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Comment
. 2020 Apr;92(4):455-459.
doi: 10.1002/jmv.25688. Epub 2020 Feb 7.

The 2019-new coronavirus epidemic: Evidence for virus evolution

Domenico Benvenuto  1 , Marta Giovanetti  2 , Alessandra Ciccozzi  1 , Silvia Spoto  3 , Silvia Angeletti  4 , Massimo Ciccozzi  2
Affiliations
Comment

The 2019-new coronavirus epidemic: Evidence for virus evolution

Domenico Benvenuto et al. J Med Virol. 2020 Apr.

Abstract

There is a worldwide concern about the new coronavirus 2019-nCoV as a global public health threat. In this article, we provide a preliminary evolutionary and molecular epidemiological analysis of this new virus. A phylogenetic tree has been built using the 15 available whole genome sequences of 2019-nCoV, 12 whole genome sequences of 2019-nCoV, and 12 highly similar whole genome sequences available in gene bank (five from the severe acute respiratory syndrome, two from Middle East respiratory syndrome, and five from bat SARS-like coronavirus). Fast unconstrained Bayesian approximation analysis shows that the nucleocapsid and the spike glycoprotein have some sites under positive pressure, whereas homology modeling revealed some molecular and structural differences between the viruses. The phylogenetic tree showed that 2019-nCoV significantly clustered with bat SARS-like coronavirus sequence isolated in 2015, whereas structural analysis revealed mutation in Spike Glycoprotein and nucleocapsid protein. From these results, the new 2019-nCoV is distinct from SARS virus, probably trasmitted from bats after mutation conferring ability to infect humans.

Keywords: SARS coronavirus; coronavirus; epidemiology; macromolecular design.

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Figures

Figure 1
Figure 1
Maximum likelihood tree of 2019‐nCoV. Along the branches, an asterisk (*) indicates a statistical value from bootstrap (>97%)
Figure 2
Figure 2
Cartoon model of the structural superposition between the homology model of the 2019‐nCoV in blue and the nucleocapsid protein of SARS coronavirus (PDB code 2jw8.1) in orange. The red circle highlights the presence of an alpha‐helix on the SARS‐CoV and the absence of the 2019‐nCoV structure, and e positional difference of the beta‐sheets. SARS, severe acute respiratory syndrome
Figure 3
Figure 3
Cartoon model of the structural superposition between the homology model of the 2019‐nCoV in blue and the spike glycoprotein of SARS coronavirus (PDB code 6acc.1) in orange. The red circle highlights the presence of a variable region on the 2019‐nCoV at the beginning of the protein, whereas the blue square highlights the presence of two beta‐sheets on the 2019‐nCoV (401:KYR and 440:LND) that are not present on the SARS‐CoV structure; SARS, severe acute respiratory syndrome
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