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International Journal of Virology

Year: 2017 | Volume: 13 | Issue: 2 | Page No.: 80-89
Research Article

Genetic Diversity and Molecular Epidemiology of Rice Yellow Mottle Virus in Central African Republic

R.D.S. Longue
Laboratoire des Sciences Biologiques et Agronomiques Pour le Developpement (LASBAD), Universite de Bangui, BP 908 Bangui, Central African Republic
LiveDNA: 236.16624
A. Galzi-Pinel
Institut de Recherche Pour le Developpement, UMR IPME (IRD-Cirad-Universite Montpellier), 911 Avenue Agropolis 34394 Montpellier, France
I. Zinga
Laboratoire des Sciences Biologiques et Agronomiques Pour le Developpement (LASBAD), Universite de Bangui, BP 908 Bangui, Central African Republic
S. Semballa
Laboratoire des Sciences Biologiques et Agronomiques Pour le Developpement (LASBAD), Universite de Bangui, BP 908 Bangui, Central African Republic
D. Fargette
Institut de Recherche Pour le Developpement, UMR IPME (IRD-Cirad-Universite Montpellier), 911 Avenue Agropolis 34394 Montpellier, France
N. Barro
Universite de Ouagadougou, UFR/SVT, Departement de Biochimie-Microbiologie, BP 7021 Ouagadougou, Burkina Faso
O. Traore
Institut de l’Environnement et de Recherches Agricoles (INERA), 01 BP 476 Ouagadougou 01, Burkina Faso
Background: Rice yellow mottle virus (RYMV) of the genus Sobemovirus is the most important viral disease of rice in Africa, mainly occurring in the lowland and irrigated ecologies. Materials and Methods: The coat protein gene of forty six isolates of RYMV collected between 2011 and 2014 in Central African Republic was amplified and sequenced. Results: Analysis of sequences revealed that the average nucleotide diversity among isolates was low, 2.0% in nucleotide and 0.9% in amino acid. The ratio of non-synonymous over synonymous nucleotide substitutions per site was 0.07, indicating a virus diversification under a high conservative selective pressure. All isolates shared the amino acids specific of the serotype Ser1, a Val115 involved in the response with monoclonal A and a Thr115 which accounts for the lack of reaction with monoclonal D. Phylogenetic analyses showed that isolates of the south of Central African Republic belong to two sister monophyletic groups related to the S1ca strain, a strain which gathers all isolates from the East of West Africa to the West of Central Africa. Molecular clock dating of the age of each of the two groups and of their common ancestor suggests that RYMV was introduced a few decades ago in Central African Republic from the West of Central Africa. Conclusion: RYMV remained at a low level and undetected in wild hosts and in traditional rice fields until recently. RYMV emergence occurred less than ten years ago, likely favored by the on-going rice intensification and resulted in the current epidemics. This is the first study of the molecular diversity of RYMV in Central African Republic. It indicates that the isolates of the South of the country belonged to the S1 strain.
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