Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: High rates of intra-species recombination - a driving force in the emergence of new strains

•147 CpCDV genomes from pulses collected across the chickpea growing regions of Sudan.•7 of the 12 known CpCDV strains are present within Sudan.•CpCDV-H alone accounted for ∼73% of the infections.•Identified four new strains of CpCDV (M, -N, -O and -P) in Sudan.•Recombination plays a significant role in the diversification of Sudanese CpCDVs.

In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.