First evidence of allexiviruses in Allium plants in Ukraine and molecular characterization of their isolates

Allexiviruses (family Alphaflexiviridae ) are widespread pathogens of vegetatively propagated Allium crops, but their occurrence has not previously been documented in Ukraine. We surveyed cultivated Allium plants collected in eight Ukrainian regions (2022–2025) and screened their samples for garlic virus B (GarV-B), garlic virus C (GarV-C) and shallot virus X (ShVX) using enzyme-linked immunosorbent assay (ELISA). GarV-B, GarV-C and ShVX were detected in 39/108 (36.1%), 23/108 (21.3%) and 21/108 (19.4%) plants, respectively, with infections which were strongly host-associated: garlic (n = 63) had high frequencies of indicated viruses (GarV-B − 61.9%; GarV-C − 36.5%; ShVX − 28.6%), whereas onion samples (n = 33) were largely negative (ShVX − 3.0%; GarV-B and GarV-C - not detected). Co-occurrence analysis within garlic revealed a nested allexivirus module in which GarV-C and ShVX occurred only in GarV-B-positive plants. RT-PCR and Sanger sequencing generated 11 partial genomes representing GarV-B, GarV-C, ShVX, GarV-A and GarV-D. Maximum-likelihood phylogenies placed Ukrainian allexivirus isolates within established global diversity and indicated both European- and Asian-affiliated lineages. These findings provide the first evidence of allexiviruses in Ukrainian Allium crops, and support their inclusion in plant health surveillance and planting-material certification.