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Momenifar N, Pirouzfar M, Hashemian Z, Daneshvar Amoli A. Development of an optimized RT-LAMP test for the detection of SARS-CoV-2. Biologicals 2023; 84:101716. [PMID: 37801803 DOI: 10.1016/j.biologicals.2023.101716] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 09/10/2022] [Revised: 06/17/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023] Open
Abstract
SARS-COV-2 is the causative agent of an acute respiratory syndrome called Coronavirus disease 2019 (COVID-19) with a varying mortality rate from 2019 to 2022. There are several measures for control and prevention of Covid-19 including using mask, vaccine injections, as well as screening the potential cases. We aimed to design and develop a molecular method (RT-LAMP) for detecting coronavirus in biological samples that is cheaper, faster and easier than conventional molecular methods. In this study, various reaction components were explored to make the optimal combination of an RT-LAMP master mix composition. The results revealed the ability of this RT-LAMP test in specifically identifying 100 copies of mixture of N and E genes in just 30-45 min. This study demonstrated the reliable performance of the RT-LAMP method for the detection of SARS-COV-2 in biological samples. Given the significant advantages of this method compared to the gold standard qRT-PCR, it can be employed as a promising tool for the diagnosis of coronavirus as well as other pathogenic viruses.
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Affiliation(s)
- Navid Momenifar
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Mohammad Pirouzfar
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Zohreh Hashemian
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
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Ebadi A, Momenifar N, Yazdani S, Gholizadeh O, Poortahmasebi V. Identification of hub genes and molecular pathways in human T-lymphotropic virus type 1 associated diseases using protein-protein interactions networks. IJM 2022; 14:125-132. [PMID: 35664724 PMCID: PMC9085549 DOI: 10.18502/ijm.v14i1.8814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Background and Objectives: Human T-lymphotropic virus type 1 (HTLV-1) is the cause of adult T-cell leukemia (ATL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The present study aims to analyze gene expression patterns in ATL and HAM/TSP. Materials and Methods: Microarray gene expression profiling of T-lymphocytes from HTLV-1 associated disease and healthy control were obtained from Gene Expression Omnibus (GEO). Several bioinformatics tools were used to identify differentially expressed genes (DEGs). Among the generated DEGs, we constructed protein-protein interaction (PPI) between HAM/TSM and ATL in comparison to asymptomatic carriers (ACs). Subsequently, gene ontology (GO) and topological analysis were performed. Results: We found that the majority of DEGs in ATL and HAM/TSP were importantly implicated in immune response categories. The nodes and edges number of normal-AC, AC-ATL and ATL-HAM/TSP PPIs were 168 and 145, 116 and 97, and 275 and 327, respectively. Based on the topological analyses of protein-protein interaction networks, APP (Amyloid Beta Precursor Protein) was detected as a critical player in progression of HTLV-1 disease. Conclusion: Dysregulation of immune response associated transcripts play a critical role in HTLV-1 disease progression. Immune response associated genes may be biomarker for prognosis in cancer development and therapeutic targets.
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Affiliation(s)
- Amin Ebadi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Navid Momenifar
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Shaghayegh Yazdani
- Department of Microbiology, Faculty of Advanced Science & Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Omid Gholizadeh
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahdat Poortahmasebi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
- Corresponding author: Vahdat Poortahmasebi, Ph.D, Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran. Tel: +98-4133364661, Fax: +98-4133364661,
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Abstract
Colorectal cancer (CRC) is one of the most malignant cancer types, characterized by elevated mortality rate and treatment resistance. Despite the progress achieved in the explanation of the molecular basis of the disease as well as introducing potential biomarkers in the clinical practice, further investigation is essential to identify innovative molecules that contribute to colorectal carcinogenesis. Circular RNAs (circRNAs) are a novel and unexplored RNA type, associated with various human pathological conditions. Recently, circRNAs have been identified to be enriched and stable in exosomes and can exert their functions when exosomes reach neighboring or distant cells. Increasing evidence indicates that these so called exosomal circRNAs (exo-circRNAs) act as signaling molecules to regulate cancer proliferation, metastasis, and sensitivity to radio- and chemotherapy. This review aims to discuss the latest progress in exo-circRNAs studies in CRC with an emphasis on their potential as promising diagnostic molecular markers and therapeutic targets.
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Affiliation(s)
- Faezeh Vakhshiteh
- Nanotechnology Research Centre, Faculty of Pharmacy, Tehran University of Medical, Sciences, Tehran, Iran.
| | - Shokoufeh Hassani
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.,Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Navid Momenifar
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Fatemeh Pakdaman
- Department of Genetics, Faculty of Science, University of Shahrekord, Shahrekord, Iran
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Hatatian F, Babakhani F, Gudarzi H, Momenifar N, Norouzi M, Shafieifar M, Kakavandi E, Sadeghi A, Sharbatdar-Alaei H, Farahmand M, Amiri-Roudy M, Jahantigh HR, Madihi M, Borhani K, Ajorloo M, Hedayat Yaghoobi M. Relative Frequency of Blood-Borne Viruses in Hemodialysis-Dependent and Kidney Transplant Recipients in Iran. Iran J Public Health 2021; 49:2136-2143. [PMID: 33708734 PMCID: PMC7917503 DOI: 10.18502/ijph.v49i11.4731] [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] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background: Hemodialysis (HD) patients and kidney transplant (KT) recipients are exposed to be infected by blood-borne viruses (BBVs). Current study was conducted to evaluate the prevalence of BBVs in HD and KT patients in the whole Iranian population. Methods: From Jan 2016 to Dec 2017, 174 hemodialysis and 139 kidney transplant recipients enrolled in this survey. After blood sampling, serum samples were detected for HBV, HCV, HCMV, HIV and HTLV antibodies. Seropositive samples confirmed by Polymerase chain reaction (PCR) method. Results: Overall, 6 (3.44%) and 3 (2.15%) of hemodialysis-dependent and transplantation patients had evidence of HCV infection, whereas no patients were HIV and HBV positive, two cases (1.14%) of hemodialysis and one case (0.71%) of transplantation patients demonstrated the HTLV-1 infection. 52 (37.4%) of patients received graft were positive for HCMV antibody. In addition, our study showed a co-infection of HCMV with HCV (3 patients, 2.15%) in transplantation patients. Conclusion: Prevalence of BBVs infection was lower in comparison to the previous studies. The current strict infection control practices in Iran appear to be effective in limiting dialysis and related infections after transplantation. Because BBVs infections constantly occur especially in dialysis and after transplantation units, our data will be useful to build a new strategic plan for the elimination of BBVs infection in kidney therapycenters.
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Affiliation(s)
- Fatemeh Hatatian
- Inflammation and Inflammatory Disease Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzad Babakhani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hoda Gudarzi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Navid Momenifar
- Human and Animal Cell Bank, Iranian Biological Resource Center, Academic Center of Education, Culture and Research, Tehran, Iran
| | - Mehdi Norouzi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Mina Shafieifar
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ehsan Kakavandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmadreza Sadeghi
- Iranian Tissue Bank and Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hedyeh Sharbatdar-Alaei
- Department of Microbial Biotechnology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Mohammad Farahmand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Maedeh Amiri-Roudy
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Jahantigh
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mobina Madihi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Kiandokht Borhani
- Department of Virology, School of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehdi Ajorloo
- Hepatitis Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran.,Department of Clinical Laboratory Sciences, School of Allied Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Mojtaba Hedayat Yaghoobi
- Department of Infectious Disease, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
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Razavi Pashabayg C, Momenifar N, Malekpour SA, Sadeghi M, Rahimi Foroushani A, Rafatpanah H, Valizadeh N, Sabet F, Jazayeri SM, Keyvani H, Rezaee SA, Norouzi M. Phylogenetic and phylodynamic study of Human T-cell lymphotropic virus Type 1 (HTLV-1) in Iran. Infect Genet Evol 2020; 85:104426. [PMID: 32561293 DOI: 10.1016/j.meegid.2020.104426] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/29/2020] [Accepted: 06/14/2020] [Indexed: 10/24/2022]
Abstract
Human T-lymphotropic virus type-1 (HTLV-1) is a retrovirus that causes the neurological disorder HTLV-1 associated myelopathy/ tropical spastic paraparesis (HAM/TSP) and/or adult T-cell leukemia/lymphoma (ATLL). Iran is one of the endemic regions of the HTLV-1 in the Middle East. To infer the origin of the virus in Iran and to follow the movements of human population and routes of virus spread to this country, phylogenetic and phylodynamic analyses were performed. To this purpose, the long terminal repeat (LTR) region of HTLV-1 was used. New LTR sequences were obtained from 100 blood samples which infected with HTLV-1. Moreover, all Iranian LTR sequences which have been reported so far, were obtained from GenBank database. Sequences were aligned and maximum-likelihood and Bayesian tree topologies were explored. After identification of Iranian specific cluster, molecular-clock and coalescent models were used to estimate time to the most recent common ancestor (tMRCA). Bayesian Skyline Plots (BSP), representing population dynamics HTLV-1 strains back to the MRCA, were estimated using BEAST software. Phylogenetic analysis demonstrated that the Iranian, Kuwaiti, German, Israelite and southern Indian isolates are located within the widespread "transcontinental" subgroup A clade of HTLV-1 Cosmopolitan subtype a. Molecular clock analysis of the Iranian cluster dated back their respective tMRCA to be 1290 AC with a 95% HPD confidence intervals (918, 1517). BSPs indicated a rapid exponential growth rate in the effective number of infections prior the 15th century. Our results support the hypothesis of a multiple introductions of HTLV-1 into Iran with the majority of introductions occurring in prior the 15th century, at the same time the Mongol invasion of Iran. Our results further suggest that HTLV-1 introduction into Iran was facilitated by the commercial/migratory linkage as known as the ancient Silk Road which linked China to Antioch (now in Turkey).
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Affiliation(s)
- Cobra Razavi Pashabayg
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Navid Momenifar
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Seyed Amir Malekpour
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran; Department of Biomedical Informatics, The Ohio State University, OH 43210, USA
| | - Mehdi Sadeghi
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran; National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Abbas Rahimi Foroushani
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Houshang Rafatpanah
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Narges Valizadeh
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Faezeh Sabet
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Jazayeri
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran; Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Keyvani
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Abdolrahim Rezaee
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mehdi Norouzi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran; Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
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