Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot

Abstract

The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at local scale remain scarce, in spite of potential implications for crop protection. Here we describe a five-years (2015-2019) monitoring of RYMV prevalence in six sites from western Burkina Faso (geographic areas of Bama, Banzon and Karfiguela). It confirmed one irrigated site as a disease hotspot, and also found one rainfed lowland site with occasional high prevalence levels. Within the studied fields, a pattern of disease aggregation was evidenced at a five-meter distance, as expected for a mechanically transmitted virus. Next, we monitored RYMV genetic diversity in the irrigated disease hotspot site, revealing a high viral diversity, with the current coexistence of various distinct genetic groups at the site-scale (ca. 520 ha), and also within various specific fields (25 meters side). One genetic lineage, named S1bzn, is the most recently emerged group and increased in frequency over the studied period (from 20% or less in 2015-2016, to more than 65% in 2019). Its genome results from a recombination between two other lineages (S1wa and S1ca). Finally, experimental work revealed that three rice varieties commonly cultivated in Burkina Faso were not different in terms of resistance level, and we also found no significant effect of RYMV genetic groups on symptom expression and viral load. We found however, that infection outcome depended on the specific RYMV isolate, with two isolates from the lineage S1bzn accumulating at highest level at early infections. Overall, this study documents a case of high viral prevalence, high viral diversity, and co-occurrence of divergent genetic lineages at small geographic scale. A recently emerged lineage, which comprises viral isolates inducing severe symptoms and high accumulation in controlled conditions, could be recently rising through natural selection. Following up the monitoring of RYMV diversity is required to confirm this trend and further understand the factors driving the local maintenance of viral diversity.

Deciphering mixed infections by plant RNA virus and reconstructing complete genomes simultaneously present within-host

“…These different approaches were carried out using RNA extracted with the GeneJET Plant RNA Purification Mini Kit (Thermo Scientific, K0802) from rice leaves inoculated by RYMV isolate BF710 collected in the irrigated perimeter of Banzon (Burkina Faso) in 2016 (S1 Table [32]). Each of the three methodologies (VN Primer, RYMV specific primers and direct cDNA) were performed twice, using RNA extracted from plant inoculated with the BF710 isolate.…”

“…Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) from rice leaves infected by different RYMV genotypes. To prepare artificial mixes, we chose a set of three RYMV genotypes from Burkina Faso (S1 Table): BF710, BF711 (Banzon, collected in 2016), [32] and BF706 (Karankasso Sambla, collected in 2014) [36]. Full-length genomes of these three isolates were obtained by Sanger sequencing.…”

“…Four rice leaves samples, symptomatic for RYMV, were collected in Banzon irrigated perimeter (south western Burkina Faso) and were chosen for application of the proposed methodology because the amplification of the RYMV ORF4 (coat protein gene) Sanger sequencing presented mixed chromatogram. First, the two samples MP1458 and MP2967, collected in 2017-2018 in Banzon (see doi.org/10.23708/8FDWIE [31] and S1 Table), and already studied in terms of OFR4 sequencing in [32] were chosen. These samples were kept dried right after sampling, and then maintained at ambient temperature [32].…”

“…4450nt, lacking 3’ polyA tail and organized in five overlapping open reading frames [30]. A recent study evidences a hotspot of rice yellow mottle disease in Burkina Faso [31, 32]. In this irrigated site, a particularly high RYMV genetic diversity was found, with at least four distinct genetic groups co-existing over years [32].…”

“…A recent study evidences a hotspot of rice yellow mottle disease in Burkina Faso [31, 32]. In this irrigated site, a particularly high RYMV genetic diversity was found, with at least four distinct genetic groups co-existing over years [32]. A fraction of samples (6/138, 4.3% of the dataset) analyzed in this study presented mixed Sanger chromatogram (ORF4 gene coding coat protein), suggesting multiple independent infections, resulting in the simultaneous presence of various RYMV genomes within plant.…”