| dc.description.abstract | Cassava brown streak ipomoviruses (Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) are extremely damaging plant pathogens affecting sustainable cultivation of cassava in Africa. The viruses are associated with losses of approximately US$100 million per year. However, little is known about the rate at which these viruses evolve and their epidemiological history. This information is central to understanding the viral evolutionary dynamics, which in turn has major implications to virus’ ability to emerge into new host species and resist RNAi approaches for control. To understand the diversity and evolutionary relationships among the viruses, the study deployed both Sanger and Illumina deep sequencing approaches.
Using the P1 gene, a novel and intermediate phylogenetic grouping tentatively called CBSV-Tanzania (CBSV-TZ) was established through computational evolutionary techniques. Virus isolates of the distinctive CBSV-TZ had nucleotide identities as low as 63.2 and 63.7% with other members of CBSV and UCBSV, respectively. Grouping of P1 gene sequences indicated distinct sub-populations of CBSV, but not UCBSV. Representatives of all three clades were found in both Tanzania and Malawi. While illumina sequencing of RNA from a cassava cutting from northern Malawi produced a genome of Ugandan cassava brown streak virus designated UCBSV-MW-NB7_2013. This was compared with twenty-two other complete genomes from Tanzania (seven), Uganda (four), Kenya (nine) and Malawi (two). Sequence comparisons revealed stronger similarity to an isolate from nearby Tanzania (93.4% pairwise nucleotide identity) than those previously reported from Malawi (86.9 – 87.0%). The study, therefore, reported for the first time a genetically divergent UCBSV isolate from Malawi with a geographically distinct monophyletic sub – cladding.
Furthermore, an ampelovirus was discovered from Malawi. The complete genome of a novel virus having a single-stranded RNA genome of 13,644 nt was assembled and the virus was assigned to the genus Ampelovirus. Virus transmission by the mealybug Phenaccocus manihotis was not successful but graft transmission of the virus was confirmed. From its original finding, a further ampelovirus sequence was identified in raw data of an experimental data set, PRJEB10634, deposited at the European Nucleic Acid Archive. In ERR996014 from which a genome of Ugandan cassava brown streak virus was assembled, an Ampelovirus sequence with 96% nt identity to the Malawi ampelovirus was re-constructed.
Using the coat protein gene, the evolutionary dynamics of the viral gene and the Bayesian coalescent approach using BEAST revealed that the CBSV CP is among the fastest evolving among studied potyviruses, with a mean rate of 4.64 x 10-4 nucleotide substitutions per site per year (95% Highest Posterior Density, 2.07 - 7.14 x 10-4 s/s/y). This rate indicates that the most recent common ancestor of CBSV existed 117 years before present (95% HPD, between years 1824-1959). The study also documented pervasive evidence of purifying selection in the CBSV CP gene, but highlighted two sites that are undergoing diversifying selection, indicating CBSV has been adapting over the last two decades. Thus, the Bayesian phylogeography and spatial migration analysis present molecular evidence that East Africa is the centre of CBSV diversity. | en_US |
