Molecular epidemiology, genetic diversity and phylogeography of cassava mosaic geminiviruses responsibles of cassava mosaic disease in Madagascar

Abstract

Cassava is a staple food for hundreds of millions of African people. Cassava mosaic disease (CMD) caused by cassava mosaic geminiviruses (CMGs) is one of the major constraints of its culture in Africa and Madagascar. This study aimed (1) to determine the genetic diversity of CMGs, (2) to identify the main epidemiological factors associated with CMD and (3) to determine the origin and the dispersal pattern of CMGs in Madagascar. Sampling surveys allowed to collect hundreds of cassava leaf samples and to identify the main epidemiological factors associated with CMD. Six CMG species were diagnosed with African cassava mosaic virus (ACMV), East African cassava mosaic Cameroon virus (EACMCV), East African cassava mosaic Kenya virus (EACMKV), East African cassava mosaic virus (EACMV), South African cassava mosaic virus (SACMV) and the new species named Cassava mosaic Madagascar virus (CMMGV). The CMD prevalence and abundance of the insect vector Bemisia tabaci were correlated with altitude. Thus, the lowlands (0-200m) were the most affected regions with the higher prevalence of CMD and abundance of B. tabaci. CMD infection was primarily due to the use of infected cuttings (> 89%) for plantings. ln addition, 21% of the samples tested were mixed infected by two to four CMG species and showed more severe symptoms. EACMCV was frequently detected in mixed infection while ACMV and SACMV were rather found in single infection. Distinct geographical distributions were observed for the six species. ACMV was more prevalent in highlands (> 800m) while EACMV-like were more prevalent in coastal lowlands. Phylogenetic and recombination analysis of the genome sequences of CMMGV allowed to determine the recombinant features of this species. With the exception of two recombinant regions that resembled a CMG, the non-recombinant part of the DNA-A component is most closely related to monopartite begomovirus infecting tomato in the south west lndian Ocean islands.