Cotton Plants Presenting Symptoms Associated with Cotton Leafroll Dwarf Virus Revealed a Novel Caulimovirid, Cotton Virus A, with Endogenous Caulimovirids in Its Hosts

Abstract

The dynamics of cotton leafroll dwarf virus (CLRDV) symptomology in Gossypium plants was investigated in Mississippi in 2019 and 2022. High-throughput sequencing of libraries constructed from ribo-depleted total RNA or total nucleic acids and bioinformatic analyses revealed a novel virus, cotton virus A (CotVA), that clusters within the family Caulimoviridae alongside two unclassified viruses related to ruflodiviruses and caulimoviruses. Endogenous CotVA elements, referred to as endogenous caulimovirids (ECVs), were identified in multiple chromosomes of 7 out of 26 Gossypium species analyzed, including two commercial species: G. hirsutum (Upland cotton) and G. barbadense (Pima cotton). The circular nature of the episomal genome of one CotVA isolate was confirmed using five overlapping primer sets. A DNase protection assay on purified virus preparations revealed evidence of CotVA virions. The presence of CotVA ECVs and/or an episomal form of CotVA in cotton fields complicates the interpretation of CLRDV symptoms, but proper studies are needed to determine if CotVA is associated with any symptomology. Possible synergistic interactions among CLRDV, CotVA, and proteins or other molecules produced by ECVs and the impact of these interactions on any possible disease progression require further investigation.