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

Yves Kwibuka,Chantal Faure,Claude Bragard,François Maclot,Arnaud G Blouin,Jean-Michel Lett,Santatra Ravelomanantsoa,Hervé Vanderschuren,Sébastien Massart,Armelle Marais,Denis Filloux,Sara Shakir,Thierry Candresse,Espoir Bisimwa

doi:10.3390/v13061030

Abstract

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.

Highlights

40% of the world’s area dedicated to the cultivation of roots and tubers is planted with cassava
We identify for the first time and characterize the genome organization of novel ampeloviruses infecting cassava plants originating from diverse geographical locations in central Africa and the southwestern Indian Ocean islands
Cuttings were collected on cassava landraces plants showing foliar cassava brown streak disease (CBSD)-like symptoms

Summary

Introduction

40% of the world’s area dedicated to the cultivation of roots and tubers is planted with cassava. In Africa, 56% of the total production of roots and tubers comes from cassava, 51% of which are from Nigeria and the Democratic Republic of Congo Cassava is one of the most important staple crops, as it ranks fourth as a source of calories for human consumption [1]. Many of the poorest farmers and most undernourished households in Africa depend on cassava as a principal nutrition source. It constitutes an important income source in rural and marginal areas and has multiple uses, most notably as a food security and regular food crop [2]. The exceptional soil carbon sequestration properties of cassava makes it a potential crop for improving the green revolution fatigue [4]

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Results

Conclusion