*Article* **Subtyping** *Cryptosporidium xiaoi***, a Common Pathogen in Sheep and Goats**

**Yingying Fan 1,2,†, Xitong Huang 1,†, Sheng Guo 1, Fang Yang 1, Xin Yang 3, Yaqiong Guo 1, Yaoyu Feng 1,2, Lihua Xiao 1,2,\* and Na Li 1,2,\***


**Abstract:** Cryptosporidiosis is a significant cause of diarrhea in sheep and goats. Among the over 40 established species of *Cryptosporidium*, *Cryptosporidium xiaoi* is one of the dominant species infecting ovine and caprine animals. The lack of subtyping tools makes it impossible to examine the transmission of this pathogen. In the present study, we identified and characterized the 60-kDa glycoprotein (*gp60*) gene by sequencing the genome of *C. xiaoi*. The GP60 protein of *C. xiaoi* had a signal peptide, a furin cleavage site of RSRR, a glycosylphosphatidylinositol anchor, and over 100 O-glycosylation sites. Based on the *gp60* sequence, a subtyping tool was developed and used in characterizing *C. xiaoi* in 355 positive samples from sheep and goats in China. A high sequence heterogeneity was observed in the *gp60* gene, with 94 sequence types in 12 subtype families, namely XXIIIa to XXIIIl. Co-infections with multiple subtypes were common in these animals, suggesting that genetic recombination might be responsible for the high diversity within *C. xiaoi*. This was supported by the mosaic sequence patterns among the subtype families. In addition, a potential host adaptation was identified within this species, reflected by the exclusive occurrence of XXIIIa, XXIIIc, XXIIIg, and XXIIIj in goats. This subtyping tool should be useful in studies of the genetic diversity and transmission dynamics of *C. xiaoi*.

**Keywords:** *Cryptosporidium xiaoi*; 60-kDa glycoprotein; *gp60*; subtyping; genetic diversity; host adaptation
