Improving the diagnosis of cassava mosaic begomoviruses using Oxford Nanopore Technology sequencing.

ABSTRACT: Cassava mosaic disease (CMD), caused by begomoviruses such as African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV), poses a threat to food security in sub-Saharan Africa. Conventional PCR assays often fail to detect viral strains in symptomatic plants due to high genetic variability and recombination. In this study, we used Oxford Nanopore Technology (ONT) sequencing on 12 cassava leaf samples that had previously tested negative by PCR. We compared two strategies: direct sequencing of total plant DNA and sequencing after rolling circle amplification (RCA-MinION). Across the samples, we obtained 7,800-36,000 reads, of which 1,327-11,749 were viral reads after host filtering. While direct sequencing of total DNA detected CMD-associated reads without yielding full

SUBMITTER: Combala M 

PROVIDER: S-EPMC12638911 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature