Geminiviruses are a group of plant viruses that contain circular single stranded (ss) DNA genomes encapsidated in small twinned icosahedral capsids . They infect a wide range of plant species and are responsible for considerable crop losses . Members of this virus family have been classified into four genera: Begomovirus, Curtovirus, Mastrevirus, and Topocuvirus, depending on genome organization, host range and type of insect vectors . The genome of cassava mosaic geminivirus (CMG) belonging to the genus Begomovirus consist of two components termed DNA A and DNA B each of ~ 2.7 - 3.0 kb [1, 4]. The virus DNA A plus strand encodes the coat protein (CP/AV1) essential for viral transmission by whiteflies (Bemisia tabaci) [1, 5]. There are three overlapping open reading frames (ORFs) on the complementary strand, of which the replication associated - protein (Rep/AC1) is absolutely required for the replication of both genomic components [6, 7]. The replication enhancer protein (REn/AC3) is not essential for infection but enhances viral DNA accumulation . The transcriptional activator protein (TrAP/AC2) is required for the transcription - activation of plus strand gene transcription, and is also involved in suppression of post - transcriptional gene silencing (PTGS) [8, 9]. The functions of two other DNA A encoded proteins AV2 and AC4 remains unclear although possible roles in movement (AV2), pathogenicity and PTGS (AC4) have been demonstrated [9, 10]. DNA B encodes the movement protein (BC1/MP) and a nuclear shuttle protein (BV1/NSP) required for cell - to - cell and long distance spread of virus in host plant . Both DNAs contain a 200-250 bp region of high sequence homology known as the common region which is a part of a large intergenic region (IR) that contains the origin of replication .
Seven species of Begomovirus have been identified so far in association with cassava mosaic disease (CMD) in Africa: African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Cameroon virus (EACMCV), East African cassava mosaic Kenya virus (EACMKV), East African cassava mosaic Malawi virus (EACMMV), East African cassava mosaic Zanzibar virus (EACMZV) and South African cassava mosaic virus (SACMV) [11–14]. The distribution of the viruses has become more complex, since they invade new geographical regions and host plants [14, 15]. This was attributed to their evolution which was more rapid than anticipated through mutational changes, recombination of double stranded (ds) DNA intermediates and re - assortment of gene components (pseudo - recombination) [12–17]. In fact, recombination played a role in the emergence of a new geminivirus that resulted in severe epidemics almost eliminating cassava (Manihot esculenta) in Uganda and Central Africa [12, 18]. The symptom severity (due to synergism) was linked to the occurrence of East African cassava mosaic virus - Uganda (EACMV - UG) arising from recombination of EACMV and ACMV) . Synergism refers to a situation where one virus affects a co - infecting virus by allowing its increased accumulation in the host plant by facilitating its replication, its movement to tissues that otherwise would not be invaded, resulting in more severe symptoms than caused by each single infection . Synergism between EACMV and ACMV is due to a selective advantage conferred by each partner linked to post transcriptional gene silencing (PTGS). In plants, PTGS operates as an adaptive immune system targeted against viruses . To counteract this defence system, viruses have developed suppressor proteins . ACMV and EACMV - UG possess two PTGS suppressors AC4 and AC2 respectively, with differential roles that target different steps in RNA silencing in a temporal and spatial manner [8, 10, 21, 22]. Therefore using more than one type of PTGS suppressor provides an advantage to viruses synergistically interacting in mixed infections, leading to more severe symptoms [9, 10]. Furthermore, geminiviruses may be associated with small sub genomic DNA molecules termed as Defective (Def) DNAs, which are the result of partial deletion to approximately half the genome, even disrupting genes [23, 24]. They may also result from sequence duplication, inversion or rearrangement of viral DNA, and recombination between DNA A and DNA B components .
Additionally, Cassava brown streak disease (CBSD), caused by Ipomoviruses (family Potyviridae), has been reported to lead to severe yield losses in cassava plantations in Africa [26–28].
Both host plants under study, cassava and Jatropha, belong to the family Euphorbiaceae. Jatropha is a drought resistant shrub native in tropical America, but is now widely grown in many tropical and subtropical regions for biodiesel production [29, 30]. Based on the genetic relationship of cassava and Jatropha and the detrimental impact of Begomoviruses in cassava, the question arose, whether Jatropha would be threatened by comparable epidemics, if planted on larger extensions, or in spatial neighbourhood. Therefore it was necessary to develop diagnostic approaches allowing reliable pathogen detection in Jatropha, which involved the amplification and sequencing of the entire DNA A molecules of 40 Kenyan isolates belonging to ACMV and EACMV - UG. This information enabled the design of novel primers to address different questions: a) primers amplifying longer sequences led to a phylogenetic tree of isolates, allowing some predictions on the evolutionary aspects of Begomoviruses in Jatropha; b) primers amplifying shorter sequences represent a reliable diagnostic tool, given that so far only limited serological tests are available.