{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T09:18:05Z","timestamp":1780996685723,"version":"3.54.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010922","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,3,10]],"date-time":"2023-03-10T00:00:00Z","timestamp":1678406400000}}],"reference-count":74,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2023,2,28]],"date-time":"2023-02-28T00:00:00Z","timestamp":1677542400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008997","name":"University of Victoria","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008997","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006112","name":"Microsoft Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006112","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Multiple coronaviruses including MERS-CoV causing Middle East Respiratory Syndrome, SARS-CoV causing SARS, and SARS-CoV-2 causing COVID-19, use a mechanism known as \u22121 programmed ribosomal frameshifting (\u22121 PRF) to replicate. SARS-CoV-2 possesses a unique RNA pseudoknotted structure that stimulates \u22121 PRF. Targeting \u22121 PRF in SARS-CoV-2 to impair viral replication can improve patients\u2019 prognoses. Crucial to developing these therapies is understanding the structure of the SARS-CoV-2 \u22121 PRF pseudoknot. Our goal is to expand knowledge of \u22121 PRF structural conformations. Following a structural alignment approach, we identify similarities in \u22121 PRF pseudoknots of SARS-CoV-2, SARS-CoV, and MERS-CoV. We provide in-depth analysis of the SARS-CoV-2 and MERS-CoV \u22121 PRF pseudoknots, including reference and noteworthy mutated sequences. To better understand the impact of mutations, we provide insight on \u22121 PRF pseudoknot sequence mutations and their effect on resulting structures. We introduce <jats:italic>Shapify<\/jats:italic>, a novel algorithm that given an RNA sequence incorporates structural reactivity (SHAPE) data and partial structure information to output an RNA secondary structure prediction within a biologically sound hierarchical folding approach. Shapify enhances our understanding of SARS-CoV-2 \u22121 PRF pseudoknot conformations by providing energetically favourable predictions that are relevant to structure-function and may correlate with \u22121 PRF efficiency. Applied to the SARS-CoV-2 \u22121 PRF pseudoknot, Shapify unveils previously unknown paths from initial stems to pseudoknotted structures. By contextualizing our work with available experimental data, our structure predictions motivate future RNA structure-function research and can aid 3-D modeling of pseudoknots.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1010922","type":"journal-article","created":{"date-parts":[[2023,2,28]],"date-time":"2023-02-28T19:50:29Z","timestamp":1677613829000},"page":"e1010922","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":10,"title":["Shapify: Paths to SARS-CoV-2 frameshifting 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