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Unraveling virus identity by detection of depleted probes with capillary electrophoresis

With the emergence of new viral infections and pandemics, there is a need to develop faster methods to unravel the virus identities in a large number of clinical samples. This report describes a virus identification method featuring high throughput, high resolution, and high sensitivity detection of...

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Autores principales: Wang, Chin-Yu, Hsiao, Tzu-Hung, Chu, Liang-Hui, Lin, Yi-Ling, Huang, Jau-Ling, Chen, Chung-Hsuan, Peck, Konan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier B.V. 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094614/
https://www.ncbi.nlm.nih.gov/pubmed/22704476
http://dx.doi.org/10.1016/j.aca.2012.04.040
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author Wang, Chin-Yu
Hsiao, Tzu-Hung
Chu, Liang-Hui
Lin, Yi-Ling
Huang, Jau-Ling
Chen, Chung-Hsuan
Peck, Konan
author_facet Wang, Chin-Yu
Hsiao, Tzu-Hung
Chu, Liang-Hui
Lin, Yi-Ling
Huang, Jau-Ling
Chen, Chung-Hsuan
Peck, Konan
author_sort Wang, Chin-Yu
collection PubMed
description With the emergence of new viral infections and pandemics, there is a need to develop faster methods to unravel the virus identities in a large number of clinical samples. This report describes a virus identification method featuring high throughput, high resolution, and high sensitivity detection of viruses. Identification of virus is based on liquid hybridization of different lengths of virus-specific probes to their corresponding viruses. The probes bound to target sequences are removed by a biotin–streptavidin pull-down mechanism and the supernatant is analyzed by capillary electrophoresis. The probes depleted from the sample appear as diminished peaks in the electropherograms and the remaining probes serve as calibrators to align peaks in different capillaries. The virus identities are unraveled by a signal processing and peak detection algorithm developed in-house. Nine viruses were used in the study to demonstrate how the system works to unravel the virus identity in single and double virus infections. With properly designed probes, the system is able to distinguish closely related viruses. The system takes advantage of the high resolution feature of capillary electrophoresis to resolve probes that differ by length. The method may facilitate virus identity screen from more candidate viruses with an automated 4-color DNA sequencer.
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spelling pubmed-70946142020-03-25 Unraveling virus identity by detection of depleted probes with capillary electrophoresis Wang, Chin-Yu Hsiao, Tzu-Hung Chu, Liang-Hui Lin, Yi-Ling Huang, Jau-Ling Chen, Chung-Hsuan Peck, Konan Anal Chim Acta Article With the emergence of new viral infections and pandemics, there is a need to develop faster methods to unravel the virus identities in a large number of clinical samples. This report describes a virus identification method featuring high throughput, high resolution, and high sensitivity detection of viruses. Identification of virus is based on liquid hybridization of different lengths of virus-specific probes to their corresponding viruses. The probes bound to target sequences are removed by a biotin–streptavidin pull-down mechanism and the supernatant is analyzed by capillary electrophoresis. The probes depleted from the sample appear as diminished peaks in the electropherograms and the remaining probes serve as calibrators to align peaks in different capillaries. The virus identities are unraveled by a signal processing and peak detection algorithm developed in-house. Nine viruses were used in the study to demonstrate how the system works to unravel the virus identity in single and double virus infections. With properly designed probes, the system is able to distinguish closely related viruses. The system takes advantage of the high resolution feature of capillary electrophoresis to resolve probes that differ by length. The method may facilitate virus identity screen from more candidate viruses with an automated 4-color DNA sequencer. Elsevier B.V. 2012-07-13 2012-05-10 /pmc/articles/PMC7094614/ /pubmed/22704476 http://dx.doi.org/10.1016/j.aca.2012.04.040 Text en Copyright © 2012 Elsevier B.V. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Wang, Chin-Yu
Hsiao, Tzu-Hung
Chu, Liang-Hui
Lin, Yi-Ling
Huang, Jau-Ling
Chen, Chung-Hsuan
Peck, Konan
Unraveling virus identity by detection of depleted probes with capillary electrophoresis
title Unraveling virus identity by detection of depleted probes with capillary electrophoresis
title_full Unraveling virus identity by detection of depleted probes with capillary electrophoresis
title_fullStr Unraveling virus identity by detection of depleted probes with capillary electrophoresis
title_full_unstemmed Unraveling virus identity by detection of depleted probes with capillary electrophoresis
title_short Unraveling virus identity by detection of depleted probes with capillary electrophoresis
title_sort unraveling virus identity by detection of depleted probes with capillary electrophoresis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094614/
https://www.ncbi.nlm.nih.gov/pubmed/22704476
http://dx.doi.org/10.1016/j.aca.2012.04.040
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