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Genetic diversity and development of improved diagnostics for Banana bunchy top virus (Nanoviridae: Babuvirus) in West and Central Africa

Adedapo Adediji: International Institute of Tropical Agriculture

<div>Bananas (<em>Musa</em> spp.) are important staple foods worldwide, especially in sub-Saharan Africa (SSA). However, its cultivation is threatened by the banana bunchy top disease (BBTD) caused by <em>Banana bunchy top virus</em> (BBTV) which results in total yield loss. There is limited information on the genetic properties of BBTV in SSA countries where BBTD has recently been reported. Hence, this study was aimed at determining the genetic diversity of BBTV in West and Central Africa and to develop improved diagnostic tools. Banana leaves with BBTD symptoms were obtained from Nigeria, Benin Republic, Cameroon, Zambia and Gabon. Full genome of the six BBTV components were amplified and compared with other worldwide sequences. New polymerase chain reaction (PCR), loop mediated isothermal amplification (LAMP) and sap-based assays were developed to target the nuclear shuttle gene (DNA-N) and compared to existing rep-based protocols. All six BBTV components were successfully amplified in symptomatic banana leaves and showed close nucleotide (98-100% identity) and amino acid (97-100% identity) similarities among the isolates. Phylogenetic analyses clustered all isolates within the Pacific-Indian ocean sub-group. No evidence of recombination was found among the populations. Comparisons of newly developed primers with existing Rep-based primers showed DNA-N-based diagnostics to be ten times more sensitive in PCR (10 pg/µl) and LAMP (100 fg/µl) assays. Also, direct-binding PCR using sap-based extracts was ten times more sensitive (1 ng/µl) than ELISA test. Direct-binding LAMP was as sensitive as conventional PCR (100 pg/µl), thus eliminating the need for nucleic acid extraction. These results confirm BBTV entry into SSA via a common source as evidenced by a low genetic diversity. Improved detection will provide better options for BBTV management.</div>