中国口蹄疫病毒同源重组研究

从GenBank数据库中获得在我国分离的16株口蹄疫病毒全基因组序列,进而运用常规的系统发生方法分析了这16株病毒的同源重组情况,发现5株重组毒株．这些重组病毒主要来源于亚洲Ⅰ型(Asia1)和O型病毒间的重组．这些重组事件的鉴定也表明口蹄疫病毒间的交叉感染在我国比较常见．另外,在我国还出现了由于Asia1型和O型病毒重组后导致病毒血清型发生转化的现象．这些结果解释了我国口蹄疫病毒(FMDV)遗传多样性和抗原多变性的成因,提示了我国在口蹄疫预防、治疗方面所面临的复杂局面．     

Avian influenza virus exhibits rapid evolutionary dynamics

Influenza A viruses from wild aquatic birds, their natural reservoir species, are thought to have reached a form of stasis, characterized by low rates of evolutionary change. We tested this hypothesis by estimating rates of nucleotide substitution in a diverse array of avian influenza viruses (AIV) and allowing for rate variation among lineages. The rates observed were extremely high, at >10(-3) substitutions per site, per year, with little difference among wild and domestic host species or viral subtypes and were similar to those seen in mammalian influenza A viruses. Influenza A virus therefore exhibits rapid evolutionary dynamics across its host range, consistent with a high background mutation rate and rapid replication. Using the same approach, we also estimated that the common ancestors of the hemagglutinin and neuraminidase sequences of AIV arose within the last 3,000 years, with most intrasubtype diversity emerging within the last 100 years and suggestive of a continual selective turnover.     

H5N1亚型禽流感病毒进化的研究进展

由H5N1流感病毒引起的高致病性禽流感,在禽类之间广泛传播。当人类接触这些禽类时,可能会被感染并产生严重的呼吸道症状,且死亡率高达60%。血凝素(hemagglutinin,HA)是H5N1病毒中和抗体的主要抗原,为了便于对病毒的HA突变进行研究,根据HA遗传基因的差异远近,所有的H5病毒株都被划分在20个分支内。对于H5N1病毒进化的研究在禽流感疫苗的研制、禽流感大流行的预防等方面均具有重要意义。现对禽流感、H5N1病毒特征、血凝素的结构功能、H5N1病毒的分支以及病毒进化的研究进行概述。     

禽流感病毒血凝素疫苗在转基因马铃薯中的表达

利用转基因马铃薯表达禽流感病毒血凝素疫苗,将含有禽流感病毒血凝素序列的表达载体导入农杆菌,再感染马铃薯的幼茎外植体。转化植株的再生及温室栽培,Western blot分析表明,83％的转化植株在其块茎组织中表达了重组血凝素,表达量占总蛋白量的0．03－0．04％,结果显示用马铃薯生产口服禽流感疫苗是可行的。     

Homologous recombination in Agrobacterium: potential implications for the genomic species concept in bacteria

According to current taxonomical rules, a bona fide bacterialspecies is a genomic species characterized by the genomic similarityof its members. It has been proposed that the genomic cohesionof such clusters may be related to sexual isolation, which limitsgene flow between too divergent bacteria. Homologous recombinationis one of the most studied mechanisms responsible for this geneticisolation. Previous studies on several bacterial models showedthat recombination frequencies decreased exponentially withincreasing DNA sequence divergence. In the present study, weinvestigated this relationship in the Agrobacterium tumefaciensspecies complex, which allowed us to focus on sequence divergencein the vicinity of the genetic boundaries of genomic species.We observed that the sensitivity of the recombination frequencyto DNA divergence fitted a log-linear function until approximately10% sequence divergence. The results clearly revealed that therewas no sharp drop in recombination frequencies at the pointwhere the sequence divergence distribution showed a "gap" delineatinggenomic species. The ratio of the recombination frequency inhomogamic conditions relative to this frequency in heterogamicconditions, that is, sexual isolation, was found to decreasefrom 8 between the most distant strains within a species to9 between the most closely related species, for respective increasesfrom 4.3% to 6.4% mismatches in the marker gene chvA. This meansthat there was only a 1.13-fold decrease in recombination frequenciesfor recombination events at both edges of the species border.Hence, from the findings of this investigation, we concludethat—at least in this taxon—sexual isolation basedon homologous recombination is likely not high enough to stronglyhamper gene flow between species as compared with gene flowbetween distantly related members of the same species. The 70%relative binding ratio cutoff used to define bacterial speciesis likely correlated to only minor declines in homologous recombinationfrequencies. Consequently, the sequence diversity, as a mechanisticfactor for the efficiency of recombination (as assayed in thelaboratory), appears to play little role in the genetic cohesionof bacterial species, and thus, the genomic species definitionfor prokaryotes is definitively not reconcilable with the biologicalspecies concept for eukaryotes.     

禽流感病毒分型基因芯片的研制

[目的]禽流感病毒是一种全球重要的人和动物呼吸道病病原,快速确定其不同亚型对于全球流感监测具有重要的意义.本研究意在研制一种可同时鉴定禽流感病毒所有亚型的方法.[方法]根据GenBank上已发表的禽流感病毒不同亚型(16个HA亚型和9个NA亚型)的基因序列,设计合成了25对特异性引物和1对通用引物,然后以各亚型病毒的参考株RNA作为模板,建立扩增不同亚型的多重RT-PCR方法.参考各亚型病毒靶cDNAs区域的保守序列设计了52条亚型特异的探针,进而利用扩增的各亚型病毒的靶cDNAs对其特异性进行评价.在此基础上,将设计好的探针点制到处理好的玻片上,制备了禽流感病毒分型鉴定基因芯片,结合所建立的扩增不同亚型的多重RT-PCR方法,开发了禽流感病毒亚型鉴定基因芯片试剂.利用收集自49个地区的2653份标本对其特异性和敏感性进行了初步评价.[结果]用于评价的各亚型参考毒株均出现良好的特异性杂交信号,检测的敏感度可达2.47 PFU/mL或2.5 ng靶DNA片段,而且与禽类常见的IBV、NDV等6种病毒均无交叉反应.[结论]证明该病毒分型基因芯片具有良好的特异性、敏感性.     

Homologous recombination: a basis for targeted genome optimization in crop species such as maize

In an attempt to understand the feasibility of future targeted genome optimization in agronomic crops, we tested the efficiency of homologous recombination-mediated sequence insertion upon induction of a targeted DNA double-strand break at the desired integration site in maize. By the development of an efficient tissue culture protocol, and with the use of an I- Sce I gene optimized for expression in maize, large numbers of precisely engineered maize events were produced in which DNA integration occurred very accurately. In a subset of events examined in detail, no additional deletions and/or insertions of short filler DNA at the integration site were observed. In 30%–40% of the recovered events, no traces of random insertions were observed. This was true for DNA delivery by both Agrobacterium and particle bombardment. These data suggest that targeted double-strand break-induced homologous recombination is a superior method to generate specific desired changes in the maize genome, and suggest targeted genome optimization of agronomic crops to be feasible.     

Genomic signature analysis of the recently emerged highly pathogenic A(H5N8) avian influenza virus: implying an evolutionary trend for bird-to-human transmission

In early 2014, a novel subclade (2.3.4.4) of the highly pathogenic avian influenza (HPAI) A(H5N8) virus caused the first outbreak in domestic ducks and migratory birds in South Korea. Since then, it has spread to 44 countries and regions. To date, no human infections with A(H5N8) virus have been reported, but the possibility cannot be excluded. By analyzing the genomic signatures of A(H5N8) strains, we found that among the 47 species-associated signature positions, three positions exhibited human-like signatures (HLS), including PA-404S, PB2-613I and PB2-702R and that mutation trend of host signatures of avian A(H5N8) is different before and after 2014. About 82% of A(H5N8) isolates collected after January of 2014 carried the 3 HLS (PA-404S/PB2-613I/PB2-702R) in combination, while none of isolates collected before 2014 had this combination. Furthermore, the HA protein had S137A and S227R substitutions in the receptor-binding site and A160T in the glycosylation site, potentially increasing viral ability to bind human-type receptors. Based on these findings, the newly emerged HPAI A(H5N8) isolates show an evolutionary trend toward gaining more HLS and, along with it, the potential for bird-to-human transmissibility. Therefore, more extensive surveillance of this rapidly spreading HPAI A(H5N8) and preparedness against its potential pandemic are urgently needed.     

修饰的痘苗病毒安卡拉株（MVA）基因组中高频的同源重组

痘苗病毒由于其外源基因容量大,表达产物后加工完善等优势而广泛用于基因工程的研究以及基因治疗,痘苗病毒基因组的同源重组现象为其基因操作带来了方便,也被用于很多痘苗病毒基因结构和功能的研究,痘苗病毒安卡拉株（MVA）是一种修饰的复制限制的痘苗病毒,由于极高的安全性,正在实验室和临床应用的很多领域取代普通的痘苗病毒,为提高重组MVA系统的安全性以及筛选重组MVA的效率,发展了一种暂时选择系统,此系统利用分子内2段同向的相同序列发生同源重组去除选择标记k1l基因,从而消除选择标记对宿主可能的危害。利用此暂时表达系统构建了4个携带编码不同长度外源多蛋白质序列的重组MVA,并估算了每次传代的重组频率,结果显示,MVA同源重组频率虽然比其他痘苗病毒株要低,但仍然是较斋的,将带有k1l基因的重组MVA经3-4次盲传（blind passage),即可获得完全去除选择标记的重组MVA。进一步证明上述利用暂时选择标记k1l基因构建重组MVA的系统具有十分可靠的安全性,适合作为人体活疫苗开发和基因治疗的载体,而且,通过盲传进行筛选,能大大提高去除选择标记的效率,降低鸺建重组MVA的成本。     

H7亚型禽流感病毒与禽类和人类的关系

2013年在中国首次发生了H7N9亚型流感病毒感染人事件,已经证实H7N9型禽流感是一种新型禽流感,是全球首次发现感染人类的新亚型流感病毒,以往这种病毒只在野生鸟类存在和传播。H7N9型禽流感病毒属于H7亚型中的一种,全球感染人的H7亚型病毒主要分为两大支系,即北美支系和欧亚支系,感染人的流感亚型也主要集中在H7N7,H7N3,H7N2等亚型上。为了清晰的了解H7亚型病毒的来龙去脉,本文重点讨论了A亚型流感病毒的宿主分布、H7亚型病毒感染禽类和人类的历史、H7亚型病毒的生物学特性以及未来研究展望。     

Phylodynamics of H5N1 avian influenza virus in Indonesia

Understanding how pathogens invade and become established in novel host populations is central to the ecology and evolution of infectious disease. Influenza viruses provide unique opportunities to study these processes in nature because of their rapid evolution, extensive surveillance, large data sets and propensity to jump species boundaries. H5N1 highly pathogenic avian influenza virus (HPAIV) is a major animal pathogen and public health threat. The virus is of particular importance in Indonesia, causing severe outbreaks among poultry and sporadic human infections since 2003. However, little is known about how H5N1 HPAIV emerged and established in Indonesia. To address these questions, we analysed Indonesian H5N1 HPAIV gene sequences isolated during 2003-2007. We find that the virus originated from a single introduction into East Java between November 2002 and October 2003. This invasion was characterized by an initially rapid burst of viral genetic diversity followed by a steady rate of lineage replacement and the maintenance of genetic diversity. Several antigenic sites in the haemagglutinin gene were subject to positive selection during the early phase, suggesting that host-immune-driven selection played a role in host adaptation and expansion. Phylogeographic analyses show that after the initial invasion of H5N1, genetic variants moved both eastwards and westwards across Java, possibly involving long-distance transportation by humans. The phylodynamics we uncover share similarities with other recently studied viral invasions, thereby shedding light on the ecological and evolutionary processes that determine disease emergence in a new geographical region.     

Human avian influenza A (H5N1) virus infection in China

Highly pathogenic influenza A (H5N1) virus causes a widespread poultry deaths worldwide. The first human H5N1 infected case was reported in Hong Kong Special Administrative Region of China in 1997. Since then, the virus re-emerged in 2003 and continues to infect people worldwide. Currently, over 400 human infections have been reported in more than 15 countries and mortality rate is greater than 60%. H5N1 viruses still pose a potential pandemic threat in the future because of the continuing global spread and evolution. Here, we summarize the epidemiological, clinical and virological characteristics of human H5N1 infection in China monitored and identified by our national surveillance systems. Chinese Nature Science Foundation Key Project (Grant No. 30599433), Chinese Basic Science Research Program (973)Key Project (Grant No. 2005CB523006)     

Development of an immunochromatographic kit for rapid diagnosis of H5 avian influenza virus infection

Highly pathogenic avian influenza (HPAI) caused by the H5N1 subtype has given rise to serious damage in poultry industries in Asia. The virus has expanded its geographical range to Europe and Africa, posing a great risk to human health as well. For the control of avian influenza, a rapid diagnosis by detecting the causative virus and identifying its subtype is essential. In the present study, a rapid diagnosis kit combining immunochromatography with enzyme immunoassay which detects the H5 HA antigen of influenza A virus was developed using newly established anti-H5 HA monoclonal antibodies. The present kit specifically detected all of the H5 influenza viruses tested, and did not react with the other HA subtypes. H5 HA antigens were detected from swabs and tissue homogenates of chickens infected with HPAI virus strain A/chicken/Yamaguchi/7/04 (H5N1) from 2 days post inoculation. The kit showed enough sensitivity and specificity for the rapid diagnosis of HPAI.     

The evolutionary potential of influenza A virus hemagglutinin is highly constrained by epistatic interactions with neuraminidase

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Homologous recombination with linear DNA to insert antigenic protein in the flagellin: improvement of the Th1 immune response

Bacterial flagellin is a surface protein with numerous advantages for the presentation of exogenous peptides. However, the production of recombinant bacteria and the expression of fusion proteins is laborious and time consuming. Here, we present a simple way to produce modified bacteria. Partially deleted, non-functional, chromosomal flagellin gene (fliC ) was changed using homologous recombination by a functional linear fliC gene in which we introduced an exogenous oligonucleotide encoding for the peptide of interest. The modified fliC gene was produced by polymerase chain amplification. Linear amplicons were introduced into the non-motile E. coli by electroporation. The formation of functional flagellar filaments allowed the discrimination of motile transformants from non-motile, non-transformed cells. Thus antibiotic selection and gene expression inductors are not required since transformed bacteria can be easily isolated and used as a vector and adjuvant for immunization. To validate this hypothesis, we studied the immune response against the N-terminal peptide of Clostridium tyrobutyricum flagellin fragment. BALB/c mice were immunized either with the protein displayed as flagellin fusion protein on the surface of E. coli, with the recombinant protein in Freund's adjuvant (FA), or with the pcDNA3 vector bearing the DNA fragment encoding this protein. Immunization with the flagellin recombinant bacteria induced a strong Th1 response as measured by high level of IFN-gamma production and the lack of IL-4 production. The results indicate that the flagellar filament protein carrying a specific epitope can be a potent inducer of the Th1 cellular response.     

Homologous recombination in DNA repair and DNA damage tolerance

Homologous recombination （HR） comprises a series of interrelated pathways that function in the repair of DNA double-stranded breaks （DSBs） and interstrand crosslinks （ICLs）. In addition, recombination provides critical support for DNA replication in the recovery of stalled or broken replication forks, contributing to tolerance of DNA damage. A central core of proteins, most critically the RecA homolog Rad51, catalyzes the key reactions that typify HR： homology search and DNA strand invasion. The diverse functions of recombination are reflected in the need for context-specific factors that perform supplemental functions in conjunction with the core proteins. The inability to properly repair complex DNA damage and resolve DNA replication stress leads to genomic instability and contributes to cancer etiology. Mutations in the BRCA2 recombination gene cause predisposition to breast and ovarian cancer as well as Fanconi anemia, a cancer predisposition syndrome characterized by a defect in the repair of DNA interstrand crosslinks. The cellular functions of recombination are also germane to DNA-based treatment modalities of cancer, which target replicating cells by the direct or indirect induction of DNA lesions that are substrates for recombination pathways. This review focuses on mechanistic aspects of HR relating to DSB and ICL repair as well as replication fork support.     

在基于BAC的EB病毒基因组中引入突变

为了在Epstein-Barr病毒(EBV)172kb的基因组中引入突变以研究基因功能,建立了一种简单有效的基因操作方法.在载体pcDNA3.1( )上操作,将两端含有重组蛋白FLP识别位点(FRT)的卡那霉素筛选标记基因(kan)与鼻咽癌(NPC)来源的、包含LMP1基因全长ORF的gDNA"无缝"连接(无外源序列插入).连接后的kan-LMP1线性DNA片段经转化、由λ噬菌体中redαβγ系统介导在E.coli中发生同源重组(ET克隆),用kan-LMP1替代了BAC-EBV(p2089)中相应的LMP1基因区域,然后经过重组蛋白FLP对FRT-kan-FRT特异性的识别,切除了引入的kan基因,留下一个69bp的FRT"疤痕".通过抗性筛选和对菌液进行PCR扩增可以鉴定突变子.这种经改进并程序化的方法.也适应于引入其它突变或在其它BAC-疱疹病毒基因组中引入突变.     

H5N8亚型高致病性禽流感病毒的全球流行概况

H5N8亚型高致病性禽流感病毒(highly pathogenic avian influenza virus,HPAIV)随候鸟的迁徙活动及商业贸易活动现已蔓延至亚洲、欧洲、非洲、美洲等国家和地区.2014-2015和2016-2019年H5N8亚型HPAIV已引发两波全球疫情,现正经历第三波疫情,导致家禽及野生鸟类...     

A codon-based model of host-specific selection in parasites,with an application to the influenza A virus

Parasites sometimes expand their host range by acquiring a new host species. After a host change event, the selective regime acting on a given parasite gene may change as a result of host-specific adaptive alterations of protein functionality or host-specific immune-mediated selection. We present a codon-based model that attempts to include these effects by allowing the position-specific substitution process to change in conjunction with a host change event. Following maximum-likelihood parameter estimation, we employ an empirical Bayesian procedure to identify candidate sites potentially involved in host-specific adaptation. We discuss the applicability of the model to the more general problem of ascertaining whether the selective regime differs in two groups of related organisms. The utility of the model is illustrated on a data set of nucleoprotein sequences from the influenza A virus obtained from avian and human hosts.     

A/H6N1亚型禽流感病毒致病性评估及与2009 A/H1N1亚型流感病毒在哺乳动物体内的遗传兼容性

目的探讨人、禽流感病毒在哺乳动物体内的遗传兼容性,为下一步研究H6亚型禽流感病毒重配和致病性变异的分子机制奠定基础。方法野鸭源A/H6N1亚型禽流感病毒A/Mallard/SanJiang/275/2007以101EID50～106EID50的攻毒剂量经鼻内途径感染小鼠,通过临床症状观察、病毒滴定和病理切片观察进行病毒学和组织学两方面检测对小鼠的致病性;同时,将此病毒与2009年A/H1N1流感病毒A/Changchun/01/2009(H1N1)混合感染豚鼠,分析两株病毒在哺乳动物体内的遗传兼容性。每天采集豚鼠鼻洗液并用噬斑纯化技术获得重配病毒,对获得的重配病毒进行全基因组序列的测定。结果 H6N1亚型禽流感病毒能直接感染小鼠,但对小鼠不致死。106EID50的攻毒剂量可有效感染小鼠,攻毒后第5天,小鼠表现出被毛较粗乱、活动减少、体重下降、呼吸急促的临床症状,但至攻毒后第10天开始康复,而对照组(MOCK)小鼠在14 d的观察期内无明显临床症状。病毒滴定结果表明,该病毒主要在小鼠肺脏和鼻甲骨中复制,病毒滴度可达104.5EID50/mL。病理学观察发现感染小鼠肺泡壁增厚,有大量炎性细胞浸润,纤维蛋白渗出并伴有轻微出血;在A/H6N1和A/H1N1混合感染豚鼠的重配实验中,经过三轮噬斑纯化从豚鼠鼻洗液中分离到6株重配病毒,说明A/H6N1亚型禽流感病毒与A/H1N1亚型流感病毒具有很好的遗传兼容性,能在豚鼠体内能发生重配。结论野鸭源A/H6N1亚型流感病毒无需适应就能够感染哺乳动物;该病毒与A/H1N1流感病毒具有很好的遗传兼容性,在哺乳动物体内能够发生基因重配,产生新的重配病毒,其公共卫生意义应引起高度关注。