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Evolutionary Analysis of SARS-2-CoV: How Mutation of Non-Structural Protein 6 (NSP6) Could Affect Viral Autophagy

13 Pages Posted: 2 Apr 2020

See all articles by Domenico Benvenuto

Domenico Benvenuto

University Campus Bio-Medico - Unit of Medical Statistics and Molecular Epidemiology

Silvia Angeletti

Policlinico Universitario Campus Biomedico - Unit of Medical Statistics and Molecular Epidemiology

Marta Giovanetti

Oswaldo Cruz Foundation (FIOCRUZ) - Laboratório de Flavivírus

Martina Bianchi

University of Rome I - Department of Biochemical Science

Stefano Pascarella

University of Rome I - Department of Biochemical Science

Roberto Cauda

Catholic University of the Sacred Heart of Milan

Massimo Ciccozzi

Policlinico Universitario Campus Biomedico - Unit of Medical Statistics and Molecular Epidemiology

Antonio Cassone

University of Siena - Center of Genomics,Genetics and Biology

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Abstract

Background: SARS-2-CoV 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-2-CoV 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 Reading Frame10 (ORF 10) adjacent regions. Amino acidic change stability analysis suggests both mutations could confer lower stability of the protein structures. Particularly, NSP6 mutation prospects as its potential relevance for modulation of cellular autophagy.

Interpretation: Our results show the presence of mutations, likely developed within the viral genome during its spread, one of which could affect virus intracellular survival. Genome follow-up of SARS-2-CoV spread is urgently needed in order to identify mutations that could significantly modify virus pathogenicity.

Funding Statement: No specific funding source has been received.

Declaration of Interests: The authors declare no competing interests.

Ethics Approval Statement: All the data used for this study have been downloaded from NCBI and GISAID databank, no personal information has been collected and no patient or animal has been directly involved in the experiment.

Keywords: SARS-2-CoV, COVID-19, Coronavirus, Bio-informatic, Autophagy, molecular evolution

Suggested Citation

Benvenuto, Domenico and Angeletti, Silvia and Giovanetti, Marta and Bianchi, Martina and Pascarella, Stefano and Cauda, Roberto and Ciccozzi, Massimo and Cassone, Antonio, Evolutionary Analysis of SARS-2-CoV: How Mutation of Non-Structural Protein 6 (NSP6) Could Affect Viral Autophagy (3/17/2020). Available at SSRN: https://ssrn.com/abstract=3558013 or http://dx.doi.org/10.2139/ssrn.3558013

Domenico Benvenuto (Contact Author)

University Campus Bio-Medico - Unit of Medical Statistics and Molecular Epidemiology ( email )

Via Álvaro del Portillo, 21
Rome, 00128
Italy

Silvia Angeletti

Policlinico Universitario Campus Biomedico - Unit of Medical Statistics and Molecular Epidemiology

Italy

Marta Giovanetti

Oswaldo Cruz Foundation (FIOCRUZ) - Laboratório de Flavivírus

Rio de Janeiro, 21040-900
Brazil

Martina Bianchi

University of Rome I - Department of Biochemical Science

Rome
Italy

Stefano Pascarella

University of Rome I - Department of Biochemical Science

Rome
Italy

Roberto Cauda

Catholic University of the Sacred Heart of Milan ( email )

Roma
Italy

Massimo Ciccozzi

Policlinico Universitario Campus Biomedico - Unit of Medical Statistics and Molecular Epidemiology

Italy

Antonio Cassone

University of Siena - Center of Genomics,Genetics and Biology

Siena
Italy

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