Predominantly anthroponotic spread and divergent Giardia assemblages drive co‑circulating lineages in pediatric infections from Egypt

Abstract Giardia duodenalis is a zoonotic protozoan causing substantial waterborne diarrheal disease, yet its genetic diversity and population structure remain under-characterized in many endemic regions. This study examined 451 diarrheic children using qPCR targeting the SSU rRNA gene and multi-locus genotyping of the tpi , gdh, and bg loci to assess prevalence, assemblage distribution, and population-genetic patterns. G. duodenalis was detected in 10.64% of children, with significantly greater prevalence in those aged 1–5 years. Assemblages A and B occurred at nearly equal frequencies, and all assemblage A isolates belonged to the human-adapted AII sub- assemblage, while assemblage B comprised diverse BIII/BIV variants. No mixed infections were detected, and animal contact did not elevate infection risk, suggesting predominantly anthroponotic transmission. Multi-locus analyses revealed striking contrasts between assemblages: assemblage A exhibited extremely low nucleotide and haplotype diversity, complete linkage disequilibrium, absence of recombination, and a highly clonal structure, whereas assemblage B displayed substantially greater polymorphism, deeper sub-structuring, elevated haplotype richness, and reticulated phylogenetic networks. AMOVA demonstrated near-complete genetic differentiation between assemblages. These findings show that assemblages A and B follow distinct evolutionary trajectories and that giardiasis transmission in this region is driven overwhelmingly by human‑to‑human spread. The strong anthroponotic signal, coupled with the high burden in children aged 1–5 and the absence of any association with animal contact, indicates that public health efforts should prioritize interrupting transmission among young children, particularly in household and childcare settings.