Cassava mosaic disease (CMD) caused by the whitefly-transmitted Begomoviruses (family Geminiviridae) is a major threat to production of cassava (Manihot esculenta Crantz) in Togo. Survey was conducted in 2020 in the 5 agroecological zones of Togo to assess the status of East African cassava mosaic virus (EACMV), East African cassava mosaic Cameroon virus (EACMCMV) and its distribution. Polymerase chain reaction (PCR) and Sanger sequencing were used for the detection of cassava mosaic Begomoviruses (CMBs) in the sampled leaves. The incidence of EACMV was 47.93% (278/580) and varied between 41.30% (Zone V) and 62.29% (Zone IV) across the agroecological zone but no significant difference was observed. The EACMCMV incidence was 13.67% (38/278) and varied significantly (p ≤ 0.001) through the agroecological zone. Phylogenetic analysis of the viral isolates showed that they are closely related to those from Nigeria, Ghana, and Ivory coast. Nucleotide sequence analysis of CP revealed an overall genetic diversity (π) of around 3.4%. These results showed that EACMV was the predominant virus and that EACMCMV incidence could be more widespread in Togo.
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