Analysis on genetic variation of pt gene of Bordetella pertussis

  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.