SARS-CoV-2 and ORF3a: Nonsynonymous Mutations, Functional Domains, and Viral Pathogenesis

MSystems
E. IssaSima T Tokajian

Abstract

The effect of the rapid accumulation of nonsynonymous mutations on the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not yet known. The 3a protein is unique to SARS-CoV and is essential for disease pathogenesis. Our study aimed at determining the nonsynonymous mutations in the 3a protein in SARS-CoV-2 and determining and characterizing the protein's structure and spatial orientation in comparison to those of 3a in SARS-CoV. A total of 51 different nonsynonymous amino acid substitutions were detected in the 3a proteins among 2,782 SARS-CoV-2 strains. We observed microclonality within the ORF3a gene tree defined by nonsynonymous mutations separating the isolates into distinct subpopulations. We detected and identified six functional domains (I to VI) in the SARS-CoV-2 3a protein. The functional domains were linked to virulence, infectivity, ion channel formation, and virus release. Our study showed the importance of conserved functional domains across the species barrier and revealed the possible role of the 3a protein in the viral life cycle. Observations reported in this study merit experimental confirmation.IMPORTANCE At the surge of the coronavirus disease 2019 (COVID-19) pandemic, we detecte...Continue Reading

References

Aug 9, 2006·Proceedings of the National Academy of Sciences of the United States of America·Wei LuBing Sun
May 8, 2007·Nucleic Acids Research·Lukas KällErik L L Sonnhammer
Nov 30, 2007·Virus Research·Krishna NarayananShinji Makino
Jan 20, 2009·Bioinformatics·Andrew M WaterhouseGeoffrey J Barton
Apr 29, 2009·The International Journal of Biochemistry & Cell Biology·Chak-Ming ChanHo Yin Edwin Chan
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Mar 20, 2014·Bioinformatics·Torsten Seemann
Jul 2, 2015·Molecular Biology and Evolution·Vincent LefortOlivier Gascuel
Dec 3, 2016·Nucleic Acids Research·Stefan BienertTorsten Schwede
Nov 6, 2018·Nucleic Acids Research·UNKNOWN UniProt Consortium
Apr 30, 2019·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Kam-Leung SiuDong-Yan Jin
Jan 30, 2020·Viruses·Lisa E Gralinski, Vineet D Menachery
Mar 29, 2020·Nature·Tommy Tsan-Yuk LamWu-Chun Cao

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Citations

Aug 1, 2020·Reviews in Medical Virology·Abdellatif Bouayad
Jun 4, 2020·Journal of Medical Virology·A S M Rubayet Ul AlamM Anwar Hossain
Jul 1, 2020·Turkish Journal of Biology = Türk Biyoloji Dergisi·Osman Mutluhan UgurelDilek Turgut-Balik
Oct 20, 2020·Frontiers in Immunology·Alessandro StellaPiero Portincasa
Oct 30, 2020·PloS One·Andreas BluhmAlbert H Werner
Oct 14, 2020·Journal of Medical Virology·María Teresa Hernández-HuertaCarlos Alberto Matias-Cervantes
Oct 27, 2020·Epidemiology and Infection·Parinita Majumdar, Sougata Niyogi
Oct 24, 2020·Glycobiology·Luís Cláudio Nascimento da SilvaMaria Tereza Dos Santos Correia
Jan 6, 2021·International Journal of Molecular Sciences·Valerie Bríd O'LearySaak Victor Ovsepian
Dec 29, 2020·International Journal of Biological Macromolecules·Martina BianchiStefano Pascarella
Dec 29, 2020·Computational and Structural Biotechnology Journal·Christos A Ouzounis
Jan 26, 2021·Gene Reports·Ahmad AlkhansaLoubna El Zein
Jan 23, 2021·Advanced Drug Delivery Reviews·Saborni ChakrabortyTaia T Wang
Jan 15, 2021·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Can ChenShigui Yang
Nov 17, 2020·Frontiers in Immunology·Alberto López-ReyesGabriela Angélica Martínez-Nava
Nov 19, 2020·Proceedings of the National Academy of Sciences of the United States of America·Hong-Li ZengErik Aurell
Nov 19, 2020·Emerging Microbes & Infections·Joy-Yan LamKin-Hang Kok
Feb 3, 2021·Biochemistry and Biophysics Reports·Gajendra Kumar Azad, Parimal Kumar Khan
Feb 16, 2021·The Journal of General Virology·Asmita GuptaMurali Dharan Bashyam
Nov 17, 2020·Frontiers in Veterinary Science·Ahmed M AlluwaimiSalah Abohelaika
Mar 8, 2021·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Ngoc-Niem BuiCheng-Wen Lin
Jun 17, 2020·Genomics·Sk Sarif HassanSiddhartha Sankar Jana
Mar 18, 2021·Microbial Pathogenesis·Behnaz BakhshandehMaryam Zamani
Oct 27, 2020·Frontiers in Microbiology·Sheng LiuJun Wan
Dec 2, 2020·Medical Hypotheses·Eduardo Pérez-Campos MayoralEduardo Pérez-Campos
Mar 27, 2021·Environmental Microbiology·Ruibang LuoAntoine Danchin
Apr 10, 2021·Frontiers in Immunology·Tatjana SchwarzVictor M Corman
Apr 15, 2021·Expert Review of Molecular Diagnostics·Davide ZellaMassimo Ciccozzi
Apr 27, 2021·Frontiers in Cellular Neuroscience·Petra TavčarJernej Jorgačevski
May 4, 2021·Virus Research·Sk Sarif HassanBidyut Roy
May 1, 2021·Epidemiology and Infection·Parinita Majumdar, Sougata Niyogi
Jun 9, 2021·Scientific Reports·Luis Fernando Saraiva Macedo TimmersStefan Laufer
May 20, 2021·Chemistry of Heterocyclic Compounds·Oskar I KoifmanMikhail O Koifman
Jun 30, 2021·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Sunil Thomas
Jun 30, 2021·Emerging Microbes & Infections·Fernando Hayashi Sant'AnnaEliana Márcia Wendland
Jun 13, 2021·Journal of Infection and Public Health·Vartika Srivastava, Aijaz Ahmad
Jul 3, 2021·Cells·Annamaria PaoliniLara Gibellini
Jul 15, 2021·BioMed Research International·Abdelmalek HakmaouiBrahim Admou
Jun 24, 2021·FEMS Microbiology Reviews·Milankumar PatelHoward E Gendelman

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Datasets Mentioned

BETA
QHR63301.1
AAU04650.1
AY572035

Software Mentioned

Phobius
MAFFT
Prokka
Protter
Protein Variation Effect Analyzer
PROVEAN
ScanProsite
FastME
BMGE
Jalview

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