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. 2020 Sep 24;10:15643. doi: 10.1038/s41598-020-72533-2

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© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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(A) The predicted minimum free energy (MFE) secondary structure of the novel coronavirus RNA in the 75 nts following the frameshift. All MFE structures displayed are those predicted by LandscapeFold; results discussed were found to be insensitive to prediction algorithm by comparison to NuPack. (B,C) Known coronaviruses with high degree of sequence and structure similarity to the novel coronavirus. (D–H) Known coronaviruses with a high degree of structure similarity to the novel coronavirus, but less sequence similarity. See main text for further discussion. (I) In addition to examining the predicted MFE structures, we considered the full free-energy landscapes. The probability of each coronavirus to form a pseudoknot in the 75 nts following the frameshift (orange), and the probability of the first stem to be part of a 3-stem pseudoknot (blue), are histogrammed.