Coinfection of cotton plants with cotton leafroll dwarf virus‐atypical and a novel cotton begomovirus

Abstract Cotton is a commercial crop of global importance whose versatile fibre is widely used in the textile industry. Cotton is vulnerable to infectious pathogens, including viruses, that are a major threat to cotton production. Cotton blue disease is caused by cotton leafroll dwarf virus (CLRDV), a polerovirus transmitted by aphids. This virus is controlled by sowing cotton varieties resistant to CLRDV, although, in recent years an atypical variant (CLRDV‐at), that breaks the resistance, has been identified. An outbreak of a disease occurred in cotton fields of the province of Chaco, in the north‐west of Argentina, in the 2014–2015 growing season. NuOpal cotton plants (a variety resistant to CLRDV and susceptible to CLRDV‐at) showed mosaic symptoms and had virus‐transmitting insect vectors, such as aphids and whiteflies ( Bemisia tabaci ). The symptoms were common for virus infections but different from those caused by CLRDV or CLRDV‐at. According to a reverse transcription‐PCR analysis with polerovirus primers and sequencing, the plants contained CLRDV‐at. To identify the complete virome of these plants, we performed a massive RNA‐based deep sequencing assay using Illumina technology. As a result, a new begomovirus that infects cotton in Argentina was identified. Structural and functional annotation indicated that its sequences corresponded to complete DNA components A and B of a novel New World bipartite begomovirus. Genetic distance and evolutionary analyses support that the detected sequences correspond to a new virus, which we propose to name cotton mosaic virus (CoMV). In addition, we report the first begomovirus and polerovirus coinfection in cotton.