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Article

Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands

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Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium
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Faculté des Sciences Agronomiques, Université Catholique de Bukavu, BP 285 Bukavu, Democratic Republic of the Congo
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Earth and Life Institute, Applied Microbiology-Phytopathology, UCLouvain, 1348 Louvain-la-Neuve, Belgium
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Université Bordeaux, INRAE, UMR BFP, CS20032, CEDEX, 33882 Villenave d’Ornon, France
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CIRAD, UMR PHIM, 34090 Montpellier, France
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PHIM Plant Health Institute, Université Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34000 Montpellier, France
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CIRAD, UMR PVBMT, Pôle de Protection des Plantes, Saint-Pierre, F-97410 Ile de la Reunion, France
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FOFIFA-CENRADERU, Laboratoire de Pathologie Végétale, BP 1444 Ambatobe, Madagascar
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Plant Genetics Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium
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Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, Biosystems Department, KU Leuven, 3000 Leuven, Belgium
*
Authors to whom correspondence should be addressed.
Academic Editors: Jan Frederik Kreuze and Adrian Fox
Viruses 2021, 13(6), 1030; https://doi.org/10.3390/v13061030
Received: 28 April 2021 / Revised: 24 May 2021 / Accepted: 25 May 2021 / Published: 29 May 2021
(This article belongs to the Special Issue Plant Virus Surveillance and Metagenomics)
Cassava is one of the most important staple crops in Africa and its production is seriously damaged by viral diseases. In this study, we identify for the first time and characterize the genome organization of novel ampeloviruses infecting cassava plants in diverse geographical locations using three high-throughput sequencing protocols [Virion-Associated Nucleotide Acid (VANA), dsRNA and total RNA], and we provide a first analysis of the diversity of these agents and of the evolutionary forces acting on them. Thirteen new Closteroviridae isolates were characterized in field-grown cassava plants from the Democratic Republic of Congo (DR Congo), Madagascar, Mayotte, and Reunion islands. The analysis of the sequences of the corresponding contigs (ranging between 10,417 and 13,752 nucleotides in length) revealed seven open reading frames. The replication-associated polyproteins have three expected functional domains: methyltransferase, helicase, and RNA-dependent RNA polymerase (RdRp). Additional open reading frames code for a small transmembrane protein, a heat-shock protein 70 homolog (HSP70h), a heat shock protein 90 homolog (HSP90h), and a major and a minor coat protein (CP and CPd respectively). Defective genomic variants were also identified in some cassava accessions originating from Madagascar and Reunion. The isolates were found to belong to two species tentatively named Manihot esculenta-associated virus 1 and 2 (MEaV-1 and MEaV-2). Phylogenetic analyses showed that MEaV-1 and MEaV-2 belong to the genus Ampelovirus, in particular to its subgroup II. MEaV-1 was found in all of the countries of study, while MEaV-2 was only detected in Madagascar and Mayotte. Recombination analysis provided evidence of intraspecies recombination occurring between the isolates from Madagascar and Mayotte. No clear association with visual symptoms in the cassava host could be identified. View Full-Text
Keywords: Manihot esculenta; Ampelovirus; high-throughput sequencing; Central Africa; Indian Ocean islands; Closteroviridae Manihot esculenta; Ampelovirus; high-throughput sequencing; Central Africa; Indian Ocean islands; Closteroviridae
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MDPI and ACS Style

Kwibuka, Y.; Bisimwa, E.; Blouin, A.G.; Bragard, C.; Candresse, T.; Faure, C.; Filloux, D.; Lett, J.-M.; Maclot, F.; Marais, A.; Ravelomanantsoa, S.; Shakir, S.; Vanderschuren, H.; Massart, S. Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands. Viruses 2021, 13, 1030. https://doi.org/10.3390/v13061030

AMA Style

Kwibuka Y, Bisimwa E, Blouin AG, Bragard C, Candresse T, Faure C, Filloux D, Lett J-M, Maclot F, Marais A, Ravelomanantsoa S, Shakir S, Vanderschuren H, Massart S. Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands. Viruses. 2021; 13(6):1030. https://doi.org/10.3390/v13061030

Chicago/Turabian Style

Kwibuka, Yves, Espoir Bisimwa, Arnaud G. Blouin, Claude Bragard, Thierry Candresse, Chantal Faure, Denis Filloux, Jean-Michel Lett, François Maclot, Armelle Marais, Santatra Ravelomanantsoa, Sara Shakir, Hervé Vanderschuren, and Sébastien Massart. 2021. "Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands" Viruses 13, no. 6: 1030. https://doi.org/10.3390/v13061030

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