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Seyran M. Artificial intelligence and clinical data suggest the T cell-mediated SARS-CoV-2 nonstructural protein intranasal vaccines for global COVID-19 immunity. Vaccine 2022; 40:4296-4300. [PMID: 35778279 PMCID: PMC9226295 DOI: 10.1016/j.vaccine.2022.06.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 11/11/2022]
Abstract
Advanced computational methodologies suggested SARS-CoV-2, nonstructural proteins ORF1AB, ORF3a, as the source of immunodominant peptides for T cell presentation. T cell immunity is long-lasting and compatible with COVID-19 pathology. Based on the supporting clinical data, nonstructural SARS-CoV-2 protein vaccines could provide global immunity against COVID-19.
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Affiliation(s)
- Murat Seyran
- The University of Vienna, Doctoral Studies in Natural and Technical Sciences (SPL 44), Währinger Straße, A-1090 Vienna, Austria.
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2
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Hassan SS, Lundstrom K, Barh D, Silva RJS, Andrade BS, Azevedo V, Choudhury PP, Palu G, Uhal BD, Kandimalla R, Seyran M, Lal A, Sherchan SP, Azad GK, Aljabali AAA, Brufsky AM, Serrano-Aroca Á, Adadi P, Abd El-Aziz TM, Redwan EM, Takayama K, Rezaei N, Tambuwala M, Uversky VN. Implications derived from S-protein variants of SARS-CoV-2 from six continents. Int J Biol Macromol 2021; 191:934-955. [PMID: 34571123 PMCID: PMC8462006 DOI: 10.1016/j.ijbiomac.2021.09.080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 01/19/2023]
Abstract
The spike (S) protein is a critical determinant of the infectivity and antigenicity of SARS-CoV-2. Several mutations in the S protein of SARS-CoV-2 have already been detected, and their effect in immune system evasion and enhanced transmission as a cause of increased morbidity and mortality are being investigated. From pathogenic and epidemiological perspectives, S proteins are of prime interest to researchers. This study focused on the unique variants of S proteins from six continents: Asia, Africa, Europe, Oceania, South America, and North America. In comparison to the other five continents, Africa had the highest percentage of unique S proteins (29.1%). The phylogenetic relationship implies that unique S proteins from North America are significantly different from those of the other five continents. They are most likely to spread to the other geographic locations through international travel or naturally by emerging mutations. It is suggested that restriction of international travel should be considered, and massive vaccination as an utmost measure to combat the spread of the COVID-19 pandemic. It is also further suggested that the efficacy of existing vaccines and future vaccine development must be reviewed with careful scrutiny, and if needed, further re-engineered based on requirements dictated by new emerging S protein variants.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal, India.
| | | | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India; Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil.
| | - Raner Jośe Santana Silva
- Department of Biological Sciences (DCB), Graduate Program in Genetics and Molecular Biology (PPGGBM), State University of Santa Cruz (UESC), Rodovia Ilheus-Itabuna, km 16, 45662-900 Ilheus, BA, Brazil
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié 45206-190, Brazil.
| | - Vasco Azevedo
- Laborat'orio de Geńetica Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciˆencias Biol'ogicas, Universidade Federal de Minas Gerais, Belo Horizonte CEP 31270-901, Brazil.
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, 203 B T Road, Kolkata 700108, India
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy.
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, India; Department of Biochemistry, Kakatiya Medical College, Warangal, Telangana, India
| | - Murat Seyran
- Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, W¨ahringer Straße, A-1090 Vienna, Austria
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA.
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Faculty of Pharmacy, Irbid 566, Jordan.
| | - Adam M Brufsky
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigaci'on Traslacional San Alberto Magno, Universidad Cat́olica de Valencia San Vicente Ḿartir, c/Guillem de Castro, 94, 46001 Valencia, Spain.
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA.
| | - Elrashdy M Redwan
- Faculty of Science, Department of Biological Science, King Abdulazizi University, Jeddah 21589, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg El-Arab, Alexandria 21934, Egypt.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan.
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden.
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russia.
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3
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Elrashdy F, Tambuwala MM, Hassan SS, Adadi P, Seyran M, Abd El-Aziz TM, Rezaei N, Lal A, Aljabali AAA, Kandimalla R, Bazan NG, Azad GK, Sherchan SP, Choudhury PP, Serrano-Aroca Á, Takayama K, Chauhan G, Pizzol D, Barh D, Panda PK, Mishra YK, Palù G, Lundstrom K, Redwan EM, Uversky VN. Autoimmunity roots of the thrombotic events after COVID-19 vaccination. Autoimmun Rev 2021; 20:102941. [PMID: 34508917 PMCID: PMC8426137 DOI: 10.1016/j.autrev.2021.102941] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 06/06/2021] [Indexed: 02/03/2023]
Abstract
Although vaccination represents the most promising way to stop or contain the coronavirus disease 2019 (COVID-19) pandemic and safety and effectiveness of available vaccines were proven, a small number of individuals who received anti-SARS-CoV-2 vaccines developed a prothrombotic syndrome. Vaccine-induced immune thrombotic thrombocytopenia (VITT) can be triggered by the adenoviral vector-based vaccine, whereas lipid nanoparticle-mRNA-based vaccines can induce rare cases of deep vein thrombosis (DVT). Although the main pathogenic mechanisms behind this rare phenomenon have not yet been identified, both host and vaccine factors might be involved, with pathology at least in part being related to the vaccine-triggered autoimmune reaction. In this review, we are considering some aspects related to pathogenesis, major risk factors, as well as peculiarities of diagnosis and treatment of this rare condition.
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Affiliation(s)
- Fatma Elrashdy
- Department of Endemic Medicine and Hepatogastroenterology, Kasr Alainy, Cairo University, Cairo, Egypt.
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Sciences, Ulster University, Coleraine, BT52 1SA, Northern Ireland, United Kingdom.
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, 722140 Paschim Medinipur, West Bengal, India
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Murat Seyran
- Doctoral Student in Natural and Technical Sciences (SPL 44), University of Vienna, Währinger Straße, A-1090 Vienna, Austria.
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA.
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Amos Lal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, USA
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Irbid 21163, P. O. BOX 566, Jordan.
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, India; Department of Biochemistry, Kakatiya Medical College, Warangal, India
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, Louisiana State University Health New Orleans, New Orleans, Louisiana, 70112, USA.
| | | | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA.
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata, 700108, West Bengal, India
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, c/Guillem de Castro 94, Valencia 46001, Spain.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan.
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnológico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, Nuevo León, Mexico.
| | - Damiano Pizzol
- Italian Agency for Development Cooperation -, Khartoum, Sudan Street 33, Al Amarat, Sudan
| | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB-721172, India; and Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil.
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
| | - Yogendra K Mishra
- University of Southern Denmark, Mads Clausen Institute, NanoSYD, Alsion 2, 6400 Sønderborg, Denmark.
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Italy.
| | | | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States.
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4
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Redwan EM, Alghamdi MF, El-Aziz TMA, Adadi P, Aljabali AAA, Attrish D, Azad GK, Baetas-da-Cruz W, Barh D, Bazan NG, Brufsky AM, Chauhan G, Hassan SKS, Kandimalla R, Lal A, Lundstrom K, Mishra YK, Choudhury PP, Palù G, Panda PK, Pizzol D, Rezaei N, Serrano-Aroca Á, Sherchan SP, Seyran M, Takayama K, Tambuwala MM, Uhal BD, Uversky VN. The mechanism behind flaring/triggering of autoimmunity disorders associated with COVID-19. Autoimmun Rev 2021; 20:102909. [PMID: 34274539 PMCID: PMC8282442 DOI: 10.1016/j.autrev.2021.102909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab, 21934 Alexandria, Egypt.
| | - Mohammed F Alghamdi
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia; Laboratory Department, University Medical Services Center, King Abdulaziz University, P.O. Box 80200, Jeddah 21589, Saudi Arabia.
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA; Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt.
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid 566, Jordan.
| | - Diksha Attrish
- Dr. B R Ambedkar Center for Biomedical Research (ACBR), University of Delhi (North Camps), Delhi 110007, India
| | | | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur WB-721172, India; Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Heath New Orleans, New Orleans 70112, USA.
| | - Adam M Brufsky
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnológico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849, Monterrey, NL, Mexico.
| | - S K Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Hyderabad 500007, Department of Biochemistry, Kakatiya Medical College, Warangal, Telangana State, India
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Yogendra Kumar Mishra
- University of Southern Denmark, Mads Clausen Institute, NanoSYD, Alsion 2, 6400 Sønderborg, Denmark.
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121, Padova, Italy.
| | - Pritam K Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, 75120 Uppsala, Sweden.
| | - Damiano Pizzol
- Italian Agency for Development Cooperation - Khartoum, Sudan Street 33, Al Amarat, Sudan
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001, Valencia, Spain.
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA.
| | - Murat Seyran
- Doctoral Student in Natural and Technical Sciences (SPL 44), University of Vienna, Währinger Straße, A-1090 Vienna, Austria; Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Austria.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8397, Japan.
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Vladimir N Uversky
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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5
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Serrano-Aroca Á, Takayama K, Tuñón-Molina A, Seyran M, Hassan SS, Pal Choudhury P, Uversky VN, Lundstrom K, Adadi P, Palù G, Aljabali AAA, Chauhan G, Kandimalla R, Tambuwala MM, Lal A, Abd El-Aziz TM, Sherchan S, Barh D, Redwan EM, Bazan NG, Mishra YK, Uhal BD, Brufsky A. Carbon-Based Nanomaterials: Promising Antiviral Agents to Combat COVID-19 in the Microbial-Resistant Era. ACS Nano 2021; 15:8069-8086. [PMID: 33826850 PMCID: PMC8043205 DOI: 10.1021/acsnano.1c00629] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/02/2021] [Indexed: 05/04/2023]
Abstract
Therapeutic options for the highly pathogenic human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the current pandemic coronavirus disease (COVID-19) are urgently needed. COVID-19 is associated with viral pneumonia and acute respiratory distress syndrome causing significant morbidity and mortality. The proposed treatments for COVID-19 have shown little or no effect in the clinic so far. Additionally, bacterial and fungal pathogens contribute to the SARS-CoV-2-mediated pneumonia disease complex. The antibiotic resistance in pneumonia treatment is increasing at an alarming rate. Therefore, carbon-based nanomaterials (CBNs), such as fullerene, carbon dots, graphene, and their derivatives constitute a promising alternative due to their wide-spectrum antimicrobial activity, biocompatibility, biodegradability, and capacity to induce tissue regeneration. Furthermore, the antimicrobial mode of action is mainly physical (e.g., membrane distortion), characterized by a low risk of antimicrobial resistance. In this Review, we evaluated the literature on the antiviral activity and broad-spectrum antimicrobial properties of CBNs. CBNs had antiviral activity against 13 enveloped positive-sense single-stranded RNA viruses, including SARS-CoV-2. CBNs with low or no toxicity to humans are promising therapeutics against the COVID-19 pneumonia complex with other viruses, bacteria, and fungi, including those that are multidrug-resistant.
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Affiliation(s)
- Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de
Investigación Traslacional San Alberto Magno, Universidad
Católica de Valencia San Vicente Mártir, 46001 Valencia,
Spain
| | - Kazuo Takayama
- Center for iPS Cell Research and Application,
Kyoto University, Kyoto 606-8397,
Japan
| | - Alberto Tuñón-Molina
- Biomaterials and Bioengineering Lab, Centro de
Investigación Traslacional San Alberto Magno, Universidad
Católica de Valencia San Vicente Mártir, 46001 Valencia,
Spain
| | - Murat Seyran
- Doctoral studies in natural and technical sciences (SPL
44), University of Vienna, Währinger Straße, A-1090
Vienna, Austria
| | - Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana
Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal,
India
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian
Statistical Institute, Kolkata 700108, West Bengal,
India
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of
Medicine, University of South Florida, Tampa, Florida 33612,
United States
| | | | - Parise Adadi
- Department of Food Science, University of
Otago, Dunedin 9054, New Zealand
| | - Giorgio Palù
- Department of Molecular Medicine,
University of Padova, Via Gabelli 63, 35121 Padova,
Italy
| | - Alaa A. A. Aljabali
- Department of Pharmaceutics and
Pharmaceutical Technology, Yarmouk University-Faculty of
Pharmacy, Irbid 21163, Jordan
| | - Gaurav Chauhan
- School of Engineering and Sciences,
Tecnológico de Monterrey, Av. Eugenio Garza Sada 2501
Sur, 64849 Monterrey, NL, Mexico
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian
Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad-500007,
India
- Department of Biochemistry,
Kakatiya Medical College, Warangal-506007, Telangana State,
India
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical
Science, Ulster University, Coleraine BT52 1SA, Northern
Ireland, U.K.
| | - Amos Lal
- Department of Medicine, Division of Pulmonary and Critical
Care Medicine, Mayo Clinic, Rochester, Minnesota 55905,
United States
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science,
Minia University, El-Minia 61519,
Egypt
- Department of Cellular and Integrative
Physiology, University of Texas Health Science Center at San
Antonio, San Antonio, Texas 78229-3900, United
States
| | - Samendra Sherchan
- Department of Environmental Health Sciences,
School of Public Health and Tropical Medicine, Tulane University of
Louisiana, New Orleans, Louisiana 70112, United
States
| | - Debmalya Barh
- Institute of Integrative
Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur,
WB-721172, India
| | - Elrashdy M. Redwan
- Biological Sciences Department,
Faculty of Science, King Abdulaziz University, P.O. Box 80203,
Jeddah 21589, Saudi Arabia
- Therapeutic and Protective Proteins
Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research
Institute, City for Scientific Research and Technology
Applications, New Borg El-Arab, Alexandria 21934,
Egypt
| | - Nicolas G. Bazan
- Neuroscience Center of Excellence,
School of Medicine, LSU Heath New Orleans, New Orleans,
Louisiana 70112, United States
| | - Yogendra Kumar Mishra
- University of Southern
Denmark, Mads Clausen Institute, NanoSYD, Alsion 2, 6400 Sønderborg,
Denmark
| | - Bruce D. Uhal
- Department of Physiology, Michigan State
University, East Lansing, Michigan 48824, United
States
| | - Adam Brufsky
- University of Pittsburgh
School of Medicine, Department of Medicine, Division of
Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania 15232,
United States
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6
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Hassan SS, Attrish D, Ghosh S, Choudhury PP, Uversky VN, Aljabali AAA, Lundstrom K, Uhal BD, Rezaei N, Seyran M, Pizzol D, Adadi P, Soares A, Abd El-Aziz TM, Kandimalla R, Tambuwala MM, Azad GK, Sherchan SP, Baetas-da-Cruz W, Lal A, Palù G, Takayama K, Serrano-Aroca Á, Barh D, Brufsky AM. Notable sequence homology of the ORF10 protein introspects the architecture of SARS-CoV-2. Int J Biol Macromol 2021; 181:801-809. [PMID: 33862077 PMCID: PMC8051021 DOI: 10.1016/j.ijbiomac.2021.03.199] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 01/01/2023]
Abstract
The current Coronavirus Disease 19 (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) shows similar pathology to MERS and SARS-CoV, with a current estimated fatality rate of 1.4%. Open reading frame 10 (ORF10) is a unique SARS-CoV-2 accessory protein, which contains eleven cytotoxic T lymphocyte (CTL) epitopes each of nine amino acids in length. Twenty-two unique SARS-CoV-2 ORF10 variants have been identified based on missense mutations found in sequence databases. Some of these mutations are predicted to decrease the stability of ORF10 in silico physicochemical and structural comparative analyses were carried out on SARS-CoV-2 and Pangolin-CoV ORF10 proteins, which share 97.37% amino acid (aa) homology. Though there is a high degree of ORF10 protein similarity of SARS-CoV-2 and Pangolin-CoV, there are differences of these two ORF10 proteins related to their sub-structure (loop/coil region), solubility, antigenicity and shift from strand to coil at aa position 26 (tyrosine). SARS-CoV-2 ORF10, which is apparently expressed in vivo since reactive T cell clones are found in convalescent patients should be monitored for changes which could correlate with the pathogenesis of COVID-19.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram 721140, India.
| | - Diksha Attrish
- Dr. B. R. Ambedkar Centre For Biomedical Research (ACBR), University of Delhi (North Campus), Delhi 110007, India
| | - Shinjini Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700009, West Bengal, India
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid 566, Jordan.
| | | | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden.
| | - Murat Seyran
- Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, Austria
| | - Damiano Pizzol
- Italian Agency for Development Cooperation - Khartoum, Sudan Street 33, Al Amarat, Sudan
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand.
| | - Antonio Soares
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA.
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA; Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt.
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, Telangana State, India; Department of Biochemistry, Kakatiya Medical College, Warangal, Telangana State, India.
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| | | | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA.
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8397, Japan.
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia, San Vicente Mártir 46001, Valencia, Spain.
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Purba Medinipur, India
| | - Adam M Brufsky
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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7
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Hassan SS, Aljabali AAA, Panda PK, Ghosh S, Attrish D, Choudhury PP, Seyran M, Pizzol D, Adadi P, Abd El-Aziz TM, Soares A, Kandimalla R, Lundstrom K, Lal A, Azad GK, Uversky VN, Sherchan SP, Baetas-da-Cruz W, Uhal BD, Rezaei N, Chauhan G, Barh D, Redwan EM, Dayhoff GW, Bazan NG, Serrano-Aroca Á, El-Demerdash A, Mishra YK, Palu G, Takayama K, Brufsky AM, Tambuwala MM. A unique view of SARS-CoV-2 through the lens of ORF8 protein. Comput Biol Med 2021; 133:104380. [PMID: 33872970 PMCID: PMC8049180 DOI: 10.1016/j.compbiomed.2021.104380] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 01/07/2023]
Abstract
Immune evasion is one of the unique characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) attributed to its ORF8 protein. This protein modulates the adaptive host immunity through down-regulation of MHC-1 (Major Histocompatibility Complex) molecules and innate immune responses by surpassing the host's interferon-mediated antiviral response. To understand the host's immune perspective in reference to the ORF8 protein, a comprehensive study of the ORF8 protein and mutations possessed by it have been performed. Chemical and structural properties of ORF8 proteins from different hosts, such as human, bat, and pangolin, suggest that the ORF8 of SARS-CoV-2 is much closer to ORF8 of Bat RaTG13-CoV than to that of Pangolin-CoV. Eighty-seven mutations across unique variants of ORF8 in SARS-CoV-2 can be grouped into four classes based on their predicted effects (Hussain et al., 2021) [1]. Based on the geo-locations and timescale of sample collection, a possible flow of mutations was built. Furthermore, conclusive flows of amalgamation of mutations were found upon sequence similarity analyses and consideration of the amino acid conservation phylogenies. Therefore, this study seeks to highlight the uniqueness of the rapidly evolving SARS-CoV-2 through the ORF8.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, 721140, India
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid, 566, Jordan
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
| | - Shinjini Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, West Bengal, India
| | - Diksha Attrish
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi (North Campus), Delhi, 110007, India
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata, 700108, West Bengal, India
| | - Murat Seyran
- Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, Austria
| | - Damiano Pizzol
- Italian Agency for Development Cooperation - Khartoum, Sudan Street 33, Al Amarat, Sudan
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin, 9054, New Zealand
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia, 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229-3900, USA
| | - Antonio Soares
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229-3900, USA
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Hyderabad, 500007, Telangana State, India
| | | | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, 70112, USA
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran and Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Sur, 64849, Monterrey, NL, Mexico Tecnológico De Monterrey, Campus Monterrey, Monterrey, Nuevo León, Mexico
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), PatnaPatna, India
| | - Elrashdy M Redwan
- King Abdulazizi University, Faculty of Science, Department of Biological Science, Saudi Arabia
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA, 70112, USA
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Translational Research Centre San Alberto Magno, Catholic University of Valencia San Vicente Mártir, C/Guillem de Castro 94, 46001, Valencia, Spain
| | - Amr El-Demerdash
- Natural Products and Medicinal Chemistry Department, Institute de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Yogendra K Mishra
- University of Southern Denmark, Mads Clausen Institute, NanoSYD, Alsion 2, 6400 Sønderborg, Denmark
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Italy
| | - Kazuo Takayama
- Center for IPS Cell Research and Application, Kyoto University, Kyoto, 606-8397, Japan
| | - Adam M Brufsky
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
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8
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Seyran M, Hassan SS, Uversky VN, Pal Choudhury P, Uhal BD, Lundstrom K, Attrish D, Rezaei N, Aljabali AAA, Ghosh S, Pizzol D, Adadi P, El-Aziz TMA, Kandimalla R, Tambuwala MM, Lal A, Azad GK, Sherchan SP, Baetas-da-Cruz W, Palù G, Brufsky AM. Urgent Need for Field Surveys of Coronaviruses in Southeast Asia to Understand the SARS-CoV-2 Phylogeny and Risk Assessment for Future Outbreaks. Biomolecules 2021; 11:398. [PMID: 33803118 PMCID: PMC7999587 DOI: 10.3390/biom11030398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 02/06/2023] Open
Abstract
Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is focused on a single isolate of bat coronaviruses (bat CoVs) which does not adequately represent genetically related coronaviruses (CoVs) [...].
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Affiliation(s)
- Murat Seyran
- Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, Währinger Straße, A-1090 Vienna, Austria;
| | - Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal, India;
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India;
| | - Bruce D. Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA;
| | | | - Diksha Attrish
- Dr. B R Ambedkar Center for Biomedical Research (ACBR), University of Delhi (North Camps), Delhi-110007, India;
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran, University of Medical Sciences, Tehran 1419733151, Iran;
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran 1419733151, Iran
| | - Alaa A. A. Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid 566, Jordan;
| | - Shinjini Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700009, West Bengal, India;
| | - Damiano Pizzol
- Italian Agency for Development Cooperation—Khartoum, Sudan Street 33, Al Amarat 13374, Sudan;
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand;
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA;
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Hyderabad 500007, Telangana State, India;
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK;
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN 55905, USA;
| | | | - Samendra P. Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA;
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941901, Brazil;
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy
| | - Adam M. Brufsky
- UPMC Hillman Cancer Center, Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA;
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9
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Seyran M, Pizzol D, Adadi P, El-Aziz TMA, Hassan SS, Soares A, Kandimalla R, Lundstrom K, Tambuwala M, Aljabali AAA, Lal A, Azad GK, Choudhury PP, Uversky VN, Sherchan SP, Uhal BD, Rezaei N, Brufsky AM. Questions concerning the proximal origin of SARS-CoV-2. J Med Virol 2020; 93:1204-1206. [PMID: 32880995 PMCID: PMC7898912 DOI: 10.1002/jmv.26478] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/11/2023]
Affiliation(s)
- Murat Seyran
- Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Doctoral Studies in Natural and Technical Sciences (SPL 44)xs, University of Vienna, Vienna, Austria.,Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Vienna, Austria
| | - Damiano Pizzol
- Italian Agency for Development Cooperation - Khartoum, Al Amarat, Sudan
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Tarek M A El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA.,Department of Zoology, Faculty of Science, Minia University, El-Minia, Egypt
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, West Bengal, India
| | - Antonio Soares
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana, India.,Kakatiya Medical College/MGM-Hospital, DME/TSPSC, Hyderabad, Warangal, Telangana, India
| | | | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, Northern Ireland, UK
| | - Alaa A A Aljabali
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Yarmouk University, Irbid, Jordan
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Pabitra P Choudhury
- Applied Statistics Unit Indian Statistical Institute, Kolkata, West Bengal, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, Louisiana, USA
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, Michigan, USA
| | - Nima Rezaei
- Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Adam M Brufsky
- Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
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10
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Seyran M, Takayama K, Uversky VN, Lundstrom K, Palù G, Sherchan SP, Attrish D, Rezaei N, Aljabali AAA, Ghosh S, Pizzol D, Chauhan G, Adadi P, Mohamed Abd El-Aziz T, Soares AG, Kandimalla R, Tambuwala M, Hassan SS, Azad GK, Pal Choudhury P, Baetas-da-Cruz W, Serrano-Aroca Á, Brufsky AM, Uhal BD. The structural basis of accelerated host cell entry by SARS-CoV-2†. FEBS J 2020; 288:5010-5020. [PMID: 33264497 PMCID: PMC7753708 DOI: 10.1111/febs.15651] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is the causative agent of the pandemic coronavirus disease 2019 (COVID‐19) that exhibits an overwhelming contagious capacity over other human coronaviruses (HCoVs). This structural snapshot describes the structural bases underlying the pandemic capacity of SARS‐CoV‐2 and explains its fast motion over respiratory epithelia that allow its rapid cellular entry. Based on notable viral spike (S) protein features, we propose that the flat sialic acid‐binding domain at the N‐terminal domain (NTD) of the S1 subunit leads to more effective first contact and interaction with the sialic acid layer over the epithelium, and this, in turn, allows faster viral ‘surfing’ of the epithelium and receptor scanning by SARS‐CoV‐2. Angiotensin‐converting enzyme 2 (ACE‐2) protein on the epithelial surface is the primary entry receptor for SARS‐CoV‐2, and protein–protein interaction assays demonstrate high‐affinity binding of the spike protein (S protein) to ACE‐2. To date, no high‐frequency mutations were detected at the C‐terminal domain of the S1 subunit in the S protein, where the receptor‐binding domain (RBD) is located. Tight binding to ACE‐2 by a conserved viral RBD suggests the ACE2‐RBD interaction is likely optimal. Moreover, the viral S subunit contains a cleavage site for furin and other proteases, which accelerates cell entry by SARS‐CoV‐2. The model proposed here describes a structural basis for the accelerated host cell entry by SARS‐CoV‐2 relative to other HCoVs and also discusses emerging hypotheses that are likely to contribute to the development of antiviral strategies to combat the pandemic capacity of SARS‐CoV‐2.
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Affiliation(s)
- Murat Seyran
- Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, Austria.,Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Vienna, Austria
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Japan
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | | | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Italy
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, USA
| | - Diksha Attrish
- Dr. B R Ambedkar Center for Biomedical Research (ACBR), University of Delhi (North Camps), Delhi, India
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid, Jordan
| | - Shinjini Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Damiano Pizzol
- Italian Agency for Development Cooperation - Khartoum, Al Amarat, Sudan
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Mexico
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, TX, USA.,Zoology Department, Faculty of Science, Minia University, El-Minia, Egypt
| | - Antonio G Soares
- Zoology Department, Faculty of Science, Minia University, El-Minia, Egypt
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Tarnaka, India.,Department of Biochemistry, Kakatiya Medical College, Warangal, India
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Paschim Medinipur, India
| | | | | | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, Valencia, Spain
| | - Adam M Brufsky
- Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI, USA
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11
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Hassan SS, Ghosh S, Attrish D, Choudhury PP, Aljabali AAA, Uhal BD, Lundstrom K, Rezaei N, Uversky VN, Seyran M, Pizzol D, Adadi P, Soares A, El-Aziz TMA, Kandimalla R, Tambuwala MM, Azad GK, Sherchan SP, Baetas-da-Cruz W, Takayama K, Serrano-Aroca Á, Chauhan G, Palu G, Brufsky AM. Possible Transmission Flow of SARS-CoV-2 Based on ACE2 Features. Molecules 2020; 25:molecules25245906. [PMID: 33322198 PMCID: PMC7763092 DOI: 10.3390/molecules25245906] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/10/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that is engendering the severe coronavirus disease 2019 (COVID-19) pandemic. The spike (S) protein receptor-binding domain (RBD) of SARS-CoV-2 binds to the three sub-domains viz. amino acids (aa) 22–42, aa 79–84, and aa 330–393 of ACE2 on human cells to initiate entry. It was reported earlier that the receptor utilization capacity of ACE2 proteins from different species, such as cats, chimpanzees, dogs, and cattle, are different. A comprehensive analysis of ACE2 receptors of nineteen species was carried out in this study, and the findings propose a possible SARS-CoV-2 transmission flow across these nineteen species.
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Affiliation(s)
- Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram 721140, India;
| | - Shinjini Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700009, India;
| | - Diksha Attrish
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi (North Campus), Delhi 110007, India;
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India;
| | - Alaa A. A. Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid 566, Jordan;
| | - Bruce D. Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA;
| | | | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran 1416753955, Iran;
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), SE-123 Stockholm, Sweden
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence:
| | - Murat Seyran
- Doctoral studies in natural and technical sciences (SPL 44), University of Vienna, 1010 Wien, Austria;
| | - Damiano Pizzol
- Italian Agency for Development Cooperation—Khartoum, Sudan Street 33, Al Amarat, Khartoum 825109, Sudan;
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand;
| | - Antonio Soares
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 77030, USA; (A.S.); (T.M.A.E.-A.)
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 77030, USA; (A.S.); (T.M.A.E.-A.)
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Hyderabad 500007, India;
- Department of Biochemistry, Kakatiya Medical College, Warangal, Telangana 500022, India
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK;
| | | | - Samendra P. Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA;
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941901, Brazil;
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8501, Japan;
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Translational Research Centre San Alberto Magno, Catholic University of Valencia San Vicente Mártir, c/Guillem de Castro 94, 46001 Valencia, Spain;
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, Monterrey 64849, Nuevo León, Mexico;
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy;
| | - Adam M. Brufsky
- Division of Hematology/Oncology, Department of Medicine, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA;
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12
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Hassan SS, Choudhury PP, Uversky VN, Dayhoff GW, Aljabali AAA, Uhal BD, Lundstrom K, Rezaei N, Seyran M, Pizzol D, Adadi P, Lal A, Soares A, Abd El-aziz TM, Kandimalla R, Tambuwala M, Azad GK, Sherchan SP, Baetas-da-cruz W, Takayama K, Serrano-aroca Á, Chauhan G, Palu G, Brufsky AM. Variability of Accessory Proteins Rules the SARS-CoV-2 Pathogenicity.. [DOI: 10.1101/2020.11.06.372227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
AbstractThe coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) which is pandemic with an estimated fatality rate less than 1% is ongoing. SARS-CoV-2 accessory proteins ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10 with putative functions to manipulate host immune mechanisms such as interferons, immune signaling receptor NLRP3 (NOD-, LRR-, and pyrin domain-containing 3) inflammasome, inflammatory cytokines such as interleukin 1β(IL-1β) are critical in COVID-19 pathology. Outspread variations of each of the six accessory proteins of all complete proteomes (available as of October 26, 2020, in the National Center for Biotechnology Information depository) of SARS-CoV-2, were observed across six continents. Across all continents, the decreasing order of percentage of unique variations in the accessory proteins was found to be ORF3a>ORF8>ORF7a>ORF6>ORF10>ORF7b. The highest and lowest unique variations of ORF3a were observed in South America and Oceania, respectively. This finding suggests that the wide variations of accessory proteins seem to govern the pathogenicity of SARS-CoV-2, and consequently, certain propositions and recommendations can be made in the public interest.
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Lundstrom K, Seyran M, Pizzol D, Adadi P, Mohamed Abd El-Aziz T, Hassan SS, Soares A, Kandimalla R, Tambuwala MM, Aljabali AAA, Kumar Azad G, Pal Choudhury P, Uversky VN, Sherchan SP, Uhal BD, Rezaei N, Brufsky AM. Viewpoint: Origin of SARS-CoV-2. Viruses 2020; 12:v12111203. [PMID: 33105685 PMCID: PMC7690418 DOI: 10.3390/v12111203] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 01/13/2023] Open
Abstract
The origin of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) virus causing the COVID-19 pandemic has not yet been fully determined. Despite the consensus about the SARS-CoV-2 origin from bat CoV RaTG13, discrepancy to host tropism to other human Coronaviruses exist. SARS-CoV-2 also possesses some differences in its S protein receptor-binding domain, glycan-binding N-terminal domain and the surface of the sialic acid-binding domain. Despite similarities based on cryo-EM and biochemical studies, the SARS-CoV-2 shows higher stability and binding affinity to the ACE2 receptor. The SARS-CoV-2 does not appear to present a mutational “hot spot” as only the D614G mutation has been identified from clinical isolates. As laboratory manipulation is highly unlikely for the origin of SARS-CoV-2, the current possibilities comprise either natural selection in animal host before zoonotic transfer or natural selection in humans following zoonotic transfer. In the former case, despite SARS-CoV-2 and bat RaTG13 showing 96% identity some pangolin Coronaviruses exhibit very high similarity to particularly the receptor-binding domain of SARS-CoV-2. In the latter case, it can be hypothesized that the SARS-CoV-2 genome has adapted during human-to-human transmission and based on available data, the isolated SARS-CoV-2 genomes derive from a common origin. Before the origin of SARS-CoV-2 can be confirmed additional research is required
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Affiliation(s)
| | - Murat Seyran
- Doctoral Studies in Natural Sciences and Technology SPL44, University of Vienna, 1010 Vienna, Austria;
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Vienna, 1010 Vienna, Austria
| | - Damiano Pizzol
- Department of Global Health, Italian Agency for Development Cooperation—Khartoum, Al Amarat 111111, Sudan;
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand;
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA; (T.M.A.E.-A.); (A.S.)
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, West Bengal 721140, India;
| | - Antonio Soares
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA; (T.M.A.E.-A.); (A.S.)
| | - Ramesh Kandimalla
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, India;
- Department of Biochemistry, Kakatiya Medical College/MGM-Hospital, Hyderabad 500007, India
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK;
| | - Alaa A. A. Aljabali
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan;
| | | | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata, West Bengal 700108, India;
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Samendra P. Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA;
| | - Bruce D. Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA;
| | - Nima Rezaei
- Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran 1419733151, Iran;
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran 1419733151, Iran
| | - Adam M. Brufsky
- UPMC Hillman Cancer Center, Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA;
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Hassan SS, Attrish D, Ghosh S, Choudhury PP, Uversky VN, Uhal BD, Lundstrom K, Rezaei N, Aljabali AAA, Seyran M, Pizzol D, Adadi P, Abd El-aziz TM, Soares A, Kandimalla R, Tambuwala M, Lal A, Azad GK, Sherchan SP, Baetas-da-cruz W, Palù G, Brufsky AM. Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2.. [DOI: 10.1101/2020.09.06.284976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
ABSTRACTThe global public health is endangered due to COVID-19 pandemic, which is caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Despite having similar pathology to MERS and SARS-CoV, the infection fatality rate of SARS-CoV-2 is likely lower than 1%. SARS-CoV-2 has been reported to be uniquely characterized by the accessory protein ORF10, which contains eleven cytotoxic T lymphocyte (CTL) epitopes of nine amino acids length each, across various human leukocyte antigen (HLA) subtypes. In this study, all missense mutations found in sequence databases were examined across twnety-two unique SARS-CoV-2 ORF10 variants that could possibly alter viral pathogenicity. Some of these mutations decrease the stability of ORF10, e.g. I4L and V6I were found in the MoRF region of ORF10 which may also possibly contribute to Intrinsic protein disorder. Furthermore, a physicochemical and structural comparative analysis was carried out on SARS-CoV-2 and Pangolin-CoV ORF10 proteins, which share 97.37% amino acid homology. The high degree of physicochemical and structural similarity of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV open questions about the architecture of SARS-CoV-2 due to the disagreement of these two ORF10 proteins over their sub-structure (loop/coil region), solubility, antigenicity and change from the strand to coil at amino acid position 26, where tyrosine is present. Altogether, SARS-CoV-2 ORF10 is a promising pharmaceutical target and a protein which should be monitored for changes which correlate to change pathogenesis and clinical course of COVID-19 infection.
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Çabuk H, Dedeoğlu SS, Adaş M, Tekin AÇ, Seyran M, Ayanoğlu S. Medial Spike and Obesity Associate with Open Reduction in Type III Supracondylar Humeral Fracture. Acta Chir Orthop Traumatol Cech 2016; 83:102-105. [PMID: 27167414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
UNLABELLED PURPOSE OF THE STUDY Although supracondylar humeral fractures represent a major part of the pediatric fractures, no classification system or radiological characteristics describes which supracondylar fractures require open reduction. We aim to evaluate the factors that lead us to perform open reduction during operation. MATERIAL AND METHODS We retrospectively evaluated 57 patients who underwent operation for type III supracondylar fracture, and divided them into two groups; those with open reduction and internal fixation, and those with closed reduction and percutaneous fixation. The two groups were compared based on age, gender, BMI by age, medial spike angle of the fracture, medial spike-skin distance and rotation angle between the fractured fragments. RESULTS Of all patients, 46 (81.71%) underwent closed reduction and percutaneous fixation (CRPF) and 11 (19.29%) were treated with open reduction and internal fixation (ORIF). BMI by age was remarkably higher in the ORIF group (p = 0.00). And medial spike angle was smaller in the ORIF group (p = 0.014). DISCUSSION Closed reduction and percutanous fixation is the main treatment of supracondylar humeral fractuers. Open reduction in supracondylar humeral fractures could be associate with complications and cosmetic lesions. Many studies indicates that obesity is high risk factor for complex fractures as well as preoperative and postoperative complications. A prominant medial spike could associate with muscle entrapment, and obliquity of the fracture line. It could be also an indirect finding of instablity of the fracture. CONCLUSION We suggest that a smaller medial spike angle and a higher BMI in children with Type III supracondylar humeral fractures may require open reduction, and it is unreasonable to avoid open reduction in cases where closed reduction is not achieved. KEY WORDS supracondylar humerus, open reduction, obesity, medial spike angle.
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Affiliation(s)
- H Çabuk
- Okmeydanı Training and Research Hospital, Department of Orthopedics and Traumatology, İstanbul, Türkiye
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Seyran M, Nischwitz C, Lewis KJ, Gitaitis RD, Brenneman TB, Stevenson KL. Phylogeny of the pecan scab fungus Fusicladium effusum G. Winter based on the cytochrome b gene sequence. Mycol Prog 2009. [DOI: 10.1007/s11557-009-0638-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Palle SR, Miao H, Seyran M, Louzada ES, da Graça JV, Skaria M. Evidence for Association of Citrus psorosis virus with Symptomatic Trees and an Olpidium -like Fungus in Texas. ACTA ACUST UNITED AC 2005. [DOI: 10.5070/c53mc2b02s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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