Complete genome sequences of two new virus isolates associated with cotton blue disease resistance breaking in Brazil

Since 2006, Brazilian cotton ( Gossypium hirsutum ) crops planted with cultivars that are resistant to cotton blue disease have developed a new disease termed “atypical” cotton blue disease or atypical vein mosaic disease. Here, we describe the complete genomes of two virus isolates associated with this disease. The new virus isolates, called CLRDV-Acr3 and CLRDV-IMA2, were found to have a high degree of nucleotide and amino acid sequence similarity to previously described isolates of cotton leafroll dwarf virus, the causal agent of cotton blue disease. However, their P0 proteins were 86.1 % identical. These results show that this new disease is caused by a new CLRDV genotype that seems to have acquired the ability to overcome cotton blue disease resistance.