不同非瘟毒株同存易形成新毒株

基因同源重组决定了非洲猪瘟病毒的遗传多样性

Homologous recombination shapes the genetic diversity of African swine fever viruses

Zhaozhong Zhu a,1, Chao-Ting Xiao a,1, Yunshi Fan a, Zena Cai a, Congyu Lu a, Gaihua Zhang b, Taijiao Jiang c,d, Yongjun Tan a, Yousong Peng a,⁎

a、College of Biology, Hunan University, Changsha, China

b、College of Life Sciences, Hunan Normal University, Changsha, 410081, China

c、Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China

d、Suzhou Institute of Systems Medicine, Suzhou, China

A B S T R A C T

TheAfrican swine fever virus (ASFV) has severely influenced the swine industry ofthe world. Currently, How to effectively control the virus is challenging. In this study,we haveanalyzed all the publicly available ASFV genomes and demonstrated that therewas a large genetic diversity of ASFV genomes. Interestingly, the geneticdiversity was mainly caused by extensive genomic insertions and/or deletions(indels) instead of the point mutations. Further analyses showed that theindels may be attributed much to the homologous recombination, as supported bysignificant associations between the occurrence of extensive recombinationevents and the indels in the ASFV genomes. Besides, the homologousrecombination also led to changes of gene content of ASFVs. Finally, repeatedelements of dozens of nucleotides in length were observed to widely distributeand cluster in the adjacent positions of ASFV genomes, which may facilitate theoccurrence of homologous recombination. This work highlighted the importance ofhomologous recombination in shaping the genetic diversity of the ASFVs, andcould help understand the evolution of the virus.

非洲猪瘟病毒(ASFV)严重影响了世界养猪业，如何有效控制非洲猪瘟病毒是一项挑战。在这项研究中，我们分析了所有公开的ASFV基因组，并证明了ASFV基因组有很大的遗传多样性。有趣的是，遗传多样性主要是由广泛的基因组插入和/或缺失引起的，而不是由点突变引起的（批注：猪场注射非洲猪瘟活毒株疫苗，如果与猪场的毒株不同，则易形成新的毒株，这个与蓝耳疫苗毒株一样）。进一步的分析表明，这些基因缺失可能在很大程度上归因于同源重组，这种广泛性的重组事件的发生与ASFV基因组缺失之间的存在显著关联。此外，同源重组也导致ASFV基因组含量的变化。最后，观察到长度为几十个核苷酸的重复元件在ASFV基因组的相邻位置广泛分布和聚集，这可能促进同源重组的发生。这项工作强调了同源重组在形成抗体遗传多样性中的重要性，并有助于理解病毒的进化。

........The large genetic diversity of ASFVs, which was supposed to hinder the development of effective vaccines or drugs against the virus(非洲猪瘟病毒的巨大遗传多样性，被认为阻碍了有效疫苗或抗病毒药物的开发)(Sanchez-Cordon et al., 2018; Escribano et al., 2013; Arabyan et al.,2018), has been investigated in many studies. The ASFV genome encodesover 150 proteins, including viral enzymes, viral transcription

and replication-related proteins, structural proteins, other proteins involvedin the virus assembly, the evading of host defence systems andthe modulation of host cell function, etc (Dixon et al., 2013; Alejo et al.,2018; Kessler et al., 2018). For example, the transcription of the virus isindependent on the host RNA polymerase because the virus containsrelevant enzymes and factors (Dixon et al., 2013). The viral genomecontains a conservative central region of about 12 kb and two variable.......

补充阅读：（来自互联网，关于蓝耳病毒的重组）

丹麦蓝耳病重组爆发事件

今年夏天，丹麦爆发一种新毒株蓝耳病毒（PRRSv）引起的蓝耳病疫情。总计35家猪场中招，对未常规进行蓝耳免疫的猪场和先天阴性场造成尤其严重的损失。

后经调查，该新毒株的出现是由于两款商用I型蓝耳病弱毒疫苗重组造成。这种重组是由于同时使用了两种类型的蓝耳活苗造成，一般在切换蓝耳病疫苗是容易发生。

两款疫苗中，其中一款是硕腾公司的名为Suvaxyn PRRS MLV的疫苗，新进入丹麦市场。丹麦环境和食品部随后将该产品撤出丹麦市场。硕腾公司对此表达了不满。另外一款疫苗为海博莱公司生产。

35个爆发猪场的病毒来源于一家名为Hatting的公猪站。病毒通过精液散播，经查明感染精液仅提供给了丹麦国内的猪场。

并不清楚公猪站如何感染该病毒，公猪站的负责人Pederson表示可能是通过空气传播。在离公猪站5km的一个母猪场发现了相同的毒株，这个猪场同时使用硕腾和海博莱的疫苗。该公猪站疫情发现于7月下旬，感染时间应该在此之前几周。该公猪站一直对蓝耳病毒进行常规监控。

Hatting公猪站在全丹麦有600多家客户，其中3-5%的客户发生了疫情，其中一些猪场仔猪死亡率达到50%。

欧洲药品管理局兽药管理委员会对蓝耳活苗的使用建议

CVMP知晓了两种I型蓝耳减毒活疫苗重组产生新的重组毒株与丹麦蓝耳先天阴性场发生的疾病的临床症状相关的事件。

不同蓝耳病毒株包括I型蓝耳弱毒苗之间的重组是经过科学证明的已知现象。因此类似丹麦出现的病毒重组毒株可以在其他地方随时产生。

CVMP做出以下蓝耳病活苗使用建议：

• 为限制不同疫苗毒株的重组风险，应当在保护动物健康的同时，尽可能避免同时或相继使用不同类型的减毒蓝耳活疫苗。

• 建议加强监控任何与蓝耳病临床症状相关的反作用事件，包括在免疫猪群中出现的蓝耳病相关症状。任何可疑的反作用事件都应当报告本国兽药管理部门或市场监管部门。蓝耳病的临床症状包括繁殖力下降、流产率增加、食欲下降、仔猪死亡率增加和呼吸窘迫。

应当指出，表明疫苗株之间或疫苗株与野毒株之间重组的序列数据应被视为相关的药物警戒数据，因此应予以报告。

姜平、杨汉春关于猪蓝耳病毒株变异与疫苗毒株重组的观点

小结：

A、目前NADC30毒株与JXA1高致病性毒株、JXA1-R疫苗毒株重组成新毒株的案例非常多，成为中毒毒力或高致病性毒力的新毒株。

B、目前JXA1-R疫苗对这种新毒株提供有限的保护，TJM-F92、 R98疫苗能够对重组毒株提供保护。

南农姜平教授研究团队研究发现1：

1、NADC30毒株与中国的高致病性毒株重组，

2、新重组毒株有类似高致病性的毒力。

3、TJM-F92、 R98疫苗能提供对重组毒株的保护。

Pathogenicity and antigenicity of anovel NADC30-like strain of porcine reproductive and respiratory syndrome virusemerged in China. Veterinary MicrobiologyVolume 197, 25 December 2016, Pages 93-101.

Highlights

1、The FJ1402 strain was a recombinantof NADC30 and the Chinese HP-PRRSV strain.

2、FJ1402 had a similar pathogenicitywith HP-PRRSV strain BB0907.

3、TJM-F92 and R98 could partly provideprotection against FJ1402 challenge.

南农姜平教授研究团队研究发现2：

1、这些结果表明 PRRSV 当前疫苗免疫压力和净化下，会出现更多的重组毒株及压力。

2、25%的重组毒株中都能发现有JXA1-R的基因特征，与之相关。

Emergence of mosaic recombinantstrains potentially associated with vaccine JXA1-R and predominant circulatingstrains of porcine reproductive and respiratory syndrome virus in differentprovinces of China.Zhao et al. Virology Journal (2017) 14:67

Highlights

1、Recombination analyses showed that nine of 28 isolatesand one isolate from other laboratory were potential complicated recombinantsbetween the vaccine JXA1-R-like strains and predominant circulating strains.

2、These results indicated an increase in recombinationrates of PRRSV under current vaccination pressure and a more pressing situationfor PRRSV eradication and control in China.

中国农大杨汉春教授研究团队研究发现1：

1、       新重组毒株TJnh1501被发现

2、       新发现的毒株基因特征是NADC30毒株与高致病性减毒活疫苗（江西毒株）的杂交的

3、       重组毒株显示出中等毒力对仔猪发病。

A recombinant type 2 porcinereproductive and respiratory syndrome virus between NADC30-like and a MLV-like:Genetic characterization and pathogenicity for piglets. Infection, Genetics and Evolution Available online 13 July 2017

Highlights

1、The genomic characterization of atype 2 PRRSV (TJnh1501) was analyzed.

2、The isolate TJnh1501 was shown to therecombinant virus between NADC30-like and MLV-like.

3、The isolate TJnh1501 sharedintermediate virulence for piglets.

中国农大杨汉春教授研究团队研究发现2：

1、   CHsx1401的NADC30毒株是中毒毒力毒株

2、    减毒活疫苗不能降低临床感染和肺部损失

3、    减毒活疫苗部分降低病毒血症

4、    减毒活苗提供有限的交叉保护对NADC30毒株

Efficacy evaluation of threemodified-live virus vaccines against a strain of porcine reproductive andrespiratory syndrome virus NADC30-like.VeterinaryMicrobiologyVolume 207, August 2017, Pages 108-116.

Highlights

1、The PRRSV NADC30-like CHsx1401 wasshown to be a moderate virulent virus for piglets.

2、MLV vaccines could not reduce theclinical signs and lung lesions of the pigs challenged.

3、MLV vaccines were partiallyefficacious in the reduction of viral loads.

4、MLV vaccines are shown to provideextremely limited cross-protection against PRRSV NADC30-like

美国报告首例蓝耳疫苗重组案例