Jun 25, 2014

Codon usage and evolutionary rates of the 2019-nCoV genes

BioRxiv : the Preprint Server for Biology
István MikóAlexandros G Georgakilas

Abstract

Severe acute respiratory syndrome coronavirus 2 (2019-nCoV), which first broke out in Wuhan (China) in December of 2019, causes a severe acute respiratory illness with a mortality ranging from 3% to 6%. To better understand the evolution of the newly emerging 2019-nCoV, in this paper, we analyze the codon usage pattern of 2019-nCoV. For this purpose, we compare the codon usage of 2019-nCoV with that of other 30 viruses belonging to the subfamily of orthocoronavirinae. We found that 2019-nCoV shows a rich composition of AT nucleotides that strongly influences its codon usage, which appears to be not optimized to human host. Then, we study the evolutionary pressures influencing the codon usage and evolutionary rates of the sequences of five conserved genes that encode the corresponding proteins (viral replicase, spike, envelope, membrane and nucleocapsid) characteristic of coronaviruses. We found different patterns of both mutational bias and nature selection that affect the codon usage of these genes at different extents. Moreover, we show that the two integral membrane proteins proteins (matrix and envelope) tend to evolve slowly by accumulating nucleotide mutations on their genes. Conversely, genes encoding nucleocapsid (N), v...Continue Reading

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Mentioned in this Paper

Mandible
WAS gene
Pteromalidae
Hymenoptera
Microscopy, Confocal
Wiskott-Aldrich Syndrome Protein
Tissue Dissection
Nasonia vitripennis
Gland
Microscopy, Confocal, Laser Scanning

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