The 2019-new coronavirus epidemic: Evidence for virus evolution - Coggle…
The 2019-new coronavirus epidemic: Evidence for virus evolution
Benvenuto D, Giovanetti M, Ciccozzi A, Spoto S, Angeletti S, Ciccozzi M. 2020. The 2019‐new coronavirus epidemic: Evidence for virus evolution. J Med Virol. 92(4):455–459. doi:10.1002/jmv.25688.
Coronaviridae is a classification of viruses that come from a certain family identified from several species to cause symptoms such as the common cold and diarrhea in humans (Benvenuto et al. 2020).
In 2003, severe acute respiratory syndrome coronavirus (SARS-COV) was connected to the SARS outbreak (Benvenuto et al. 2020)
2019-nCoV known as the novelty coronavirus identified from the Orthocoronavirinae subfamily emerged from Wuhan, China infecting humans (Benvenuto et al. 2020).
FUBAR analysis shows the nucleocapsid and the spike glycoprotein have sites that are under positive pressure (Benvenuto et al. 2020).
Homology model shows molecular and structural differences between viruses (Benvenuto et al. 2020).
The 2019-nCoV showed genetic similarities to the bat SARS according to the phylogenetic tree but the structural analysis showed mutations occurred in spike glycoprotein and nucleocapsid protein (Benvenuto et al. 2020).
The results indicated 2019-nCoV is distinct from the SARS virus correlating to the transmittance from bats after going through mutations developing the ability to infect humans (Benvenuto et al. 2020).
Material and Methods
Complete genome sequences were downloaded using GISAID and GenBank.
5 similar sequences for SARS, 2 sequences for middle east respiratory syndrome (MERS), and 5 sequences for bat SARS were used to help identify the sequences.
Fast unconstrained Bayesian approximation (FUBAR) were used to help identify pervasive selection from specific sites, episodic selection from individual sites, and episodic diversifying selection across regions of interest.
The 2019-nCoV showed a significant relationship to the bat SARS isolated from Rhinolophus sinicus in 2015
Sites under positive pressure were found on the spike glycoprotein in the 2019-nCoV showing signs of asparagine residue located on the 536th aminoacidic position.
Bat SARS showed glutamine residue (536th aminoacidic position)
SARS virus showed aspartic acid residue (536th aminoacidic position)
2019-nCoV showed threonine residue located on the 644th aminoacidic position
Bat SARS showed serine residue (644th aminoacidic position)
SARS virus showed alanine residue (644th aminoacidic position)
Bat SARS is homologous and genetically similar to the 2019-nCoV
The spike glycoprotein is responsible for virus entering the cell after binding to a cell receptor
The nucleocapsid is responsible for the virion assembly and transcription
Mutations of the spike and nucleocapsid proteins have shown similar characteristics of the 2019-nCoV
Some characteristic is the enhance ability to infect more than the bat SARS showing lower pathogenicity.
Bat origin of infection can clarify the transmission mechanics of the 2019-nCoV