Please enable JavaScript.
Coggle requires JavaScript to display documents.
The 2019‐new coronavirus epidemic: Evidence for virus evolution - Coggle…
The 2019‐new coronavirus epidemic: Evidence
for virus evolution
Abstract
Methods
The virus was analyzed using a phylogenetic tree
15 available whole genome sequences and 12 similar genome sequences were used to construct the tree
Sequences taken from Severe acute respiratory syndromes, 2 from middle east respiratory syndrome and 5 from bat SARS-like coronavirus.
Results
Homology showed clear structural and molecular differences between the viruses, structurally and molecularly
Bayesian approximation analysis shows that the nucleocapsid and spike protein have sites under positive selection pressures
The phylogenetic tree showed that 2019-nCoV clustered with bat SARS like coronavirus sequences.
2019-nCoV likely transferred from bats to humans after a mutation allowed for it.
Introduction
There is a worldwide concern about the ability of 2019-nCoV virus causing a pandemic.
This article provides a preliminary analysis of the virus' epidemiology
Introduction
the family Coronaviridae comprises a group of large single stranded RNA viruses
Known to cause cold symptoms and diarrhea.
New coronavirus strain arose in 2003. SARS-CoV, severe acute respiratory syndrome.
A new strain emerged in 2019 from Wuhan, China.
Cases of unexplained pneumonia arose in China starting in December 2019
This strain is part of the sub-family of Orthocoronavirinae
Most patients visited local animal markets
It is likely that the virus originated through animal to human transmission.
Prompt diagnosis and isolation are the proposed methods of controlling the epidemic
A phylogenetic tree could also provide information on the genetic variability, evolution rate and disease progression. These would help in vaccine manufacturing.
Materials & Methods
The complete genomes of 15 2019-nCoV sequences were downloaded
A dataset created from 5 similar SARS, 2 MERS and 5 bat-SARS-like sequences.
Duplicated sequences were excluded from the dataset and the remaining sequences were aligned.
Maximum likelihood methods employed to calculate the probability of certain hypotheses based on the specific phylogenetic tree
The adaptive evolution server was used to find sites under negative and positive selection
Homology models were built to determine if the 2019 variant differed structurally and molecularly
Results
Phylogenetic tree
MERS sequences formed a distinct clade from SARS, Bat-SARS and 2019-nCoV in Clade I
Clade II consisted of all viruses except MERS
Clade II was split into 2 different clusters
Cluster IIa contained bat-SARS and 2019-nCoV
Cluster IIb contained bat-SARS and SARS virus
2019-n-CoV is specifically related to bat-SARS from Rhinolophus sinicus. A species of bat found in China
FUBAR
The Wuhan virus sequence there is a glutamine at 380bp and a threonine at 410bp
Sites of positive selection found on the spike glycoprotein
2019-nCoV has amino acids that differ from the other viruses on the glycoprotein.
Pervasive negative selection was identified
Refrences
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.
Discussion
Since 2019-nCoV landed in cluster IIa with bar-SARS, it is likely the 2019 strain arose from animal to human transmission due to a mutation that allowed cross-species transmission.
The viral spike protein is responsible for virus entry into the cell. This why there is positive selection seen in the spike glycoprotein
Mutation of this protein could result in higher infection rates of the virus