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The 2019‐new coronavirus epidemic: Evidence for virus evolution - Coggle…
The 2019‐new coronavirus epidemic: Evidence for virus evolution
Introduction
The family Coronaviridae includes many large, single, plus-stranded RNA viruses that has previously been known to cause the common cold and diarrhea in humans.
In 2003, a new coronavirus was found that also cause severe acute respiratory syndrome (SARS-CoV) hence the new name
In 2019, a new corona virus emerged in Wuhan China that was part of the Orthocoronavirinae subfamily
Molecular epidemiology, evolutionary models, and phylogenic analysis is being implemented to see if there are positive or negative selection pressures in regions where the virus is prevalent.
Methods
The complete genomes of 15 of the 2019-nCov were downloaded and analyzed for similarity using a basic local alignment tool.
Sites of positive or negative selection were found using a test called fast unconstrained Bayesian approximation (FUBAR).
Homology models were built using the website SwissModel
They were validated using the QMEAN tool and analyzed the structures using PyMOL
Results
The phylogenic Tree
The MERS virus formed its own clade
So did the 2019-nCoV virus from bats, which was split into two sub clusters where the 2019-nCoV was most closely related to the bat isolated CoV
The FUBAR analysis
There was pervasive episodic selection found on the N and S regions both under negative selection.
There were no sites under positive selection in the E and M regions
The Homology model
The N region has proven to be the most stable and similar model produced using this technique.
There are multiple substitutions in residues that were identified in the various strains of CoV and those under positive selection were different for the spike glycoprotein.
Discussion
The new 2019-nCoV is tightly related to the sequence from the SARS-like bat coronavirus from 2015.
Homology analysis showed that this bat CoV from 2015 is more alike to the new 2019-nCoV than to other bat SARS-like CoV.
The spike protein S and the nucleocapsid N protein have proven to be under selection in these strains.
Mutations of these proteins are under investigation since they are prevalent in the new 2019n-CoV virus
These finding support the infection control policies during the ongoing epidemic.
Reference:
Benvenuto D, Giovanetti M, Ciccozzi A, Spoto S, Angeletti S, Ciccozzi M. 2020 Feb 7. The 2019‐new coronavirus epidemic: Evidence for virus evolution. Journal of Medical Virology. doi:10.1002/jmv.25688.