1
|
Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma. Diagnostics (Basel) 2022; 12:diagnostics12071599. [PMID: 35885505 PMCID: PMC9322174 DOI: 10.3390/diagnostics12071599] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/21/2022] [Accepted: 06/26/2022] [Indexed: 11/16/2022] Open
Abstract
Nucleic acid extraction from biological samples is an important step for hepatitis C virus (HCV) diagnosis. However, such extractions are mostly based on silica-based column methodologies, which may limit their application for on-site diagnosis. A simple, rapid, and field-deployable method for RNA extraction is still needed. In this study, we evaluated the efficacy of four simple RNA extraction methods for the detection of HCV in plasma samples: a silica-membrane-based method, a magnetic-beads-based method, boiling with diethyl pyrocarbonate (DEPC)-treated distilled water, and using a commercial lysis buffer. HCV RNA was detected using both real-time reverse transcription polymerase chain reaction (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP). Using real-time RT-PCR, extracted RNA from the silica-membrane-based and magnetic-beads-based methods had a 100% detection rate for RNA extraction from plasma. Using RT-LAMP, extracted RNA from the silica-membrane-based method showed a 66% detection rate, while the magnetic-beads-based method had a 62% detection rate. In summary, magnetic-beads-based extraction can be used as an alternative RNA extraction method for on-site HCV detection. Boiling with DEPC-treated distilled water was not appropriate for low HCV load samples, and boiling with a lysis buffer was not recommended.
Collapse
|
2
|
Nasir S, Majeed MI, Nawaz H, Rashid N, Ali S, Farooq S, Kashif M, Rafiq S, Bano S, Ashraf MN, Abubakar M, Ahmad S, Rehman A, Amin I. Surface enhanced Raman spectroscopy of RNA samples extracted from blood of hepatitis C patients for quantification of viral loads. Photodiagnosis Photodyn Ther 2020; 33:102152. [PMID: 33348077 DOI: 10.1016/j.pdpdt.2020.102152] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/23/2020] [Accepted: 12/14/2020] [Indexed: 01/31/2023]
Abstract
BACKGROUND Raman spectroscopy is a promising technique to analyze the body fluids for the purpose of non-invasive disease diagnosis. OBJECTIVES To develop a surface-enhanced Raman spectroscopy (SERS) based method for qualitative and quantitative analysis of HCV from blood samples. METHODS SERS was employed to characterize the Hepatitis C viral RNA extracted from different blood samples of hepatitis C virus (HCV) infected patients with predetermined viral loads in comparison with total RNA of healthy individuals. The SERS measurements were performed on 27 extracted RNA samples including low viral loads, medium viral loads, high viral loads and healthy/negative viral load samples. For this purpose, silver nanoparticles (Ag NPs) were used as SERS substrates. Furthermore, multivariate data analysis technique, Principal Component Analysis (PCA) and Partial Least Square Regression (PLSR) were also performed on SERS spectral data. RESULTS The SERS spectral features due to biochemical changes in the extracted RNA samples associated with the increasing viral loads were established which could be employed for HCV diagnostic purpose. PCA was found helpful for the differentiation between Raman spectral data of RNA extracted from hepatitis infected and healthy blood samples. PLSR model is established for the determination of viral loads in HCV positive RNA samples with 99 % accuracy. CONCLUSION SERS can be employed for qualitative and quantitative analysis of HCV from blood samples.
Collapse
Affiliation(s)
- Saira Nasir
- Department of Chemistry, University of Agriculture Faisalabad, 38040, Pakistan
| | | | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, 38040, Pakistan.
| | - Nosheen Rashid
- Department of Chemistry, University of Central Punjab, Lahore, Faisalabad Campus, Pakistan
| | - Saqib Ali
- Department of Chemistry, University of Agriculture Faisalabad, 38040, Pakistan
| | - Sidra Farooq
- Department of Chemistry, University of Agriculture Faisalabad, 38040, Pakistan
| | - Muhammad Kashif
- Department of Chemistry, University of Agriculture Faisalabad, 38040, Pakistan
| | - Sidra Rafiq
- Department of Chemistry, University of Agriculture Faisalabad, 38040, Pakistan
| | - Saira Bano
- Department of Chemistry, University of Agriculture Faisalabad, 38040, Pakistan
| | | | - Muhammad Abubakar
- Department of Chemistry, University of Agriculture Faisalabad, 38040, Pakistan
| | - Shamsheer Ahmad
- Department of Chemistry, University of Agriculture Faisalabad, 38040, Pakistan
| | - Asma Rehman
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P. O. Box 577, Jhang Road Faisalabad, Pakistan
| | - Imran Amin
- PCR Laboratory, PINUM Hospital, Faisalabad, Pakistan
| |
Collapse
|
3
|
Gurunathan S, Qasim M, Choi Y, Do JT, Park C, Hong K, Kim JH, Song H. Antiviral Potential of Nanoparticles-Can Nanoparticles Fight Against Coronaviruses? NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E1645. [PMID: 32825737 PMCID: PMC7557932 DOI: 10.3390/nano10091645] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/08/2020] [Accepted: 08/18/2020] [Indexed: 12/12/2022]
Abstract
Infectious diseases account for more than 20% of global mortality and viruses are responsible for about one-third of these deaths. Highly infectious viral diseases such as severe acute respiratory (SARS), Middle East respiratory syndrome (MERS) and coronavirus disease (COVID-19) are emerging more frequently and their worldwide spread poses a serious threat to human health and the global economy. The current COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of 27 July 2020, SARS-CoV-2 has infected over 16 million people and led to the death of more than 652,434 individuals as on 27 July 2020 while also causing significant economic losses. To date, there are no vaccines or specific antiviral drugs to prevent or treat COVID-19. Hence, it is necessary to accelerate the development of antiviral drugs and vaccines to help mitigate this pandemic. Non-Conventional antiviral agents must also be considered and exploited. In this regard, nanoparticles can be used as antiviral agents for the treatment of various viral infections. The use of nanoparticles provides an interesting opportunity for the development of novel antiviral therapies with a low probability of developing drug resistance compared to conventional chemical-based antiviral therapies. In this review, we first discuss viral mechanisms of entry into host cells and then we detail the major and important types of nanomaterials that could be used as antiviral agents. These nanomaterials include silver, gold, quantum dots, organic nanoparticles, liposomes, dendrimers and polymers. Further, we consider antiviral mechanisms, the effects of nanoparticles on coronaviruses and therapeutic approaches of nanoparticles. Finally, we provide our perspective on the future of nanoparticles in the fight against viral infections.
Collapse
Affiliation(s)
- Sangiliyandi Gurunathan
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea; (S.G.); (Y.C.); (J.T.D.); (C.P.); (K.H.); (J.-H.K.)
| | - Muhammad Qasim
- Center of Bioengineering and Nanomedicine, Department of Food Science, University of Otago, Dunedin 9054, New Zealand;
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea; (S.G.); (Y.C.); (J.T.D.); (C.P.); (K.H.); (J.-H.K.)
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea; (S.G.); (Y.C.); (J.T.D.); (C.P.); (K.H.); (J.-H.K.)
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea; (S.G.); (Y.C.); (J.T.D.); (C.P.); (K.H.); (J.-H.K.)
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea; (S.G.); (Y.C.); (J.T.D.); (C.P.); (K.H.); (J.-H.K.)
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea; (S.G.); (Y.C.); (J.T.D.); (C.P.); (K.H.); (J.-H.K.)
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea; (S.G.); (Y.C.); (J.T.D.); (C.P.); (K.H.); (J.-H.K.)
| |
Collapse
|
4
|
Carinelli S, Martí M, Alegret S, Pividori MI. Biomarker detection of global infectious diseases based on magnetic particles. N Biotechnol 2015; 32:521-32. [PMID: 25917978 DOI: 10.1016/j.nbt.2015.04.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 04/17/2015] [Accepted: 04/17/2015] [Indexed: 10/23/2022]
Abstract
Infectious diseases affect the daily lives of millions of people all around the world, and are responsible for hundreds of thousands of deaths, mostly in the developing world. Although most of these major infectious diseases are treatable, the early identification of individuals requiring treatment remains a major issue. The incidence of these diseases would be reduced if rapid diagnostic tests were widely available at the community and primary care level in low-resource settings. Strong research efforts are thus being focused on replacing standard clinical diagnostic methods, such as the invasive detection techniques (biopsy or endoscopy) or expensive diagnostic and monitoring methods, by affordable and sensitive tests based on novel biomarkers. The development of new methods that are needed includes solid-phase separation techniques. In this context, the integration of magnetic particles within bioassays and biosensing devices is very promising since they greatly improve the performance of a biological reaction. The diagnosis of clinical samples with magnetic particles can be easily achieved without pre-enrichment, purification or pretreatment steps often required for standard methods, simplifying the analytical procedures. The biomarkers can be specifically isolated and preconcentrated from complex biological matrixes by magnetic actuation, increasing specificity and the sensitivity of the assay. This review addresses these promising features of the magnetic particles for the detection of biomarkers in emerging technologies related with infectious diseases affecting global health, such as malaria, influenza, dengue, tuberculosis or HIV.
Collapse
Affiliation(s)
- Soledad Carinelli
- Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Mercè Martí
- Laboratory of Cellular Immunology, Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Salvador Alegret
- Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - María Isabel Pividori
- Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain.
| |
Collapse
|
5
|
Albertoni G, Castelo Girão MJB, Schor N. Mini review: current molecular methods for the detection and quantification of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus type 1. Int J Infect Dis 2014; 25:145-9. [PMID: 24927665 DOI: 10.1016/j.ijid.2014.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 04/01/2014] [Accepted: 04/09/2014] [Indexed: 12/11/2022] Open
Abstract
The detection of acute human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) infection is vital for controlling the spread of HIV, HBV, and HCV to uninfected individuals. Considering that these viruses have high replication rates and are undetectable by serological markers, early detection upon transmission is crucial. Various nucleic acid assays have been developed for diagnostics and therapeutic monitoring of infections. In the past decade, rapid and sensitive molecular techniques such as PCR have revolutionized the detection of a variety of infectious viruses, including HIV, HCV, and HBV. Here, we describe two of the most commonly used licensed methods for the detection and quantification of HIV, HCV, and HBV: the cobas TaqScreen MPX (PCR) test and the Tigris System. We used transcription-mediated amplification to review and compare the development and efficiency of these technologies.
Collapse
Affiliation(s)
- Guilherme Albertoni
- Federal University of São Paulo (UNIFESP), Department of Medicine, Nephrology Division, Rua Botucatu 740, São Paulo, 04023-900, SP, Brazil; Colsan (Associação Beneficente de Coleta de Sangue), São Paulo, SP, Brazil.
| | | | - Nestor Schor
- Federal University of São Paulo (UNIFESP), Department of Medicine, Nephrology Division, Rua Botucatu 740, São Paulo, 04023-900, SP, Brazil
| |
Collapse
|
6
|
Albertoni G, Arnoni CP, Latini FRM, Andrade SS, Araújo PRB, Rodrigues FK, Rozenchan PB, Mendes-Correa MC, Leite OHM, Schor N, Girão MJCB, Barreto JA. Altered of apoptotic markers of both extrinsic and intrinsic pathways induced by hepatitis C virus infection in peripheral blood mononuclear cells. Virol J 2012; 9:314. [PMID: 23256595 PMCID: PMC3554545 DOI: 10.1186/1743-422x-9-314] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 12/07/2012] [Indexed: 01/09/2023] Open
Abstract
Background Chronic hepatitis C (CHC) has emerged as a leading cause of cirrhosis in the U.S. and across the world. To understand the role of apoptotic pathways in hepatitis C virus (HCV) infection, we studied the mRNA and protein expression patterns of apoptosis-related genes in peripheral blood mononuclear cells (PBMC) obtained from patients with HCV infection. Methods The present study included 50 subjects which plasma samples were positive for HCV, but negative for human immunodeficiency virus (HIV) or hepatitis B virus (HBV). These cases were divided into four groups according to METAVIR, a score-based analysis which helps to interpret a liver biopsy according to the degree of inflammation and fibrosis. mRNA expression of the studied genes were analyzed by reverse transcription of quantitative polymerase chain reaction (RT-qPCR) and protein levels, analyzed by ELISA, was also conducted. HCV genotyping was also determined. Results HCV infection increased mRNA expression and protein synthesis of caspase 8 in group 1 by 3 fold and 4 fold, respectively (p < 0.05). In group 4 HCV infection increased mRNA expression and protein synthesis of caspase 9 by 2 fold and 1,5 fold, respectively (p < 0.05). Also, caspase 3 mRNA expression and protein synthesis had level augumented by HCV infection in group 1 by 4 fold and 5 fold, respectively, and in group 4 by 6 fold and 7 fold, respectively (p < 0.05). Conclusions HCV induces alteration at both genomic and protein levels of apoptosis markers involved with extrinsic and intrinsic pathways.
Collapse
|