Serotyping dengue virus with isothermal amplification and a portable sequencer

Abstract The recent development of a nanopore-type portable DNA sequencer has changed the way we think about DNA sequencing. We can perform sequencing directly in the field, where we collect the samples. Here, we report the development of a novel method to detect and genotype tropical disease pathog...

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Autores principales:	Junya Yamagishi, Lucky R. Runtuwene, Kyoko Hayashida, Arthur E. Mongan, Lan Anh Nguyen Thi, Linh Nguyen Thuy, Cam Nguyen Nhat, Kriengsak Limkittikul, Chukiat Sirivichayakul, Nuankanya Sathirapongsasuti, Martin Frith, Wojciech Makalowski, Yuki Eshita, Sumio Sugano, Yutaka Suzuki
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b2194db746994341ba4af5192538c1fd
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spelling	oai:doaj.org-article:b2194db746994341ba4af5192538c1fd2021-12-02T16:07:04ZSerotyping dengue virus with isothermal amplification and a portable sequencer10.1038/s41598-017-03734-52045-2322https://doaj.org/article/b2194db746994341ba4af5192538c1fd2017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-03734-5https://doaj.org/toc/2045-2322Abstract The recent development of a nanopore-type portable DNA sequencer has changed the way we think about DNA sequencing. We can perform sequencing directly in the field, where we collect the samples. Here, we report the development of a novel method to detect and genotype tropical disease pathogens, using dengue fever as a model. By combining the sequencer with isothermal amplification that only requires a water bath, we were able to amplify and sequence target viral genomes with ease. Starting from a serum sample, the entire procedure could be finished in a single day. The analysis of blood samples collected from 141 Indonesian patients demonstrated that this method enables the clinical identification and serotyping of the dengue virus with high sensitivity and specificity. The overall successful detection rate was 79%, and a total of 58 SNVs were detected. Similar analyses were conducted on 80 Vietnamese and 12 Thai samples with similar performance. Based on the obtained sequence information, we demonstrated that this approach is able to produce indispensable information for etiologically analyzing annual or regional diversifications of the pathogens.Junya YamagishiLucky R. RuntuweneKyoko HayashidaArthur E. MonganLan Anh Nguyen ThiLinh Nguyen ThuyCam Nguyen NhatKriengsak LimkittikulChukiat SirivichayakulNuankanya SathirapongsasutiMartin FrithWojciech MakalowskiYuki EshitaSumio SuganoYutaka SuzukiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Junya Yamagishi Lucky R. Runtuwene Kyoko Hayashida Arthur E. Mongan Lan Anh Nguyen Thi Linh Nguyen Thuy Cam Nguyen Nhat Kriengsak Limkittikul Chukiat Sirivichayakul Nuankanya Sathirapongsasuti Martin Frith Wojciech Makalowski Yuki Eshita Sumio Sugano Yutaka Suzuki Serotyping dengue virus with isothermal amplification and a portable sequencer
description	Abstract The recent development of a nanopore-type portable DNA sequencer has changed the way we think about DNA sequencing. We can perform sequencing directly in the field, where we collect the samples. Here, we report the development of a novel method to detect and genotype tropical disease pathogens, using dengue fever as a model. By combining the sequencer with isothermal amplification that only requires a water bath, we were able to amplify and sequence target viral genomes with ease. Starting from a serum sample, the entire procedure could be finished in a single day. The analysis of blood samples collected from 141 Indonesian patients demonstrated that this method enables the clinical identification and serotyping of the dengue virus with high sensitivity and specificity. The overall successful detection rate was 79%, and a total of 58 SNVs were detected. Similar analyses were conducted on 80 Vietnamese and 12 Thai samples with similar performance. Based on the obtained sequence information, we demonstrated that this approach is able to produce indispensable information for etiologically analyzing annual or regional diversifications of the pathogens.
format	article
author	Junya Yamagishi Lucky R. Runtuwene Kyoko Hayashida Arthur E. Mongan Lan Anh Nguyen Thi Linh Nguyen Thuy Cam Nguyen Nhat Kriengsak Limkittikul Chukiat Sirivichayakul Nuankanya Sathirapongsasuti Martin Frith Wojciech Makalowski Yuki Eshita Sumio Sugano Yutaka Suzuki
author_facet	Junya Yamagishi Lucky R. Runtuwene Kyoko Hayashida Arthur E. Mongan Lan Anh Nguyen Thi Linh Nguyen Thuy Cam Nguyen Nhat Kriengsak Limkittikul Chukiat Sirivichayakul Nuankanya Sathirapongsasuti Martin Frith Wojciech Makalowski Yuki Eshita Sumio Sugano Yutaka Suzuki
author_sort	Junya Yamagishi
title	Serotyping dengue virus with isothermal amplification and a portable sequencer
title_short	Serotyping dengue virus with isothermal amplification and a portable sequencer
title_full	Serotyping dengue virus with isothermal amplification and a portable sequencer
title_fullStr	Serotyping dengue virus with isothermal amplification and a portable sequencer
title_full_unstemmed	Serotyping dengue virus with isothermal amplification and a portable sequencer
title_sort	serotyping dengue virus with isothermal amplification and a portable sequencer
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/b2194db746994341ba4af5192538c1fd
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Serotyping dengue virus with isothermal amplification and a portable sequencer

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