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Archives of Virology | Page 2

Yubing Jiao, Junyun Jiang, Mengnan An, Zihao Xia, Yuanhua Wu
Maize chlorotic mottle virus (MCMV), an important quarantine virus, causes lethal necrosis in maize when coinfected with a potyvirid, which is seriously threatening the production of maize worldwide. In this study, recombinase polymerase amplification (RPA), a novel isothermal DNA amplification and detection technique, was developed to detect MCMV in maize crops. A pair of specific primers was designed based on the conserved sequences of the MCMV coat protein region. The RT-RPA assay was carried out as an isothermal reaction at 38 °C that was complete within 30 min, and no cross-reactivity was detected with other viruses infecting maize in China...
July 29, 2019: Archives of Virology
Guehwan Jang, Jonghyun Park, Changhee Lee
Porcine epidemic diarrhea virus (PEDV) is a deadly epizootic swine coronavirus that is of importance to the world pork industry. Since the re-emergence of the virulent genotype 2b (G2b) in 2014, Jeju Island in South Korea has faced periodic outbreaks, leading to the occurrence of endemics in provincial herds. In this study, we examined the complete genome sequences and molecular characteristics of novel G2b PEDV variants with a two-amino-acid deletion in the neutralizing epitope of the spike (S) gene, which were concurrently identified on a re-infected farm and its neighboring farm on Jeju Island...
July 26, 2019: Archives of Virology
Alfredo Diaz-Lara, Reid S Brisbane, Kamyar Aram, Deborah Golino, Maher Al Rwahnih
Recently, five new viruses from the genus Vitivirus were identified and named grapevine virus G, H, I, J and L. These viruses were targeted in a survey to evaluate their prevalence in different grapevine populations in California. Excluding a single detection of GVJ, other vitiviruses were detected infecting several grapevine selections via RT-PCR and later confirmed by sequencing. This paper represents the first report of GVG, GVH and GVI in California. In a preliminary analysis, the sequence diversity between identified isolates of GVG, GVH, GVI and GVL was investigated using distance matrices and phylogenetics...
July 25, 2019: Archives of Virology
Tahereh Donyavi, Farah Bokharaei-Salim, Khadijeh Khanaliha, Maryam Sheikh, Mohammad-Navid Bastani, Najmeh Moradi, Roghayeh Babaei, Zahra Habib, Atousa Fakhim, Maryam Esghaei
One of the pathological forms of chronic hepatitis C is occult HCV infection (OCI), in which there is no detectable HCV RNA in plasma specimens but HCV RNA is present in PBMCs and liver biopsy specimens. The aim of this study is to estimate the prevalence of OCI in HIV-positive people who are injection drug users (IDUs). From April 2015 to August 2018, 161 Iranian IDUs with HIV infection enrolled in the study. Viral RNA was extracted from plasma and PBMC samples of participants, and the presence of HCV RNA was examined using RT nested PCR with primers from two conserved regions (5´-UTR and NS5B)...
July 25, 2019: Archives of Virology
Rodolfo De La Torre-Almaráz, Vicente Pallás, Jesús A Sánchez-Navarro
The complete genome sequence of a trichovirus was obtained from peach samples collected from Mexico and found to be 7985 nucleotides long, excluding the poly(A) tail. Phylogenetic analysis using the complete nucleotide sequence revealed that the virus is a member of the genus Trichovirus and is closely related to peach mosaic virus (PcMV) and cherry mottle leaf virus (CMLV). The highest nucleotide sequence identity was 70% to both PcMV and CMLV, indicating that this virus, which we have tentatively named "peach virus M" (PeVM) should be considered a member of a new trichovirus species...
July 25, 2019: Archives of Virology
Xiaoran Chang, Qian Lin, Junying Hu, Xu Wang, Xin Li, Menglu Cai, Weiyu Wang, Zecai Zhang, Xinping Wang
Here, we report two novel enteroviruses, designated as SD-S67 and SD-S68, isolated from a goat farm. Their complete genome sequences were determined and found to be 7455 and 7465 nucleotides in length, respectively. Molecular characterization revealed that SD-S67 is closely related to bovine enterovirus strain 261 and that SD-S68 to caprine enterovirus strain CEV-JL14. Phylogenetic analysis showed that SD-S67 clustered with members of the species Enterovirus F, and that SD-S68 clustered with enteroviruses of goats and sheep...
July 18, 2019: Archives of Virology
Thamiris Vaz Gago Prata, Dayane de Souza Rodrigues da Silva, Caroline Manchiero, Bianca Peixoto Dantas, Celso Carmo Mazza, Arielle Karen da Silva Nunes, Edson Abdala, Gerusa Maria Figueiredo, Fátima Mitiko Tengan, Mariana Cavalheiro Magri
Polymorphisms in the microsomal triglyceride transfer protein (MTTP) gene were genotyped in individuals who were chronically infected with hepatitis C virus (HCV). In the 236 patients, the frequencies of risk alleles of the -164T/C (rs1800804), -400A/T (rs1800803) and H297Q (rs2306985) polymorphisms were 0.30, 0.41 and 0.50, respectively. A significant association between the risk alleles of the -164T/C and -400A/T polymorphisms combined with HCV genotype 3 infection and the occurrence of steatosis was detected (p = 0...
July 18, 2019: Archives of Virology
Min Xu, Song Zhang, Zhiyou Xuan, Jiaxing Wu, Peng Dong, Yan Zhou, Ruhui Li, Mengji Cao
A new virus with a circular double-stranded DNA genome was discovered in green Sichuan pepper with vein clearing symptoms. Its complete genome of 8,014 bp contains three open reading frames (ORF) on the plus strand, which is typical of members of the genus Badnavirus in the family Caulimoviridae. Sequence comparisons revealed that the new virus has the highest nucleotide sequence identity with grapevine vein-clearing virus (GVCV). In particular, the identity of the two viruses in the ORF3 RT-RNase H region is 71...
July 18, 2019: Archives of Virology
Wei Li, Cixiu Li, Lifang Liu, Xia Liu, Shiqiang Shang, Haiyan Mao, Yanjun Zhang
Enteroviruses (EVs) are the major cause of hand, foot, and mouth disease (HFMD) and herpangina in children. In this study, we conducted a molecular investigation of EVs in throat swab samples from children in Hangzhou, China with a diagnosis of HFMD or herpangina. EVs were detected using one-step real-time RT-PCR, and their serotypes were determined based on partial VP1 gene sequences. The molecular typing results revealed the presence of six different EV serotypes in HFMD cases, including coxsackievirus (CV) A16 (20/30, 66...
July 18, 2019: Archives of Virology
Thanyaporn Sirihongthong, Kunlakanya Jitobaom, Supinya Phakaratsakul, Chompunuch Boonarkart, Ornpreya Suptawiwat, Prasert Auewarakul
Codon usage is biased in most species, and the pattern of codon usage bias is specific to each species or group of closely related species. Although viruses use the host translational machinery for synthesis of their proteins, their codon usage patterns do not match those of their host. Viral codon usage is determined by a complex interplay of mutational bias, genome composition constraints, translational adaptation to the host, and host cellular innate defense. The codon usage of parvoviruses was previously shown not to be strongly biased and selective pressure was found to be a dominating factor driving codon usage...
July 18, 2019: Archives of Virology
Karel Petrzik, Abu Bakar Siddique
A novel bisegmented double-stranded RNA virus was identified in the mycoparasitic and opportunistic fungus Hypomyces chrysospermus. The RNA1 genome segment comprises 1866 bp and encodes an RNA-dependent RNA polymerase (RdRp). The RNA2 segment comprises 1822 bp and encodes a capsid protein. Phylogenetic analysis of the RdRp protein indicated that this virus is a new member of genus Alphapartitivirus in the family Partitiviridae. We have designated this mycovirus as "Hypomyces chrysospermus partitivirus 1" (HcPV1)...
July 17, 2019: Archives of Virology
Thanuja Thekke-Veetil, Thien Ho
A new virus belonging to the genus Vitivirus in the family Betaflexiviridae was identified by next-generation sequencing of a blueberry plant showing green mosaic symptoms. The genome organization of the virus, which is tentatively named "blueberry green mosaic-associated virus" (BGMaV), is typical of vitiviruses, with five open reading frames (ORFs) and a polyadenylated 3' terminus. The ORFs code for the viral replicase, a 16K protein of unknown function, a movement protein, a coat protein (CP), and a nucleic acid binding protein...
July 16, 2019: Archives of Virology
Rayan M Asil, Martin Ludlow, Abdelgadir Ballal, Saafass Alsarraj, Wegdan H Ali, Baraa A Mohamed, Shaza M Mutwakil, Nussieba A Osman
In May 2017, many free-ranging dorcas gazelles (Gazella dorcas) with suspected signs of peste des petits ruminants (PPR) were reported in Dinder National Park, South-Eastern Sudan. Peste des petits ruminants virus (PPRV) antigen and nucleic acid were detected in specimens from these gazelles using an immunocapture ELISA and a reverse transcription polymerase chain reaction (RT-PCR) assays. PPRV was also detected in four healthy semi-captive dorcas gazelles from two areas of Khartoum State. Phylogenetic analysis showed that these PPRV strains belonged to the lineage IV genotype...
July 15, 2019: Archives of Virology
Mundia M Phiri, Evans Kaimoyo, Katendi Changula, Isaac Silwamba, Herman M Chambaro, Penjaninge Kapila, Masahiro Kajihara, Martin Simuunza, John Bwalya Muma, Girja S Pandey, Ayato Takada, Aaron S Mweene, Simbarashe Chitanga, Edgar Simulundu
Whilst bovine leukemia virus (BLV) causes considerable economic losses to the dairy industry worldwide, information on its molecular epidemiology and economic impact in beef cattle is limited. Here, blood from 880 animals from Zambia's major cattle-rearing provinces was screened for BLV by nested PCR. Positive pools were sequenced and phylogenetically analyzed. The estimated pooled prevalence was 2.1%. All strains belonged to genotype 1 and formed a distinct phylogenetic cluster. The study suggests circulation of genotype 1 BLV in beef cattle in these regions...
July 12, 2019: Archives of Virology
S Marton, D Szalay, S Kecskeméti, B Forró, F Olasz, Z Zádori, I Szabó, T Molnár, K Bányai, Á Bálint
Porcine reproductive and respiratory syndrome virus 1 is a major cause of swine morbidity and mortality in various parts of the world, including Hungary. A national elimination programme to reduce the associated economic burden was initiated in Hungary in 2012. Using extensive laboratory surveillance, we identified and isolated an unusual PRRSV strain. The complete coding sequence of this isolate was determined and analyzed. The genome of this Hungarian PRRSV1 strain, HUN60077/16, is 15,081 nucleotides in length...
July 12, 2019: Archives of Virology
Natalia Langenfeld Fuoco, Elaine Raniero Fernandes, Fernanda Guedes, Sandriana Dos Ramos Silva, Leticia Patricia Guimarães, Nayara Ugeda Silva, Orlando Garcia Ribeiro, Iana Suly Santos Katz
Rabies is a lethal viral disease that can affect a wide range of mammals. Currently, Rabies virus (RABV) in some European and American countries is maintained primarily in wild species. The regulation of viral replication is one of the critical mechanisms involved in RABV pathogenesis. However, the relationship between replication and the pathogenesis of RABV isolated from wild animals remains poorly understood. In the present study, we evaluated the pathogenicity of the street viruses Nyctinomops laticaudatus bat-associated RABV (NYBRV) and Cerdocyon thous canid-associated RABV (CECRV)...
July 10, 2019: Archives of Virology
Yang Song, Yu Pei, Yawen Bu, Wenfeng Jia, Guozhong Zhang
In this study, we investigated which structural proteins of pigeon paramyxovirus type 1 (PPMV-1) are responsible for its low pathogenicity in chickens. The results revealed that the pathogenicity of the virus is determined by multiple genes. The NP protein and F protein were found to have the strongest individual effect on virulence, and this effect further enhanced when the two proteins were expressed in combination. Our study highlights the influence of the NP and F proteins on the pathogenicity of PPMV-1 in chickens...
July 8, 2019: Archives of Virology
Shiqing Wei, Xiaorong He, Die Wang, Jinyou Xiang, Yide Yang, Shu Yuan, Jing Shang, Hui Yang
Tobacco vein banding mosaic virus (TVBMV) is of increasing importance in tobacco production. Knowledge of the genetic structure and variability of the virus population is vital for developing sustainable management. In this study, 24 new TVBMV isolates from Sichuan Province together with 46 previous isolates were studied based on their coat protein sequences. Two distinguishable clades were supported by phylogenetic analysis. The summary statistics PS, AI and MC showed a strong TVBMV-geography association between the isolates from Southwest China (SW) and Mainland China (MC)...
July 8, 2019: Archives of Virology
Yuyu Yuan, Feiyang Zhao, Lili Wang, Demeng Tan, Cong Cong, Xiaoyu Li, Yongping Xu
This work describes the characterization and genome annotation of a new lytic Enterococcus faecalis siphovirus, vB_EfaS_AL3 (referred to as AL3), isolated from wastewater samples collected in Liaoning Province, China. The genome of phage AL3 is composed of linear double-stranded DNA that is 40,789 bp in length with a G + C content of 34.84% and 61 putative protein-coding genes. Phylogenetic and comparative genomic analyses indicate that phage AL3 should be considered a novel phage.
July 5, 2019: Archives of Virology
Deli Xia, Liping Huang, Yongxing Xie, Xiaoqian Zhang, Yanwu Wei, Dan Liu, Hongzhen Zhu, Haiqiao Bian, Li Feng, Changming Liu
A total of 472 samples from domestic pigs collected in China from 2015 to 2018 were tested for the presence of porcine circovirus types 2 and 3 (PCV2 and PCV3, respectively) by conventional polymerase chain reaction analysis. The prevalence of PCV2, PCV3, and PCV2/3 co-infection was 50.0%, 13.3%, and 6.78%, respectively. The complete genomic sequences of 66 PCV2 isolates and four PCV3 isolates were determined. Based phylogenetic analysis, the PCV2 isolates were assigned to three genotypes, PCV2a, PCV2b, and PCV2d, representing 13...
July 4, 2019: Archives of Virology
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