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Covid Origin - Coggle Diagram
Covid Origin
FUBAR analysis of these genomes shows significant pervasive selection and negative selection compared to the reference strain in the S and N regions.
Results suggest that the S region could be highly conserved with 1065 sites under pervasive negative selection.
Specifically, two sites in both the S and N regions show significant pervasive episodic selection.
In 2019, the 2019-nCoV, a large, single plus‐stranded RNA virus, originated in Wuhan, China and was suggested to arise from animal to human transmission.
Phylogenetic analysis of viruses is important in estimating evolutionary rate and variability, which are important for understanding the disease and developing proper treatment.
The authors performed phylogenetic analyses to identify regions of positive and negative selection in the 2019-nCoV virus.
The authors obtained 15 complete 2019-nCoV sequences from GISAID and GenBank databases and compared them to five SARS, two MERS and five bat SARS-like coronavirus sequences.
The maximum likelihood methods were used to find the best phylogenetic tree, which was reconstructed using time-reversible plus gamma distribution and invariant sites.
The fast unconstrained Bayesian approximation test (FUBAR) was used to identify episodic selection at individual sites.
Then, homology models were built from the SwissModel website.
The phylogenetic tree hows MERS forming its own clade while bat SARS-like coronavirus, SARS virus and 2019-nCoV formed their own clade.
The sequences 2019-nCoV and a bat SARS-like coronavirus formed a cluster within the clade while the other bat SARS-like coronavirus sequences and SARS virus formed their own cluster.
The results show that 2019-nCoV is closely related to the bat SARS-like coronavirus isolated in china in 2015.
The data suggest that 2019-nCoV is homologous to the bat SARS-like coronavirus sequence from 2015 and not the other sequences or SARS or MERS sequences, which suggest that it was transmitted to human from the bat.
Analysis of the N and S region confirm that there are significant similarities in the two sequences.
The mutations in the N and S region give stability to the virus increasing its ability to infect and enhancing pathogenicity making it worse than the bat SARS-like coronavirus but better than SARS.
Positive selection could have played a role in the evolution of the epidemic that favored enhanced pathogenicity and increased transmission rates.
Structural and molecular analysis of the Nucleoapsid region show 2019-nCoV shares the same aminoacid sequence as the bat SARS-like coronavirus and not the SARS virus. In the S region, all SARS, bat SARS-like coronavirus and 2019-nCoV vary in aminoacid sequence.
Another paper mentioned by the authors suggest Bungarus milticinctus snakes are a probable reservoir because of the codon usage similarities in the snakes and the spike glycoprotein of 2019-nCoV that favors cross-species transmission.
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. 92:455-459.