yesheng Zhou, Dandi Li, Zhaojun Duan

    Abstract The discovery of novel viruses in wild animals allows the prediction of their potential threat to the health of humans and other animals. We report a highly divergent picornavirus (tentatively named “mobovirus A”), identified in a fecal sample from Macaca mulatta in Yunnan province, China, using viral metagenomic analysis, with viral loads of 2 × 107 copies/g. The complete genomic sequence of mobovirus A is 8,325 nucleotides in length. Phylogenetic analysis showed that it clustered with Guangxi changeable lizard picornavirus 1 and Guangxi Chinese leopard gecko picornavirus, with less than 38%, 40%, and 40% amino acid identity in the P1, P2, and P3 protein, respectively. The viruses in this cluster were most closely related to members of the genera Harkavirus, Tremovirus and Hepatovirus. Genomic analysis revealed that mobovirus A has the typical genomic organization and motifs of a picornavirus. Additionally, its codon usage bias complements that of M. mulatta, suggesting that this feature is not restricted only to hepatoviruses. Thus, according to the guidelines of the Picornaviridae Study Group of the International Committee on Taxonomy of Viruses, mobovirus A should be considered a member of a new genus (tentatively named for Monkey-borne virus, “Mobovirus”) in the family Picornaviridae. These data will facilitate the understanding of the genetic diversity and evolution of picornaviruses. Further studies are needed to understand the epidemiology and potential pathogenicity of the virus in M. mulatta.

    更新日期:2020-01-04
  • Distinctive features of bovine alphaherpesvirus types 1 and 5 and the virus-host interactions that might influence clinical outcomes
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-16
    Maia Marin, Mercedes Burucúa, Daniel Rensetti, Juan José Rosales, Anselmo Odeón, Sandra Pérez

    Bovine herpesvirus types 1 (BoHV-1) and 5 (BoHV-5) are two closely related alphaherpesviruses. BoHV-1 causes several syndromes in cattle, including respiratory disease and sporadic cases of encephalitis, whereas BoHV-5 is responsible for meningoencephalitis in calves. Although both viruses are neurotropic, they differ in their neuropathogenic potential. This review summarizes the findings on the specific mechanisms and pathways known to modulate the pathogenesis of BoHV-1 and BoHV-5, particularly in relation to respiratory and neurological syndromes, which characterize BoHV-1 and BoHV-5 infections, respectively.

    更新日期:2020-01-04
  • A novel jumbo Tenacibaculum maritimum lytic phage with head-fiber-like appendages.
    Arch. Virol. (IF 2.261) Pub Date : 2019-12-02
    Yasuhiko Kawato,Indah Istiqomah,Alkhateib Y Gaafar,Makoto Hanaoka,Katsuya Ishimaru,Motoshige Yasuike,Issei Nishiki,Yoji Nakamura,Atushi Fujiwara,Toshihiro Nakai

    A novel jumbo bacteriophage (myovirus) is described. The lytic phage of Tenacibaculum maritimum, which is the etiological agent of tenacibaculosis in a variety of farmed marine fish worldwide, was plaque-isolated from seawater around a fish aquaculture field in Japan. The phage had an isometric head 110-120 nm in diameter, from which several 50- to 100-nm-long flexible fiber-like appendages emanate, and a 150-nm-long rigid contractile tail. The full genomes of the two representative phages (PTm1 and PTm5) were 224,680 and 226,876 bp long, respectively, both with 29.7% GC content, and the number of predicted open reading frames (ORFs) was 308 and 306, respectively. The average nucleotide sequence identity between PTm1 and PTm5 was 99.95%, indicating they are quite similar to each other. A genetic relationship was found in 15.0-16.6% of the predicted ORFs among the T. maritimum phages PTm1 and PTm5, the Tenacibaculum spp. phage pT24, and the Sphingomonas paucimobilis phage PAU. Phylogenetic analysis based on the terminase large subunit genes revealed that these four phages (PTm1, PTm5, pT24 and PAU) are more closely related than the other 10 jumbo myoviruses that have similar genome sizes. Transmission electron microscopy observations suggest that the head fibers of the T. maritimum phage function as tentacles to search and recognize the host cell surface to facilitate infection.

    更新日期:2019-11-01
  • Complete genomic sequence of crow-dipper mosaic-associated virus, a novel macluravirus infecting Pinellia ternata.
    Arch. Virol. (IF 2.261) Pub Date : null
    Rong Wang,Bingwei Chen,Yong Li,Tianyou Wang,Wanlong Ding

    A new macluravirus infecting Pinellia ternata in China was identified by high-throughput sequencing (HTS) and tentatively named "crow-dipper mosaic-associated virus" (CrdMV). The complete genome sequence of CrdMV was determined by reverse transcription (RT) PCR and rapid amplification of cDNA ends (RACE) PCR. The genomic RNA of CrdMV consists of 8,454 nucleotides (nt), excluding the poly(A) tail at the 3' end. CrdMV has a genomic structure typical of macluraviruses, with large open reading frame encoding a polyprotein of 2,696 amino acids (aa). CrdMV shares 54.40%-59.37% nt sequence identity at the genome sequence level, 48.00%-58.58% aa sequence identity, at the polyprotein sequence level and 37.27%-49.22% aa sequence identity at the CP sequence level with other members of the genus Macluravirus. These values are well below the species demarcation threshold for the family Potyviridae. Phylogenetic analysis based on the amino acid sequences of polyproteins confirmed that CrdMV clusters closely with broad-leafed dock virus A (BDVA, GenBank accession no. KU053507). These results suggest that CrdMV should be considered a distinct member of the genus Macluravirus.

    更新日期:2019-11-01
  • Novel positive-sense single-stranded RNA virus related to alphavirus-like viruses from Fusarium graminearum.
    Arch. Virol. (IF 2.261) Pub Date : null
    Xing Zhang,Haotian Zhang,Dongfang Ma,Huaigu Chen,Wei Li

    A putative novel positive-sense (+) RNA virus was detected in isolate CF16158 of the fungus Fusarium graminearum, the causal agent of Fusarium head blight and crown rot in wheat in China. The full genome of this virus was sequenced and characterized. The complete cDNA sequence is 7,051 nt long and contains four open reading frames (ORFs). ORF2 is predicted to encode helicase (Hel) and RNA-dependent RNA polymerase (RdRp) domains that are conserved among the alphavirus-like viruses. Pairwise comparisons and phylogenetic analysis of the deduced amino acid sequences of Hel and RdRp indicated that this (+) RNA mycovirus is a novel member of a new, yet to be established family of alphavirus-like viruses. Therefore, we named this virus "Fusarium graminearum alphavirus-like virus 1" (FgALV1). This is the first report of a full-length genomic sequence of a putative alphavirus-like virus in F. graminearum.

    更新日期:2019-11-01
  • Subclinical infection of captive Asian elephants (Elephas maximus) in Thailand with elephant endotheliotropic herpesvirus.
    Arch. Virol. (IF 2.261) Pub Date : null
    Supaphen Sripiboon,William Ditcham,Rebecca Vaughan-Higgins,Bethany Jackson,Ian Robertson,Chatchote Thitaram,Taweepoke Angkawanish,Sakuna Phatthanakunanan,Preeda Lertwatcharasarakul,Kristin Warren

    Elephant endotheliotropic herpesvirus (EEHV) infection is a conservation threat to the endangered Asian elephant (Elephas maximus), causing fatal hemorrhagic disease in juvenile elephants throughout the world, including Thailand. This study revealed a subclinical EEHV1 infection rate of 5.5% in healthy captive Asian elephants in Thailand (n = 362). The virus was detected in all age classes above one year old, in both sexes, and across the country - even in facilities with no history of hemorrhagic disease (EEHV HD). Subclinical EEHV infection in Thailand urgently requires proper health management.

    更新日期:2019-11-01
  • Correction to: Complete genome sequence of a phage hyperparasite of Candidatus Xenohaliotis californiensis (Rickettsiales) - a pathogen of Haliotis spp (Gasteropoda).
    Arch. Virol. (IF 2.261) Pub Date : 2018-02-06
    Roberto Cruz-Flores,Jorge Cáceres-Martínez,Miguel Ángel Del Río-Portilla,Alexei F Licea-Navarro,Ricardo Gonzales-Sánchez,Abraham Guerrero

    Unfortunately, the family name of the co-author Roberto Cruz-Flores was incorrectly published in the original publication and corrected here by this correction. The original article has been corrected.

    更新日期:2019-11-01
  • Mitochondrial bioenergy alterations in avian HD11 macrophages infected with infectious bronchitis virus.
    Arch. Virol. (IF 2.261) Pub Date : 2018-01-06
    Sergio E L da Silva,Helena L Ferreira,Andrea F Garcia,Felipe E S Silva,Roberto Gameiro,Carolina U F Fabri,Dielson S Vieira,Tereza C Cardoso

    To establish an association between mitochondrial dysfunction and apoptosis following infectious bronchitis virus (IBV) infection, HD11 avian macrophage cells were infected with the Massachusetts 41 (M41) strain. Our results show that the M41 strain of IBV induced cytopathic effects followed by the release of new viral particles. Elevated numbers of apoptotic cells were observed at 24, 48 and 72 h post-infection (p.i.). Viral infection was associated with mitochondrial membrane depolarization and reactive oxygen species (ROS) production at all of the examined timepoints p.i. In summary, IBV M41 replication in infected HD11 macrophages seems to induce mitochondrial bioenergy failure, acting as a respiratory chain uncoupler, without compromising viral replication.

    更新日期:2019-11-01
  • Complete genome sequence of a novel polerovirus in Ornithogalum thyrsoides from South Africa.
    Arch. Virol. (IF 2.261) Pub Date : null
    I Mostert,M Visser,I Gazendam,M Cloete,J T Burger,H J Maree

    Ornithogalum thyrsoides, commonly known as chincherinchee, is an indigenous ornamental plant widely cultivated in South Africa. It is commercially valued as a flowering pot plant and for the production of cut flowers. Virus infections resulting in the development of severe necrotic mosaic symptoms threaten the success of commercial cultivation. The virome of an O. thyrsoides plant displaying necrotic mosaic symptoms was determined using high-throughput sequencing (HTS). In this plant, ornithogalum mosaic virus and ornithogalum virus 3 were identified, as well as a previously unknown virus. The full genome sequence of this virus was confirmed by Sanger sequencing using overlapping amplicons combined with rapid amplification of cDNA ends (RACE). Based on genome organisation and phylogenetic analysis, this novel virus can be classified as a polerovirus.

    更新日期:2019-11-01
  • Absence of bovine leukemia virus proviral DNA in Japanese human blood cell lines and human cancer cell lines.
    Arch. Virol. (IF 2.261) Pub Date : null
    Susumu Saito,Yuri Kitamura-Muramatsu,Fumiko Komine,Meripet Polat,Shin-Nosuke Takeshima,Masami Takei,Yoko Aida

    Bovine leukemia virus (BLV) infects cattle worldwide and causes B-cell lymphoma in cattle. BLV has been identified in human breast and lung cancer and in blood, but the association of BLV and human cancer is controversial. In this study, we investigated the existence of BLV in 145 Japanese human blood cell lines and 54 human cancer cell lines, using a new highly sensitive PCR assay that can amplify even one copy of BLV using LTR primers different from those in previous studies on BLV provirus in breast cancer. All samples were found negative for BLV provirus, suggesting that BLV is unlikely to infect humans.

    更新日期:2019-11-01
  • Genomic characterization of Malus domestica virus A (MdoVA), a novel velarivirus infecting apple.
    Arch. Virol. (IF 2.261) Pub Date : null
    Igor Koloniuk,Jaroslava Přibylová,Jana Fránová,Josef Špak

    Screening of apple samples using a high-throughput sequencing (HTS) approach led to the discovery of a novel virus, tentatively named "Malus domestica virus A" (MdoVA). Its genomic organisation and phylogenetic relationship showed relatedness to viruses of the genus Velarivirus in the family Closteroviridae. It is not clear whether MdoVA has any impact on its host, as the analysed apple tree contained other viruses and a viroid.

    更新日期:2019-11-01
  • Maize Iranian mosaic virus (family Rhabdoviridae) improves biological traits of its vector Laodelphax striatellus.
    Arch. Virol. (IF 2.261) Pub Date : null
    Pedram Moeini,Alireza Afsharifar,Keramatollah Izadpanah,Seyed Ebrahim Sadeghi,Sanford D Eigenbrode

    Plant viruses can alter the behavior or performance of their arthropod vectors, either indirectly (through effects of virus infection on the host plant) or directly (from virus acquisition by the vector). Given the diversity of plant viruses and their arthropod vectors, the effects for any specific system are not possible to predict. Here, we present experimental evidence that acquisition of maize Iranian mosaic virus (MIMV, genus Nucleorhabdovirus, family Rhabdoviridae) modifies the biological traits of its insect vector, the small brown planthopper (SBPH) Laodelphax striatellus. MIMV is an economically important virus of maize and several other grass species. It is transmitted by SBPHs in a persistent-propagative manner. We evaluated the effects of MIMV acquisition by SBPH on its life history when reared on healthy barley plants (Hordeum vulgare). We conclude that 1) MIMV acquisition by SBPHs increases female fecundity, duration of the nymph stage, adult longevity, and survival of SBPHs, (2) the mortality rate and female-to-male sex ratio are reduced in MIMV-infected planthoppers, and (3) MIMV infection increases the concentration of some biochemical components of the infected plants, including carbohydrates, some amino acids, and total protein, which might influence the life traits of its insect vector. The results indicate the potential of MIMV to improve the ecological fitness of its vector, SBPH, through direct or indirect effects, with the potential to increase the spread of the virus.

    更新日期:2019-11-01
  • Molecular characterization of common bean curly stunt virus: a novel recombinant geminivirus in China.
    Arch. Virol. (IF 2.261) Pub Date : null
    Ruonan Zhang,Xiaoyun Wu,Xue Jiang,Xiaoxia Wu,Xiaoyan Luan,Xiaofei Cheng

    A new geminivirus was identified in common bean (Phaseolus vulgaris) showing severe stunt and leaf curling symptoms in Heilongjiang province of China, via sequencing and assembly of small RNAs. The genome of this geminivirus comprises 2,959 nucleotides (nt) and shares 21.77-54.97% nt sequence identity with other geminiviruses. The coat protein (CP) shares the highest amino acid (aa) sequence identity (23.5%) with that of sesame curly top virus (SeYMV; genus Turncurtovirus), whereas the C1 (Rep) shares the highest aa sequence identity (66.5%) with that of beet severe curly top virus (BSCTV; genus Curtovirus). This geminivirus neighbors the turncurtoviruses in phylogenetic trees based on the full genome sequence or the amino acid sequence of the Rep protein, but it forms a distinct clade in the phylogenetic tree based on the coat protein. Recombination analysis showed that parts of the C1 coding region of this geminivirus were recombined from a curtovirus or turncurtovirus. Based on these results, the name "common bean curly stunt virus" (CBCSV) is proposed for this virus.

    更新日期:2019-11-01
  • First report of fowl aviadenovirus serotypes FAdV-8b and FAdV-11 associated with inclusion body hepatitis in commercial broiler and broiler-breeder flocks in Turkey.
    Arch. Virol. (IF 2.261) Pub Date : 2019-11-05
    İsmail Şahindokuyucu,Fethiye Çöven,Hamza Kılıç,Özge Yılmaz,Mustafa Kars,Öznur Yazıcıoğlu,Ercüment Ertunç,Zafer Yazıcı

    Inclusion body hepatitis (IBH), hydropericardium syndrome (HS), and gizzard erosion (GE) are all economically important diseases in the poultry industry worldwide and are all caused by fowl aviadenovirus (FAdV). It is important to identify the serotype of the virus to differentiate these diseases. In the present study, a total of six recent FAdV serotypes were isolated and identified in broiler and broiler-breeder flocks in Izmir, Manisa, and Aydın provinces of the Aegean region of Turkey between January and March 2019. The viruses were isolated from livers and pooled organs of chickens using primary chicken embryo kidney cell cultures (CEKC). Virus isolates were identified by PCR amplification of the loop 1 (L1) variable region of the hexon gene followed by Sanger sequencing. Sequence analysis revealed the presence of both FAdV-D (serotype 11) and FAdV-E (serotype 8b). The viruses that were isolated were associated with IBH, which is typically characterized by gross lesions such as enlarged and pale yellow liver with multiple petechial hemorrhages. Histopathological examination also showed necrotizing hepatitis with intranuclear inclusion bodies in hepatocytes. This study is the first report of the isolation and identification of FAdV serotypes associated with IBH in commercial broilers and broiler-breeder flocks in Turkey. The results of sequence analysis showed that FAdV-8b and FAdV-11 were the circulating serotypes that caused recent field outbreaks of IBH in the Aegean region between January and March, 2019.

    更新日期:2019-11-01
  • R18C is a new viable P2-like bacteriophage of rabbit origin infecting Citrobacter rodentium and Shigella sonnei strains.
    Arch. Virol. (IF 2.261) Pub Date : 2019-10-24
    Domonkos Sváb,Balázs Horváth,Manfred Rohde,Gergely Maróti,István Tóth

    Here, we report a novel virulent P2-like bacteriophage, R18C, isolated from rabbit faeces, which, in addition to Escherichia coli K-12 strains, was able to be propagated on Citrobacter rodentium strain ICC169 and a range of Shigella sonnei strains with high efficiency of plating (EOP). It represents the first lytic bacteriophage originating from rabbit and the first infectious P2-like phage of animal origin. In the three characteristic moron-containing regions of P2-like phages, R18C contains genes with unknown function that have so far only been found in cryptic P2-like prophages.

    更新日期:2019-11-01
  • Identification and genomic characterization of grapevine Kizil Sapak virus, a novel grapevine-infecting member of the family Betaflexiviridae.
    Arch. Virol. (IF 2.261) Pub Date : 2019-10-17
    Maher Al Rwahnih,Olufemi J Alabi,Min Sook Hwang,Kristian Stevens,Deborah Golino

    A novel virus with a (+) single-stranded RNA genome was detected by high-throughput sequencing (HTS) in a sample of grapevine (Vitis vinifera) cv. Kizil Sapak (sample/isolate 127) that originated from Turkmenistan. The complete genome of the virus, tentatively named "grapevine Kizil Sapak virus" (GKSV), is 7,604 nucleotides in length, excluding the poly(A) tail. The genome organization of GKSV, encoded genes, and sequence domains are typical for members of the family Betaflexiviridae, specifically those belonging to the subfamily Trivirinae. Phylogenetic analysis placed GKSV within the subfamily Trivirinae, in the same clade as fig latent virus 1 (FLV-1) but distinct from the clades formed by members of other genera. A comparative analysis of GKSV-127 with the HTS-derived sequences obtained from two additional isolates showed that they are genetic variants of the same virus species. Based on current ICTV species and genus demarcation criteria, and the results of the sequence and phylogenetic analyses, we propose that GKSV and FLV-1 represent a new genus within the subfamily Trivirinae.

    更新日期:2019-11-01
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