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Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma

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 e...

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Autores principales: Hongjaisee, Sayamon, Jabjainai, Yosita, Sakset, Suthasinee, Preechasuth, Kanya, Ngo-Giang-Huong, Nicole, Khamduang, Woottichai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9322174/
https://www.ncbi.nlm.nih.gov/pubmed/35885505
http://dx.doi.org/10.3390/diagnostics12071599
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author Hongjaisee, Sayamon
Jabjainai, Yosita
Sakset, Suthasinee
Preechasuth, Kanya
Ngo-Giang-Huong, Nicole
Khamduang, Woottichai
author_facet Hongjaisee, Sayamon
Jabjainai, Yosita
Sakset, Suthasinee
Preechasuth, Kanya
Ngo-Giang-Huong, Nicole
Khamduang, Woottichai
author_sort Hongjaisee, Sayamon
collection PubMed
description 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.
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spelling pubmed-93221742022-07-27 Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma Hongjaisee, Sayamon Jabjainai, Yosita Sakset, Suthasinee Preechasuth, Kanya Ngo-Giang-Huong, Nicole Khamduang, Woottichai Diagnostics (Basel) Communication 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. MDPI 2022-06-30 /pmc/articles/PMC9322174/ /pubmed/35885505 http://dx.doi.org/10.3390/diagnostics12071599 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Communication
Hongjaisee, Sayamon
Jabjainai, Yosita
Sakset, Suthasinee
Preechasuth, Kanya
Ngo-Giang-Huong, Nicole
Khamduang, Woottichai
Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma
title Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma
title_full Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma
title_fullStr Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma
title_full_unstemmed Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma
title_short Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma
title_sort comparison of simple rna extraction methods for molecular diagnosis of hepatitis c virus in plasma
topic Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9322174/
https://www.ncbi.nlm.nih.gov/pubmed/35885505
http://dx.doi.org/10.3390/diagnostics12071599
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