Pathogen Detection and Genotyping With Trace Sample by A Phi29 Based Unbiased Exponential Amplification

Abstract Ticks are vectors for many infectious diseases such as spotted fever group (SFG) rickettsioses and borrelioses. Ticks are valuable material for pathogen ecology study. Ticks have several growth stages with significant varying size, and therefore, in most cases, the collected ticks cannot provide sufficient DNA for subsequent studies, particularly for multiple pathogen screening and genotyping. Unbiased pretreatment of the tick samples for subsequent analysis is an urgent need for subsequent ecological survey and other studies. Phi29 DNA polymerase, an enzyme with strand displacement activity, could exponentially amplify DNA randomly and non-biasedly, generating large quantities of DNA. In the present study, we developed a Phi29 based unbiased exponential amplification (PEA) assay for unbiased treatment of sample nucleic acid to provide sufficient DNA for genetic analysis. By using tick borne pathogen detection and genotype as a model, we tested and evaluated the feasibility of the assay. Nucleic acid were extracted from single ticks and subjected to PEA. The results showed that tick DNA could be amplified up to 10 5 folds. The amplified products were successfully used for pathogen screening and genotyping. With the amplified DNA from single tick, Rickettsia was successfully detected and genotyped. A new genotype of Rickettsia was identified from ticks collected from Dandong city, Liaoning province, Northeast China. This PEA assay is universal and can also be extended to other applications where samples are greatly limited.