Open Access Open Badges Research article

East African cassava mosaic-like viruses from Africa to Indian ocean islands: molecular diversity, evolutionary history and geographical dissemination of a bipartite begomovirus

Alexandre De Bruyn12, Julie Villemot1, Pierre Lefeuvre1, Emilie Villar1, Murielle Hoareau1, Mireille Harimalala1, Anli L Abdoul-Karime3, Chadhouliati Abdou-Chakour4, Bernard Reynaud1, Gordon W Harkins5, Arvind Varsani678, Darren P Martin9 and Jean-Michel Lett1*

  • * Corresponding author: Jean-Michel Lett

  • † Equal contributors

Author Affiliations

1 CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l’IRAT, Saint-Pierre, Ile de La Réunion, 97410, France

2 Université de La Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l’IRAT, Saint-Pierre, Ile de La Réunion, 97410, France

3 Service de Protection des Végétaux - Direction de l’Agriculture et de la Forêt, B.P 103, Mamoudzou, Mayotte, 97600, France

4 Institut National de Recherche pour l’Agriculture, la Pêche et l’Environnement, BP289, Moroni, Grande Comore, Union des Comores

5 South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa

6 School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand

7 Biomolecular interaction centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand

8 Electron Microscope Unit, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa

9 Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, Cape Town, South Africa

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BMC Evolutionary Biology 2012, 12:228  doi:10.1186/1471-2148-12-228

Published: 27 November 2012



Cassava (Manihot esculenta) is a major food source for over 200 million sub-Saharan Africans. Unfortunately, its cultivation is severely hampered by cassava mosaic disease (CMD). Caused by a complex of bipartite cassava mosaic geminiviruses (CMG) species (Family: Geminivirideae; Genus: Begomovirus) CMD has been widely described throughout Africa and it is apparent that CMG's are expanding their geographical distribution. Determining where and when CMG movements have occurred could help curtail its spread and reveal the ecological and anthropic factors associated with similar viral invasions. We applied Bayesian phylogeographic inference and recombination analyses to available and newly described CMG sequences to reconstruct a plausible history of CMG diversification and migration between Africa and South West Indian Ocean (SWIO) islands.


The isolation and analysis of 114 DNA-A and 41 DNA-B sequences demonstrated the presence of three CMG species circulating in the Comoros and Seychelles archipelagos (East African cassava mosaic virus, EACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV). Phylogeographic analyses suggest that CMG’s presence on these SWIO islands is probably the result of at least four independent introduction events from mainland Africa occurring between 1988 and 2009. Amongst the islands of the Comoros archipelago, two major migration pathways were inferred: One from Grande Comore to Mohéli and the second from Mayotte to Anjouan. While only two recombination events characteristic of SWIO islands isolates were identified, numerous re-assortments events were detected between EACMV and EACMKV, which seem to almost freely interchange their genome components.


Rapid and extensive virus spread within the SWIO islands was demonstrated for three CMG complex species. Strong evolutionary or ecological interaction between CMG species may explain both their propensity to exchange components and the absence of recombination with non-CMG begomoviruses. Our results suggest an important role of anthropic factors in CMGs spread as the principal axes of viral migration correspond with major routes of human movement and commercial trade. Finer-scale temporal analyses of CMGs to precisely scale the relative contributions of human and insect transmission to their movement dynamics will require further extensive sampling in the SWIO region.

Cassava; Begomoviruses; Dissemination; Africa; Phylogeography; Recombination