Nation-wide virome survey of banana plantations and surrounding plants in Malawi

A nationwide virome survey of banana plantations and their surrounding plants was carried-out using virion associated nucleic acids (VANA) high throughput sequencing (HTS) of plants. Two novel viruses were detected, their genomes characterized and compared with the NCBI ref. seqs. 9 first time detection and 13 endemic viruses were identified. In total, 24 plant viruses were detected among which two novel viruses, nine viruses identified for the first time in Malawi. New host species for three viruses were found among 24. No viral exchange between banana and surrounding plants was observed. The detection of novel viruses and of 9 species new to Malawi and their host plants was independently confirmed by RT-PCR. The results obtained with the VANA protocol applied on pools of samples were compared to previous results obtained with targeted PCR tests applied on individual samples. The diagnostic sensitivity of HTS was superior to the (RT)-PCR for detecting BanMMV and BSMYV. The diagnostic sensitivity of (RT)-PCR was higher than HTS for BBTV, BSOLV, BSGFV, BSIMV, BSVLac and BSCAV detection. Overall, our research confirms the assets of high throughput sequencing technologies for plant virus territory surveillance but underlines also weaknesses for achieving high sensitivity depending on the protocol and the virus to be detected.