目的
了解百日咳毒素（
pt
）基因启动子区及不同亚基编码区遗传变异特点及进化规律，为分子流行病学监控和疫苗研究提供参考依据。
方法
从GenBank数据库中下载已公开发表的百日咳菌株
pt
基因启动子区序列及S1～S5亚基编码序列，利用PhyML 3.0 软件构建系统发育树，确定进化簇；利用MEGA 7.0软件计算遗传距离；通过VESPA分析工具，分析不同进化簇的特征性核苷酸/氨基酸位点；利用SNAP v2.1.1软件计算不同区域选择压力。
结果
获得启动子区序列797条，含有4个进化簇，平均遗传距离为1.89×10
−3
；获得S1区序列786条，含有4个进化簇，平均遗传距离为2.43×10
−4
，dn/ds>1；获得S2区序列772条，含有2个进化簇，平均遗传距离为4.31×10
−5
，dn/ds>1；获得S3区序列772条，含有1个进化簇，平均遗传距离为3.96×10
−6
；获得S4区序列775条，含有1个进化簇，平均遗传距离为2.36×10
−5
；获得S5区序列776条，含有1个进化簇，所有序列无差异，平均遗传距离为0。
结论
pt
基因不同区域遗传变异度及进化特点存在明显差别。针对
pt
基因的分子流行病学研究和疫苗研发应重点关注启动子区，S1亚基及S2亚基。
Abstract:
Objective
To understand the genetic variation and evolution of promoter region and different subunit coding region of pertussis toxin (
pt
) gene of
Bordetella pertussis
and provide evidence for the molecular epidemiological surveillance and vaccine development.
Methods
Gene promoter region sequence and S1–S5 subunit coding sequence of
pt
gene of
B. pertussis
were collected from GenBank database. Software PhyML 3.0 was used to construct phylogenetic tree and determine the evolutionary cluster. The genetic distance was calculated by software MEGA 7.0. VESPA analysis tool was used to analyze the characteristic sites of different evolutionary clusters. Software SNAP v2.1.1 was used to calculate selection pressures in different gene regions.
Results
A total of 797 promoter sequences were obtained, which contained 4 evolutionary clusters, and the average genetic distance was 1.89×10
−3
. A total of 786 sequences of S1 region were obtained, which contained 4 evolutionary clusters, the average genetic distance was 2.43×10
−4
, dn/ds>1. A total of 772 sequences of S2 region were obtained, which contained 2 evolutionary clusters, the average genetic distance was 4.31×10
−5
, dn/ds>1. A total of 772 sequences of S3 region were obtained, containing 1 evolutionary clusters, with an average genetic distance of 3.96×10
−6
. A total of 775 sequences of S4 region were obtained, which contained 1 evolutionary clusters, the average genetic distance was 2.36×10
−5
. A total of 776 sequences of S5 region were obtained, which only contained 1 evolutionary cluster, and all the sequences were identical the average genetic distance was 0.
Conclusion
There were significant differences in genetic variation and evolutionary characteristics among different regions of
pt
gene of
B. pertussis
. Molecular epidemiological studies of
pt
gene of
B. pertussis
and development of vaccine for pertussis should focus on the promoter region, S1 subunit and S2 subunit.
