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

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


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.

MeSH terms

  • Autophagy
  • Betacoronavirus / genetics*
  • COVID-19
  • Capsid Proteins / genetics*
  • Coronavirus Infections / virology*
  • Coronavirus Nucleocapsid Proteins
  • Evolution, Molecular
  • Gene Expression Regulation, Viral
  • Genome, Viral
  • Humans
  • Likelihood Functions
  • Models, Molecular
  • Mutation*
  • Open Reading Frames
  • Pandemics
  • Pneumonia, Viral / virology*
  • Protein Conformation
  • SARS-CoV-2


  • Capsid Proteins
  • Coronavirus Nucleocapsid Proteins
  • NSP6 protein, SARS-CoV-2