coviz

Interesting topics

DNA

Alignments between 2019CoV and other known coronaviruses, bat CoV

https://onlinelibrary.wiley.com/doi/full/10.1002/jmv.25762

Analysis of the mutations in human strains.

https://www.biorxiv.org/content/10.1101/2020.03.30.016790v1.full.pdf

Interesting but inconclusive paper on the different human strains, according to this the 5 major strains, that are occupy different geographic areas, are the consequence of the founder effect and not some other cause (better fitness in the environment).

Highlightning of each part of the sequence whose role is known

Nextrains aligns all known strains all the virus, highlighting mutations on their RNA sequence and showing connections on the world map. I think we can take this as a reference for content.

Functional Genomics:

(from wikipedia)

4 structural proteins:

S: Spike (attach human cells at ACE2 receptor?),
E: Envelope,
M: Membrane,
N: Nucleocapside (folds RNA?),

Genetic information of coronavirus is highly complex, unsurprisingly, since all the informatiin is packed into ~30kb (b stands for bases, not bytes, but the concept is ridicolusly similart). Evolution and function of the RNA sequence is reviewed here: https://www.cell.com/trends/microbiology/fulltext/S0966-842X(16)30133-0

this review does not include the actual virus, which is very similar to the SARS-Cov

Notes:

2 big overlapping open reading frames (1a and 1b) --> 16 non structural proteins,
rest at 3' --> structural proteins (S, E, M, N) + accessory proteins (???)

add more notes here

Interactome

Map of interactome between human and 2019CoV, with highlight of the interactions whose role is known/important

CoV2019 DNA has 29 proteins written over 14 ORFs. Out of those 29, only 26 were analyzed against the proteome of a human cell to find any interaction between human proteins and viral ones, and 332 interactions have been found.

The human tissue that most expresses these proteins is, as expected, the lung. Comparing this interactome with other known from other viruses, the most similar ones are the tuberculosis and West Nile virus, both causing pulmonary conditions.

Out of the initial 332 interactions, 62 (66 with more relaxed thresholds) were selected because they already have drugs or preclinical molecules targetting and modulating them.