Use of S1 nuclease in deep sequencing for detection of double-stranded RNA viruses

Metagenomic approach using next-generation DNA sequencing has facilitated the detection of many pathogenic viruses from fecal samples. However, in many cases, majority of the detected sequences originate from the host genome and bacterial flora in the gut. Here, to improve efficiency of the detection of double-stranded (ds) RNA viruses from samples, we evaluated the applicability of S1 nuclease on deep sequencing. Treating total RNA with S1 nuclease resulted in 1.5–28.4- and 10.1–208.9-fold increases in sequence reads of group A rotavirus in fecal and viral culture samples, respectively. Moreover, increasing coverage of mapping to reference sequences allowed for sufficient genotyping using analytical software. These results suggest that library construction using S1 nuclease is useful for deep sequencing in the detection of dsRNA viruses.     

反向遗传学技术及在RNA病毒研究中的应用

RNA病毒的反向遗传学技术是指由病毒的cDNA克隆获取RNA病毒的一项技术,该技术通过人为加入DNA基因片段,实现了在DNA水平上对RNA病毒基因组的人工操作。反向遗传系统可以对RNA病毒直接进行遗传操作,为RNA病毒的分子生物学研究提供了一种强大的工具。自20世纪70年代后期第一例RNA病毒感染性克隆构建成功以来,RNA病毒的分子生物学研究取得了长足的进展,这在很大程度上归功于各种RNA病毒反向遗传系统的建立。文章介绍了反向遗传学技术的基本特点、技术方法及其在正、负链RNA病毒的基因功能、致病机制及新型病毒载体等方面的研究及应用情况。     

Implementation of next-generation sequencing for virus identification in veterinary diagnostic laboratories

The value of next-generation sequencing (NGS)-based applications for testing purposes in human medicine is widely recognized. Although NGS-based metagenomic screening may be of interest in veterinary medicine, in particular for intensively farmed livestock species such as pigs, there is a lack of protocols tailored to veterinary requirements, likely because of the high diversity of species and samples. Therefore, we developed an NGS-based protocol for use in veterinary virology and present here different applications in porcine medicine. To develop the protocol, each step of sample preparation was optimized using porcine samples spiked with various RNA and DNA viruses. The resulting protocol was tested with clinical samples previously confirmed to be positive for specific viruses by a diagnostic laboratory. Additionally, we validated the protocol in an NGS viral metagenomics ring trial and tested the protocol on viral multiplex reference material (NIBSC, U.K.). We applied our ViroScreen protocol successfully for 1) virus identification, 2) virus characterization, and 3) herd screening. We identified torque teno sus virus and atypical porcine pestivirus in a neurologic case, determined the full-length genome sequence of swine influenza A virus in field samples, and screened pigs using pen floor fecal samples and chewing rope liquid.     

检测CSFV、JEV、PRRSV三种RNA病毒多重RT-PCR方法的建立

猪瘟病毒(CSFV)、流行性乙型脑炎病毒(JEV)和猪繁殖与呼吸综合征病毒(PRRSV)是引起严重的种猪繁殖障碍的病原,而且经常混合感染,及时准确诊断是防治的前提。根据GenBank发表序列选取3对引物建立检测CSFV、JEV和PRRSV病毒的多重RT-PCR方法,扩增产物分别为508 bp、380 bp、263 bp。经与IDEXX商品化的检测CSW抗原试剂盒比较,二者的符合率为96.7%;扩增JEV和PRRSV PCR产物分别经EcoR V和Sau3A I酶切得到预期的片段。建立的多重RT-PCR检测JEV、PRRSV和CSFV敏感度分别为12.5个TCID_(50)、10个TCID_(50)和10~(-3)ng总RNA。结果表明该多重RT-PCR方法具有很好的特异性和敏感性,可用于临床三种病毒核酸的检测。     

动物RNA病毒感染性cDNA的研究进展

RNA病毒不仅对各国畜牧业的发展带来了严重的破坏,而且影响着畜产品进出口。感染性cDNA的研究虽然起步晚,但发展迅速。文章探讨了构建感染性cDNA的主要策略,并对正、负链RNA病毒感染性cD-NA的研究现状、国内外研究进展和应用情况,如基因组功能、研制标记疫苗和基因工程疫苗等做了综述,认为在此病毒上构建感染性cDNA有着广阔的前景,值得作进一步的探索,这对预防和控制RNA病毒引起的疾病将起重要的作用。     

单细胞转录组测序技术及其在肌内脂肪细胞研究中的应用

单细胞转录组测序(single-cell RNA sequencing, scRNA-seq)技术在单细胞水平对转录组进行测序,可从表达量、细胞量及细胞组成等多种角度描述样本,主要包括单细胞分离、mRNA反转录、文库构建、转录组测序和数据分析等步骤。单细胞分离是scRNA-seq技术操作的第一步,常用的细胞分离方法有连续稀释法、显微操作法、荧光激活流式细胞术、激光捕获显微切割术和微流控技术。基于不同细胞捕获、cDNA扩增和文库构建开发了许多scRNA-seq方法,如CEL-seq2、Drop-seq、MARS-seq、SCRB-seq、Smart-seq、Smart-seq2等。与传统测序方法相比,scRNA-seq可识别单个细胞的基因表达信息、记录细胞的空间位置、跟踪不同细胞谱系在分化过程中的轨迹,这为研究难以大量提取的肌内脂肪细胞分子特异性和发生分化过程带来极大便利。作者简要介绍了scRNA-seq技术的关键步骤,比较分析了单细胞分离和转录组测序方法的优缺点,综述了肌内脂肪细胞的起源以及scRNA-seq在肌内脂肪细胞的亚群和标记基因鉴定以及细胞分化轨迹追踪中的应用,以期为肌内脂肪...     

Next-generation sequencing for the genetic characterization of Maedi/Visna virus isolated from the northwest of China

BackgroundMaedi/Visna virus (MVV) is a contagious viral pathogen that causes considerable economic losses to the sheep industry worldwide.ObjectivesIn China, MVV has been detected in several regions, but its molecular characteristics and genetic variations were not thoroughly investigated.MethodsTherefore, in this study, we conducted next-generation sequencing on an MVV strain obtained from northwest China to reveal its genetic evolution via phylogenetic analysis.ResultsA MVV strain obtained from Inner Mongolia (NM) of China was identified. Sequence analysis indicated that its whole-genome length is 9193 bp. Homology comparison of nucleotides between the NM strain and reference strains showed that the sequence homology of gag and env were 77.1%–86.8% and 67.7%–75.5%, respectively. Phylogenetic analysis revealed that the NM strain was closely related to the reference strains isolated from America, which belong to the A2 type. Notably, there were 5 amino acid insertions in variable region 4 and a highly variable motif at the C-terminal of the surface glycoprotein (SU5).ConclusionsThe present study is the first to show the whole-genome sequence of an MVV obtained from China. The detailed analyses provide essential information for understanding the genetic characteristics of MVV, and the results enrich the MVV library.     

T7 RNA多聚酶基因的克隆、序列测定及其在E.coli中的表达

从BL21(DE3)E．coli菌株中以PCR的方法扩增得到了与T7RNA多聚酶(T7RNApolymerase，T7pol)基因大小一致的DNA片断。将PCR产物纯化后直接克隆到pGEM—T载体中，经酶切鉴定和DNA序列分析表明克隆得到了正确的T7pol基因。将T7pol基因亚克隆入pET-28b( )中，构建得到原核表达质粒pET28T7。该质粒的BL21(DE3)pLysS转化菌在IPTG的诱导下可表达约98800的蛋白，这与T7pol的相对分子质量一致。将该质粒转化DH5α、JMl09、HBl01、BL21(DE3)和BL21(DE3)pLysS等5种不同的宿主菌，仅有转化T7pol酶活性受到抑制的宿主菌BL21(DE3)pLysS才能得到转化子，而其余4种T7T7pol酶活性不受抑制的E．coli宿主菌不能得到转化子。pET28T7原核表达质粒这种仅能在T7pol酶活性受到抑制的宿主菌中才能存活的现象说明本试验所克隆的T7pol基因能正确表达出具有RNA转录酶活性的蛋白。     

Detection of severe fever with thrombocytopenia syndrome virus and other viruses in cats via unbiased next-generation sequencing

We used unbiased next-generation sequencing (NGS) to detect unknown viruses in cats. Serum or plasma samples were obtained from clinically ill cats with suspected acute viral infections. Nucleic acid was extracted from serum or plasma samples to construct a complementary DNA library for NGS. Comprehensive nucleotide sequencing analyses enabled detection of the genomes of various viruses, including the severe fever with thrombocytopenia syndrome virus, feline immunodeficiency virus, feline morbillivirus, parvovirus, and Torque teno felis virus. Our findings indicate that comprehensive nucleotide analyses of serum or plasma samples can be used to detect infections with unknown viruses in cats.     

反义RNA重组逆转录病毒逆转录套式PCR检测方法的建立

为探求一种快速检测反义RNA重组逆转录病毒效价的新方法，用脂质体介导法将反义RNA重组逆转录病毒载体pLXSA、pLXSB分别转染包装细胞系PA317，经G418筛选，获得数个稳定的产毒细胞克隆，择优挑选7个细胞克隆扩增培养，收集细胞上清，用异硫氰酸胍-酚一步法提取病毒RNA，进行逆转录套式PCR，检测细胞上清中的反义RNA重组逆转录病毒效价，同时用传统方法（小鼠成纤维放大法）进行测定。2种方法检测结果的比较表明，逆转录套式PCR法的特异性和敏感性均高于小鼠成纤维放大法，是一种敏感性高、特异性强、操作简便、快速的检测逆转录病毒效价的新方法。     

动物RNA病毒检测关键试剂—反转录酶(M-MLV RTase)的制备

反转录酶是动物RNA病毒分子诊断用到的关键试剂之一。为获得纯度高、活性高、制备简单经济的M-MLV RTase,本试验将M-MLV RTase的基因序列进行密码子优化,合成并构建表达载体。将表达载体转化到大肠杆菌E.coli Rosetta宿主菌种,经IPTG诱导后实现M-MLV RTase的可溶性表达。利用Ni2+柱亲和层析纯化载有6x His标记的重组MMLV RTase,对重组酶进行Western Blotting试验,鉴定为M-MLV RTase。通过对动物流感病毒RNA的普通RT-PCR和荧光RT-PCR检测来评价重组酶的活性并估测其活性单位。将活性单位相当的重组酶和商品酶进行比较,结果显示,制备的重组酶活性高,对不同浓度病毒RNA的检测结果与商品酶相当。研制的M-MLV RTase可以用于动物RNA病毒的分子诊断。     

鼠伤寒沙门菌小RNA GcvB靶基因的预测与验证

为筛选鼠伤寒沙门菌小RNA GcvB调控的靶基因,本研究通过TargetRNA2软件预测能与GcvB R1、R2和R3区产生作用的基因,将鼠伤寒沙门菌gcvB基因敲除株的转录组测序结果注释到KEGG数据库以及GO富集分析,并利用荧光定量PCR对预测的靶基因进行验证。TargetRNA2的预测结果显示,杂交能量最高的narY、yeaK、trpB和STM2732基因均能够和小RNA GcvB产生至少7个连续的碱基互补,narY、yeaK和trpB基因分别与鼠伤寒沙门菌无氧呼吸、脯氨酸与tRNA的识别以及色氨酸的合成相关。荧光定量PCR检测结果显示,narY、yeaK、trpB和STM2732基因在gcvB基因敲除条件下转录水平分别上调3.4、9.8、12.1和18.37倍。以上结果表明,narY、yeaK、trpB和STM2732基因受小RNA GcvB的负调控且可能为直接负调控。本研究为进一步探明小RNA GcvB与靶基因相互作用、小RNA的调控机制以及沙门菌致病机制奠定了基础。     

猪链球菌2型分泌性核酸酶A(SsnA)活性检测及其基因序列的克隆与测序分析

对8株猪链球菌2型重庆分离株的核酸酶A全基因进行克隆测序,结果表明该基因长度为3 126 bp,与Gen-Bank发表的唯一的该基因的序列相比,核苷酸同源性高于98%,推导的氨基酸同源性高于94%。根据核酸酶A基因的测序结果建立扩增片段长度为301 bp的PCR检测方法,并用甲苯胺蓝DNA酶琼脂对猪链球菌分泌性核酸酶A的活性进行检测。检测了从病猪内脏分离的猪链球菌致病株35株,33株核酸酶A基因PCR检测阳性(阳性比例为94.3%),其中有24株分泌活性检测为阳性(阳性比例68.6%);正常猪扁桃体分离株14株,PCR检测为阳性的10株(阳性比例71.4%),其中有核酸酶A分泌活性为8株(阳性比例57.1%),检测菌株中有2型猪链球菌44株,38株扩增出核酸酶A基因的片段PCR检测阳性并且分泌活性为阳性的有32株,猪链球菌1型、7型、9型、13型、1/2型各1株,均能扩增出核酸酶A基因的片段,但只有13型猪链球菌有核酸酶A分泌活性。对猪链球菌在不同生长时期核酸酶活性的检测显示,猪链球菌在培养4、8、16、32、48 h均有核酸酶A的分泌,并且C a2 和M g2 为分泌性核酸酶A的活性必需因子。     

非编码RNA及其在畜禽中的应用研究进展

在真核生物基因组转录过程中,除了一些蛋白质编码RNA以外,还有一些不同类型的非编码RNA(non-coding RNA,ncRNA)也参与了复杂生命活动过程的调节。近年来,全转录组测序技术的出现和生物信息学的快速发展极大地促进了人们对ncRNA的研究,ncRNA在生物领域的多个方面具有重要作用,如在人类肿瘤、非肿瘤等方面的疾病治疗,在动物胚胎发育、肌肉生长、脂肪沉积、免疫应答及皮肤毛囊调控等领域都有了很大的进展。作者主要综述了全转录组测序技术、ncRNA分类、主要作用机制和ncRNA在畜禽中的应用,为探究ncRNA在动物中的调控机制提供理论依据。     

Indirect fluorescent antibody techniques for demonstration of trout viruses and corresponding antibody

Two variations of the indirect fluorescent antibody technique (FAT) have been utilized in the work concerning two important virus diseases of trout, viral haemorrhagic septicaemia (VHS) and infectious pancreatic necrosis (IPN). A “two layer” indirect FAT allowed demonstration of the respective viruses in cell cultures and a “three layer” indirect FAT allowed demonstration of trout antibody to the viruses. Antibody, by means of the latter technique, could be demonstrated only in artificially immunized trout.     

海兰鸡白细胞介素-18全基因的克隆与序列分析

白细胞介素-18（Interleukin-18，IL-18）是一种能诱导产生IFN-γ的新型细胞因子，在调节Th1型细胞免疫应答中起重要作用。根据GenBank发表的鸡IL-18cDNA基因序列，自行设计一对引物，经植物血凝素（PHA）活化60日龄海兰鸡的脾淋巴细胞后，提取其总RNA，经反转录-聚合酶链反应（RT—PCR）扩增，扩增产物进行了T-A克隆、测序，获得了中国海兰鸡IL-18基因全序列，其大小为597bp，与在GenBank中查得的鸡IL-18基因进行比较发现，中国海兰鸡IL-18基因与Schneider报道的鸡IL-18基因序列完全一致，为进一步研究鸡IL-18基因表达、生物学活性和应用奠定了基础。     

RNA病毒重组及发生机制

重组在RNA病毒中很常见,但有关重组的许多关键问题目前尚无法解释.本文主要针对RNA重组的发生机制及其影响因素,解释重组频率发生变化的原因,阐述RNA重组未来仍需解决的问题.RNA重组是RNA病毒特殊的遗传信息交换方式,其频率在不同的RNA病毒中显著不同.目前,研究者普遍认为重组发生的机制可分为复制型、非复制型重组以及...     

Current status and future perspectives for sequencing livestock genomes

Only in recent years, the draft sequences for several agricultural animals have been assembled. Assembling an individual animal’s entire genome sequence or specific region(s) of interest is increasingly important for agricultural researchers to perform genetic comparisons between animals with different performance. We review the current status for several sequenced agricultural species and suggest that next generation sequencing (NGS) technology with decreased sequencing cost and increased speed of sequencing can benefit agricultural researchers. By taking advantage of advanced NGS technologies, genes and chromosomal regions that are more labile to the influence of environmental factors could be pinpointed. A more long term goal would be addressing the question of how animals respond at the molecular and cellular levels to different environmental models (e.g. nutrition). Upon revealing important genes and gene-environment interactions, the rate of genetic improvement can also be accelerated. It is clear that NGS technologies will be able to assist animal scientists to efficiently raise animals and to better prevent infectious diseases so that overall costs of animal production can be decreased.