Molecular Prevalence and Genotypic Diversity of Theileria equi in Xinjiang, China, Based on Three Genes

Equine theileriosis, caused by the protozoan parasite <i>Theileria equi</i>, represents a significant economic threat to the equine industry. In Xinjiang, China, an endemic area for this disease, systematic research on the genetic diversity of <i>T. equi</i> has been notably lacking. The aim of this study was to obtain molecular epidemiological data pertaining to the parasite in selected regions of Xinjiang, China, and analyze the genetic characteristics (including <i>18S</i> rRNA, <i>EMA-1</i>, and <i>COI</i> genes) and genotype distribution patterns of isolates from these regions, providing a scientific basis for developing targeted prevention and control strategies. Blood samples were collected from 440 horses across four regions (Altay, Ili, Tacheng, and Urumqi) and subjected to PCR assays. Positive samples were sequenced for phylogenetic and haplotype network analyses, and genetic diversity indices were calculated. The overall infection rate of <i>T. equi</i> was 38.41% (169/440), with Tacheng having the highest prevalence (86.27%) and Altay the lowest (20.88%); these regional differences were statistically significant. Phylogenetic analysis identified two genotypes of the <i>18S</i> rRNA gene: genotype E (predominant) and genotype A. All <i>EMA-1</i> sequences clustered exclusively within genotype A. Notably, all <i>COI</i> gene sequences formed a monophyletic group, exhibiting closer genetic relationships to isolates from France and Senegal. This study presents the first comprehensive genotyping of <i>T. equi</i> in Xinjiang based on three target genes and constructs an associated haplotype network. The analysis identified <i>18S</i> rRNA genotype E and <i>EMA-1</i> genotype A as the predominant genotypes. Furthermore, the genetic diversity of <i>T. equi</i> was found to be higher in Urumqi than in the other regions studied.