Geminiviruses are a large family of plant viruses with circular, single-stranded DNA (ssDNA) genomes packaged within geminate particles. The family Geminiviridae is divided into four genera (Mastrevirus, Curtovirus, Topocuvirus, and Begomovirus) according to their genome organizations and biological properties [1,2]. Members of the genus Begomovirus have caused significant yield losses in many crops worldwide  and are transmitted by whiteflies (Bemisia tabaci) to dicotyledonous plants. The genome of cassava mosaic geminiviruses (CMGs) in the genus Begomovirus consists of two DNA molecules, DNA-A and DNA-B, each of about 2.8 kbp , which are responsible for different functions in the infection process. DNA-A encodes genes responsible for viral replication [AC1 (Rep), and AC3 (Ren)], regulation of gene expression [AC2 (Trap)] and particle encapsidation [AV1 (CP)]. DNA-B encodes for two proteins, BC1 (MP) and BV1 (NSP) involved in cell-to-cell movement within the plant, host range and symptom modulation . CMGs have been reported from many cassava-growing countries in Africa and the cassava mosaic disease (CMD) induced by them constitutes a formidable threat to cassava production .
Representatives of six distinct CMG species have been found to infect cassava in Africa: African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Cameroon virus (EACMCV), East African cassava mosaic Malawi virus (EACMMV), East African cassava mosaic Zanzibar virus (EACMZV) and South African cassava mosaic virus (SACMV) . Recent studies have uncovered much variation in CMGs including evidence that certain CMGs, when present in mixtures, employ pseudo-recombination or reassortment strategies and recombination at certain hot spots such as the origin of replication [6-10] resulting in the emergence of 'new' viruses with altered virulence. For instance, an ACMV-EACMV recombinant component A, designated EACMV-UG2, and a pseudo-recombinant component B, designated EACMV-UG3 , have been implicated in the pandemic of severe CMD currently devastating cassava in much of east and central Africa . In 1997, only ACMV and EACMV were known to occur in Tanzania with the former occurring only in the western part of the country . The discovery of EACMZV on the island of Zanzibar  together with the recent spread into Tanzania of the EACMV-UG2 associated pandemic of severe CMD [4,13] has aggravated the CMD situation. Consequently, there is much to be learned about the identity, distribution, molecular variability, and the threat that these emerging geminiviruses pose to cassava production in Tanzania and more generally in Africa.
In 1997, the first recombination between two species of geminiviruses was recorded [7,8]. This mechanism is now known to be widely used by all geminiviruses and is probably the most important molecular mechanism for generating genetic changes that allow novel geminiviruses to exploit new ecological niches [2,14].
This paper describes the results of a molecular study of the sequences of CMGs collected from the major cassava-growing areas of Tanzania in an effort towards identifying, determining molecular variability and mapping the distribution of CMGs. In addition, because East Africa seems to be unusually rich in virus biodiversity and because the most recent cassava pandemic was first reported in East Africa, we investigated the extent of inter-CMG recombinations and examined their role in the evolution of CMGs in Africa.