Detection and molecular characterisation of beet chlorosis virus in sugar beet in the Czech Republic

Beet chlorosis virus (BChV; species Polerovirus BCHV ) is an economically important pathogen causing significant yield losses in sugar beet worldwide. This study reports the first detection and genetic diversity of BChV in the Czech Republic. Thirty‐seven symptomatic sugar beet samples collected from multiple locations were screened using one‐enzyme RTX‐PCR. BChV was detected in 12 samples from seven locations. All positive isolates were analysed by Sanger sequencing of the coat protein‐readthrough domain (CP‐RTD; ORF3–ORF5) region, which served as the primary dataset for diversity analysis. One representative isolate, PX088834 (B_V1_CZ; Bezno_CZ), was further analysed by high‐throughput sequencing (HTS) to obtain a near‐complete genome sequence. HTS produced a near‐complete BChV genome sequence of 5779 nt. The sequence confirmed the expected polerovirus genomic organisation of the PX088834 (B_V1_CZ; Bezno_CZ) isolate, and genome‐wide pairwise identity analysis placed it within the European BChV lineage. CP‐RTD phylogenetic analysis of 12 Czech isolates revealed three phylogenetic lineages, designated A, B, and B1. Three Czech isolates (L_V8; Jizerní Vtelno_CZ, L_V11; Němčice_CZ, and L_V16; Radonice_CZ) clustered within lineage A together with isolates from the United Kingdom and the United States, whereas the remaining nine isolates fell within lineages B and B1 alongside other European isolates. The co‐occurrence of these lineages, including at the same sampling location, is consistent with multiple independent introductions. Sliding‐window similarity analysis confirmed a clear gradient of divergence from closely related European isolates to the most divergent US isolate. Codon‐based analysis demonstrated significant purifying selection acting on the CP‐RTD region, and recombination analysis identified one putative event in the near‐complete genome and two additional events in the CP‐RTD dataset. These findings expand current knowledge of BChV distribution and genetic diversity in Europe and provide a foundation for future surveillance efforts.