Interspecies recombination between cassava brown streak disease-causing viruses

Cassava brown streak disease (CBSD) significantly limits cassava production in East and Central Africa. There is significant interest in the two viruses that cause CBSD (cassava brown streak virus [CBSV] and Ugandan cassava brown streak virus [UCBSV]) and how these viruses interact. We analyzed recombination events in publicly available sequences of these two ipomoviruses to detect recombination hotspots. We detected 27 recombination events in 67 polyprotein-coding sequences of CBSV (all supported P ≤ 1.36x10 ^-20 ) and 16 recombination events in 81 sequences of UCBSV (P ≤ 1.081x10 ^-41 ). The breakpoints from both analyses were concentrated in the 3’ end of the genome, appearing mainly in the NIb, Ham1h and CP genes. Importantly, each analysis detected a recombination event with an unknown parent that is likely a member of the other species, demonstrating recombination between CBSV and UCBSV for the first time. A combined recombination analysis on both viruses revealed 11 well-supported interspecific recombination events resulting in four recombinant sequences. Our results reveal that the frequent coinfection of these two ipomoviruses in the field has led to the expected mixing of their genomic material, especially in the extreme 3’ (CP protein-coding) end of the polyprotein open reading frame, and suggest that more hybrid genomes may be found as both viruses increase their range in Africa.