Diversity of Cotton leafroll dwarf virus in Thailand and Timor-Leste

Abstract

One of the aims of a current CRDC-funded project is to determine the genetic relatedness of Cotton leafroll dwarf virus (CLRDV) from Thailand and East Timor to the ‘atypical’ strains from South America which are known to overcome CRLDV-resistance. Some recent reports from Brazil and Argentina (da Silva et al. 2015; Cascardo et al. 2015; Agrofoglio et al. 2017) showed that the PO gene is the most variable region of the CLRDV genome and shows the greatest differences between the standard and resistant-breaking strains of CLRDV. The P0 protein is reported to control the ability of the virus to overcome plant resistance. I have now sequenced the partial PO gene from 12 isolates of CLRDV from Thailand, Timor-Leste and Uzbekistan, and compared these to published sequences of standard and resistance-breaking strains from Brazil and Argentina. The standard (typical) and resistance-breaking strains from Brazil and Argentina form their own clades which share about 90-91% nt identity. By contrast, the PO gene sequences from Uzbekistan, Thailand and Timor-Leste show greater diversity. In fact, the diversity between CLRDV samples from two sites in Timor-Leste separated by only 21 km (Lospalos and Luro), share about 86 % nt identity, which represents greater diversity than that between the standard and resistance-breaking CLRDV samples from across vast distances and the two countries of Brazil and Argentina. Further diversity is also present in the CLRDV samples from Thailand and Uzbekistan which both form their own clades.
While the CLRDV strains from Timor-Leste are different to the ‘atypical’ strains from South America, there may be enough diversity in the CLRDV strains present in Timor-Leste to overcome a resistance gene in cotton. The industry should remain vigilant to minimise the risk of incursion or spread of CLRDV.