Epidemiological investigation and molecular detection of coccidial infection in yaks in parts of Qinghai Province, China.

To inform coccidiosis control in Qinghai's yak regions, we examined Eimeria species composition and prevalence in grazing yaks, and assessed infection associations with season and mixed sheep grazing. Age-related data were unavailable due to unrecorded birth dates in pastoral systems. From September 2024 to April 2025, 559 fecal samples from yaks with suspected coccidiosis were collected across five counties: Tianjun, Haiyan, Gangcha, Maduo, and Gonghe. DNA extracted by fecal sedimentation was subjected to nested PCR of the 18S rRNA gene; positive amplicons were sequenced and identified by BLAST. Haplotype diversity was analyzed with DnaSP v6, networks constructed with PopArt, and a neighbor-joining tree built using Nosema portugal (AF033316) as an outgroup. The overall infection prevalence was 35.6% (199/559), with all counties affected and the highest rates in Maduo (53.2%), Gangcha (43.8%), and Haiyan (38.6%). Ten Eimeria species were identified, predominated by E. bovis (9.8%), E. ahsata (9.8%), and E. auburnensis (7.0%). E. bovis (20 haplotypes) had the dominant haplotype EmbH1 across all counties; E. ahsata and E. auburnensis (10 each) had EmsH3 and EmuH4 as dominant, respectively. Phylogenetic analysis placed all ten species in well-supported clades with reference sequences, with bovine-derived Eimeria clustering together, indicating host-parasite co-evolution. These findings reveal severe endemic status and high species and haplotype diversity. An integrated strategy comprising optimized feeding management, strategic anticoccidial treatment, and environmental sanitation is essential to reduce the epidemiological burden.