First Report of Mal de Rio Cuarto Virus and a Picorna-Like Virus Naturally Infecting Rice (Oryza sativa) in Argentina

HomePlant DiseaseAhead of PrintFirst Report of Mal de Rio Cuarto Virus and a Picorna-Like Virus Naturally Infecting Rice (Oryza sativa) in Argentina PreviousNext DISEASE NOTE OPENOpen Access licenseFirst Report of Mal de Rio Cuarto Virus and a Picorna-Like Virus Naturally Infecting Rice (Oryza sativa) in ArgentinaV. E. Solís, C. E. Luciani, M. F. Brugo Carivali, M. C. Perotto, S. A. Gutierrez, and M. G. CelliV. E. SolísConsejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Cordoba, ArgentinaUniversidad Nacional del Nordeste – UNNE, Corrientes, ArgentinaSearch for more papers by this author, C. E. LucianiInst. de Patología Vegetal (IPAVE-CIAP, INTA), Córdoba, ArgentinaSearch for more papers by this author, M. F. Brugo CarivaliConsejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Cordoba, ArgentinaUnidad de Fitopatología y Modelización Agrícola (UFyMA, CONICET-INTA), Cordoba, ArgentinaSearch for more papers by this author, M. C. Perottohttps://orcid.org/0000-0002-3408-0067Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Cordoba, ArgentinaInst. de Patología Vegetal (IPAVE-CIAP, INTA), Córdoba, ArgentinaSearch for more papers by this author, S. A. GutierrezUniversidad Nacional del Nordeste – UNNE, Corrientes, ArgentinaSearch for more papers by this author, and M. G. Celli†Corresponding author: M. G. Celli; E-mail Address: [email protected]https://orcid.org/0000-0002-9256-6305Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Cordoba, ArgentinaUnidad de Fitopatología y Modelización Agrícola (UFyMA, CONICET-INTA), Cordoba, ArgentinaSearch for more papers by this authorAffiliationsAuthors and Affiliations V. E. Solís1 2 C. E. Luciani3 M. F. Brugo Carivali1 4 M. C. Perotto1 3 S. A. Gutierrez2 M. G. Celli1 4 † 1Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Cordoba, Argentina 2Universidad Nacional del Nordeste – UNNE, Corrientes, Argentina 3Inst. de Patología Vegetal (IPAVE-CIAP, INTA), Córdoba, Argentina 4Unidad de Fitopatología y Modelización Agrícola (UFyMA, CONICET-INTA), Cordoba, Argentina Published Online:14 Aug 2023https://doi.org/10.1094/PDIS-11-22-2581-PDNAboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat The first rice virus detected in Argentina was rice stripe necrosis virus (RSNV), a benyvirus known to cause “entorchamiento” due to its characteristic symptom of leaf crinkling. As part of this study, it was proposed to sequence plants naturally infected with RSNV that presented other symptoms such as thickening of veins, serrated edges, chlorosis that turns necrotic, and dwarfism to detect the presence of other viruses in mixed infections. We investigated 20 rice plants sampled in the San Javier area (Santa Fe, Argentina), and the samples were positive for RSNV by serology using anti-RSNV antiserum. Total RNA of 5-mg leaf tissue from each plant was extracted separately using a Qiagen RNeasy Plant RNA kit. Ten micrograms of the pooled sample was sent for library preparation using Ribo-Zero Plant Kit + TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 1500, 150-nucleotide (nt) flow cell at the IABIMO-CONICET/INTA (Argentina). The 177,005,442 reads generated were mapped to the Oryza sativa genome (RefSeq GCF_001433935) using Geneious software v.9.1.8 (Biomatters, Auckland, New Zealand) to remove rice reads. The remaining reads (63,756,284) were assembled de novo using rnaviralSPAdes, Galaxy tools (https://usegalaxy.org.au/). Contigs were annotated using the BEST HIT of BLASTN versus nt and BLASTX versus the nonredundant sequence database. Forty virus sequences were analyzed using the ORF finder and BLAST tools at NCBI (http://www.ncbi.nlm.nih.gov/). The nt identity was calculated using the SDT 1.2 program (Muhire et al. 2014). The BLASTN results showed the presence of 38 contigs (636 reads) with high nt identity (higher than 97.6%) with Mal de Rio Cuarto virus (MRCV), with 58% genome coverage. Two other contigs (120 reads) had high nt identity to Fuyang picorna-like virus 2 (FpiV2, GenBank accession MT317172), with 38% genome coverage. MRCV is a species of the genus Fijivirus, family Reoviridae, with a linear dsRNA genome composed of 10 segments encoding 12 proteins (Matthijnssens et al. 2022). In this work, it was possible to partially sequence the 10 segments of MRCV. Contigs with lengths greater than 1,000 nt were detected that correspond to segments S1 (2,029 nt), S2 (2,308 nt), S3 (1,249 nt), and S4 (1,067 nt) and showed 98.32, 98.48, 97.68, and 97.75% nt identity with the reference sequences (GenBank accession NC_008733, NC_008730, NC_008732, and NC_008729), respectively. A contig of 400 nt was identified as a capsid protein (CP) gene fragment (S10) with 98.75% nt identity to the reference sequence (NC_008734). The presence of MRCV was confirmed in 3 of the 20 samples by the DAS-ELISA serological test using anti-MRCV antiserum. FpiV2 was reported for the first time infecting rice in China and, due to its genomic structure, was proposed as a new member of the Picornaviridae family, but without an assigned genus (Chao et al. 2021). It is a monopartite virus, with a linear ssRNA(+) genome of 9.2 kb. Analysis of two sequence fragments (1,587 nt and 2,086 nt) revealed that they corresponded to the putative RdRp with 83.9% nt identity (90.2% aa) and the putative CP sequence with 86.7% nt identity (96.3% aa) with the GenBank sequence MT317172, respectively. Detection of this picorna-like virus was further confirmed in 2 of the 20 samples by RT-PCR and Sanger sequencing with virus-specific primers (PL2Fw: 5′-TTATTTGTGAGTAACAGCCCAGCAC-3′; PL2Rv: 5′-AGACCGAGGACTATGGAAGCCTTTC-3′, 540 nt). To our knowledge, this is the first report of rice as a natural host of MRCV and may be the second detection of FpiV2 worldwide.The author(s) declare no conflict of interest.References:Chao, S., et al. 2021. Viruses 13:2464. https://doi.org/10.3390/v13122464 Crossref, Google ScholarMatthijnssens, J., et al. 2022. J. Gen. Virol. 103:001782. https://doi.org/10.1099/jgv.0.001782 Google ScholarMuhire, B. M., et al. 2014. PLoS One 9:e108277. https://doi.org/10.1371/journal.pone.0108277 Crossref, ISI, Google ScholarFunding: This study was funded by the Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (Agencia i+d+i, PICT2020-1819), Argentina, the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), and the Instituto Nacional de Tecnología Agropecuaria (INTA).The author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Just PublishedSubscribeISSN:0191-2917e-ISSN:1943-7692 Metrics Article History Published: 14 Aug 2023First Look: 1 Mar 2023Accepted: 18 Feb 2023 Information© 2023 The American Phytopathological SocietyFundingAgencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la InnovaciónGrant/Award Number: PICT2020-1819Consejo Nacional de Investigaciones Científicas y TécnicasInstituto Nacional de Tecnología AgropecuariaKeywordsFijivirusMRCVPicornaviridaeReoviridaeThe author(s) declare no conflict of interest.PDF download