Complete genomic sequence of bluetongue virus serotype 16 from China

We report here the complete genomic sequence of the Chinese bluetongue virus serotype 16 (BTV16) strain BN96/16. This work is the first to document the complete genomic sequence (segments 1 to 10) of a BTV16 strain. The sequence information provided herein will help determine the geographic origin of BTV16 and define the phylogenetic relationship of BTV16 to other BTV strains.     

Full Genome Sequence of Bluetongue Virus Serotype 4 from China

The complete genomic sequence of a bluetongue virus serotype 4 (BTV-4) strain (strain YTS-4), isolated from sentinel cattle in Yunnan Province, China, is reported here. This work is the first to document the complete genomic sequence of a BTV-4 strain from China. The sequence information will help determine the geographic origin of Chinese BTV-4 and provide data to facilitate future analyses of the genetic diversity and phylogenetic relationships of BTV strains.     

Complete genomic sequence of duck flavivirus from china

We report here the complete genomic sequence of the Chinese duck flavivirus TA strain. This work is the first to document the complete genomic sequence of this previously unknown duck flavivirus strain. The sequence will help further relevant epidemiological studies and extend our general knowledge of flaviviruses.     

蓝舌病病毒基因节段2与6的重配导致病毒血清型与增殖特性的改变

[背景]蓝舌病病毒(Bluetongue Virus,BTV)是一种侵染反刍动物的虫媒病毒,基因重配可引起病毒的快速变异.[目的]通过我国强致病性BTV-16型毒株与弱致病性BTV-4型毒株间Seg-2与Seg-6基因节段的重配,探讨病毒基因重配与表型变异之间的关系.[方法]采用全长cDNA扩增与高通量测序获取BTV-...     

Sequence analysis of VP7 gene of Indian bluetongue virus serotype-23 shows its close phylogenetic relationship to Australian and Chinese serotypes.

Bluetongue, an arthropod borne viral disease of wild and domestic ruminants, causes heavy economic losses throughout the world. In the present study, full-length VP7 gene of Indian bluetongue virus (BTV) serotype 23 was sequenced and compared with prototype strains of BTV reported from different countries. Nucleotide sequence analysis of VP7 gene revealed Indian BTV serotype 23 to have 1154 nucleotides with the deletion of two nucleotides at 3' non-coding region and a unique amino acid change 211S-N. The Indian virus also demonstrated a maximum similarity of 94.2% with Australian serotype 1 and a minimum similarity of 67.4% with Australian serotype 15. However, at deduced amino acid level, it had maximum similarity of 99.7% and a minimum of 82.5% with Chinese serotypes 1, 2 and 4 and Australian serotype 15, respectively. Deduced amino acid sequence analysis of putative receptor binding domain (121-249) revealed all the nine hydrophilic domains to be conserved across the serotypes. Functional motifs present in VP7 protein were also conserved in almost all the BTV serotypes including Indian serotype 23. Phylogenetic analysis based on VP7 gene sequence revealed Indian BTV serotype 23 segregating into a monophyletic group along with Australian serotype 1 and Chinese serotypes 1, 2 and 4, indicating its close evolutionary relationship with these Australian and Chinese serotypes.     

我国肾综合征出血热疫苗生产株LR1株的全基因组序列分析

为测定我国肾综合征出血热疫苗生产株LR1株的全基因组序列 ,了解该株分子基础 ,从提取的细胞总RNA逆转录PCR扩增 ,产物纯化后克隆T载体纯化后测序 ,结果证明 ,LR1株全基因组序列由L6 5 33、M36 16、S片段的16 92个核苷酸组成 ,依各自读码框架分别编码 2 15 1、1135、42 9个氨基酸。序列同源比较分析表明 ,LR1毒株与国外HTN型毒株高度同源 ,属同一亚型 ,尤其与HTN代表株 76 - 1183个片段同源率高达 99 3%～ 99 8% ,而与国内的HTN型病毒差异较大 ,同源率仅为 79 4%～ 84 6 %。氨基酸比较也显示了同样的结果。     

Phylogenetic comparison of the S3 gene of United States prototype strains of bluetongue virus with that of field isolates from California.

To better define the molecular epidemiology of bluetongue virus (BTV) infection, the genetic characteristics and phylogenetic relationships of the S3 genes of the five U.S. prototype strains of BTV, the commercially available serotype 10 modified live virus vaccine, and 18 field isolates of BTV serotypes 10, 11, 13, and 17 obtained in California during 1980, 1981, 1989, and 1990 were determined. With the exception of the S3 gene of the U.S. prototype strain of BTV serotype 2 (BTV 2), these viruses had an overall sequence homology of between 95 and 100%. Phylogenetic analyses segregated the prototype U.S. BTV 2 strain to a unique branch (100% bootstrap value), whereas the rest of the viruses clustered in two main monophyletic groups that were not correlated with their serotype, year of isolation, or geographical origin. The lack of consistent association between S3 gene sequence and virus serotype likely is a consequence of reassortment of BTV gene segments during natural mixed infections of vertebrate and invertebrate hosts. The prototype strain of BTV 13, which is considered an introduction to the U.S. like BTV 2, presents an S3 gene which is highly homologous to those of some isolates of BTV 10 and especially to that of the vaccine strain. This finding strongly suggests that the U.S. prototype strain of BTV 13 is a natural reassortant. The different topologies of the phylogenetic trees of the L2 and S3 genes of the various viruses indicate that these two genome segments evolve independently. We conclude that the S3 gene segment of populations of BTV in California is formed by different consensus sequences which cocirculate and which cannot be grouped by serotype.     

水稻矮缩病毒第11号组分基因序列和编码蛋白的功能分析

水稻矮缩病毒(Rice Dwarf Virus-RDV)广泛分布于中国、日本及东南亚地区,侵染水稻和禾本科其它一些作物,是造成水稻减产的主要原因之一,对农作物危害极大。RDV属于呼肠孤病毒科(Re-oviridae)中的植物呼肠孤病毒属(Phytoreovirus)成员,其病毒粒子直径70nm,为20面体,有双层     

Complete Genome Sequence of Duck Tembusu Virus,Isolated from Muscovy Ducks in Southern China

We report here the complete genomic sequence of the duck Tembusu virus (DTMUV) WJ-1 strain, isolated from Muscovy ducks. This is the first complete genome sequence of DTMUV reported in southern China. Compared with the other strains (TA, GH-2, YY5, and ZJ-407) that were previously found in eastern China, WJ-1 bears a few differences in the nucleotide and amino acid sequences. We found that there are 47 mutations of amino acids encoded by the whole open reading frame (ORF) among these five strains. The whole-genome sequence of DTMUV will help in understanding the epidemiology and molecular characteristics of duck Tembusu virus in southern China.     

库蠓源蓝舌病病毒1型的分离和初步鉴定

为监测云南边境地区虫媒库蠓蓝舌病病毒携带情况,本研究对2013年-2017年从云南6个口岸及周边地区采集到的约5 400只库蠓样本,分180组。采用荧光定量RT-PCR检测、鸡胚和细胞分离、目的基因克隆测序分析和间接免疫荧光试验等进行病毒分离与鉴定。结果显示:采集库蠓样本中有20组检出蓝舌病病毒核酸,检出率为11.11%(20/180);接种后有1份样本能导致鸡胚胚体充血出血和死亡以及BHK-21细胞呈现明显的细胞病变;RT-PCR能从感染细胞样本中扩增出蓝舌病病毒VP7基因特异性片段,且该片段序列与国外BTV-1毒株相应序列的相似性达95%~99%;间接免疫荧光试验显示分离病毒能与BTV-1抗体发生特异性结合。结果表明,云南边境地区库蠓携带有蓝舌病病毒,且为BTV-1,因此应加强对云南边境地区蓝舌病的预防与控制。     

Complete sequences of two highly divergent european isolates of TT virus

TT virus is a virus distantly related to the Circoviridae family. We report here the complete genome characterization of two European human isolates (T3PB and TUPB) using a new and simple protocol for sequencing GC-rich genomic regions. Sequence analysis confirmed the existence of two major ORFs, of a CAV-like VP2 motif in ORF2 and of potential stem-loop structures in non-coding regions. Phylogenetic analyses based on complete genomic sequences of human isolates suggested that three different lineages exist at least. The first lineage includes genotypes 1, 2, and 3, and two other lineages include viruses related to the Japanese SANBAN and to the North American TUS01 isolates respectively. Sequence comparison made it possible to assign strain T3PB to genotype 3, and strain TUPB to the TUS01 group. Consequently, this study reports the first full-length sequence of a genotype 3 isolate and demonstrates that viruses belonging to the TUS01 lineage are present in the Old Word.     

Complete genome sequence analysis of a reference strain of bluetongue virus serotype 16

The entire genome of the reference strain of bluetongue virus (BTV) serotype 16 (strain RSArrrr/16) was sequenced (a total of 23,518 base pairs). The virus was obtained from the Orbivirus Reference Collection (ORC) at IAH, Pirbright, United Kingdom. The virus strain, which was previously provided by the Onderstepoort Veterinary Research Institute in South Africa, was originally isolated from the Indian subcontinent (Hazara, West Pakistan) in 1960. Previous phylogenetic comparisons show that BTV RNA sequences cluster according to the geographic origins of the virus isolate/lineage, identifying distinct BTV topotypes. Sequence comparisons of segments Seg-1 to Seg-10 show that RSArrrr/16 belongs to the major eastern topotype of BTV (BTV-16e) and can be regarded as a reference strain of BTV-16e for phylogenetic and molecular epidemiology studies. All 10 genome segments of RSArrrr/16 group closely with the vaccine strain of BTV-16 (RSAvvvv/16) that was derived from it, as well as those recently published for a Chinese isolate of BTV-16 (>99% nucleotide identity), suggesting a very recent common ancestry for all three viruses.     

GiSAO.db: a database for ageing research

Background

Infectious laryngotracheitis virus (ILTV) is an alphaherpesvirus that causes acute respiratory disease in chickens worldwide. To date, only one complete genomic sequence of ILTV has been reported. This sequence was generated by concatenating partial sequences from six different ILTV strains. Thus, the full genomic sequence of a single (individual) strain of ILTV has not been determined previously. This study aimed to use high throughput sequencing technology to determine the complete genomic sequence of a live attenuated vaccine strain of ILTV.

Results

The complete genomic sequence of the Serva vaccine strain of ILTV was determined, annotated and compared to the concatenated ILTV reference sequence. The genome size of the Serva strain was 152,628 bp, with a G + C content of 48%. A total of 80 predicted open reading frames were identified. The Serva strain had 96.5% DNA sequence identity with the concatenated ILTV sequence. Notably, the concatenated ILTV sequence was found to lack four large regions of sequence, including 528 bp and 594 bp of sequence in the UL29 and UL36 genes, respectively, and two copies of a 1,563 bp sequence in the repeat regions. Considerable differences in the size of the predicted translation products of 4 other genes (UL54, UL30, UL37 and UL38) were also identified. More than 530 single-nucleotide polymorphisms (SNPs) were identified. Most SNPs were located within three genomic regions, corresponding to sequence from the SA-2 ILTV vaccine strain in the concatenated ILTV sequence.

Conclusions

This is the first complete genomic sequence of an individual ILTV strain. This sequence will facilitate future comparative genomic studies of ILTV by providing an appropriate reference sequence for the sequence analysis of other ILTV strains.     

猪Ⅱ型圆环病毒豫A株的全基因组克隆与序列分析

参照国外发表的猪Ⅱ型圆环病毒(porcine circovirus type 2,PCV-2)全基因组序列,设计一对PCV-2特异性引物,用该室分离的PCV-2豫A株感染PK-15细胞,从中提取PCV-2复制型基因组DNA,并以之为模板进行PCR扩增.回收PCR产物,构建重组测序质粒T-PCV-2.测序结果表明,猪Ⅱ型圆环病毒豫A株的全基因组为1767bp,与GenBank收录的PCV-2国外分离株核苷酸的同源性可高达97%.序列分析表明,复制型豫A株的基因组包含10个读码框架,其中ORF1、ORF2是其两个最主要的读码框架,分别编码314、234个氨基酸.豫A株和PCV-1间的ORF1、ORF2的氨基酸序列同源性分别为85%、66%,与其它PCV-2毒株间的ORF1氨基酸同源性均在98%以上,而ORF2的氨基酸同源性为92%～97%.     

口蹄疫病毒Asia1/YNBS/58株全基因组序列分析

口蹄疫是由口蹄疫病毒(Foot-and-mouth dis-ease virus,FMDV)感染引起的偶蹄动物(猪、牛、羊、骆驼等)共患的一种急性、烈性、接触性传染病。FMDV是小核糖核酸病毒科(Picornaviridae)口蹄疫病毒属(Aphthovirus)的成员,有7个血清型,分别为O、A、C、Asia1、SAT1、SAT2、SAT3,完整     

Complete genome sequence of a novel field strain of rearranged porcine circovirus type 2 in southern china

We report here the complete genomic sequence of a novel porcine circovirus type 2 (PCV2) strain, which is supposed to be the result of natural genetic recombination between the ORF1 gene of genotype PCV2b-1B and the ORF2 gene of PCV2b-1C. Further analyses revealed that this novel PCV2 strain arose from recombination between PCV2a and PCV2b strains within the ORF2 gene. To our knowledge, this is the first report of both inter- and intragenotype PCV2 gene rearrangement in the field, and it will help in understanding the epidemiology and molecular characteristics of porcine circovirus type 2(PCV2) in southern China.     

Full genome sequence of bluetongue virus serotype 1 from India

We report the full-genome sequence of an Indian isolate of bluetongue virus serotype 1 (BTV-1), strain IND1992/01. This is the first report of the entire genome sequence (Seg-1 to Seg-10) of an Eastern (e) strain of BTV-1. These sequence data provide a reference for BTV-1e that will help to define the phylogenetic relationships and geographic origins of distinct Indian lineages of BTV-1 as well as their relationships with other BTV strains from around the world. The availability of data for all 10 genome segments of this strain will also help to identify reassortment events involving this and other virus lineages.     

Complete Genome Sequence of a Duck Hepatitis A Virus Type 3 Identified in Eastern China

We report here the complete genome sequence of a novel duck hepatitis A virus type 3 (DHAV-3) isolated from a dead Cherry Valley duckling in eastern China. The whole genomic nucleotide sequence and polyprotein amino acid sequence of the virus had higher homology with those of Chinese DHAV-3 isolates, medium homology with those of Korean DHAV-3 isolates, and the lowest homology with those of Vietnamese isolate DN2. The result indicated that the genetic evolution of DHAV-3 isolates had obvious geographical features.     

Sequence analysis for the complete proviral genome of reticuloendotheliosis virus Chinese strain HA9901

The genomic DNA extracted from chicken embryo fibroblast (CEF) infected with a Chinese field isolate HA9901 of reticuloendotheliosis virus (REV) was used as the template to amplify the REV proviral genomic cDNA by PCR with 6 pairs of primers according to published sequences. Six overlapping fragments were amplified, cloned into the TA vector and sequenced, including a fragment which was amplified from the circular proviral cDNA and covering both 5′-and 3′-ends. The complete sequence of the whole genome was established and analyzed with a DNAstar software. Comparisons of the sequence with two other strains demonstrated that the genomes of REV were relatively conservative, the homogenecity for all genes or LTR fragments of the 3 strains was over 92%, no matter whether they were isolated from different species and regions in different years. But, the homology of Chinese strain HA9901 to a fowl pox virus-associated strain from Chickens was higher than that to strain SNV isolated from ducks.     

Sequence analysis for the complete proviral genome of reticuloendotheliosis virus Chinese strain HA9901

Reticuloendotheliosis virus (REV), a member of avian retrovirus, can cause tumor, immune suppression and a runting disease syndrome[1,2]. With several clas-sical reference strains, such as strain SNV from ducks, a replication defective oncogenic strain T …