Map annotations from SARS-CoV

[gtauriello]

Since SARS-CoV (which caused the 2002–2004 SARS outbreak) is better studied than SARS-CoV-2 a lot of knowledge can be mapped from there.

This issue is to explore annotations for SARS-CoV which could be mapped to SARS-CoV-2. Preferably such a mapping should also include an estimation of the quality of the mapping and annotation to avoid false confidence (e.g. in the predicted sites, such as immunogenic positions, or mutations giving rise to drug resistance).

Related to this a good mapping of variability comparing SARS-CoV and SARS-CoV-2 could be a worthwhile effort (handled in #23).

[DCGenomics]

This is likely a good place to start!
https://pubmed.ncbi.nlm.nih.gov/28636671/

[DCGenomics]

e.g. We should check if SARS S-667 (req'd for TMPRSS cleavage) maps to CoVID-19 S-614 (amino acid space)

[DCGenomics]

Note that S-614 is variable in CoVID --

[gtauriello]

@all-contributors please add @DCGenomics for ideas, content

[allcontributors]

@gtauriello

I've put up a pull request to add @DCGenomics! 🎉

[gtauriello]

Also along those lines I noticed the nextprot annotations (see here). Indeed TMPRSS (see here for our structural model of it) has escaped our attention so far. Annotations on its interactions with SARS-CoV-2 would certainly be helpful since there are no structures for that interaction (as opposed to the spike-ACE2-complex).

[gtauriello]

The annotation system should also work to map annotations on ACE2 (UniProtKB AC 'Q9BYF1') and TMPRSS (UniProtKB AC 'O15393') btw.