Analyses of Twelve New Whole Genome Sequences of Cassava Brown Streak Viruses and Ugandan Cassava Brown Streak Viruses from East Africa: Diversity, Supercomputing and Evidence for Further Speciation

Abstract

Cassava brown streak disease is caused by two devastating viruses, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) which are frequently found infecting cassava, one of sub-Saharan Africa’s most important staple food crops. Each year these viruses cause losses of up to $100 million USD and can leave entire families without their primary food source, for an entire year. Twelve new whole genomes, including seven of CBSV and five of UCBSV were uncovered in this research, doubling the genomic sequences available in the public domain for these viruses. These new sequences disprove the assumption that the viruses are limited by agro-ecological zones, show that current diagnostic primers are insufficient to provide confident diagnosis of these viruses and give rise to the possibility that there may be as many as four distinct species of virus. Utilizing NGS sequencing technologies and proper phylogenetic practices will rapidly increase the solution to sustainable cassava production.

Viruses infecting common bean (Phaseolus vulgaris L.) in Tanzania: A review on molecular characterization, detection and disease management options

“…These methods are robust in detection of plant viruses from different families and have led to discovery of novel plant viruses (Adams et al, 2009;Kreuze et al, 2009;Boonham et al, 2014;Zheng et al, 2017). Some studies conducted in or using plant samples from Tanzania have employed NGS to detect plant viruses but not those infecting common bean (Mbanzibwa et al, 2014;Ndunguru et al, 2015). Elsewhere, viruses infecting common bean have been detected and sequenced using NGS (Kehoe et al, 2014;Maina et al, 2016).…”

Occurrence and estimated losses caused by cassava viruses in Migori County, Kenya

“…Mixed infections of CBSV and UCBSV with high prevalence, incidence and severity in the mid altitude areas (1181 to 1467 m above sea level (m asl)) of Western Kenya have been reported by Mware et al (2009) and Osogo et al (2014). In similar studies, Ndunguru et al (2015) detected the presence of both CBSV and UCBSV in low, mid and high altitude areas of Tanzania disapproving the assumption that the viruses are limited by agro-ecological zones. The results in both studies demonstrate a wide distribution of the disease in almost all cassava-growing areas, which confirms that other areas in the East African region previously unaffected by CBSD are now at risk of spread and increased prevalence of the disease.…”

“…The CBSD is caused by two distinct viruses: cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), both of which have (+)ss RNA genomes belong to the genus Ipomovirus in the family Potyviridae, and generally produce similar symptoms in infected plants (Winter et al, 2010;Ndunguru et al, 2015;Vanderschuren et al, 2012;Legg et al, 2011). UCBSV has however been reported to cause milder symptoms than CBSV, and also lower pathogenicity (Vanderschuren et al, 2012).…”

Incidence of viruses and virus-like diseases of watermelons and pumpkins in Uganda, a hitherto none-investigated pathosystem

“…Moreover, virus diseases in nonpriority crops at local or regional scale when ignored or left to 'fallow' may constitute none investigated pathosystems as sources of harmful viruses in surrounding cropping systems (Jones et al, 2010;Lebeda and Burdon, 2013). An example is the watermelon/pumpkin pathosystem in eastern Africa including Uganda that has not been studied, despite pumpkins being common intercrops of other well characterized pathosystems such as cassava (Legg et al, 2011;Ndunguru et al, 2015) and sweetpotato (Valverde, 2007;Clark et al, 2012).…”