An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2

PeerJ

Ramesh Kandimalla¹  Pabitra Pal Choudhury²  Ángel Serrano-Aroca³  Kazuo Takayama⁴  Debmalya Barh⁵  Raner José Santana Silva⁶  Vasco Azevedo⁷  Tarek Mohamed Abd El-Aziz⁸  Parise Adadi⁹  Vaishnavi Kodakandla^1,10  Sk. Sarif Hassan^1,11  Adam M. Brufsky^1,12  Giorgio Palù^1,13  Vladimir N. Uversky^1,14  Alaa A.A. Aljabali^1,15  Gajendra Kumar Azad^1,16  Amos Lal^1,17  Elrashdy M. Redwan^1,18  Bruno Silva Andrade^1,19  Nikolas G. Bazan^2,20  Kenneth Lundstrom^2,21  Gaurav Chauhan^2,22  Murtaza Tambuwala^2,23  Wagner Baetas-da-Cruz^2,24 

[1] Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India;Applied Statistics Unit, Indian Statistical Institute, Kolkata, India;Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Catolica de Valencia San Vicente Martir, Valencia, Spain;Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan;Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and 46 Applied Biotechnology (IIOAB), Nonakuri, India;Departamento de Ciencias Biologicas (DCB), Programa de Pos-Graduacao em Genetica e Biologia Molecular (PPGGBM), Universidade Estadual de Santa Cruz (UESC), Ilheus, Brazil;Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil;Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States;Department of Food Science, University of Otago, University of Otago, Dunedin, New Zealand;Department of Life sciences, Sophia College For Women, University of Mumbai, Mumbai, India;Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, India;Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States;Department of Molecular Medicine, University of Padova, Padova, Italy;Department of Molecular Medicine, University of South Florida, Tampa, FL, United States;Department of Pharmaceutics and Pharmaceutical, Yarmouk University, Irbid, Jordan;Department of Zoology, Patna University, Patna, India;Division of Pulmonary and Critical Care Medicine, Mayo Clinic Rochester, Rochester, NY, United States;Faculty of Science, Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia;Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil;Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA, United States;PanTherapeutics, Lutry, Switzerland;School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico;School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK;Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil;

关键词: ORF8;    SARS-CoV-2;    COVID-19;    Truncated;    Intrinsically disordered region;    Truncation mutation;   

DOI  :  10.7717/peerj.13136

来源: DOAJ

【 摘 要 】

Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.

【 授权许可】

Unknown