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2019 Coronavirus Epidemic - Coggle Diagram
2019 Coronavirus Epidemic
Citation
Benvenuto D, Giovanetti M, Ciccozzi A, Spoto S, Angeletti S, Ciccozzi M. 2020. The 2019‐new coronavirus epidemic: Evidence for virus evolution. Journal of Medical Virology. 92(4):455–459. doi:10.1002/jmv.25688
Introduction
2019-nCoV originated from Wuhan, China causing severe respiratory infections.
Currently, there are 1,975 pneumonia cases confirmed in this region (China).
Animal to human transmission is thought to be the start of the epidemic.
“Molecular epidemiology, evolutionary models, and phylogenetic analysis estimates genetic variability and evolutionary rate” which can be useful in disease, drug, and vaccine findings (Benvenuto et. al 2020).
Material and Methods
A dataset was built with...
-5 sequences for SARS -2 sequences for MERS -5 sequences for bat SARS-like
Duplicated sequences were excluded.
Maximum likelihood (ML) were used to test and compare the probability of an evolution model.
“Datamonkey.org was used to find eventual sites of positive or negative selection which was based on P-value less than 0.5.” This was to further test the fast unconstrained Bayesian approximation (FUBAR) to infer that site-specific selection (Benvenuto et. al 2020).
SwissModel was used to build homology models and validated using the QMEAN tool.
3-dimensional structures were analyzed using PyMOL.
Results
In the ML phylogenetic tree, MERS sequences formed clade 1 from the Bat SARS-like, SARS, and 2019-nCoV that clustered together in clade 2 (Benvenuto et. al 2020).
For negative selection...
Using FUBAR, multiple sites in the N region had a P-value less than 0.5.
The 380th nucleotide had a glutamine residue rather than an asparagine.
The 410th nucleotide had a threonine residue rather than an alanine.
An additional 6 sites were also found.
Using FUBAR, multiple sites in the S region had a P-value less than 0.5.
The 536th nucleotide had aasparagine rather than an apartic acid.
The 644th nucleotide had a threonine residue rather than an alanine.
An additional 1065 sites were also found.
For positive selection...
No sites in the E and M regions were found.