Genetic Diversity and Distribution of Cassava Brown Streak Virus and Ugandan Cassava Brown Streak Virus in Major Cassava-growing Regions in Kenya

Cassava brown streak disease (CBSD) is caused by two viruses; Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) that are genetically distinct. The disease can cause losses of up to 100 million US Dollars and it has a big impact on cassava yields. There is relatively little genetic information of CBSVs, their distribution and genetic diversities in Kenya. This study was therefore to establish the extent of distribution and diversity of CBSV and UCBSV strains in the Kenya. A survey was conducted in Coast, Western and Nyanza which are the major cassava-growing areas of Kenya. The mean disease incidence in Coast was 47.8%, Western 33.0% and Nyanza 55.9%. The average mean severity score cassava brown streak virus was 2.0 for Coast, 2.4 for Western and 2.6 for Nyanza. A reverse transcriptase polymerase chain reaction (RT-PCR) was used to screen 131 samples and of these 24 positive and negatives samples representing each region were selected for next generation sequencing. RT-PCR detected single infections of CBSV, UCBSV and co infections 19.8%, 22.1% and 34.4% of the positive reactions respectively countrywide. Alignment from assembled coat protein sequences revealed two clusters representing the two strains. The study also revealed a mixed infection in the samples from the surveyed fields. The widespread distribution of CBSV and UCBSV in Coast, Western and Nyanza farmer’s field in Kenya has implications in the cassava production in those regions.