Genomic analyses of a widespread blueberry virus in the United States

•Genomic and evolutionary analysis of blueberry virus (BlVL), a new luteovirus.•A cryptic ORF is under strong positive selection.•BlVL is present in almost 80% of the more than 600 samples tested.•Most widespread blueberry virus in the United States.•Given the BlVL diversity movement by propagation material is highly unlikely. Screening of blueberry accessions using high throughput sequencing revealed the presence of a new virus. Genomic structure and sequence are similar to that of nectarine stem pitting associated virus (NSPaV), a member of the genus Luteovirus, family Tombusviridae. The full genome of the new luteovirus, tentatively named blueberry virus L (BlVL), was characterized and analyzed. Similar to NSPaV, BlVL does not contain readily identifiable movement proteins in any of the seven isolates sequenced. More than 600 samples collected from five states were screened and 79% were found infected, making BlVL the most widespread blueberry virus in the United States.