Genetic Variation and Population Structure of Clonorchis sinensis: An In Silico Analysis

Abstract

Clonorchis sinensis is an important zoonotic parasite that is mainly prevalent in China, Korea, Vietnam and the Russian Far East. To explore the genetic variation and population structure of C. sinensis, an in silico analysis was conducted based on mitochondrial cytochrome c oxidase subunit 1 (COX1), ribosomal internal transcribed spacer 1 (ITS1) and ribosomal internal transcribed spacer 2 (ITS2) sequences. The sequences obtained from NCBI were truncated for further analyses, including haplotype network, phylogenetic, gene flow, diversity and neutrality analyses. The results showed that there were 20, 11 and 4 haplotypes for COX1, ITS1 and ITS2, respectively. The results of both the haplotype network and phylogenetic analyses indicated that the haplotypes for each type of sequence from the same country were not all clustered together. Haplotype diversity values were all lower than 0.5. Values of nucleotide diversity were higher than 0.005, except for ITS2. Tajima’s D and Fu’s Fs values were all negative, and p-values showed significant differences, indicating that the population of C. sinensis is growing. Fst values were all lower than 0.05. In conclusion, this study found that there are specific variations of C. sinensis in different countries, and the population of this parasite is growing with less genetic variation. The findings provide a crucial foundation for understanding the molecular epidemiology and population dynamics of C. sinensis.