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Based on bioinformatic analyses and a mutagenesis strategy monitored with electrophoretic experiments and viral replication assays, we report that, in addition to the local pseudoknot in the 3\u2032UTR, 3SL2 can establish a distal tertiary contact with an exposed sequence in the ORF7b gene located 1847 nucleotides upstream in the SARS-CoV-2 genome. The bases involved in this contact are highly conserved in all SARS-like coronaviruses and sequencing data indicate that this motif may form an alternative polymerase binding site enabling the synthesis of non-canonical subgenomic RNA. These findings provide a foundation for investigating the molecular mechanisms governing the processes of replication, discontinuous transcription, and recombination in these viruses.<\/jats:p>","DOI":"10.1093\/nar\/gkag701","type":"journal-article","created":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T07:13:08Z","timestamp":1784099588000},"source":"Crossref","is-referenced-by-count":0,"title":["A potential RNA\u2013RNA distal interaction competing with a functional pseudoknot in the 3\u2032-untranslated region of SARS-like coronaviruses"],"prefix":"10.1093","volume":"54","author":[{"given":"Sergio","family":"L\u00f3pez-N\u00fa\u00f1ez","sequence":"first","affiliation":[{"name":"Centro de Investigaci\u00f3n Traslacional San Alberto Magno, Universidad Cat\u00f3lica de Valencia , 46001 Valencia ,","place":["Spain"]},{"name":"Escuela de Doctorado, Universidad Cat\u00f3lica de Valencia , 46001 Valencia 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