First report of maize streak Reunion virus infecting rice in Burkina Faso

Among the 19 viruses reported to infect rice, only rice stripe necrosis virus (RSNV; Benyvirus, Benyviridae) and rice yellow mottle virus (RYMV; Sobemovirus, Solemoviridae) have been characterised in Africa (Wang et al., 2022). To expand our knowledge of viruses infecting rice in Africa, we used a virion-associated nucleic acids (VANA) Illumina HiSeq approach (Moubset et al., 2022; Fouad et al., 2024) on 85 pools of 16 rice plants each, collected at random (without regard to disease symptoms) in 2016 and 2017 from 57 rice fields across six sites in Burkina Faso (Barro et al., 2021). From the 288,971,924 raw sequences produced by Illumina sequencing, we first identified maize streak virus (MSV, Mastrevirus, Geminiviridae) (Fouad et al., 2024). We also obtained 63 contigs sharing a mean of 96.7% nucleotide identity with maize streak Reunion virus (MSRV, Mastrevirus, Geminiviridae). All of these contigs were identified in a pooled sample collected in 2017 from a field at the Karfiguela site in Burkina Faso (field/sample hereafter referred to as 17KA02). After total DNA extraction using the CTAB protocol and a rolling circle amplification (RCA) step (Fouad et al., 2024), a PCR to detect MSRV (MSRV-F613bp: 5′-TTGGCAAGACCCGTCTGTAC-3′ / MSRV-R613bp: 5′-GGAGCCTCTACATCGTTGGG-3′) was performed on 172 pooled rice samples (2016-2019) and 17 pooled or individual wild Poaceae collected within or nearby the previously sampled rice fields (https://doi.org/10.23708/1IPJAU). Although no rice field other than 17KA02 was positive for MSRV, we detected the virus at two other sites located in a 100 × 100 km region, one in a pooled wild Poaceae sample (17SZ07w) and the other a symptomatic plant of Rottboellia exaltata (17BM02w). Both plants were collected in 2017, at the Senzon and Bama sites, respectively. Full MSRV genomes were obtained by Sanger sequencing (Azenta, USA) of two PCR overlapping fragments done with specific primers (MSRV2F: 5′-ATACTGCTTAGGGCGAAGAGACAGC-3′/MSRVqPCR1R: 5′-TCCAGAGGTACTTTCATTCCCAGAG-3′; MSRVqPCR1F: 5′-CTTGCTGGTTGTGGTTTCGATAATG-3′/MSRV4R: 5′-AACTCCCTGCCATCGGTCTCGTA-3′) using RCA products as template. Complete genome sequences were assembled and deposited in GenBank (Accession Nos. PQ424982-PQ424984). A phylogenetic tree showed that all three MSRV isolates obtained in this study were genetically related to two isolates from wild species reported from Nigeria (Figure 1). Based on the rice MSRV isolate, an infectious MSRV clone (pCAMBIA0380::MSRV) was synthesized (Azenta, USA) and agroinoculated into 200 plants of Oryza sativa spp. indica cv. IR64 and of O. glaberrima cv. Tog5673 as described by Fouad et al. (2024). Light to moderate streaks (Figure 2) appeared 28 days after inoculation (dpi) on a few leaves of four IR64 plants and three Tog5673 plants. However, these symptoms never developed into clear and distinct streaks on whole plants, and no reduction in the plant growth was observed at 60 dpi. MSRV presence was confirmed in the symptomatic leaves by PCR and Sanger sequencing. Although MSRV has so far only been described on maize and wild grasses (Kraberger et al., 2017), our study shows that rice is an alternative host for this virus. However, our results suggest that MSRV infection of rice is less frequent than MSV infection (Fouad et al., 2024). Nevertheless, MSRV has been described in African and Asian rice-producing countries and our results are important to consider when undertaking disease surveillance of rice fields worldwide. Funding: French National Research Agency ANR-10-LABX-001-01, ANR-20-CE35-0008-01, CGIAR Research Program on Rice.