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Archives of Virology

Weiyao Hu, Zengping Li, Xiaoye Wang, Wenbo Liu, Chaohao Huang, Weiguo Miao, Hongguang Cui
A macluravirus, tentatively named alpinia oxyphylla mosaic virus (AloMV), was identified in Alpinia oxyphylla, and its complete genomic sequence determined. The positively single-stranded RNA genome is comprised of 8213 nucleotides excluding the poly (A) tail, and contains one large open reading frame encoding a polyprotein of 2,626 amino acids. Blastp search showed that the polyprotein of AloMV shared 48%~68% aa sequence identities with other reported macluraviruses. Phylogenetic analysis based on the nucleotide sequence of the polyprotein showed that AloMV, together with all other macluraviruses, clustered into the same group most closely related to cardamom mosaic virus, sharing 66...
May 21, 2018: Archives of Virology
Sabrina Koberg, Stefanie Gieschler, Erik Brinks, Mareike Wenning, Horst Neve, Charles M A P Franz
Psychrotrophic gram-negative Pseudomonas spp. represent a serious problem in the dairy industry as they can cause spoilage of milk and dairy products. Bacteriophages have moved into focus as promising biocontrol agents for such food spoilage bacteria. The virulent Siphoviridae phage PMBT14 was isolated on a mutant variant of P. fluorescens DSM 50090 challenged with an unrelated virulent P. fluorescens DSM 50090 Podoviridae phage (i.e., mutant strain DSM 50090R ). PMBT14 has a 47,820-bp dsDNA genome with 76 predicted open reading frames (ORFs)...
May 21, 2018: Archives of Virology
Koki Fujisaki, Chika Tateda, Asuka Shirakawa, Mari Iwai, Yoshiko Abe
The DECS (dsRNA isolation, exhaustive amplification, cloning and sequencing) analysis technique for viral diagnosis detected a tombusvirus in Japanese gentian not displaying severe symptoms. We tentatively named this virus "gentian virus A" (GeVA). GeVA systemically but inefficiently infected Japanese gentian without causing visible symptoms, while it led to severe symptoms in some other plants. The complete genome sequence of GeVA indicated a typical tombusvirus-like structure. Phylogenetic analysis of the deduced amino acid sequences of four tombusvirus-encoded proteins did not reveal other known tombusviruses that were closely-related to GeVA, suggesting that it is a novel tombusvirus...
May 21, 2018: Archives of Virology
Yan Wang, Wen Zhang, Zhijian Liu, Xingli Fu, Jiaqi Yuan, Jieji Zhao, Yuan Lin, Quan Shen, Xiaochun Wang, Xutao Deng, Eric Delwart, Tongling Shan, Shixing Yang
Recombination occurs frequently between enteroviruses (EVs) which are classified within the same species of the Picornaviridae family. Here, using viral metagenomics, the genomes of two recombinant EV-Gs (strains EVG 01/NC_CHI/2014 and EVG 02/NC_CHI/2014) found in the feces of pigs from a swine farm in China are described. The two strains are characterized by distinct insertion of a papain-like protease gene from toroviruses classified within the Coronaviridae family. According to recent reports the site of the torovirus protease insertion was located at the 2C/3A junction region in EVG 02/NC_CHI/2014...
May 21, 2018: Archives of Virology
Faith Sigei, Fredrick Nindo, Silvanos Mukunzi, Zipporah Ng'ang'a, Rosemary Sang
Sindbis virus (SINV) is a mosquito borne virus maintained in nature in a mosquito-bird cycle, with human outbreaks known to occur in Northern Europe and parts of Africa. We analyzed five SINV strains isolated in Kenya from five different mosquito species and geographic locations between 2007 and 2013. Phylogenetic relationships and evolutionary inferences were performed using maximum likelihood and Bayesian phylogenetic inference approaches. Selection analyses were carried out based on the virus envelope glycoproteins (E1, E2) and non-structural protein (nsP4) genes...
May 21, 2018: Archives of Virology
Nada Madi, Wassim Chehadeh, Mohammed Asadzadeh, Mariam Al-Turab, Anfal Al-Adwani
Respiratory syncytial virus (RSV) is the most frequently identified viral agent in infants, children, and elderly people with acute respiratory tract infections (ARTIs). This study is the only one of its kind in Kuwait, and its purpose was to investigate the genetic variability of the G protein gene in RSV strains prevalent in Kuwait. Respiratory samples were collected from patients with ARTIs in various hospitals in Kuwait and subjected to reverse transcription PCR (RT-PCR) amplifying a fragment of the G gene of RSV...
May 19, 2018: Archives of Virology
Saif Ul Islam, Wenzhong Lin, Ran Wu, Chen Lin, Waqar Islam, Muhammad Arif, Zhenguo Du, Zujian Wu
Three cycloviruses (genus Cyclovirus, family Circoviridae) were recovered from a dragonfly (Odonata: Anisoptera) captured in Fuzhou, China. The three cycloviruses, named dragonfly associated cyclovirus 9, 10 and 11 (DfCyV-9, -10, -11), respectively, show 56.1-79.6% genome-wide identity to known cycloviruses and 61.6-65.1% among themselves. Thus, according to the current species demarcation criteria, they represent three novel cycloviruses. Notably, DfCyV-10 has a predicted replication-associated protein (Rep) that is most similar to that of bat associated cyclovirus 2 (BatACyV-2), a cyclovirus discovered in China, with 79...
May 17, 2018: Archives of Virology
Dan Yin, Yanan Zhu, Kaifeng Wang, Jing Wang, Xiru Zhang, Min Han, Yaqing He, Qing Chen, Guifang Hu
Enterovirus 71 (EV71) is one of the most common pathogens of hand, foot, and mouth disease (HFMD). A rapid reverse transcription recombinase polymerase amplification (RT-RPA) assay was established to detect EV71 subgenotype C4 (EV71-C4). The 95% detection limit of the RT-RPA was 3.767 log10 genomic copies (LGC)/reaction. The specificity was 100%. In a clinical sample evaluation, this approach demonstrated sufficient clinical performance when compared with a commercial RT-qPCR diagnostic kit. Thus, the RT-RPA assay may be a promising alternative for the detection of EV71-C4...
May 16, 2018: Archives of Virology
Wencheng Lin, Piaopiao Lu, Aijun Li, Yu Wu, Hongxin Li, Feng Chen, Jingyun Ma, Qingmei Xie
Avian encephalomyelitis virus (AEV) causes typical neurological symptoms in young chicks and a transient drop in egg production and hatchability in adult laying birds, resulting in huge economic losses in the poultry industry. An effective way to control and prevent this disease is vaccination of the flocks. Here, we assessed the efficacy of the live vaccine candidate strain GDt29 against avian encephalomyelitis virus. The GDt29 strain has low virulence, was confirmed safe, and showed no signs of pathogenicity...
May 16, 2018: Archives of Virology
Yurgis A V Yomantas, Elena G Abalakina, Juliya S Lobanova, Victor A Mamontov, Nataliya V Stoynova, Sergey V Mashko
The genomes of two new lytic phages of Corynebacterium glutamicum ATCC 13032, φ673 and φ674, were sequenced and annotated (GenBank: MG324353, MG324354). Electron microscopy studies of both virions revealed that taxonomically they belong to the Siphoviridae family and have a polyhedral head with a width of 50 nm and a non-contractile tail with a length of 250 nm. The genomes of φ673 and φ674 consist of linear double-stranded DNA molecules with lengths of 44,530 bp (G+C = 51.1%) and 43,193 bp (G+C = 50...
May 15, 2018: Archives of Virology
Kazuki Shiba, Chiharu Hatta, Shinsaku Sasai, Motoaki Tojo, Satoshi T Ohki, Tomofumi Mochizuki
The mycoparasitic oomycete Pythium nunn isolate UZ415 contains two double-stranded RNAs (dsRNAs) of different sizes. The 1707-nt dsRNA1 and the 1475-nt dsRNA2 potentially encode an RNA-dependent RNA polymerase (RdRp) and a coat protein (CP), respectively, with sequence similarity to the RdRp and CP of gammapartitiviruses (< 57% and < 36%). Phylogenetic analysis of the deduced RdRp amino acid sequences indicated that the virus identified from P. nunn is classifiable as a distinct member of the genus Ganmmapartitivirus in the family Partitiviridae...
May 12, 2018: Archives of Virology
Andrew M Q King, Elliot J Lefkowitz, Arcady R Mushegian, Michael J Adams, Bas E Dutilh, Alexander E Gorbalenya, Balázs Harrach, Robert L Harrison, Sandra Junglen, Nick J Knowles, Andrew M Kropinski, Mart Krupovic, Jens H Kuhn, Max L Nibert, Luisa Rubino, Sead Sabanadzovic, Hélène Sanfaçon, Stuart G Siddell, Peter Simmonds, Arvind Varsani, Francisco Murilo Zerbini, Andrew J Davison
This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses in February 2018. A total of 451 species, 69 genera, 11 subfamilies, 9 families and one new order were added to the taxonomy. The current totals at each taxonomic level now stand at 9 orders, 131 families, 46 subfamilies, 803 genera and 4853 species. A change was made to the International Code of Virus Classification and Nomenclature to allow the use of the names of people in taxon names under appropriate circumstances...
May 12, 2018: Archives of Virology
Caitlin A O'Brien, Sonja Hall-Mendelin, Jody Hobson-Peters, Georgia Deliyannis, Andy Allen, Ala Lew-Tabor, Manuel Rodriguez-Valle, Dayana Barker, Stephen C Barker, Roy A Hall
Ixodes holocyclus, the eastern paralysis tick, is a significant parasite in Australia in terms of animal and human health. However, very little is known about its virome. In this study, next-generation sequencing of I. holocyclus salivary glands yielded a full-length genome sequence which phylogenetically groups with viruses classified in the Iflaviridae family and shares 45% amino acid similarity with its closest relative Bole hyalomma asiaticum virus 1. The sequence of this virus, provisionally named Ixodes holocyclus iflavirus (IhIV) has been identified in tick populations from northern New South Wales and Queensland, Australia and represents the first virus sequence reported from I...
May 11, 2018: Archives of Virology
Andreia Elisa Cursino, Ana Paula Pessoa Vilela, Ana Paula Moreira Franco-Luiz, Jaquelline Germano de Oliveira, Márcia Furlan Nogueira, João Pessoa Araújo Júnior, Daniel Moura de Aguiar, Erna Geessien Kroon
Equine infectious anemia (EIA) has a worldwide distribution, and is widespread in Brazil. The Brazilian Pantanal presents with high prevalence comprising equine performance and indirectly the livestock industry, since the horses are used for cattle management. Although EIA is routinely diagnosed by the agar gel immunodiffusion test (AGID), this serological assay has some limitations, so PCR-based detection methods have the potential to overcome these limitations and act as complementary tests to those currently used...
May 11, 2018: Archives of Virology
Louise Hock, Annika Gillis, Jacques Mahillon
Bacteriophage Deep-Purple, isolated from an agricultural soil in Belgium, lyses the emetic Bacillus weihenstephanensis strain LH002 and exhibits a lytic activity against 55% of emetic Bacillus cereus and B. weihenstephanensis strains. Deep-Purple is able to complete its lytic cycle within 45 min and is stable to a large range of pHs and temperatures below 60 °C. It possesses an icosahedral head of about 63 nm in diameter and a non-contractile tail of approximately 165 nm in length. The genome of this newly classifiable Siphoviridae family member is 36,278 bp long, with a G+C content of 38...
May 11, 2018: Archives of Virology
Fenjiao Zhang, Kechong Huang, Xiaojing Yang, Li Sun, Jiajia You, Xuewei Pan, Xiaoli Cui, Hongjiang Yang
Phage O4 of Pseudomonas aeruginosa was previously visualized as a short-tailed virus using a transmission electron microscope. In this work, the O4 genome was characterized to be a linear dsDNA molecule comprising 50509 bp with 76 predicted genes located in five clusters. Mass spectrometry showed that the O4 virion contains 6 putative structural proteins, 2 putative enzymes, and 7 hypothetical proteins. By analyzing a Tn5G transposon mutation library, eight genes, wbpR, wbpV, wbpO, wbpT, wbpS, wbpL,  galU, and wzy, were identified and confirmed responsible for the phage-resistant phenotype; all of them are related to the synthesis of O-specific antigen (OSA) of lipopolysaccharide (LPS), indicating that OSA is the receptor for the adsorption of phage O4...
May 10, 2018: Archives of Virology
Shao-Lun Zhai, Tao Lin, Xia Zhou, Zhang-Fu Pei, Zu-Zhang Wei, He Zhang, Xiao-Hui Wen, Qin-Ling Chen, Dian-Hong Lv, Wen-Kang Wei
Porcine reproductive and respiratory syndrome virus (PRRSV) is considered an important economic pathogen for the international swine industry. At present, both PRRSV-1 and PRRSV-2 have been confirmed to be co-circulating in China. However, there is little available information about the prevalence or distribution of PRRSV-1 in Guangdong province, southern China. In this study, we performed molecular detection of PRRSV-1 in 750 samples collected from 50 farms in 15 major pig farming regions in this province...
May 10, 2018: Archives of Virology
Soumita Das, Akshay Hegde, P V Shivaprasad
Begomoviruses (family Geminiviridae) cause important diseases in many crops. In addition, many wild plants are reservoirs of begomoviruses, which are a potential menace for nearby crops. A novel begomovirus was isolated from a weed of the species Synedrella nodiflora (Compositae) exhibiting yellow vein symptoms in South India. This virus had a typical monopartite Old World begomovirus genome and was accompanied by a betasatellite. Sequence comparison revealed that this virus represents a new species in the genus Begomovirus...
May 9, 2018: Archives of Virology
Rob W Briddon, Darren P Martin, Philippe Roumagnac, Jesús Navas-Castillo, Elvira Fiallo-Olivé, Enrique Moriones, Jean-Michel Lett, F Murilo Zerbini, Arvind Varsani
Nanoviruses and geminiviruses are circular, single stranded DNA viruses that infect many plant species around the world. Nanoviruses and certain geminiviruses that belong to the Begomovirus and Mastrevirus genera are associated with additional circular, single stranded DNA molecules (~ 1-1.4 kb) that encode a replication-associated protein (Rep). These Rep-encoding satellite molecules are commonly referred to as alphasatellites and here we communicate the establishment of the family Alphasatellitidae to which these have been assigned...
May 9, 2018: Archives of Virology
Juliana Galera Castilho, Samira Maria Achkar, Rafael de Novaes Oliveira, Enio Mori, Pedro Carnieli, Carla Isabel Macedo
The genetic lineage of rabies virus (RABV) associated with dogs has not been found in the state of São Paulo since 1998, and all cases of rabies in domestic animals reported since then have involved the RABV lineage that circulates in bats. As there has been a change in the rabies transmission cycle in cats and dogs, we decided to analyze the tests used to diagnose rabies in these animals in the 15-year period from 2002 to 2016 in the state of São Paulo. During this period, 85,508 central nervous system (CNS) samples from dogs and cats were submitted to the Rabies Diagnosis Section at the Pasteur Institute of São Paulo for testing...
May 8, 2018: Archives of Virology
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