Next generation sequencing approach to elucidate CSSV species profiles

Muller Emmanuelle, Wetten Andrew, Allainguillaume Joel, Abrokwah Francis Kwame, Kouakou Koffie, Dzahini-Obiatey Henry. 2018. Next generation sequencing approach to elucidate CSSV species profiles. . COST-DIVAS. Liège : COST-DIVA, Résumé, 1 p. Final Meeting of COST-DIVAS Action: HTS Technologies for the study and diagnostic of plant viruses, Liège, Belgique, 26 November 2018/30 November 2018.

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Abstract : Cacao swollen shoot virus (CSSV) is a member of the family Caulimoviridae, genus Badnavirus and is naturally transmitted to Theobroma cacao by several mealybug species. The virus is restricted to West Africa, while the cacao tree originates from the Americas, and has therefore most probably an indigenous origin on the West African subcontinent. The resultant disease has caused enormous economic damage in Ghana since the 1930's but was restricted to small areas in Togo and Côte d'Ivoire until recently. Now, renewed outbreaks in the main producing areas in Côte d'Ivoire, Ghana and Togo, cause serious yield losses and tree death. CSSV populations in West African countries are genetically structured into several different groups according to the diversity in the first part of ORF3 corresponding to the movement protein. To unravel the extent of isolate diversity we used Illumina HiSeq technology and reconstructed 21 new complete genomes corresponding to the different groups of CSSV sequences. In this way we were able to compare the partial sequences of the RTase region (recognised as the taxonomical region by ICTV using a 20% threshold of nucleotide divergence to denote separate species), and thereby identifying nine different CSSV species. These results will now be used to improve the detection of all badnaviruses present in cacao leaf samples, a vital tool in efforts to halt the spread of the disease and confirm the healthy status of new plantations.

Mots-clés libres : Cacao, CSSV, HTS sequencing

Auteurs et affiliations

  • Muller Emmanuelle, CIRAD-BIOS-UMR BGPI (FRA)
  • Wetten Andrew, University of Reading (GBR)
  • Allainguillaume Joel, University of the West of England (GBR)
  • Abrokwah Francis Kwame, University of Cape Coast (GHA)
  • Kouakou Koffie, World Cocoa Foundation (CIV)
  • Dzahini-Obiatey Henry, CRIG (GHA)

Source : Cirad-Agritrop (

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