Genotype constellations and segment-specific phylogenetic incongruence in bovine rotavirus A associated with fatal neonatal calf diarrhoea in Türkiye.

Neonatal calf diarrhoea (NCD) is a major cause of morbidity and mortality in cattle worldwide, with group A rotaviruses (RVA) recognised as a principal viral aetiological agent. Despite extensive genotyping studies, the relationship between RVA genotypes, segmental phylogenetic patterns, lineage-level diversity, and intestinal pathology in fatal cases remains poorly defined, particularly in Türkiye. In this study, RVA strains detected in fatal NCD cases were investigated through integrated molecular characterisation of the VP7, VP4, and VP6 genes and histopathological examination of small intestinal tissues. Phylogenetic analyses revealed G6-P[1]-I2 and G8-P[1]-I2 genotype constellations and demonstrated segment-specific phylogenetic incongruence, with discordant clustering patterns between VP7 and VP4/VP6 gene segments, consistent with reassortment. Notably, G8 strains clustered within multi-host-associated lineages, including bovine-like human and caprine RVA strains, suggesting potential interspecies transmission dynamics, whereas G6 strains were associated with more host-restricted bovine lineages. Histopathological findings, including villus atrophy, epithelial desquamation, crypt necrosis, and lymphoid depletion, were consistent across cases and showed no genotype-associated differences. These findings highlight reassortment as a key driver of bovine RVA evolution and demonstrate that lineage-level diversity may reflect host adaptation and cross-species transmission processes. The integration of molecular epidemiology with pathological assessment provides a more comprehensive understanding of RVA-associated disease. It supports the need for coordinated surveillance of bovine and multi-host RVA populations.