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Is there anything known about the RNA structures of coronaviruses? More specifically - do they have any interesting known structures in the translatable region, like RRE of HIV or the double loops in flaviviruses?

Update
Here is a recent development on the side of structure prediction.

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  • $\begingroup$ Excellent @vadim, thank you this is very informative. You can of course edit your question and then place your answer below, because you have essentially answered your own question. Also thank you for your question. When I've a minute I'll answer your 'RNA structure and vaccines' in more detail $\endgroup$ – M__ Mar 9 '20 at 18:43
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    $\begingroup$ Thank you for this suggestion. I am thinking to do a bit more reading, perhaps I will have a more complete answer. $\endgroup$ – Vadim Mar 9 '20 at 21:08
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To add a more complete answer: the current coronavirus is closely related to the SARS virus that caused the outbreak in 2004, and on which much research has been done.

Here is a general review of the coronavirus epidemiology, life cycle etc.

I haven't found yet any materials about the RNA structures in the translatable region, however the structures in the 3' and 5' terminal regions are well studied and are known to be crucial for initiating viral replication and for its packaging.

This recent article addresses in details the RNA structures in 5' terminal of human coronaviruses, whereas this older article describes the structures both in 3' and 5' terminals.

Finally, the interesting algorithmic developments for the link that I added to the question are described here.

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  • $\begingroup$ huge thanks. This is a very interesting question and your answer is particulalrly good. The only point I'd like to add is compensatory mutations which are well known in viral RNA secondary structure. $\endgroup$ – M__ Mar 10 '20 at 22:05

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