塞内卡病毒CH/ZZ/2016株全基因组测序与分析

为了解塞内卡病毒分离株SVA/CH/ZZ/2016全基因组序列,设计4对相互重叠的特异性引物扩增基因片段,将扩增产物分别克隆至pCE2TA/Blunt-Zero载体并进行测序,拼接校正后获得SVA/CH/ZZ/2016株全基因组。结果显示,该毒株基因组全长7 292 bp,包括5''UTR（670 bp）、ORF（6 546 bp）以及3''UTR（76 bp）。选择国内外其他9株参考毒株序列,对编码区12个基因的核苷酸及编码氨基酸进行比对。结果显示,核苷酸同源性最高的是3B基因,最低的是VP1基因,其余基因的核苷酸序列同源性均在85.2%~100%之间。VP1基因遗传进化分析显示,SVA/CH/ZZ/2016株与美国分离株USAIL_Purdue_43_2016和USAIN_Purdue_3698_2016株亲缘关系最近,属同一进化分支,与原始毒株SVV-001株亲缘关系最远。对SVA/CH/ZZ/2016株和原始毒株SVV-001 VP1蛋白的氨基酸序列进行比对,发现共有10处氨基酸差异。本研究通过对SVA/CH/ZZ/2016株全基因组测序及分析,为进一步开展SVA分子生物学研究及流行病学调查提供了基础数据。     

一株塞内卡病毒A全基因组序列测定与致病性分析

本研究旨在明确塞内卡病毒A（Senecavirus A，SVA）FJLY株的基因组特性及其与其他毒株的同源性关系，并了解SVA-FJLY株的致病性。以分离自福建省某养殖场中的一株SVA-FJLY株为研究对象，参照其原型毒株SVV-001（GenBank No.DQ641257.1）全基因组序列设计5对引物，通过RT-PCR扩增、测序、拼接，获得SVA-FJLY株全基因组序列并进行序列分析；并通过滴鼻攻毒3~4周龄仔猪。结果表明，SVA-FJLY株基因组全长7 275 bp（不包括PolyA），SVA-FJLY株基因组存在一个多聚蛋白、VP1蛋白和VP2蛋白。SVA-FJLY株与参考毒株之间的基因组一级结构有较高的相似性，与HeB01-2017株（MF967574.1）相似性最高，达98.5%；而与SVA原型毒株SVV-001株（DQ641257.1）的相似性较低，为93.9%。SVA-FJLY株与国内几个毒株属于同一个分支，与国内的HeB01-2017株亲缘关系最近，同时与国外Colombia-2016株（KX857728.1）的亲缘关系最近。通过动物试验发现试验组猪攻毒10 d后，试验组2/3发病，对照组3/3正常，未出现仔猪死亡。通过全基因组序列测定获得了SVA-FJLY株全基因组序列并进行序列分析，明确SVA-FJLY株的基因组特性及其与其他毒株的相似性关系，了解了SVA-FJLY株的致病性，为SVA的反向遗传学和疫苗的研制提供参考依据，同时也丰富了SVA的基因组信息数据库。     

一株塞内卡病毒A全基因组序列测定与致病性分析

本研究旨在明确塞内卡病毒A(Senecavirus A, SVA)FJLY株的基因组特性及其与其他毒株的同源性关系,并了解SVA-FJLY株的致病性。以分离自福建省某养殖场中的一株SVA-FJLY株为研究对象,参照其原型毒株SVV-001(GenBank No.DQ641257.1)全基因组序列设计5对引物,通过RT-PCR扩增、测序、拼接,获得SVA-FJLY株全基因组序列并进行序列分析;并通过滴鼻攻毒3～4周龄仔猪。结果表明,SVA-FJLY株基因组全长7 275 bp(不包括PolyA),SVA-FJLY株基因组存在一个多聚蛋白、VP1蛋白和VP2蛋白。SVA-FJLY株与参考毒株之间的基因组一级结构有较高的相似性,与HeB01-2017株(MF967574.1)相似性最高,达98.5%;而与SVA原型毒株SVV-001株(DQ641257.1)的相似性较低,为93.9%。SVA-FJLY株与国内几个毒株属于同一个分支,与国内的HeB01-2017株亲缘关系最近,同时与国外Colombia-2016株(KX857728.1)的亲缘关系最近。通过动物试验发现试验组猪攻毒10 d后,试验组2/3发病,对照组3/3正常,未出现仔猪死亡。通过全基因组序列测定获得了SVA-FJLY株全基因组序列并进行序列分析,明确SVA-FJLY株的基因组特性及其与其他毒株的相似性关系,了解了SVA-FJLY株的致病性,为SVA的反向遗传学和疫苗的研制提供参考依据,同时也丰富了SVA的基因组信息数据库。     

新型鸭肝炎病毒分离株JFX08全基因组测定与分析

对我国鸭病毒性肝炎病毒(Duck hepatitis virus,DHV)分离株JFX08的全基因组进行了序列测定与分析。结果表明,JFX08毒株的基因组全长为7793nt,包括652nt的5’UTR,6753nt的ORF,366nt的3’UTR以及19nt的poly(A)尾巴。JFX08毒株的ORF编码2251个氨基酸,各基因均与韩国新型毒株的氨基酸序列相似性最高,与1型DHV和台湾新型DHV的序列相似性均较低。其中VP1较1型DHV存在2个氨基酸的插入和较多氨基酸位点的突变,高变区主要集中在180～194位和213～219位。JFX08毒株的非编码区核苷酸序列之间存在大量碱基突变和插入/缺失。多聚蛋白、VP0、VP3、VP1、2C和3D基因进化分析结果均表明,JFX08分离株与韩国新型DHV的遗传距离最近,属基因C型。     

番鸭源鸭肝炎病毒CH12株的分离与全基因组序列分析

从浙江省某疑似鸭病毒性肝炎的发病番鸭群分离到1株鸭肝炎病毒（Duck hepatitis virus,DHV）CH12株,分离毒株经动物回归试验、ELD50测定、中和试验等确定为DHV-1（基因A型DHV）。通过RT-PCR方法对DHV CH12株的全基因组序列进行分段扩增并测序。结果表明,CH12株的全基因组长度为7690 bp（不包括PolyA）,包括626 bp的5′UTR,6747 bp的ORF和317 bp的3′UTR。CH12株各基因均与基因A型DHV毒株的序列相似性较高,与基因B型和基因C型DHV毒株的序列相似性较低。全基因组核苷酸、多聚蛋白、VP0、VP3、VP1、2C和3D基因的进化分析均显示,CH12株均与基因A型DHV在同一进化分支上,亲缘关系较近,属于基因A型DHV。     

广西地区犬细小病毒检测及VP2基因序列分析

为了调查广西地区犬细小病毒(CPV)的优势毒株及其遗传变异情况,试验利用PCR方法对采自广西地区的423份犬血清样本进行CPV检测并扩增其VP2基因,利用MegAlign软件进行同源性比对并分析VP2蛋白主要突变的氨基酸位点,同时利用MEGA 7.0软件采用邻接法构建遗传进化树。结果表明：共获得55份CPV阳性血清样本,阳性率约为13.0%。PCR扩增得到大小约为1 755 bp的VP2基因。55株分离毒株之间的相似性为98.6%～100%;分离毒株与国内外参考毒株的相似性为97.4%～100%,与疫苗株Pfizer/vaccine/06的相似性为98.3%～98.9%。扩增序列的推导氨基酸主要在第5,297,370,426,440位发生变异。在55株分离毒株中,有32株为New CPV-2a亚型毒株,20株为CPV-2c亚型毒株,3株为New CPV-2b亚型毒株。55株分离毒株形成3个主要的流行分支,与国内参考毒株的亲缘关系较近,而与国外参考毒株、猫细小病毒的亲缘关系较远。说明New CPV-2a、CPV-2c、New CPV-2b亚型毒株在广西地区流行广泛,正逐步取代CPV-2a...     

Ⅰ型鸭肝炎病毒R株VP1基因克隆与序列分析

本研究克隆了DHVI-R株VP1基因,分析其与目前GenBank上发表的DHVI VP1基因的遗传变异,发现DHV I-R株与GenBank上发表的其他中国毒株VP1基因的核苷酸序列相似性92.2%～100%,而氨基酸序列相似性为95.0%～100%,变异程度不大.但各毒株的亲缘关系相差较大.     

2007～2009年华南地区鸭肝炎病毒流行病学调查及分离株的VP1基因变异分析

为了分析华南地区鸭肝炎病毒(Duck hepatitis virus,DHV)的遗传进化情况,本试验对2007～2009年华南地区各鸭场发病雏鸭进行DHV的病原学检测以及VP1基因扩增、克隆和测序,并运用生物信息学软件对VP1基因进行了序列分析。结果表明:所分离的R、SS1、ZJ株为DHV-A、VP1 DHV-A参考毒株核苷酸序列相似性分别为93.8%～100%、93.7%～99.6%、91.7%～98.9%,氨基酸序列相似性分别为94.5%～100.0%、94.1%～99.2%、95.0%～99.2%。其余15株DHV-C分离病毒株与台湾新型DHV核苷酸和氨基酸序列相似性均在71.4%～72.0%和78.2%～79.0%之间,与韩国新型DHV相似性在94.0%～95.1%和91.6%～93.3%之间,与国内分离的新型DHV相似性均在97.9%～100.0%和97.5%～100.0%之间。VP1氨基酸序列比对分析表明:VP1的高变区主要分布在46～64、95～149、180～223位,尤其是C′末端,存在点突变或连续变异。在第145～146位,15株新型DHV毒株比3株Ⅰ型DHV多2个氨基酸(G和G)。小RNA病毒科的VP1蛋白中保守的RGD基序,在DHV中分别显示为SGD和QSD。结果表明,危害华南地区鸭场的DHV已经发生变异,且存在两种基因型毒株的流行。     

猪圆环病毒2型贵州株全基因组的克隆与序列分析

应用PCR方法对采自贵州长顺、清镇和仁怀地区疑似断奶仔猪多系统衰竭综合征的病料进行了猪圆环病毒2型(PCV2)全基因组扩增、克隆和测序分析。结果表明:所扩增克隆的3株PCV2中,GZ-QZ1(JQ809463)和GZ-RH1(JQ809464)2个PCV2毒株基因组全长为1 767 bp,GZ-CS1(JQ809462)株为1 768 bp;3株PCV2之间的核苷酸序列相似性介于94.5%⁹9.9%,与国内外参考毒株核苷酸序列相似性为93.6%99.9%,与国内外参考毒株核苷酸序列相似性为93.6%⁹9.9%;全基因组序列比对分析表明,GZ-QZ1和GZ-RH1两个毒株属于PCV2b,GZ-CS1株属于PCV2a。对3株病毒编码Cap蛋白的ORF2基因分析发现,GZ-QZ1和GZ-RH1毒株与GZ-CS1毒株相比在696位缺失了一个碱基A,导致移码突变,使得末端氨基酸序列变由L K P变为L N P R。     

A亚群禽白血病病毒GD08株的分离与全基因组序列测定

通过DF-1细胞培养、ELISA抗原检测和特异聚合酶链式反应(PCR)从疑似禽白血病感染的黄羽肉种鸡中,分离并鉴定出1株A亚群禽白血病病毒(ALV-A),命名为GD08。依据A亚群原型株RAV-1前病毒全基因组序列设计并合成3对引物,首次完成了ALV-A中国分离株的全基因组序列测定。测序结果显示GD08株基因组序列全长7 704 bp,其中gp85全长为1 018 bp,预计编码339个氨基酸。序列分析发现GD08株的gp85与国内外各参考毒株的相应核苷酸序列相似性在44.2%～89.4%之间,其中与A亚群MAV-1株相似性最高(89.4%),与J亚群原型株HPRS-103相似性最低(44.2%)。基于ALVgp85核苷酸序列的系统发育进化树表明:GD08株与MAV-1株的亲缘关系最近。结果表明,在J亚群禽白血病普遍流行的情况下,ALV-A引起禽白血病病例在我国华南地区依然存在,提示了我国华南地区地方品种鸡禽白血病的流行呈现复杂化趋势。     

Molecular characterizations of avian polyomavirus isolated from budgerigar in China

Budgerigar fledgling disease is an acute viral infectious disease caused by avian polyomavirus (APV). In this study, 34 liver tissue samples of young, dead budgerigar with typical symptoms were collected in 2004. All the samples had positive polymerase chain reaction (PCR) test based on the VP1 specific primers. VP1 genes of these samples were sequenced and had high similarities to each other (99%-100%). A strain (HBYM02) was isolated and sequenced. As shown in the phylogenetic tree, there are two branches. One branch was composed by strains isolated from Passeriformes, and the other was composed only by one strain isolated from Falconiformes. The genome similarities between our isolate and other reported isolates were very high (> 99%), and the evolution distances in the phylogenetic tree were very short (< 0.005), which suggests that APV in China has the same genotype as those in other regions. The results will be useful for the diagnoses of, and vaccine development for, APV.     

1株库蠓源版纳病毒的分离与全基因组序列分析

为分析云南省虫媒病毒的种类与遗传特征,在云南省师宗县采集库蠓进行病毒的分离与鉴定;通过全长cDNA扩增与高通量测序技术获取病毒全基因组序列,进行序列比对与系统发生树构建。结果显示,从采集的库蠓样本中分离出1株可在C6/36细胞上引起细胞病变的毒株（YNSZ043）,病毒基因组为分节段双链RNA,琼脂糖凝胶电泳呈"2-4-3"的带型特征;电镜观察可见直径为70~80 nm,呈"指环状",表面具有纤维突起的病毒粒子。全基因组测序结果显示,YNSZ043毒株为版纳病毒（Banna virus,BAV）,基因组大小为20 683 bp,由Seg-1（3 762 bp）至Seg-12（861 bp）12个基因节段组成,与中国BAV毒株各基因节段的核苷酸序列相似性在64.8%~99.6%之间,氨基酸序列相似性在58.8%~100%之间,在系统发生树上YNSZ043毒株与中国分离的BAV聚为一簇,形成独立的中国进化支系。对决定BAV基因型的Seg-12分析结果显示,YNSZ043毒株属于A2基因型,该毒株的Seg-5/VP5与越南分离BAV毒株的核苷酸和氨基酸序列相似性高达97.1%和97.6%,表明该毒株的Seg-5基因节段很可能与越南毒株之间发生了基因重配。研究结果丰富了中国BAV的基因组序列,为开展云南省BAV的流行病学研究提供了参考。     

Molecular characterization of avian polyomavirus isolated from psittacine birds based on the whole genome sequence analysis

Seven avian polyomaviruses (APVs) were isolated from seven psittacine birds of four species. Their whole genome sequences were genetically analyzed. Comparing with the sequence of BFDV1 strain, nucleotide substitutions in the sequences of seven APV isolates were found at 63 loci and a high level of conservation of amino acid sequence in each viral protein (VP1, VP2, VP3, VP4, and t/T antigen) was predicted. An A-to-T nucleotide substitution was observed in non-control region of all seven APV sequences in comparison with BFDV1 strain. Two C-to-T nucleotide substitutions were also detected in non-coding regions of one isolate. A phylogenetic analysis of the whole genome sequences indicated that the sequences from the same species of bird were closely related. APV has been reported to have distinct tropism for cell cultures of various avian species. The present study indicated that a single amino acid substitution at position 221 in VP2 was essential for propagating in chicken embryonic fibroblast culture and this substitution was promoted by propagation on budgerigar embryonic fibroblast culture. For two isolates, three serial amino acids appeared to be deleted in VP4. However, this deletion had little effect on virus propagation.     

Sequence analysis of the VP2 hypervariable region of eight very virulent infectious bursal disease virus isolates from the northeast of China

Nucleotide sequences of the VP2 gene of eight infectious bursal disease viruses isolated from vaccinated chicken flocks in the northeast of China were determined. The sequence analysis showed that all of the isolates were also characterized by the vvIBDV conserved amino acid residues: 222A, 256I, 294I, and 299S. Four of them had one amino acid change (D-->N) at position 212 in VP2 major hydrophilic peak A, while two of the four isolates had another one (A-->V) at position 321 in major hydrophilic peak B. The other isolates were similar to the UK661 strain. Our findings demonstrated that the vvlBDV strains in the northeast of China could be diverse.     

广西梧州地区近十年传染性法氏囊病病毒vVP2变化特征分析

为了解近10年来广西梧州地区鸡传染性法氏囊病病毒(IBDV)分子进化情况,对2013年—2014年间来自该地区传染性法氏囊病(Infectious bursal disease,IBD)的法氏囊样品进行IBDV的分离鉴定,并对分离株以及课题组2006年—2013年间分离的毒株,共24株的VP2高变区(vVP2)进行序列分析和遗传进化分析。结果表明,QX0601等23个分离株在关键氨基酸位点上具有256I、284A、294I等超强毒株(vvIBDV)的分子特征,遗传进化分析表明,这23株分离株与UK661、HK46等超强毒参考株同处一个分支中,亲缘关系较近;QX110603在关键性氨基酸位点上则具有256V、284T、294L等弱毒株的特征,遗传进化分析显示,其与BJ836等致弱株处于同一分支,亲缘关系较近。对所有分离株进行氨基酸位点分析发现,该地区IBDV进化出现了新的特点,212D-212N符合国内近年来的分离株的变化趋势,209T-209A、338R-338H、359T-359R则表现出地域特点,未曾见过相似报道。研究结果表明,具有vvIBDV分子特征的分离株是该地区近10年来主要流行毒株,该地区IBDV毒株在vVP2序列上仍处于不断进化中,且带有地域特点。     

不同动物源脑心肌炎病毒的分离、鉴定和全基因组序列分析

为研究脑心肌炎病毒（encephalomyocarditis virus,EMCV）对不同动物宿主的感染情况。本试验应用改进的＂细胞接种与RT-PCR方法相结合＂技术,成功分离到国内首株地方土猪源EMCV、首株家养野猪源EMCV、1株鼠源EMCV和3株良种猪源EMCV,并进行了全基因组序列测定和分析。结果显示,6株EMCV分离毒的基因组全长从7 724~7 735bp不等,ORF长度均为6 879bp,彼此间核苷酸同源性为99.3%~99.8%,与其他不同动物源EMCV参考毒株的同源性为79.9%~99.9%,与国内猪源、鼠源分离毒的同源性均在99.4%以上;各基因片段中,以VP1和2A变异幅度最大,VP2和3D最为保守;基于EMCV全基因组、ORF和VP1基因序列绘制的系统发育进化树显示,EMCV可分为G1、G2和G3 3个群,猪源EMCV主要分布在G1、G2群,鼠源EMCV在G1、G3群中均有分布;6株EMCV分离毒与其他国内参考毒株同属于G1群,但分布并不完全集中。结果表明,地方土猪和家养野猪可感染EMCV并引起发病,提醒在进行地方品种养殖和野生动物家养时要充分考虑人兽共患疫病传播的生态学;鼠在良种猪、家养野猪和地方土猪EMCV之间的交叉感染、传播与流行中起到重要媒介作用;不同EMCV地方流行株间存在较大的地域差异,其传播具有一定的区域限制性;EMCV在感染不同动物时可能会发生某些突变,以适应新的宿主。     

Genetic diversity of avian infectious bronchitis coronavirus in recent years in China

Fifty-six isolates of avian infectious bronchitis virus (IBV) were obtained from different field outbreaks in China in 2010, and they were genotyped by comparison with 19 reference strains in the present study. The results showed that LX4-type isolates are still the predominant IBVs circulating in chicken flocks in China, and these isolates could be grouped further into two clusters. Viruses in each cluster had favored amino acid residues at different positions in the S1 subunit of the spike protein. In addition, a recombination event was observed to have occurred between LX4- and tl/CH/LDT3/03I-type strains, which contributed to the emergence of a new strain. The most important finding of the study is the isolation and identification of Taiwan II-type (TW II-type) strains of IBV in mainland China in recent years. The genome of TW II-type IBV strains isolated in mainland China has experienced mutations and deletions, as demonstrated by comparison of the entire genome sequence with those of IBV strains isolated in Taiwan. Pathogenicity testing and sequence analysis of the 3' terminal untranslated region revealed that TW II-type IBV strains isolated in mainland China have a close relationship with the embryo-passaged, attenuated TW2296/95.     

Comparison of Chinese field strains of avian leukosis subgroup J viruses with prototype strain HPRS-103 and United States strains

Eight Chinese field strains of subgroup J avian leukosis viruses (ALV-J) were isolated from broilers or parent stocks during January 1999 to April 2001. One strain, SD9902, was an acute transforming virus, able to induce typical myelocytomatosis in 22-38 days after inoculation of 1-day-old meat-type chicks. The envelope protein and 3'-untranslated region (UTR) of the eight field strains were compared with the U.K. prototype HPRS-103 and several U.S. field strains isolated in 1993-97. All Chinese strains shared an almost identical deletion with the U.S. strain 4817 in the E element region of 3'-UTR when compared with the prototype HPRS-103, indicating that they have a very close phylogenic relationship. Every year, China has to import grandparent stocks of meat-type chickens, mainly from the United States. Chinese isolates should represent a part in the phylogenic tree of U.S. ALV-J evolution. Envelope protein gp85 amino acid sequence analysis demonstrated that, interestingly, all recent Chinese isolates were more closely related to HPRS-103 and the earliest U.S. isolates but not to the late U.S. isolates. The result implies that envelope gp85 may not have diverged from prototype and older strains. It is also possible that some recently imported birds could have been infected by the older viruses that were introduced in the late 1990s.     

鹦鹉幼雏病病毒福建株VP1基因的克隆及序列分析

为明确虎皮鹦鹉源鹦鹉幼雏病病毒（budgerigar fledgling disease polyomavirus,BFPyV）福建株（命名为FJ-2016株）结构蛋白VP1基因特征,本研究针对BFPyV VP1基因特点设计特异性引物,利用PCR方法扩增获得FJ-2016株VP1基因全长序列,目的片段经胶回收后进行克隆测序。结果显示,BFPyV FJ-2016株VP1基因全长为1 032 bp,编码343个氨基酸。所编码VP1蛋白的理论等电点为5.77,不稳定指数为40.91,是不稳定蛋白;脂肪系数为74.72;总平均疏水性指数为-0.366。将获得的VP1基因序列提交至GenBank,登录号为：MG148345。核苷酸同源性分析表明,不同时间、地区和品种BFPyV的VP1基因十分保守,相互之间的核苷酸同源性均在99.1%以上。遗传进化分析发现,不同时间和地域BFPyV相互之间亲缘关系较近,但可细分为两个大的遗传进化分支（Clade 1和Clade 2）。从宿主品种来看,虎皮鹦鹉源BFPyV各分离株的遗传进化与分离时间及地域无明显关系,虎皮鹦鹉源BFPyV分离株在Clade 1和Clade 2分支均有分布。本研究首次证实福建地区虎皮鹦鹉中存在BFPyV感染,相关研究结果为丰富不同地区BFPyV分子流行病学数据提供参考。