Identification of a Cotton Leafroll Dwarf Virus-like Polerovirus Infecting Cotton in Alabama during 2017-2018

Cotton (Gossypium hirsutum) is one of the most economically important crops in the southeast United States. Cotton blue disease has been associated with isolates of the exotic Cotton leafroll dwarf virus (CLRDV) known from Argentina and Brazil. The virus is thought to be endemic in Africa or Asia and to have spread to South America only recently. During 2017, an aphid-transmitted poleroviruses, was identified for the first time infecting symptomatic cotton plants in Alabama. Provisional identification was based on 1143 bp fragment based on Illumina RNA sequencing, and cloned viral amplicons obtained by RT-PCR amplification. To determine the full-length viral genome, RNA was isolated from symptomatic cotton leaves and petioles collected in Barbour and Macon counties during 2018 and subjected to Illumina sequencing. Analysis of the assembled contigs revealed a 5771 bp fragment that most closely matched six Cotton leafroll dwarf virus isolates from South America. Based on pairwise distance analysis, the polerovirus isolate from Alabama shares its highest nucleotide (nt) identity with CLRDV from Brazil [HQ827780], at 95.6%. The apparently full-length genome contains six open reading frames (ORFs), ORF0-ORF5. The most divergent coding region among the six available genomes is ORF0 (which encodes a viral suppressor of host-gene silencing), at 90.6-92.0% nt identity and 82.4-88.5% amino acid similarity. In 2018, the extent of its distribution in Alabama cotton plantings was investigated using reverse transcriptase-PCR and previously validated primers. The expected amplicon size of 310 bp was detected in 196 of 400 cotton samples from Alabama. Selected amplicons were cloned and sequenced, confirming virus identity, and therefore its distribution in at least 20 AL counties during 2018.