Deep sequencing of High Plains wheat mosaic virus from sweet corn to guide seed health testing reveals multiple variants for all eight genome segments and two major isolate types

High Plains wheat mosaic virus (HPWMoV) is a virus that can infect both wheat and maize crops, raising concerns of seed transmission. Due to the potential to spread the virus through seed imports, sweet corn seed lots are now required to test negative for the presence of HPWMoV in certain countries. To develop more effective diagnostic primers for seed health testing and phytosanitary certification, researchers conducted deep sequencing of HPWMoV-positive tissue samples collected from fields in two major sweet corn seed production regions: the Columbia Basin and Treasure Valley.

Through this process, they were able to achieve near-complete genome coverage (95%) for 21 HPWMoV isolates.

The researchers used de novo assembly of the eight viral genome segments to uncover a high level of diversity within each segment. They identified at least two variants for each RNA segment, with three variants for RNA3, RNA6, and RNA8. Generally, only one variant of each RNA segment was present within a single sample, except for RNA3, which helped categorize the isolates into two distinct types: type A and type B. These two types accounted for all but one previously sequenced HPWMoV isolate.

In two specific samples, at least two variants of every RNA were detected, totaling 17 genome segments, suggesting a co-infection involving both type A and type B isolates.

Despite the observed variability, the researchers successfully created two primer and probe sets for reverse transcription-quantitative polymerase chain reactions (RT-qPCR) diagnostics. These primers were able to detect all 20 HPWMoV isolates tested in a duplex diagnostic assay. This assay proved capable of screening seed lots for HPWMoV, providing a suitable solution for seed health testing and phytosanitary certification in regions where the virus is a concern.