High Genetic Variation in the COI Gene Complicates Molecular Identification of Eimeria Species in Goats from South Korea

Abstract

Despite the growth in South Korea’s goat industry, epidemiological data on goat coccidiosis—an intestinal disease caused by Eimeria spp., causing diarrhea and productivity losses, particularly in kids—remain limited. In 2025, fecal samples from 67 farms across 12 regions in Gyeongsangnam-do were analyzed for oocyst detection, oocysts per gram (OPG) quantification, and cytochrome c oxidase subunit I (COI) sequencing. Farm-level prevalence was high at 83.6% (56/67; range, 66.7–100%), with a mean OPG of 1136 (range: 250–7033) among positive samples. Morphologically, the observed oocysts resembled E. christenseni, E. arloingi, and E. hirci. COI-based BLAST analysis showed high identity with E. christenseni and E. arloingi, whereas phylogenetic analysis revealed affinities extending to E. hirci and sequences from cattle (E. bovis, E. zuernii) and sheep (E. ahsata). However, substantial COI heterogeneity, pooled sampling, and potential preferential amplification during Sanger sequencing limited confident species assignment. Here, findings demonstrate farm-level Eimeria detection but do not establish clinical or subclinical coccidiosis since clinical status was not systematically assessed. Nevertheless, these data establish a useful epidemiological and genetic baseline and highlight the need for multi-locus analysis (18S rRNA, internal transcribed spacer [ITS], and COI) to improve species-level resolution for surveillance and control strategies.