Cotton Leafroll Dwarf Virus: An Emerging Threat to the U.S. Cotton Industry.

Cotton leafroll dwarf virus (CLRDV), first detected in the US in 2018 in Alabama, is associated with cotton leafroll dwarf disease on cotton. The virus was subsequently detected in Florida, Georgia, Mississippi, South Carolina, and Texas in 2019, suggesting a widespread presence in the cotton-growing region of the U.S. In Georgia, the virus was detected in 14 and 18 counties in 2018 and 2019, respectively. Disease symptoms vary with crop growth stage, time of virus infection and varieties. Early symptoms include reddening of leaves and petioles, downward drooping, and wilting of leaves. As the season progresses, leaf distortion and deformation, stacking of internodes, loss of squares and bolls, absence of pollen, deformed bolls with few seeds, and elongation of the mainstem have been observed in symptomatic plants. The virus was also detected in common weeds including henbit, pigweed, overwintering cotton, and perennial peanuts indicating, that the virus likely overwinters in non-crop hosts that possibly serve as a reservoir for the virus. Genomic composition and diversity were determined by identifying and characterizing the full-length virus genome sequence in isolates from six GA counties from plants at different crop stages that showed diverse symptoms. The genome of CLRDV was determined to be 5,868 nucleotides encoding seven open reading frames, and the 5’ and 3’ end non-coding regions were 70 and 151 bp respectively. Pairwise sequence analysis showed that the virus was 93-95% identical with a strain of CLRDV that causes Atypical Cotton Blue Disease in Brazil and Argentina. The GA isolates were 96-97% identical with the Alabama isolates, suggesting the presence of similar genotypes in the region. Multidisciplinary coordinated efforts across the state lines is needed to develop management strategies and understand the etiology and ecology of the disease, the virus’ genomics, and its interaction with the host and the vector.