Next generation sequencing elucidates cacao badnavirus diversity and reveals the existence of more than ten viral species

Muller Emmanuelle, Ravel Sébastien, Agret Clément, Abrokwah Francis, Dzahini-Obiatey Henry, Galyuon I., Kouakou K., Jeyaseelan E.C., Allainguillaume Joel, Wetten Andrew. 2018. Next generation sequencing elucidates cacao badnavirus diversity and reveals the existence of more than ten viral species. Virus Research, 244 : 235-251.

https://doi.org/10.1016/j.virusres.2017.11.019

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Quartile : Q3, Sujet : VIROLOGY

Résumé : Cacao swollen shoot virus is a member of the family Caulimoviridae, genus Badnavirus and is naturally transmitted to Theobroma cacao (L.) by several mealybug species. CSSV populations in West African countries are highly variable and genetically structured into several different groups based on the diversity in the first part of ORF3 which encodes the movement protein. To unravel the extent of isolate diversity and address the problems of low titer and mixed viral sequences in samples, we used Illumina MiSeq and HiSeq technology. We were able to reconstruct de novo 20 new complete genomes from cacao samples collected in the Cocoa Research Institute of Ghana (CRIG) Museum and from the field samples collected in Côte d'Ivoire or Ghana. Based on the 20% threshold of nucleotide divergence in the reverse transcriptase/ribonuclease H (RT/RNase H) region which denotes species demarcation, we conclude there exist seven new species associated with the cacao swollen shoot disease. These new species along with the three already described leads to ten, the total number of the complex of viral species associated with the disease. A sample from Sri Lanka exhibiting similar leaf symptomology to West African CSSD-affected plants was also included in the study and the corresponding sequence represents the genome of a new virus named cacao bacilliform SriLanka virus (CBSLV).

Mots-clés Agrovoc : Theobroma cacao, virus des végétaux, phylogénie, séquence nucléotidique, virologie

Mots-clés géographiques Agrovoc : Afrique occidentale, Sri Lanka, Ghana, Côte d'Ivoire

Mots-clés complémentaires : Cacao swollen shoot virus (CSSV), Badnavirus

Classification Agris : H20 - Maladies des plantes

Champ stratégique Cirad : Axe 4 (2014-2018) - Santé des animaux et des plantes

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