A novel strain of Beet western yellows virus infecting sugar beet with two distinct genotypes differing in the 5′-terminal half of genome

Abstract

The complete genomic sequences of two distinct Beet western yellows virus (BWYV) genotypes infecting sugar beet in Bei**g, named as BWYV-BJ^A and BWYV-BJ^B (GenBank accession number HM804471, HM804472, respectively), were determined by RT-PCR sub-cloning approach. BWYV-BJ^A and BWYV-BJ^B were 5674 and 5626nt in length, respectively. BWYV-BJ^B was 48nt shorter than BWYV-BJ^A in the regions 1589–1615 and 1629–1649nt. Sequence alignment analysis showed that the full length of BWYV-BJ^A and BWYV-BJ^B shared 93% nucleotide sequence identity, with relatively high variability within ORFs 0, 1, 2 (at the nucleotide level was 86.3–88.8%) and high conservation within ORFs 3, 4, 5 (at the nucleotide level was 99.3–99.5%). The complete nucleotide sequences of BWYV-BJ^A and BWYV-BJ^B were most related to BWYV-US (80.6 and 79.0%, respectively). ORFs 1, 2 of BWYV-BJ^A and BWYV-BJ^B shared the highest homology with BWYV-US (nucleotide identity 91.2–93.3, 86.7–89.5%, respectively) and their ORFs 3, 4 were more closely related to BWYV-IM. However, their ORF5 were more closely related to that of Cucurbit aphid-borne yellows virus China strain (CABYV-CHN), with 68.1 and 68.5% nucleotide identity, respectively. Based on the sequence and phylogenetic analysis, we proposed that BWYV-BJ was at least a novel strain of BWYV, and BWYV-BJ^A, BWYV-BJ^B were two distinct genotypes of BWYV-BJ. In addition, phylogenetic analysis and recombination analysis suggested that BWYV-BJ^A and BWYV-BJ^B might be recombinant viruses.