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The genome of SARS-CoV-2 is one of the largest among known RNA viruses, comprising of at least 26 known protein-coding loci. Studies thus far have outlined the coding capacity of the positive-sense strand of the SARS-CoV-2 genome, which can be used directly for protein translation. However, it has been recently shown that transcribed negative-sense viral RNA intermediates that arise during viral genome replication from positive-sense viruses can also code for proteins. No studies have yet explored the potential for negative-sense SARS-CoV-2 RNA intermediates to contain protein-coding loci. Thus, using sequence and structure-based bioinformatics methodologies, we have investigated the presence and validity of putative negative-sense ORFs (nsORFs) in the SARS-CoV-2 genome. Nine nsORFs were discovered to contain strong eukaryotic translation initiation signals and high codon adaptability scores, and several of the nsORFs were predicted to interact with RNA-binding proteins. Evolutionary conservation analyses indicated that some of the nsORFs are deeply conserved among related coronaviruses. Three-dimensional protein modeling revealed the presence of higher order folding among all putative SARS-CoV-2 nsORFs, and subsequent structural mimicry analyses suggest similarity of the nsORFs to DNA\/RNA-binding proteins and proteins involved in immune signaling pathways. Altogether, these results suggest the potential existence of still undescribed SARS-CoV-2 proteins, which may play an important role in the viral lifecycle and COVID-19 pathogenesis.<\/jats:p>","DOI":"10.1093\/bib\/bbac045","type":"journal-article","created":{"date-parts":[[2022,2,23]],"date-time":"2022-02-23T15:16:43Z","timestamp":1645629403000},"source":"Crossref","is-referenced-by-count":18,"title":["Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4415-2220","authenticated-orcid":false,"given":"Martin","family":"Bartas","sequence":"first","affiliation":[{"name":"Department of Biology and Ecology, University of Ostrava, Ostrava 710 00, Czech Republic"}]},{"given":"Adriana","family":"Voln\u00e1","sequence":"additional","affiliation":[{"name":"Department of Physics, University of Ostrava, Ostrava 710 00, Czech Republic"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0232-0281","authenticated-orcid":false,"given":"Christopher A","family":"Beaudoin","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, UK"}]},{"given":"Ebbe Toftgaard","family":"Poulsen","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark"}]},{"given":"Ji\u0159\u00ed","family":"\u010cerve\u0148","sequence":"additional","affiliation":[{"name":"Department of Biology and Ecology, University of Ostrava, Ostrava 710 00, Czech Republic"}]},{"given":"V\u00e1clav","family":"Br\u00e1zda","sequence":"additional","affiliation":[{"name":"Institute of Biophysics, Czech Academy of Sciences, Brno, 612 65, Czech Republic"}]},{"given":"Vladim\u00edr","family":"\u0160punda","sequence":"additional","affiliation":[{"name":"Department of Physics, University of Ostrava, Ostrava 710 00, Czech Republic"},{"name":"Global Change Research Institute, Czech Academy of Sciences, Brno, 603 00, Czech Republic"}]},{"given":"Tom L","family":"Blundell","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, UK"}]},{"given":"Petr","family":"Pe\u010dinka","sequence":"additional","affiliation":[{"name":"Department of Biology and Ecology, University of 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