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Abbasi H, Behrouzikhah M, Divbandi M, Tabaraei A, Khosravi A, Razavi Nikoo H. Genomic analysis of SARS-CoV-2 variants: diagnosis and vaccination challenges. J Biomol Struct Dyn 2023; 41:14939-14951. [PMID: 37676289 DOI: 10.1080/07391102.2023.2252069] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 02/18/2023] [Indexed: 09/08/2023]
Abstract
SARS-CoV-2 put a heavy financial burden on the healthcare system, with millions of laboratory-confirmed cases and deaths worldwide in the last 2 years. During the seventh wave of this pandemic, the continuously evolving nature of SARS-CoV-2 resulted in the emergence of new variants that harbor different mutations. Mutations are associated with changes in the virus behavior, including increased transmissibility, increased virulence, and evasion of neutralizing antibodies. Currently, we need detailed and comprehensive genomic information on all SARS-CoV-2 variants. One of the key points in this study was the genome survey of mutation profiles across variants as a genomic data source, to determine the efficiency of RT-qPCR assays. We also used the source to calculate the binding affinity changes of neutralizing antibodies-mutant receptor binding domain (RBD) complexes and determine vaccine efficacy. Our result revealed that the number of nucleotide mismatches is variable in the WHO-recommended primer-probe sets. Mismatches located at the 3' ends of the oligonucleotide, may lead to false-negative results. Only the primer-probe sets designed by the Ministry of Public Health of Thailand were exclusive and cannot detect the omicron variant reliably. Binding affinity changes showed that E484K was more deleterious than other mutations and decreased stability between the mutant RBD protein and neutralizing antibodies. The Omicrons show the highest change in binding affinity which may lead to immune escape and increase transmissibility. Additionally, the 7D6 monoclonal antibody in the 7eam complex could neutralize all variants of SARS-CoV-2. We strongly recommend creating and improving a matrix accuracy by processing a large number of SARS-CoV-2 sequences to update RT-qPCR assays and identified immunogenic residues among conserved RBD. Also, a detail computational analysis is needed to investigate distinctive amino acid substitution patterns which may be foundational in the vaccines. Finally, designing in-vitro studies can help confirm the present study and manage COVID-19 patients.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hamidreza Abbasi
- Department of Medical Biotechnology, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mehdi Behrouzikhah
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Marzieh Divbandi
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Alijan Tabaraei
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ayyoob Khosravi
- Stem Cell Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Molecular Medicine, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
| | - Hadi Razavi Nikoo
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
- Infectious Disease Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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Hassanpour M, Tazarghi A, Teimoori A, Tabaraei A, Erfani-Moghadam V, Sedigheh AY, Nikoo HR. Curcumin inhibits the replication of rotavirus in vitro. Acta Virol 2022; 66:166-171. [DOI: 10.4149/av_2022_206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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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Abbasi H, Tabaraei A, Hosseini SM, Khosravi A, Nikoo HR. Real-time PCR Ct value in SARS-CoV-2 detection: RdRp or N gene? Infection 2021; 50:537-540. [PMID: 34331262 PMCID: PMC8323962 DOI: 10.1007/s15010-021-01674-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022]
Affiliation(s)
- Hamidreza Abbasi
- Department of Medical Biotechnology, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
| | - Alijan Tabaraei
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, P.O. Box: 4934174515, Gorgan, Iran
| | - Seyed Mehran Hosseini
- Department of Physiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ayyoob Khosravi
- Stem Cell Research Center, Golestan University of Medical Sciences, P.O. Box: 4934174515, Gorgan, Iran. .,Department of Molecular Medicine, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran.
| | - Hadi Razavi Nikoo
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, P.O. Box: 4934174515, Gorgan, Iran. .,Infectious Disease Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
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Masoudi M, Teimoori A, Tabaraei A, Shahbazi M, Divbandi M, Lorestani N, Yamchi A, Nikoo HR. Advanced sequence optimization for the high efficient yield of human group A rotavirus VP6 recombinant protein in Escherichia coli and its use as immunogen. J Med Virol 2021; 93:3549-3556. [PMID: 32940917 DOI: 10.1002/jmv.26522] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/14/2020] [Accepted: 09/08/2020] [Indexed: 11/09/2022]
Abstract
Rotavirus is the important etiological agents of infectious diarrhea among children under 5 years old. Rotaviruses are divided into 10 serogroups (A-J) and each group is based on genetic properties of major structural protein VP6. We designed a novel VP6 sequence optimization to increase the expression level of this protein. Numerous factors such as codon adaptation index, codon pair bias, and guanine-cytosine content were adapted based on Escherichiacoli codon usage. In addition, the ribosome binding site (RBS) of pET-15b was redesigned by the RBS calculator and the secondary structure of VP6 messenger RNA was optimized in the whole length of the coding sequence. Various factors including isopropyl beta- d-thiogalactoside (IPTG) concentration, temperature, and induction time were analyzed for the optimization of the best expression in E. coli by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and western blotting. The recombinant VP6 (rVP6) protein was purified by the Ni-sepharose and then the hyperimmune sera were generated against rVP6 in rabbits. Among three different temperatures, IPTG concentrations, and postinductions, the level of rVP6 was higher at 37°C, 1 mM of IPTG, and 8 h, respectively. Also, the high expression level of rVP6 was obtained in the insoluble aggregate form (43.8 g/L). After purification, the yield of rVP6 was 10.83 g/L. The rVP6 specific antiserum was confirmed by both immunofluorescent and western blotting. The versatile sequence optimization was the reason to produce a high level of rVP6 compared to other reports and can potentially apply to produce cheaper commercial kits to diagnose serological tests and new rotavirus vaccines.
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Affiliation(s)
- Maha Masoudi
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ali Teimoori
- Department of Virology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Alijan Tabaraei
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Majid Shahbazi
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Marzieh Divbandi
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Nazanin Lorestani
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ahad Yamchi
- Department of Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Hadi Razavi Nikoo
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
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Raeisi M, Tabaraei A, Hashemi M, Behnampour N. Effect of sodium alginate coating incorporated with nisin, Cinnamomum zeylanicum , and rosemary essential oils on microbial quality of chicken meat and fate of Listeria monocytogenes during refrigeration. Int J Food Microbiol 2016; 238:139-145. [DOI: 10.1016/j.ijfoodmicro.2016.08.042] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 08/20/2016] [Accepted: 08/29/2016] [Indexed: 11/25/2022]
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Ayasi H, Dastar B, Ghoorchi T, Hashemi S, Tabaraei A. Effect of utilization of maize silage in moult inducing diets on performance, immune response and bone quality in laying hens. J Anim Feed Sci 2016. [DOI: 10.22358/jafs/65587/2016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Kaleji H, Tabaraei A, Abbasi A, Javeed N, Bazoori M, Golmohamadi R, Moradi A. Expression Analysis of Cellular Mir-29a and mir-29b in HIV Positive Patients. mljgoums 2015. [DOI: 10.18869/acadpub.mlj.9.5.23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Ghaemi A, Soleimanjahi H, Razeghi S, Gorji A, Tabaraei A, Moradi A, Alizadeh A, Vakili MA. Genistein induces a protective immunomodulatory effect in a mouse model of cervical cancer. Iran J Immunol 2012; 9:119-127. [PMID: 22735799] [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: 06/01/2023]
Abstract
BACKGROUND Genistein (GEN), a naturally occurring flavonoid present in soy bean, has attracted scientific interest for its possible benefits in cancer. OBJECTIVE The potential immunomodulatory effects of genistein on the immune system and against TC-1 tumor cell line were evaluated in adult female C57BL/6 mice. METHODS Mice were treated with GEN 10 days before to 10 days after the tumor induction. Thirty days after the last GEN treatment, lymphocyte proliferation, Lactase Dehydrogenase (LDH) cytolytic activity and cytokine secretion were analyzed in GEN and control groups. RESULTS The results showed that ingestion of genistein significantly increased lymphocyte proliferation and LDH release. Furthermore, the treatment with genistein also caused a significant increment in interferon gamma (IFN-γ). In addition, the treatment achieved significant therapeutic effect in tumor models compared to the control group. These results indicated that the effect of GEN on tumor growth may be attributed to its effect on lymphocyte proliferation, cytolytic activity and IFN-γ production. CONCLUSION These results demonstrate that GEN exerts an immunomodulatory effect in a mouse model of Human Papillomavirus (HPV) associated-cervical cancer.
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Affiliation(s)
- Amir Ghaemi
- Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran, e-mail:
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