Bing du xue bao = Chinese journal of virology最新文献

{"title":"[Influence of Synonymous Codon Bias on the RNA Secondary Structure in Influenza-A Viruses].","authors":"Ruifang Li,&nbsp;Zhifen Yu,&nbsp;Qiao Huang,&nbsp;Chunyang Guo,&nbsp;Xue Li","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Influenza-A viruses were selected as samples. Then, the relationship between synonymous codon bias and mRNA secondary structures was analyzed. Our data will provide a theoretical basis for further research on the synonymous codon and RNA properties of the influenza-A virus. Information on the nucleic-acid sequence of all influenza-A viruses in the National Center for Biotechnology Information was collected. The secondary structure of each nucleic-acid sequence was predicted. Then, the loop structure, stem structure, and free replicating energy of RNA were calculated. Based on this information, the specific flexibility of RNA was worked out. Simultaneously, the synonymous codon bias in each nucleic-acid sequence was counted. A database on the RNA secondary structure of the influenza-A virus was set up. Then, the relationship between the synonymous codon bias and the content of loop structure, stem structure, and flexibility were analyzed.Codon usage of 50% of amino acids was correlated significantly with the content of stem structure or the content of loop structure.Also,60% of amino acids were correlated significantly with average unit folding free energy. In addition, codon usage of 50% of amino acids was correlated significantly with the specific flexibility of RNA. For codons that were correlated significantly with stem structure and loop structure, the correlation between their usage with two types of structural content was completely contrary .Also, the correlation between specific flexibility with synonymous codon bias was better than that observed for other parameters. These results suggest that synonymous codon usage bias has important influences on RNA secondary structure.</p>","PeriodicalId":8776,"journal":{"name":"Bing du xue bao = Chinese journal of virology","volume":"32 6","pages":"773-81"},"PeriodicalIF":0.0,"publicationDate":"2016-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36309478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[Research Advances in VP16 of the Herpes Virus].","authors":"Yuwei Zhang,&nbsp;Anchun Chen,&nbsp;Mingshu Wang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Viral protein(VP)16is an important tegument protein of the herpes virus. It is involved in early transcription activation of viral genes as well as virion assembly and release in host cells.VP16 of some herpes viruses have deubiquitinating protease activity and can help the virus counteract the host immune response. In this review, we explain the function and complex interactions between VP16 and other proteins based of the structural characteristics of VP16.This summary provides a reference for further research of maturation of the herpes virus as well as interactions between VP16 and other proteins.</p>","PeriodicalId":8776,"journal":{"name":"Bing du xue bao = Chinese journal of virology","volume":"32 6","pages":"817-24"},"PeriodicalIF":0.0,"publicationDate":"2016-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36309484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[The Epidemiology and Etiology Characteristics of Hand-foot-mouth Disease in Chongqing, China,2014～2015].","authors":"Xinrui Gu,&nbsp;Hua Zhao,&nbsp;Tianjiao Ji,&nbsp;Qin Li,&nbsp;Hua Ling,&nbsp;Shuangli Zhu,&nbsp;Yong Zhang,&nbsp;Qian Yang,&nbsp;Yang Song,&nbsp;Wei Huang,&nbsp;Wenbo Xu","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In this study, the epidemiology of Hand-foot-mouth disease(HFMD)composition of enterovirus (EV) pathogen and VP1 coding gene of Enterovirus A71(EV-A71)were analyzed in Chongqing from 2014 to 2015,to provide a scientific basis for strategies of prevention and control of HFMD in Chongqing. It is reported that there were a total of 100,176 cases of HFMD, of which 284 cases of severe,37 cases of death in Chongqing.39counties(autonomous counties)of Chongqing have reported cases, and the urbans reported incidence rate(298.83/100,000)was significantly higher than the suburbs(103.37/100,000),children 3and under 3years old accounted for 83.21%%,and 5and under 5years old accounted for 95.64%of reported cases, the big peak of epidemics of HFMD was from April to July and the small peak took shape from October to November. Severe cases(96.83%)and deaths(100%)were concentrated in the age group of 5years old and below. The severe cases were mainly in the three districts, WanZhou District, Liangping County and FuLing District, accounting for 74.65% of reported cases, and death cases were widely distributed, scattered in 17 counties.7503nucleic acid of clinical specimens of HFMD were detected, suggested that EV-A71,CV-A16,non-EV-A71/CV-A16 of other EV accounted for 23.54%,33.21%,43.25% respectively,Non-EV-A71/ CV-A16 of other EV became the dominant pathogen of HFMD in Chongqing, but EV-A71 was still the dominant pathogen in severe and death cases. The results showed that 54 strains belonged to C4a and one strain belonged to B5 in the analyses of the VP1 sequences of 55 strains during2014-2015 in Chongqing. This study provides important epidemiological and etiological data for HFMD prevention and control strategies and reduction of severe and death caused by EV-A71 in Chongqing.</p>","PeriodicalId":8776,"journal":{"name":"Bing du xue bao = Chinese journal of virology","volume":"32 6","pages":"707-12"},"PeriodicalIF":0.0,"publicationDate":"2016-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36309593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[Development and Application of Reverse Transcription Loop-mediated Isothermal Amplification Method for Detection of Porcine Rotavirus of Swine].","authors":"Xingyi Hu,&nbsp;Shuangxiang Zhang,&nbsp;Xufang Feng,&nbsp;Bijun Zhou,&nbsp;Ming Wen,&nbsp;Zhentao Cheng,&nbsp;Wei Wang,&nbsp;Kaigong Wang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We wished to establish a method for rapid and sensitive detection of reverse transcription loop-mediated isothermal amplification(RT-LAMP)for the rapid and sensitive detection of porcine rotavirus (PoRV). According to the published PoRV VP7 sequences in GenBank,6specific primers were designed. According to the concentrations of foward and reverse primers, Bst DNA polymerase, Mg(2+), and dNTP, reaction conditions were optimized. Results revealed the concentration ratio of foward and reverse primers to be 200 nmol/L:2, 400 nmol (1:12), Bst DNA polymerase concentration to be 0.64U/μL,Mg2+concentration to be 2.5mmol/L, and dNTP concentration to be 1.0mmol/L in 1hat 60℃.The amplification effect achieved a \"ladder\" effect, with amplified bands being shown only for PoRV. RT-LAMP was specific and did not elicit a cross reaction with porcine epidemic diarrhea virus, transmissible gastroenteritis virus of pigs, or classical swine fever virus. The sensitivity of RT-LAMP was 1.0×10(2) copies/μL. After the reaction, inspection by the naked eye revealed positive amplification products to appears as cloudy-white precipitates, and addition of SYBR Green I showed a color change. These data demonstrate that RT-LAMP is suitable for the rapid and sensitive detection of PoRV.</p>","PeriodicalId":8776,"journal":{"name":"Bing du xue bao = Chinese journal of virology","volume":"32 6","pages":"740-6"},"PeriodicalIF":0.0,"publicationDate":"2016-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36308997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[Current Status of Middle East Respiratory Syndrome Vaccines].","authors":"Yi Fan,&nbsp;Zhiyi Jiang,&nbsp;Ping Li,&nbsp;Yicao Den,&nbsp;Jianbo Huang,&nbsp;Ling Zhu,&nbsp;Zhiwen Xu","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Middle East respiratory syndrome is a kind of respiratory disease Caused by Middle East respiratory syndrome Coronavirus. Now the disease has spread to 27 countries around the world, more than 1806 people infected and more than 600 people were killed, and four countries have reported cases of camel infection MERS. Prevention of the disease are very important measures to research and development related to the vaccine. In order to have more resources into the development of safe and effective vaccine, this article summarizes the current some candidate vaccine of MERS research progress for the prevention and treatment of the disease that could trigger a global public health security problems ahead.</p>","PeriodicalId":8776,"journal":{"name":"Bing du xue bao = Chinese journal of virology","volume":"32 6","pages":"825-9"},"PeriodicalIF":0.0,"publicationDate":"2016-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36309485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[Establishment of a Model of Infection by Enterovirus 71 in ICR Mice].","authors":"Zhaopeng Dong,&nbsp;Zhenjie Zhang,&nbsp;Leiying Yang,&nbsp;Dong Li,&nbsp;Weifeng Shi","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We aimed to study infections in neonatal ICR mice of different ages infected with Enterovirus 71(EV-A71)through three routes of infection, and to explore the dynamic distribution and infection mechanism of EV-A71 in vivo.Three-,5-and 9-day-old neonatal ICR mice were infected with an EV-A71 strain isolated from a child with severe hand, foot and mouth disease through intramuscular(IM), intraperitoneal (IP)and intracerebral (IC)injection, respectively. Consequently, blood, brain, hind-limb muscle, heart, and intestines of mice were collected at regular intervals. Changes in viral load in organs were measured using real-time polymerase chain reaction. Hematoxylin and eosin staining and immunohistochemical (IHC)analyses were undertaken to detect pathogenic and pathologic changes in infected mice.Five-day-old neonatal mice infected with EV-A71 through IM,IP or IC routes had obvious neurologic symptoms and a high mortality rate. Symptoms were alleviated slightly with increasing age of mice upon injection. However, the pathogenicity associated with IM and IP injections was more severe than that of IC injection. Also, the mortality rates of IM and IP injections were significantly higher than that of IC injection. Compared with the control group, the mean body weight(in g)of 3-day-old neonatal mice at 6days post-infection(dpi)injected by IM,IP and IC routes decreased by 1.54(31.43%),1.31(15.06%)and 2.52(44.28%),respectively. Similarly, the mean body weight(in g)of 5-day-old neonatal mice at 6dpi injected by IM and IP decreased by 0.605(8.95%),0.886(15.51%),whereas that of mice injected by IC increased by 0.904(14.70%).The body weight of all infection groups was significantly lower than that of the control group(P<0.05).All 3-day-old neonatal mice infected with EV-A71 through IM,IP and IC routes died at 9dpi.Survival rates of 5-day-old neonatal mice infected through IM,IP and IC routes at 9dpi and14 dpi were 42.8%,25%,and 87.5%,and 0%,0%,and 25%,respectively.Those of 9-day-old neonatal mice at 14 dpi were 70%,69.23% and 100%,respectively.Pathologic and IHC examination showed that EV-A71 had a strong preference for infecting nervous systems and skeletal muscle, and could also lead to: viremia; necrosis of brain neurons and skeletal muscle; myocardial interstitial edema; inflammatory response of multiple organs. These data suggest that 5-day-old ICR neonatal mice injected through IM or IP routes can establish an ideal model of infection by EV-A71 in mice.</p>","PeriodicalId":8776,"journal":{"name":"Bing du xue bao = Chinese journal of virology","volume":"32 6","pages":"671-82"},"PeriodicalIF":0.0,"publicationDate":"2016-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36309588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[Genetic Characterization of Coxsackievirus A6 Strains Isolated in Ningxia Region, China, 2013～2015].","authors":"Fang Yuan,&nbsp;Hui Chen,&nbsp;Jiangtao Ma,&nbsp;Xueming Ma,&nbsp;Jun Zhan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>To study the genetic characteristics of coxsackievirus (CV)-A6 strains isolated from hand, food and mouth(HFMD)cases in Ningxia Province, China, in 2013~2015.A total of 998 specimens identified as non-EV71,non-CVA16 enteroviruses by real-time polymerase chain reaction were collected in 2013~2015and cultured using RD cells. The viral protein(VP)1gene of isolated strains was amplified by reverse transcription-polymerase chain reaction with degenerate primers and sequenced.Sequences were compared using the GenBank database by the BLAST algorithm to identify virus genotypes. All CV-A6 stains identified underwent homologous comparison and phylogenetic analyses. A total of 227 virus strains were isolated from 998 clinical specimens, and 61 stains were identified as CV-A6.Homologies of nucleotides and amino acids among Ningxia CV-A6 strains were 96.1%~99.8% and 98%~100%,respectively.The nucleotide homogeneity of Ningxia CV-A6 strains with Gudla strains, and the similarity of nucleotides and amino-acid sequences with VP1 of CV-A6 were 82.0%~83.5% and 93.8%~95.7%,respectively.CVA6 was the main pathogen of HFMD apart from EV71 and CV-A16 in Ningxia Province in 2013~2015.</p>","PeriodicalId":8776,"journal":{"name":"Bing du xue bao = Chinese journal of virology","volume":"32 6","pages":"702-6"},"PeriodicalIF":0.0,"publicationDate":"2016-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36309592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[Molecular Epidemiology of Astrovirus Infection Among Hospitalized Infants in Kunming City, China, 2013～2014].","authors":"Sida Yang,&nbsp;Yuheng Ren,&nbsp;Lili Deng,&nbsp;Jinghui Yang,&nbsp;Yongying Xiong,&nbsp;Shenrong Jing,&nbsp;Li Li","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We investigated the infection and molecular-epidemiologic characteristics of human astrovirus (HAstV) of hospitalized infants in Kunming City from the year 2013 to 2014.Infection and genotype of HAstV of 63 samples of diarrheal feces and 42 controls were analyzed by reverse transcription-polymerase chain reaction(RT-PCR).The complete genome sequence of a HAstV strain was amplified and sequenced. The positive rate of HAstV in 63 feces samples was 41.27%(26/63).The main circulating genotype of HAstV was HAstV1.Only 1sample was positive for HAstV in 42controls(2.38%).A complete genome sequence of the HAstV strain was identified as HAstV1 by phylogenetic analyses. These data provide an important theoretical basis for the control of viral diarrhea in infants in Kunming City.</p>","PeriodicalId":8776,"journal":{"name":"Bing du xue bao = Chinese journal of virology","volume":"32 6","pages":"752-7"},"PeriodicalIF":0.0,"publicationDate":"2016-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36310085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[Isolation and Identification of the Nam Dinh Virus from Mosquitoes on the China-Laos-Myanmar Border].","authors":"Wenwen Lei,&nbsp;Xiaofang Guo,&nbsp;Shihong Fu,&nbsp;Yun Feng,&nbsp;Jingdong Song,&nbsp;Hongning Zhou,&nbsp;Guodong Liang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Three strains of an insect nidovirus, the Nam Dinh virus (NDiV), isolated in Yunnan Province, China, have been identified. Aedes albopictus C6/36 cells were used to isolate NDiV from mosquitoes collected in Yunnan Province in 2012.Culture supernatants with a positive cytopathic effect were harvested for virus identification by sequence-independent single primer amplification. Transmission electron microscopy revealed virion structure to be spherical with a diameter of 60~80nm.Reverse transcription-polymerase chain reaction was applied to amplify sequences of RNA-dependent RNA-polymerase (RdRp), HEL1(superfamily 1helicase)and spike protein. The amino-acid sequences of three isolates from Yunnan Province showed>98% homology with NDiV strains. Phylogenetic analyses showed that these three isolates, along with NDiV, could be classified into the family Mesoniviridae.</p>","PeriodicalId":8776,"journal":{"name":"Bing du xue bao = Chinese journal of virology","volume":"32 6","pages":"782-9"},"PeriodicalIF":0.0,"publicationDate":"2016-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36309479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[Genetic Characteristics of the VP1 Region of the Coxsackie A16 Virus from Jiangsu Province, China, in 2015].","authors":"Junhong Li,&nbsp;Hong Ji,&nbsp;Huan Fan,&nbsp;Qiong Li,&nbsp;Fengming Wang,&nbsp;Ping Yao,&nbsp;Jun Shan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The aim of this study was to analyze the genetic characteristics of the VP1 gene of coxsackievirus A16(CA16)strains isolated from Jiangsu Province, China, in 2015.The VP1 regions of 20CA16 virus strains from Jiangsu Province in 2015 were amplified, and the amplification products were sequenced. Mega 6.0and DNA Star software were applied to build the phylogenetic tree and analyze the homogeneity of nucleotides and amino acids. The sequence homologies of the nucleotides and amino acids of the VP1 gene were 88.2%~100.0%and 98.0%~100.0%among 20CA16 isolates, respectively. Comparison with the sequence of the prototype strain A-G10 showed 75.3%~77.4% homologies in nucleotide sequence and90.6%~92.3%in amino-acid sequences, respectively. Comparison with the sequence of the representative strain B1 showed 88.3%~98.4% homologies in nucleotide sequence and 96.3%~100.0%in amino-acid sequence, respectively. Comparison with the sequence of the representative strain B2 showed 88.4%~90.8% homologies in nucleotide sequence and 96.6%~100.0%in amino-acid sequence, respectively. Twenty CA16 isolates were subgenotype B1.One isolate was subgenotype B1a, whereas the remainder of isolates was subgenotype B1b among 20 CA16 isolates. A subgenotype B1b transmission chain was also noted. The CA16 strains isolated from Jiangsu Province in 2015 belonged to subgenotype B1.There were two evolutionary branches, whereby B1 a and B1bwere co-circulating and evolving together. The epidemic strain was subgenotype B1b.</p>","PeriodicalId":8776,"journal":{"name":"Bing du xue bao = Chinese journal of virology","volume":"32 6","pages":"689-93"},"PeriodicalIF":0.0,"publicationDate":"2016-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36309590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}