S.E. Bull¹, H.W. Karakacha⁴, R.W. Briddon^1*, S. Nzioki², M.N. Maruthi³, J. Stanley¹ and S. Winter⁴

¹ Department of Disease and Stress Biology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, U.K.
² Kenya Agricultural Research Institute, P.O. Box 57811, Nairobi, Kenya
³ Plant, Animal & Human Health Group, Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent ME4 4TB, U.K.
⁴ DSMZ-Deutsche Sammlung von Mikroorganismen and Zellkulturen GmBH, Plant Virus Division, Biologisches Bundesanstalt, Messeweg 11/12, D-38104 Braunschweig, Germany.

*rob.briddon@bbsrc.ac.uk

Accepted for publication 01/04/03

Cassava is a staple crop grown throughout central and southern Africa. Losses to cassava production occur in all areas due to cassava mosaic disease (CMD), caused by various begomoviruses (family Geminiviridae). During the 1990s a particularly severe CMD pandemic spread through Uganda and into surrounding countries, including Kenya. The severity of the pandemic was attributed to a synergistic interaction between African cassava mosaic virus (ACMV) and a recombinant strain of East African cassava mosaic virus (EACMV), known as the Uganda variant (EACMV-UG; Zhou et al., 1997). Recently Maruthi et al. (2001) showed the presence of an additional begomovirus species, East African cassava mosaic Zanzibar virus (EACMZV) on the island of Zanzibar.

Figure 1. Phylogenetic dendrogram derived from an alignment of African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Malawi virus (EACMV), East African cassava mosaic Zanzibar virus (EACMV), Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosaic virus (SLCMV) DNA A nucleotide sequences. The position of EACMZV-KE is highlighted with a black box and the "East African cluster" of cassava mosaic begomoviruses is indicated. The tree was rooted on the DNA A sequence of Tomato mottle virus (ToMoV), a distantly related begomovirus originating from Florida. The numbers at nodes indicate bootstrap confidence values (1000 replicates).

Cassava stem cuttings were collected in Kenya during 1999. EACMV was found in coastal areas from Kilifi to Kwale. Four symptomatic cassava samples failed to produce products in diagnostic PCR. For these samples, DNA A-specific primers (virion-sense 5'-GGTACCACATGTTGACGCGCTCCACTACTT-3', complementary-sense 5'-GGTACCATTGTTAAACGATTTCCCTGAA-3') were designed from the sequence of PCR products produced with genus-specific primers (Deng et al., 1994). The full-length PCR product was cloned into pQA (Qiagen) and sequenced (EMBL Acc. No. AJ516003). The DNA A component is 2,784 nucleotides in length and shows the arrangement of genes typical of Old World bipartite begomoviruses (Stanley and Gay, 1983). It is most similar to EACMZV (96.4% nucleotide identity) and closely related to other CMD-associated begomoviruses including EACMV-Tanzania (85%) and EACMV-UG (83.4%).

Figure 2. Foliar symptoms of cassava naturally infected with EACMZV-KE.

The virus isolate from coastal Kenya is a strain of EACMZV which we designate EACMZV-Kenya (EACMZV-KE). This virus may be widespread along the coast of East Africa and probably diverged from other cassava-infecting begomoviruses due to geographic isolation. The cassava growing region of coastal Kenya is separated from cultivated areas inland by an arid belt which does not support intensive agriculture. This suggests that there has been little, if any, movement of cassava and associated viruses between these two regions, thus protecting the coastal belt from the severe CMD pandemic and allowing EACMZV-KE to be maintained.

Research at the JIC and KARI was supported by the EU-funded INCO-DEV programme. HWK was supported by a grant from the German Academic Exchange Service, DAAD.

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The British Society for Plant Pathology