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. 2020 Jul;81(1):e24-e27.
doi: 10.1016/j.jinf.2020.03.058. Epub 2020 Apr 10.

Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy

Domenico Benvenuto  1 , Silvia Angeletti  2 , Marta Giovanetti  3 , Martina Bianchi  4 , Stefano Pascarella  4 , Roberto Cauda  5 , Massimo Ciccozzi  6 , Antonio Cassone  7
Affiliations

Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy

Domenico Benvenuto et al. J Infect. 2020 Jul.

Abstract

Background: SARS-CoV-2 is a new coronavirus that has spread globally, infecting more than 150000 people, and being declared pandemic by the WHO. We provide here bio-informatic, evolutionary analysis of 351 available sequences of its genome with the aim of mapping genome structural variations and the patterns of selection.

Methods: A Maximum likelihood tree has been built and selective pressure has been investigated in order to find any mutation developed during the SARS-CoV-2 epidemic that could potentially affect clinical evolution of the infection.

Finding: We have found in more recent isolates the presence of two mutations affecting the Non-Structural Protein 6 (NSP6) and the Open Reding Frame10 (ORF 10) adjacent regions. Amino acidic change stability analysis suggests both mutations could confer lower stability of the protein structures.

Interpretation: One of the two mutations, likely developed within the genome during virus spread, could affect virus intracellular survival. Genome follow-up of SARS-CoV-2 spread is urgently needed in order to identify mutations that could significantly modify virus pathogenicity.

Keywords: Autophagy; Bio-informatic; COVID-19; Coronavirus; Molecular evolution; SARS-CoV-2.

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Conflict of interest statement

Declaration of Competing Interest We declare no competing interests.

Figures

Fig. 1:
Fig. 1
I-TASSER model of NSP6. Residue under positive selective pressure with a p< 0.05 is shown as a sphere. Residues found in the structure proximity are shown in sticks. All residues are marked by the corresponding labels.
Fig. 2:
Fig. 2
Results obtained with Protter and TMHMM are shown in panel A and B, respectively. In the panel A, the residue under positive pressure with p< 0.05 is marked by the red arrow (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.).
See this image and copyright information in PMC

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