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

A nation-wide virome survey of banana plantations and their surrounding plants was carried-out using Virion Associated Nucleic Acids (VANA) high throughput sequencing of plants pooled in batches with proper internal and external alien controls. In total, 24 plant viruses were detected among which two novel viruses, whose genomes have been characterized and compared, 9 viruses identified for the first time in Malawi and new host species for three viruses. No viral exchange between banana and surrounding plants was observed. The detection of novel viruses and 9 species new to Malawi was independently confirmed and their host plants were confirmed by RT-PCR. The results obtained by the VANA protocol applied on pools of samples were compared to previous results obtained with targeted PCR tests applied on individual samples. The HTS was superior compared to the (RT)-PCR by detecting BanMMV and BSMYV in many pools. The (RT)-PCR outclassed HTS by detection BBTV, BSOLV, BSGFV, BSIMV, BSVLac and BSCAV. 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.