鸽新城疫病毒BJ-C分离株基因组测序及系统发育分析

Genome sequencing and phylogenetic analysis of Newcastle disease virus BJ-C strain in pigeons

摘要:

【背景】鸽新城疫是由鸽Ⅰ型副黏病毒(pigeon paramyxovirus type Ⅰ，PPMV-1)感染引起的危害最严重的疫病之一，至今尚无有效的防控制剂。【目的】分析鸽新城疫病毒BJ-C株的基因组信息及系统发育关系，为鸽新城疫的防控提供科学依据。【方法】设计首尾重叠的6对特异性引物，利用分段扩增的方法，以鸽新城疫病毒BJ-C株基因组cDNA为模板，分别扩增、测序后进行全基因组序列拼接。以NCBI数据库中发布的新城疫病毒序列为参考，针对鸽新城疫病毒BJ-C株的基因组、F基因建立系统发育树。【结果】鸽新城疫病毒BJ-C株的基因组全长为15192nt。基于全基因组的系统发育分析发现其与PPMV-1/BJ-01/CH株的系统发育关系最近，核苷酸相似性为99.96%，氨基酸相似性高达100%，属于同一个分支，而与LaSota疫苗株等其他新城疫毒株的亲缘关系相对较远。基于F基因序列的系统发育树分析发现BJ-C株F基因与我国的BJP2013株同属一个分支。ClassⅡ类Ⅵ亚型F基因高变区序列(47-420nt)比对结果显示，安徽株Pigeon/Anhui/2369/2012、广东株Pigeon/Guangdong/GZ288/2013、北京株BJP13、浙江株Pigeon/Zhejiang/2036/2012及比利时株PPMV-1/Belgium/11-09620/2011等与BJ-C毒株处于同一个分支，同属Ⅵb亚型。【结论】本研究获得了鸽新城疫病毒BJ-C株全基因组序列，分析了其系统发育关系，确定其属于ClassⅡ类Ⅵb型，为后续防控产品的开发提供了理论依据。

关键词:鸽新城疫病毒;全基因组测序;F基因;系统发育分析

Abstract:

[Background] Pigeon Newcastle disease (ND), caused by pigeon paramyxovirus type Ⅰ (PPMV-1), is a severe infectious disease. However, there is no effective method to control this disease. [Objective] To elucidate the phylogenetic analysis of BJ-C and provide a scientific basis for the prevention and control of pigeon ND. [Methods] Six pairs of specific primers overlapped at the beginning and ending were designed. The genomic cDNA sequence of BJ-C strain was used as the template for amplification and sequencing. The phylogenetic tree of BJ-C strain was established by sequence alignment with the published PPMV-1 and NDV strains on the NCBI website. [Results] The genome length of BJ-C strain was 15 192 nt. BJ-C strain had the closest genetic relationship with PPMV-1/BJ-01/CH strain based on the whole genome analysis, with nucleotide similarity of 99.96% and amino acid similarity of 100%. BJ-C strain shared the same branch with PPMV-1/BJ-01/CH strain, whereas it was far from other ND virus strains such as the LaSota vaccine strain. The phylogenetic tree built based on F gene showed that BJ-C strain was in the same branch with BJP2013 strain isolated in China. The sequence alignment of the hypervariable region (47-420 nt) of F gene showed that the Ⅵb subtype strains including Pigeon/Anhui/2369/2012, Pigeon/Guangdong/GZ288/2013, BJP13, Pigeon/ Zhejiang/2036/2012, PPMV-1/Belgium/11-09620/2011, and BJ-C were in the same clade. [Conclusion] The full-length genome sequence of BJ-C strain was obtained and the strain was grouped to the class Ⅱ Ⅵb type based on phylogenetic analysis. Our results are of theoretical significance for the development of pigeon ND vaccines and other prevention and control methods.

Key words:Newcastle disease virus of pigeon;full-length genome sequencing;fusion gene;phylogenetic analysis