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Archives of Virology

Xiang Wu, Yongfeng Wu, Ya Tang, Bingcheng Gan
We isolated a Pseudomonas phage infecting Pseudomonas fluorescens SA1 separated from a soil sample collected in Sichuan Province, China. This phage, which we named PPSC2, has a genome that is composed of a 97,330-bp-long linear double-stranded DNA with 47.51% G+C content and 168 putative protein-coding genes. We identified 20 tRNA genes in the genome of PPSC2, and the tRNA GC content ranged from 44.2% to 58.4%. Phylogenetic and BLASTn analysis revealed that the Pseudomonas phage PPSC2 should be considered a new member of the family Myoviridae...
March 14, 2018: Archives of Virology
Xian Qi, Xiaofei An, Yongjun Jiao, Huiyan Yu, Ke Xu, Lunbiao Cui, Shenjiao Wang, Fei Deng, Xiang Huo, Haodi Huang, Qigang Dai, Changjun Bao
Five epidemic waves of human infection with influenza A (H7N9) virus have emerged in China since spring 2013. We previously described the epidemiological characterization of the fifth wave in Jiangsu province. In this study, 41 H7N9 viruses from patients and live-poultry markets were isolated and sequenced to further elucidate the genetic features of viruses of the fifth wave in Jiangsu province. Phylogenetic analysis revealed substantial genetic diversity in the internal genes, and 18 genotypes were identified from the 41 H7N9 virus strains...
March 14, 2018: Archives of Virology
Cecilia M Lotufo, Maximiliano Wilda, Adrian N Giraldez, Pablo R Grigera, Nora M Mattion
A foot-and-mouth disease virus (FMDV) DNA-launched reporter replicon containing a luciferase gene was used to assess the impact of non-structural (NS) protein 3A on viral replication. Independent deletions within the N-terminal region (amino acid [aa] residues 6 to 24) and the central hydrophobic region (HR, aa 59 to 76) of FMDV NS protein 3A were engineered, and luciferase activity in lysates of control and mutated replicon-transfected cells was measured. Triple alanine replacements of the N-terminal triplet Arg 18- His 19 -Glu 20 and a single alanine substitution of the highly charged Glu 20 residue both resulted in a 70-80% reduction in luciferase activity when compared with wild-type controls...
March 13, 2018: Archives of Virology
Reuban Toby D'cruz, Cheryl Chien-Li Lau, Thomas Paulraj Thamboo
Cytomegalovirus (CMV) typically causes gastrointestinal infections in immunocompetent patients. Colonic perforations secondary to CMV are exceeding rare. We describe a 88-year-old male presenting with a week-long history of intractable abdominal discomfort, bloating, nausea and diarrhea. Flexible sigmoidoscopy revealed significant ulceration with yellowish slough. Emergency surgery was performed subsequently in view of multiple perforations in the rectosigmoid junction. CMV gastrointestinal infections demonstrated an ischemic process secondary to vasculitis, which accelerated the pathway to colonic perforation...
March 12, 2018: Archives of Virology
Rong Wang, Jiali Dong, Zhen Wang, Tao Zhou, Yong Li, Wanlong Ding
A new virus causing a serious stunt disease of chrysanthemum was identified in China by high-throughput sequencing (HTS) and named chrysanthemum virus R (CVR). The complete sequence of CVR was determined by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The genomic RNA of CVR consists of 8,874 nucleotides (nt), excluding the poly(A) tail, contains six putative open reading frames (ORFs), and has a genomic organization typical of members of the genus Carlavirus...
March 10, 2018: Archives of Virology
G Theillet, A Rubens, F Foucault, P Dalbon, C Rozand, I Leparc-Goffart, F Bedin
The incidence of flavivirus infections has increased dramatically in recent decades in tropical and sub-tropical areas worldwide, affecting hundreds of millions of people each year. Dengue viruses are typically transmitted by mosquitoes and can cause a wide range of symptoms from flu-like fever to organ impairment and death. Although conventional diagnostic tests can provide early diagnosis of acute dengue infections, access to these tests is often limited in developing countries. Consequently, there is an urgent need to develop affordable, simple, rapid, and robust diagnostic tools that can be used at 'Point of Care' settings...
March 10, 2018: Archives of Virology
Min Liao
In this paper, I describe the genomic characteristics of a Ralstonia phage infecting Ralstonia solanacearum. The Ralstonia phage RPSC1 was isolated from a soil sample collected in Sichuan Province, in southwestern China. The complete genome of RPSC1 is composed of a linear double-stranded DNA 39,628 bp in length, with G+C content of 61.55%, and 43 putative protein-coding genes. All the putative protein-coding genes were on the same strand. No tRNA-encoding genes were identified. Phylogenetic and comparative genomics analyses indicate that Ralstonia phage RPSC1 should be considered a new member of the family Podoviridae...
March 9, 2018: Archives of Virology
Sanne Charles Bodjo, Jean-de-Dieu Baziki, Nick Nwankpa, Ethel Chitsungo, Yao Mathurin Koffi, Emmanuel Couacy-Hymann, Mariame Diop, Daniel Gizaw, Idris Badri Adam Tajelser, Mamadou Lelenta, Adama Diallo, Karim Tounkara
Peste des petits ruminants (PPR) is a contagious and economically important disease affecting production of small ruminants (i.e., sheep and goats). Taking into consideration the lessons learnt from the Global Rinderpest Eradication Programme (GREP), PPR is now targeted by the international veterinary community as the next animal disease to be eradicated. To support the African continental programme for the control of PPR, the Pan African Veterinary Vaccine Centre of the African Union (AU-PANVAC) is developing diagnostics tools...
March 8, 2018: Archives of Virology
Bouchra Kitab, Michinori Kohara, Kyoko Tsukiyama-Kohara
Dengue is the most prevalent arboviral disease in humans and leads to significant morbidity and socioeconomic burden in tropical and subtropical areas. Dengue is caused by infection with any of the four closely related serotypes of dengue virus (DENV1-4) and usually manifests as a mild febrile illness, but may develop into fatal dengue hemorrhagic fever and shock syndrome. There are no specific antiviral therapies against dengue because understanding of DENV biology is limited. A tetravalent chimeric dengue vaccine, Dengvaxia, has finally been licensed for use, but its efficacy was significantly lower against DENV-2 infections and in dengue-naïve individuals...
March 8, 2018: Archives of Virology
Waqas Ali, Mudasser Habib, Rai Shafqat Ali Khan, Muhammad Ashir Zia, Muhammad Farooq, Sanaullah Sajid, Muhammad Salah Ud Din Shah
This study reports the molecular characterization of foot-and-mouth disease virus (FMDV) in the provinces of Punjab and Sindh, Pakistan during 2014-17. FMDV genome was detected in 42 and 41 out of 46 samples (epithelial tissue and saliva) by reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and reverse transcriptase polymerase chain reaction (RT-PCR), respectively. Sequences of the complete VP1 coding region of the samples (n = 33) was achieved showing that 10, 4 and 19 samples belonged to serotype O, A and Asia1 respectively...
March 7, 2018: Archives of Virology
Alfredo Diaz-Lara, Deborah Golino, Maher Al Rwahnih
This paper describes the nucleotide sequence and genome organization of a novel RNA virus detected in grapevine (Vitis vinifera) cultivar 'Kizil Sapak' by high-throughput sequencing (HTS) and tentatively named "grapevine virus J" (GVJ). The full genome of GVJ is 7,390 nucleotides in length, which comprises five open reading frames (ORFs), including a 20K ORF (ORF 2) between the replicase (ORF 1) and the movement protein (ORF 3) genes. According to the level of sequence homology and phylogenetics, GVJ is proposed as a new member of the genus Vitivirus (subfamily Trivirinae; family Betaflexiviridae), with the closest characterized virus being grapevine virus D (GVD)...
March 7, 2018: Archives of Virology
Max L Nibert, Austin R Manny, Humberto J Debat, Andrew E Firth, Laura Bertini, Carla Caruso
Because so few viruses in the family Barnaviridae have been reported, we searched for more of them in public sequence databases. Here, we report the complete coding sequence of Colobanthus quitensis associated barnavirus 1, mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis. The 4.2-kb plus-strand sequence of this virus encompasses four main open reading frames (ORFs), as expected for barnaviruses, including ORFs for a protease-containing polyprotein, an RNA-dependent RNA polymerase whose translation appears to rely on - 1 ribosomal frameshifting, and a capsid protein that is likely to be translated from a subgenomic RNA...
March 7, 2018: Archives of Virology
Marcelo Marques da Silveira, Stéfhano Luis Candido, Valéria Dutra, Selma Samiko Miyazaki, Luciano Nakazato
Nine free-ranging jaguars (Panthera onca) were captured, and rectal swabs were collected in the Pantanal of Cáceres, Mato Grosso, Brazil. Reverse transcription polymerase chain reaction specific for noroviruses was performed. Six jaguars (66.6%) tested positive for norovirus genotype GII.11.
March 7, 2018: Archives of Virology
Lamia Yacoubi, Ségolène Brichler, Frédéric Le Gal, Henda Triki, Emmanuel Gordien
While Tunisia is endemic for hepatitis B virus (HBV), a recent large-scale retrospective study, revealed a very low prevalence (2%) of hepatitis Delta virus (HDV) (Yacoubi et al. in J Clin Virol 72:126-132, 2015). All strains were classified within the genotype 1 (HDV-1) as assessed by nucleotide sequencing of the so-called 'R0' region of the genome described previously. In this study, we aimed to determine the full-length genome sequence of HDV isolates in order to fully characterize the HDV strains spreading in Tunisia...
March 7, 2018: Archives of Virology
Takako Ujihara, Jumpei Uchiyama, Tadahiro Nasukawa, Hiroki Ando, Hironobu Murakami, Naoya Ohara, Midori Ogawa, Toshio Yamazaki, Masanori Daibata, Masahiro Sakaguchi, Shigenobu Matsuzaki
Mycobacteriophage archival stocks have been kept for ca. 20-50 years in Japan. In this study, we attempted to recover mycobacteriophages from 50 archival stocks and briefly analyzed the recovered phages. The phages were recovered from 72.2% (13/18) of the lyophilized stocks that had been stored for 47-56 years. Moreover, the analysis of 12 representative recovered phages led to their classification as belonging to the family Siphoviridae, and seven of them were typed by polymerase chain reaction (PCR) targeting the gene that encodes the tape measure protein...
March 6, 2018: Archives of Virology
Fırat Dogan, Selvi Deniz Dorttas, Seval Bilge Dagalp, Veysel Soydal Ataseven, Feray Alkan
Papillomaviruses (PVs) are epitheliotropic viruses that cause benign proliferative lesions in the skin (warts or papillomas) and mucous membranes of their natural hosts. Recently, new PVs have been found in many animal species. The most common current approach for identifying novel PV types is based on PCR, using various consensus or degenerated primer (broad-range primers), designed on the basis of the multiple alignment of nucleotide or amino acid sequences of a large number of different human papillomaviruses (HPV)...
March 3, 2018: Archives of Virology
Yuliana M Gallo-García, Helena Jaramillo-Mesa, Luisa F Toro-Fernández, Mauricio Marín-Montoya, Pablo A Gutiérrez
As part of an initiative to characterize viruses infecting Cape gooseberry in the province of Antioquia (Colombia), we report the genome sequence of a new member of the genus Ilarvirus (family Bromoviridae). This virus was identified in a Cape gooseberry plot in the municipality of Marinilla in a mixed infection with potato virus Y (PVY) as part of high-throughput sequencing initiative. Results were confirmed by nested RT-PCR and DAS-ELISA. Phylogenetic analysis suggested that the Cape gooseberry ilarvirus is a new member of subgroup 1 and it is most closely related to ageratum latent virus (AgLV)...
March 3, 2018: Archives of Virology
Jeremie Williams, Karthikeya Venkatesan, Joseph Atia Ayariga, Doba Jackson, Hongzhuan Wu, Robert Villafane
P22 bacteriophage has been studied extensively and has served as a model for many important processes such as in vivo protein folding, protein aggregation and protein-protein interactions. The trimeric tailspike protein (TSP) serves as the receptor-binding protein for the P22 bacteriophage to the bacterial host. The homotrimeric P22 tail consists of three chains of 666aa in which the first 108aa form a trimeric dome-like structure which is called the N-terminal domain (NTD) and is responsible for attachment of the tailspike protein to the rest of the phage particle structure in the phage assembly pathway...
March 2, 2018: Archives of Virology
Song Zhang, Pan Shen, Min Li, Xin Tian, Changyong Zhou, Mengji Cao
Next-generation sequencing of small RNAs and PCR amplification with two pairs of back-to-back primers, followed by cloning and sequencing, allowed identification of a novel geminivirus isolate provisionally named camellia chlorotic dwarf-associated virus (CaCDaV). The complete genome sequence of CaCDaV comprises 3,687 nucleotides (nts) and six open reading frames (ORFs). The genome and putative proteins of CaCDaV were most closely related to those of two unclassified geminiviruses: citrus chlorotic dwarf-associated virus (CCDaV, 3,640 nt) and mulberry mosaic dwarf-associated virus (MMDaV, 2,952 nt)...
March 2, 2018: Archives of Virology
Nozomi Shiwa, Kazunori Kimitsuki, Daria Llenaresas Manalo, Satoshi Inoue, Chun-Ho Park
During rabies virus infections, the minor salivary glands are one of the important organs for virus replication and excretion into the oral cavity. However, details of pathological findings and viral antigen distribution in the minor salivary glands remain poorly understood. In this study, we conducted pathological tests on the tongues of 71 rabid dogs in the Philippines; the minor salivary glands (von Ebner's glands, lingual glands), circumvallate papilla, autonomic ganglia, and skeletal muscles were evaluated...
March 2, 2018: Archives of Virology
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