{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T14:20:19Z","timestamp":1787581219823,"version":"build-2736575974"},"reference-count":35,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T00:00:00Z","timestamp":1787529600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Major Project of Guangzhou National Laboratory","award":["GZNL2024A01003"],"award-info":[{"award-number":["GZNL2024A01003"]}]},{"award":["GZNL2024A01003"],"award-info":[{"award-number":["GZNL2024A01003"]}],"id":[{"id":"https:\/\/ror.org\/03ybmxt82","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>RNA large language models (RNA LLMs) show potential for predicting viral RNA\u2013RNA interactions (RRIs), but their ability to transfer between viruses remains unclear. Here, we evaluated three nucleotide language models using vRIC-seq-derived RRI datasets from two members of the Coronaviridae family, SARS-CoV-2 and porcine deltacoronavirus (PDCoV). We compared within-virus five-fold cross-validation with bidirectional cross-virus testing. DNABERT achieved within-virus AUC values of 0.9595 for PDCoV and 0.9741 for SARS-CoV-2. Under cross-virus transfer, its AUC decreased to 0.8372 when trained on PDCoV and tested on SARS-CoV-2 and to 0.8116 in the reverse direction, with corresponding F1 scores of 0.7847 and 0.7617. RNAErnie retained similar but slightly lower cross-virus discrimination, whereas the Nucleotide Transformer approached random discrimination. These results provide a two-virus proof of concept that sequence-based models can retain partially shared discriminative signals across coronavirus genera. They do not establish functional, tropism-related, or receptor-dependent transferability, and broader evaluation across additional viruses and orthogonal structural validation will be required before application to emerging-virus screening.<\/jats:p>","DOI":"10.3390\/ijms27177565","type":"journal-article","created":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T13:20:43Z","timestamp":1787577643000},"page":"7565","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Cross-Virus RNA Language Models for Within-Family RNA\u2013RNA Interaction Prediction in SARS-CoV-2 and Porcine Deltacoronavirus"],"prefix":"10.3390","volume":"27","author":[{"given":"Xu","family":"Yang","sequence":"first","affiliation":[{"name":"Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiwei","family":"Shen","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China"},{"name":"School of Life Sciences, Shanghai University, Shanghai 200444, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yixue","family":"Li","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China"},{"name":"Guangzhou National Laboratory, Guangzhou 510000, China"},{"name":"The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Laboratory, GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou 510000, China"},{"name":"Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8334-0216","authenticated-orcid":false,"given":"Liucun","family":"Zhu","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Shanghai University, Shanghai 200444, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1975-9693","authenticated-orcid":false,"given":"Tao","family":"Huang","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1038\/s41597-024-03975-w","article-title":"RNA Architecture of Porcine Deltacoronavirus Genome inside Virions Detected by vRIC-Seq","volume":"11","author":"Sun","year":"2024","journal-title":"Sci. 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