Population structure, evolution and detection of blackberry leaf mottle-associated virus, an emerging emaravirus

Blackberry leaf mottle-associated virus (BLMaV) is a recently described emaravirus associated with yellow vein disease, the main constraint of blackberry production in the southern USA. The population structure and genetic variation of BLMaV, based on the nucleocapsid and movement protein genes was resolved. BLMaV diversity is low when compared to other emaraviruses, with the genes studied being under strong negative selection. Phylogenetic analyses suggest long distance migration of the virus whereas incongruent phylogenetic relatedness and predicted reassortment events suggest that genetic exchange could play an important role in BLMaV evolution. A quantitative PCR (qPCR) protocol was developed based on the knowledge obtained through the population structure of the virus; this is a sensitive test able to detect all the isolates studied. The assay was optimized and applied successfully on multiple samples collected from several regions in the United States. Comparison between a previously developed test and the new protocol illustrated that the latter is at least 1000 times more sensitive.