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1. A bioinformatics pipeline to search functional motifs within whole-proteome data: a case study of poxviruses

Author:
Sobhy, Haitham
Source:
Virus genes 2017 v.53 no.2 pp. 173-178
ISSN:
0920-8569
Subject:
Poxviridae; amino acid sequences; bioinformatics; case studies; data collection; protein composition; proteins; proteomics; viruses
Abstract:
... Proteins harbor domains or short linear motifs, which facilitate their functions and interactions. Finding functional motifs in protein sequences could predict the putative cellular roles or characteristics of hypothetical proteins. In this study, we present Shetti-Motif, which is an interactive tool to (i) map UniProt and PROSITE flat files, (ii) search for multiple pre-defined consensus patterns ...
DOI:
10.1007/s11262-016-1416-9
PubMed:
28000080
PubMed Central:
PMC5357487

2. A new look at the origins of gibbon ape leukemia virus

Author:
McKee, J.; Clark, N.; Shapter, F.; Simmons, G.
Source:
Virus genes 2017 v.53 no.2 pp. 165-172
ISSN:
0920-8569
Subject:
Gibbon ape leukemia virus; Hylobatidae; humans; patients; rodents; viruses; Papua New Guinea
Abstract:
... Is the origin of gibbon ape leukemia virus (GALV) human after all? When GALV was discovered and found to cause neoplastic disease in gibbons, it stimulated a great deal of research including investigations into the origins of this virus. A number of publications have suggested that the GALV progenitor was a retrovirus present in one of several species of South East Asian rodents that had close con ...
DOI:
10.1007/s11262-017-1436-0

3. Assessment of HCV genotypes in Yunnan Province of Southwest China

Author:
Li, Qiongfen; Yao, Yufeng; Shen, Yunsong; Cao, Danfeng; Li, Yalin; Zhang, Shuqiong; Cun, Wei; Sun, Mingbo; Yu, Jiankun; Shi, Li; Dong, Shaozhong
Source:
Virus genes 2017 v.53 no.2 pp. 190-196
ISSN:
0920-8569
Subject:
Hepatitis C virus; drugs; genotype; intravenous injection; patients; phylogeny; polymerase chain reaction; China; Vietnam
Abstract:
... Recently, we reported that the frequency of hepatitis C virus (HCV) genotypes and subtypes has rapidly changed among intravenous drug users (IDUs) in Yunnan Province over the last 5 years; this is especially true for subtype 6a which has increased in frequency from 5 to 15%. Here, we assessed 120 HCV-positive plasma samples from the general population (GP). HCV NS5B fragments were amplified and se ...
DOI:
10.1007/s11262-016-1420-0

4. Comparative genomic analysis of three white spot syndrome virus isolates of different virulence

Author:
Li, Fang; Gao, Meiling; Xu, Limei; Yang, Feng
Source:
Virus genes 2017 v.53 no.2 pp. 249-258
ISSN:
0920-8569
Subject:
White spot syndrome virus; genes; genetic variation; genomics; pathogenesis; virulence
Abstract:
... Three white spot syndrome virus (WSSV) isolates of different virulence were identified in our previous study, the high-virulent strain WSSV-CN01, the moderate-virulent strain WSSV-CN02 and the low-virulent strain WSSV-CN03. In this study, the genomes of these three WSSV isolates were sequenced, annotated and compared. The genome sizes for WSSV-CN01, WSSV-CN02, and WSSV-CN03 are 309,286, 294,261, a ...
DOI:
10.1007/s11262-016-1421-z

5. Complete genomic sequence of an infectious pancreatic necrosis virus isolated from rainbow trout (Oncorhynchus mykiss) in China

Author:
Ji, Feng; Zhao, Jing-zhuang; Liu, Miao; Lu, Tong-yan; Liu, Hong-bai; Yin, Jiasheng; Xu, Li-Ming
Source:
Virus genes 2017 v.53 no.2 pp. 215-225
ISSN:
0920-8569
Subject:
Infectious pancreatic necrosis virus; Oncorhynchus mykiss; RNA-directed RNA polymerase; financial economics; genes; mortality; necrosis; nucleotide sequences; nucleotides; phylogeny; polyproteins; serotypes; viral nonstructural proteins; China; Japan
Abstract:
... Infectious pancreatic necrosis (IPN) is a significant disease of farmed salmonids resulting in direct economic losses due to high mortality in China. However, no gene sequence of any Chinese infectious pancreatic necrosis virus (IPNV) isolates was available. In the study, moribund rainbow trout fry samples were collected during an outbreak of IPN in Yunnan province of southwest China in 2013. An I ...
DOI:
10.1007/s11262-016-1408-9

6. Complete nucleotide sequences and construction of full-length infectious cDNA clones of cucumber green mottle mosaic virus (CGMMV) in a versatile newly developed binary vector including both 35S and T7 promoters

Author:
Park, Chan-Hwan; Ju, Hye-Kyoung; Han, Jae-Yeong; Park, Jong-Seo; Kim, Ik-Hyun; Seo, Eun-Young; Kim, Jung-Kyu; Hammond, John; Lim, Hyoun-Sub
Source:
Virus genes 2017 v.53 no.2 pp. 286-299
ISSN:
0920-8569
Subject:
Cucumber green mottle mosaic virus; Hepatitis delta virus; Kyuri green mottle mosaic virus; Nicotiana benthamiana; Pepper mild mottle virus; Tobacco mosaic virus; Tomato mosaic virus; Zucchini green mottle mosaic virus; agroinfiltration; amino acid sequences; clones; complementary DNA; crops; gene silencing; genome; messenger RNA; nucleotide sequences; pathogenicity; phylogeny; ribozymes; transcription (genetics); viruses; watermelons; Canada; China; India; Israel; Japan; Korean Peninsula; Russia; Spain; Taiwan
Abstract:
... Seed-transmitted viruses have caused significant damage to watermelon crops in Korea in recent years, with cucumber green mottle mosaic virus (CGMMV) infection widespread as a result of infected seed lots. To determine the likely origin of CGMMV infection, we collected CGMMV isolates from watermelon and melon fields and generated full-length infectious cDNA clones. The full-length cDNAs were clone ...
DOI:
10.1007/s11262-016-1415-x

7. Establishment of mouse leukemia cell lines expressing human CD4/CCR5 using lentiviral vectors

Author:
Li, Ya-jing; ZhuGe, Fu-yan; Zeng, Chang-chun; He, Jin-yang; Tan, Ning; Liang, Juan
Source:
Virus genes 2017 v.53 no.2 pp. 197-204
ISSN:
0920-8569
Subject:
CCR5 receptor; Cytomegalovirus; HIV infections; Human immunodeficiency virus 1; Murine leukemia virus; Western blotting; animal models; antiviral agents; enzyme-linked immunosorbent assay; genes; humans; mice; neoplasm cells; pathogenesis; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; transcription (genetics); transfection; transgenic animals; virus replication
Abstract:
... A low-cost rodent model of HIV infection and which presents high application value is an effective tool to investigate HIV infection and pathogenesis. However, development of such a small animal model has been hampered by the unsuitability of rodent cells for HIV-1 replication given that the retrovirus HIV-1 has high selectivity to its host cell. Our study used the mouse leukemia cell lines L615 a ...
DOI:
10.1007/s11262-016-1423-x

8. Full-length infectious clone of an Iranian isolate of chicken anemia virus

Author:
Kaffashi, Amir; Eshratabadi, Fatemeh; Shoushtari, Abdelhamed
Source:
Virus genes 2017 v.53 no.2 pp. 312-316
ISSN:
0920-8569
Subject:
Chicken anemia virus; Marek disease; birds; cell culture; chicks; cytopathogenicity; electroporation; glutamine; mutation; plasmids; specific pathogen-free animals; vaccines; viral proteins; viruses
Abstract:
... An Iranian field strain of chicken anemia virus (CAV), designated IR CAV, was isolated in the Marek’s disease virus-transformed lymphoblastoid cell line MDCC-MSB1 (MSB1) culture for the first time. The full-length CAV DNA of this strain was cloned in the bacterial plasmid pTZ57R/T to create the molecular clone pTZ-CAV. The nucleotide and deduced amino acid sequences of viral proteins of IR CAV wer ...
DOI:
10.1007/s11262-016-1417-8

9. Genetic analysis of H9N2 avian influenza viruses circulated in broiler flocks: a case study in Iraq in 2014–2015

Author:
Kraidi, Qayssar Ali; Madadgar, Omid; Ghalyanchi Langeroudi, Arash; Karimi, Vahid
Source:
Virus genes 2017 v.53 no.2 pp. 205-214
ISSN:
0920-8569
Subject:
Influenza A virus; alanine; broiler chickens; case studies; flocks; genes; genetic analysis; hemagglutinins; histidine; leucine; nucleotide sequences; sequence analysis; sialidase; viruses; Iran; Iraq; Pakistan
Abstract:
... H9N2 avian influenza viruses (AIVs) have been recorded in Eurasian for several years. Since 2004–2005, the disease has become endemic in Iraq, causing serious economic losses in the poultry industry. The hemagglutinin (HA) and neuraminidase (NA), two out of eight protein-coding genes, play an important role during the early stage of infection and hinder virus assembling. Little is known about the ...
DOI:
10.1007/s11262-016-1407-x

10. Identification and characterization of host cell proteins interacting with Scylla serrata reovirus non-structural protein p35

Author:
Yuan, Yangyang; Fan, Dongyang; Zhu, Sidong; Yang, Jifang; Chen, Jigang
Source:
Virus genes 2017 v.53 no.2 pp. 317-322
ISSN:
0920-8569
Subject:
Reoviridae; Scylla serrata; cDNA libraries; complementary DNA; hemocyanin; molecular weight; rapid amplification of cDNA ends; screening; two hybrid system techniques; viral nonstructural proteins
Abstract:
... We have previously shown that non-structural protein p35, encoded by Scylla serrata reovirus (SsRV) S10, may act as a viroporin. To characterize the role of p35 protein in the modulation of cellular function, a yeast two-hybrid system was used to screen a cDNA library derived from S. serrata to find its interacting partner. Protein interactions were confirmed in vitro by GST pull-down. Full cDNAs ...
DOI:
10.1007/s11262-016-1418-7

11. Inhibition of porcine transmissible gastroenteritis virus infection in porcine kidney cells using short hairpin RNAs targeting the membrane gene

Author:
Wang, Li; Dai, Xianjin; Song, Han; Yuan, Peng; Yang, Zhou; Dong, Wei; Song, Zhenhui
Source:
Virus genes 2017 v.53 no.2 pp. 226-232
ISSN:
0920-8569
Subject:
RNA interference; Transmissible gastroenteritis virus; cell culture; cytopathogenicity; fluorescent antibody technique; genes; kidney cells; plasmids; quantitative polymerase chain reaction; small interfering RNA; swine; tissue culture; viruses
Abstract:
... The membrane (M) protein is the most abundant component of the porcine transmissible gastroenteritis virus (TGEV) particle. To exploit the possibility of using RNA interference (RNAi) as a strategy against TGEV infection, three plasmids (pRNAT-1, pRNAT-2, and pRNAT-3) expressing short hairpin RNAs were designed to target three different coding regions of the M gene of TGEV. The plasmids were const ...
DOI:
10.1007/s11262-016-1409-8

12. Isolation and complete genome characterization of novel reassortant orthoreovirus from common vole (Microtus arvalis)

Author:
Fehér, Enikő; Kemenesi, Gábor; Oldal, Miklós; Kurucz, Kornélia; Kugler, Renáta; Farkas, Szilvia L.; Marton, Szilvia; Horváth, Győző; Bányai, Krisztián; Jakab, Ferenc
Source:
Virus genes 2017 v.53 no.2 pp. 307-311
ISSN:
0920-8569
Subject:
Clethrionomys glareolus; Hantavirus; Mammalian orthoreovirus; Microtus arvalis; amino acids; genome; humans; lungs; mice; zoonoses; Germany
Abstract:
... A novel mammalian orthoreovirus (MRV) strain was isolated from the lung tissue of a common vole (Microtus arvalis) with Tula hantavirus infection. Seven segments (L1–L3, M2–M3, S2, and S4) of the Hungarian MRV isolate MORV/47Ma/06 revealed a high similarity with an MRV strain detected in bank vole (Myodes glareolus) in Germany. The M1 and S3 segment of the Hungarian isolate showed the closest rela ...
DOI:
10.1007/s11262-016-1411-1

13. Molecular characterization of a distinct monopartite begomovirus associated with betasatellites and alphasatellites infecting Pisum sativum in Nepal

Author:
Shahid, M. S.; Pudashini, B. J.; Khatri-Chhetri, G. B.; Briddon, R. W.; Natsuaki, K. T.
Source:
Virus genes 2017 v.53 no.2 pp. 300-306
ISSN:
0920-8569
Subject:
Begomovirus; Pisum sativum; leaves; nucleotide sequences; peas; plant diseases and disorders; plant viruses; sequence analysis; viruses; Nepal
Abstract:
... Pea (Pisum sativum) plants exhibiting leaf distortion, yellowing, stunted growth and reduction in leaf size from Rampur, Nepal were shown to be infected by a begomovirus in association with betasatellites and alphasatellites. The begomovirus associated with the disease showed only low levels of nucleotide sequence identity (<91%) to previously characterized begomoviruses. This finding indicates th ...
DOI:
10.1007/s11262-016-1424-9

14. Molecular genetic analysis and evolution of begomoviruses and betasatellites causing yellow mosaic disease of bhendi

Author:
Kumar, R. Vinoth; Prasanna, H. C.; Singh, A. K.; Ragunathan, D.; Garg, G. K.; Chakraborty, S.
Source:
Virus genes 2017 v.53 no.2 pp. 275-285
ISSN:
0920-8569
Subject:
Begomovirus; evolution; gene flow; genes; genetic analysis; genetic variation; microsatellite repeats; mutation; okra; India
Abstract:
... In India, Bhendi yellow vein mosaic disease (BYVMD) is one of the most economically important diseases of bhendi/okra and is caused by a complex of monopartite begomovirus (Bhendi yellow vein mosaic virus—BYVMV) and betasatellite (Bhendi yellow vein betasatellite—BYVB). In this study, we have analyzed the role of possible evolutionary factors involved in the evolution of BYVMV and BYVB isolates. E ...
DOI:
10.1007/s11262-016-1414-y

15. Phylogenetic analysis of Wheat dwarf virus isolates from Iran

Author:
Parizipour, Mohamad Hamed Ghodoum; Schubert, Jörg; Behjatnia, Seyed Ali Akbar; Afsharifar, Alireza; Habekuß, Antje; Wu, Beilei
Source:
Virus genes 2017 v.53 no.2 pp. 266-274
ISSN:
0920-8569
Subject:
Wheat dwarf virus; genetic recombination; genome; mixed infection; phylogeny; sequence analysis; wheat; Iran
Abstract:
... Wheat dwarf virus (WDV) adversely affects cereal production in Asia, Europe, and North Africa. In this study, sequences of several WDV isolates from Iran which is located in the Fertile Crescent were analyzed. Analysis revealed a new geographic cluster for WDV-Wheat from Iran. Recombination analysis demonstrated the existence of several breakpoints in different regions of the viral genome. Data an ...
DOI:
10.1007/s11262-016-1412-0

16. Pig BVDV-2 non-structural protein (Npro) links to cellular antiviral response in vitro

Author:
Tao, Jie; Liao, Jinhu; Wang, Jianye; Zhang, Xinjun; Zhang, Qian; Zhu, Liqian; Zhang, Weiping; Liu, Huili; Zhu, Guoqiang
Source:
Virus genes 2017 v.53 no.2 pp. 233-239
ISSN:
0920-8569
Subject:
Bovine viral diarrhea virus 2; cattle; chronic diseases; complementary DNA; gene expression regulation; gene overexpression; interferons; mutants; plasmids; polypeptides; swine; viral nonstructural proteins; viruses
Abstract:
... In this study, we constructed for the first time a full-length cDNA clone of pig-original bovine viral diarrhea virus 2 (BVDV-2) strain SH-28, modified the cDNA clone (pASH28) for mutant pASHΔNᵖʳᵒ and derived virus strain vASHΔNᵖʳᵒ by deleting the genomic region encoding the Nᵖʳᵒ polypeptide, and examined significance of protein Nᵖʳᵒ for antiviral responses in vitro. Data showed that Nᵖʳᵒ-deletion ...
DOI:
10.1007/s11262-016-1410-2

17. Rotavirus NSP486–175 interacts with H9c2(2-1) cells in vitro, elevates intracellular Ca2+ levels and can become cytotoxic: a possible mechanism for extra-intestinal pathogenesis

Author:
Xiong, Xiaoshun; Hu, Yinyin; Liu, Caixia; Li, Xiangyang
Source:
Virus genes 2017 v.53 no.2 pp. 179-189
ISSN:
0920-8569
Subject:
Rotavirus; antibodies; calcium; cytopathogenicity; cytotoxicity; enterotoxins; gastroenteritis; gastrointestinal system; integrins; microfilaments; pathogenesis
Abstract:
... Rotavirus (RV) is the predominant cause of infantile gastroenteritis with multiple pathogenic factors, among which enterotoxin NSP4 is the most significant factor. NSP4 has been shown to induce elevation of the intracellular calcium concentration, alteration of the cytoskeleton organization, and cytopathic effect among other processes. However, increasing evidence suggests that RVs can escape from ...
DOI:
10.1007/s11262-016-1419-6

18. Splicing features in the expression of the complementary-sense genes of Beet curly top Iran virus

Author:
Bozorgi, Naghmeh; Heydarnejad, Jahangir; Kamali, Mehdi; Massumi, Hossain
Source:
Virus genes 2017 v.53 no.2 pp. 323-327
ISSN:
0920-8569
Subject:
Beet curly top Iran virus; eukaryotic cells; farms; genes; introns; messenger RNA; nucleotides; plant viruses; reverse transcriptase polymerase chain reaction; sequence analysis; transcription (genetics); Iran
Abstract:
... Beet curly top Iran virus (BCTIV) is a distinct geminivirus which has been reported from sugar-beet-growing farms in Iran. In this study, the role of the splicing in expression of complementary-sense genes of BCTIV was studied. Total RNA was extracted from BCTIV-infected tissue, and the predicted intron position of complementary-sense mRNA transcripts was amplified by RT-PCR followed by cloning of ...
DOI:
10.1007/s11262-016-1422-y

19. The fourth central polypurine tract guides the synthesis of prototype foamy virus plus-strand DNA

Author:
Chen, Dongxue; Song, Jing; Sun, Yan; Li, Zhi; Wen, Didi; Liu, Qingmei; Liu, Wanhong; He, Xiaohua
Source:
Virus genes 2017 v.53 no.2 pp. 259-265
ISSN:
0920-8569
Subject:
DNA; Human immunodeficiency virus 1; gene therapy; genome; mutation; nucleotide sequences; nucleotides; virion; viruses
Abstract:
... Foamy virus (FV) is a nonpathogenic retrovirus that has the potential to serve as a gene therapy vector. In retroviral replication, the central polypurine tract (cPPT) is used as a primer to synthesize plus-strand DNA. The cPPT is subsequently degraded to produce a single-stranded gap in the double-stranded viral DNA molecule. In the prototype foamy virus (PFV), four cPPT-like motifs have been pre ...
DOI:
10.1007/s11262-016-1425-8

20. The genetic diversity and complete genome analysis of two novel porcine deltacoronavirus isolates in Thailand in 2015

Author:
Lorsirigool, Athip; Saeng-chuto, Kepalee; Madapong, Adthakorn; Temeeyasen, Gun; Tripipat, Thitima; Kaewprommal, Pavita; Tantituvanont, Angkana; Piriyapongsa, Jittima; Nilubol, Dachrit
Source:
Virus genes 2017 v.53 no.2 pp. 240-248
ISSN:
0920-8569
Subject:
Deltacoronavirus; amino acids; diarrhea; genes; genetic analysis; genetic variation; nucleotides; phylogeny; piglets; sequence diversity; China; Thailand; United States
Abstract:
... Porcine deltacoronavirus (PDCoV) was identified in intestinal samples collected from piglets with diarrhea in Thailand in 2015. Two Thai PDCoV isolates, P23_15_TT_1115 and P24_15_NT1_1215, were isolated and identified. The full-length genome sequences of the P23_15_TT_1115 and P24_15_NT1_1215 isolates were 25,404 and 25,407 nucleotides in length, respectively, which were relatively shorter than th ...
DOI:
10.1007/s11262-016-1413-z