Insights into the mysterious genetic variation profile oftprKinTreponema pallidumunder the development of natural human syphilis infection

Although the variations of the tprK gene in Treponema pallidum were considered to play a critical role in the pathogenesis of syphilis, how actual variable characteristics of tprK in the course of natural human infection enabling the pathogen’s survive has thus far remained unclear. Here, we performed NGS to investigate tprK of T. pallidum directly from primary and secondary syphilis samples. Compared with diversity in tprK of the strains from primary syphilis samples, there were more mixture variants found within seven V regions of the tprK gene among the strains from secondary syphilis samples, and the frequencies of predominant sequences within V regions of tprK were generally decreased (less than 80%) with the proportion of minor variants in 10-60% increasing. Noteworthy, the variations within V regions of tprK always obeyed a strict 3 bp changing pattern. And tprK in the strains from the two-stage samples kept some stable amino acid sequences within V regions. Particularly, the amino acid sequences IASDGGAIKH and IASEDGSAGNLKH in V1 not only presented a high proportion of inter-population sharing, but also presented a relatively high frequency (above 80%) in the populations. Besides, tprK always demonstrated remarkable variability in V6 at both the intra- and inter-strain levels regardless of the course. These findings unveiled that the different profile of tprK in T. pallidum directly from primary and secondary syphilis samples, indicating that throughout the development of syphilis T. pallidum constantly varies its domain tprK gene to obtain the best adaptation to the host. While this changing was always subjected a strict gene conversion mechanism to keep an abnormal TprK. The highly stable peptides found in V1 would probably be promising potential vaccine components. And the highly heterogenetic regions (e.g. V6) could provide insight into the mysterious role of tprK in immune evasion. Author summary Although the variations of the tprK gene in Treponema pallidum were considered to play a critical role in the pathogenesis of syphilis, how actual variable characteristics of tprK in the course of natural human infection enabling the pathogen’s survive has thus far remained unclear. Here, we performed next-generation sequencing, a more sensitive and reliable approach, to investigate tprK of Treponema pallidum directly from primary and secondary syphilis patients, revealing that the profile of tprK in T. pallidum from the two-stage samples was different. Within the strains from secondary syphilis patients, more mixture variants within seven V regions of tprK were found, the frequencies of their predominant sequences were generally decreased with the proportion of minor variants in 10-60% was increased. And the variations within V regions of tprK always obeyed a strict 3 bp changing pattern. Noteworthy, the amino acid sequences IASDGGAIKH and IASEDGSAGNLKH in V1 presented a high proportion of inter-population sharing and presented a relatively high frequency in the populations. And V6 region always demonstrated remarkable variability at intra- and inter-patient levels regardless of the course. These findings provide insights into the mysterious role of TprK in immune evasion and for further exploring the potential vaccine components.