Genomic analysis of Echinococcus granulosus sensu stricto: genetic diversity and population structure.
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Anijalg Liina, Korhonen Pasi K, Young Neil D, Cai Huimin, Li Junhua, Yang Huanming, Wang Daxi, Wang Tao, Yang Bicheng, Laurimäe Teivi, Jenkins David J, Casulli Adriano, Rostami-Nejad Mohammad, Acosta-Jamett Gerardo, Irshadullah Malik, Mirhendi Hossein, Sharbatkhori Mitra, Kia Eshrat Beigom, Ponce-Gordo Francisco, Simsek Sami, Zait Houria, de la Rue Mario Luiz, Soriano Silvia Viviana, Lazzarini Lorena Evelina, Romig Thomas, Wassermann Marion, Aghayan Sargis A, Gevorgyan Hasmik, Ibrahim Mohamed Mousa, Rehbein Steffen, Šnábel Viliam, Manfredi Maria Teresa, Chang Bill C H, Saarma Urmas, Gasser Robin B
Аннотация
METHODS: We conducted a genomic study of 137 E granulosus ss samples from endemic regions across five continents, derived from previously collected parasite material from livestock, wildlife, and human infections. Using a chromosome-scale reference genome, we applied population genomic approaches to investigate genome-wide nuclear genetic diversity, population structure, and patterns of evolutionary constraint.
FINDINGS: We identified 1 071 085 nuclear single-nucleotide polymorphisms across 137 samples, with heterozygosity ranging from 46% to 93% per sample. Genome-wide analyses identified two major clades associated with geographical origin. Distinct regions of genetic differentiation were observed, particularly on chromosome 9. Conserved genes under purifying selection included those involved in glycan biosynthesis and core cellular functions, whereas variable genes were enriched in pathways such as ribosome biogenesis. Mitochondrial genotypes (G1 and G3) did not align with the nuclear genomic structure.
INTERPRETATION: To the best of our knowledge, this study provides the first broad atlas of nuclear genomic diversity in E granulosus ss, uncovering genetic diversity and population structure. The findings have important implications for molecular epidemiology, genomic surveillance, and translational development of diagnostics and vaccines. Incorporating genomic data into cystic echinococcosis control programmes could enhance WHO-aligned efforts to reduce the burden of this neglected tropical disease.
FUNDING: Australian Research Council and the Estonian Ministry of Education and Research.