Occurrence and molecular characterization of begomoviruses associated with cassava across agro-ecological zones in Cross River State, Nigeria

Abstract: Cassava (Manihot esculenta Crantz) is a major root crop in sub-Saharan Africa, including Cross River State, Nigeria, where the crop is cultivated as a staple food in many communities. Cassava mosaic begomoviruses (CMBs) have limited cassava production across Africa. Thus, between March and August 2021, forty-five samples of symptomatic cassava leaves across the state were collected and evaluated for CMBs using molecular techniques. Partial sequencing of the African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV) coat protein genes produced sequence lengths of 620 bp for representative isolates from Okpoma (MZ507578), Ababene (MZ507579) and Idundu (MZ507580), and 554 bp for an Ovonum isolate, respectively. BLASTn results for MZ507578 and MZ507580 showed a percentage similarity of 99.35 and 99.03%, respectively with the nucleotide sequence of ACMV (MH251339) from Nigeria for MZ507579, percentage similarity was 99.84% with ACMV (MG250088) from Ghana. Conversely, the Ovonum isolate showed a 100% percentage similarity with EACMV (MW826364) from Nigeria. Phylogenetic analysis clustered the Calabar isolates (MZ507578, MZ507579 and MZ507580) with MH251339 from Nigeria, MG250088 from Ghana and EU155147 from Togo while the Ovonum isolate was grouped with MW826364 and MT571462, both from Nigeria. The two main CMBs in Nigeria, ACMV and EACMV, were identified and characterized from Cross River state in this study, indicating that disease monitoring should be continuous and more virus-resistant cultivars should be introduced for proper virus management.