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

Giorgio Palù, Vladimir N Uversky, Raner José Santana Silva, Bruno Silva Andrade, Nikolas G Bazan, Vasco Azevedo, Debmalya Barh, Wagner Baetas-da-Cruz, Adam M Brufsky, Murtaza Tambuwala, Parise Adadi, Gaurav Chauhan, Sk Sarif Hassan, Alaa A A Aljabali, Gajendra Kumar Azad, Ángel Serrano-Aroca, Amos Lal, Ramesh Kandimalla, Kazuo Takayama, Tarek Mohamed Abd El-Aziz, Pabitra Pal Choudhury, Kenneth Lundstrom, Elrashdy M Redwan, Vaishnavi Kodakandla

Journal: PeerJ 2023;10():e13136

PMID: 35341060

Free Full Text on PubMed Central View on PubMed

Abstract

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.

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

DOI: 10.7717/peerj.13136

Link outs

Free resources

Full Text Sources:

Medical:

https://medlineplus.gov/covid19coronavirusdisease2...

Miscellaneous:

https://assays.cancer.gov/CPTAC-438

Research Materials:

https://antibodies.cancer.gov/detail/CPTC-HLA-C-1

MeSH Terms: Humans, SARS-CoV-2, COVID-19, Open Reading Frames, Antigens, Viral