Field diagnosis and genotyping of chikungunya virus using a dried reverse transcription loop-mediated isothermal amplification (LAMP) assay and MinION sequencing.
Detection and sequencing of chikungunya virus (CHIKV) genome was performed using a combination of a modified reverse transcription loop-mediated isothermal amplification (RT-LAMP) method and a MinION sequencer. We developed the protocol for drying all the reagents for the RT-LAMP in a single reactio...
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Online Access: | https://doi.org/10.1371/journal.pntd.0007480 https://doaj.org/article/8d2ec082313445329eb6a430de2c153d |
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ftdoajarticles:oai:doaj.org/article:8d2ec082313445329eb6a430de2c153d 2023-05-15T15:04:36+02:00 Field diagnosis and genotyping of chikungunya virus using a dried reverse transcription loop-mediated isothermal amplification (LAMP) assay and MinION sequencing. Kyoko Hayashida Yasuko Orba Patricia C Sequeira Chihiro Sugimoto William W Hall Yuki Eshita Yutaka Suzuki Lucky Runtuwene Patricia Brasil Guilherme Calvet Cintia D S Rodrigues Carolina C Dos Santos Maria A M Mares-Guia Junya Yamagishi Ana M B de Filippis Hirofumi Sawa 2019-06-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0007480 https://doaj.org/article/8d2ec082313445329eb6a430de2c153d EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pntd.0007480 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0007480 https://doaj.org/article/8d2ec082313445329eb6a430de2c153d PLoS Neglected Tropical Diseases, Vol 13, Iss 6, p e0007480 (2019) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2019 ftdoajarticles https://doi.org/10.1371/journal.pntd.0007480 2022-12-31T11:51:02Z Detection and sequencing of chikungunya virus (CHIKV) genome was performed using a combination of a modified reverse transcription loop-mediated isothermal amplification (RT-LAMP) method and a MinION sequencer. We developed the protocol for drying all the reagents for the RT-LAMP in a single reaction tube. Using this system, the CHIKV genome was effectively amplified under isothermal conditions, and used as a template for MinION sequencing with a laptop computer. Our in-house RT-LAMP method and MinION sequencing system were also validated with RNAs and serum samples from recent outbreaks of CHIKV patients in Brazil. The obtained sequence data confirmed the CHIKV outbreaks and identified the genotype. In summary, our established inexpensive on-site genome detection and sequencing system is applicable for both diagnosis of CHIKV infected patients and genotyping of the CHIKV virus in future outbreak in remote areas. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLOS Neglected Tropical Diseases 13 6 e0007480 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
spellingShingle |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Kyoko Hayashida Yasuko Orba Patricia C Sequeira Chihiro Sugimoto William W Hall Yuki Eshita Yutaka Suzuki Lucky Runtuwene Patricia Brasil Guilherme Calvet Cintia D S Rodrigues Carolina C Dos Santos Maria A M Mares-Guia Junya Yamagishi Ana M B de Filippis Hirofumi Sawa Field diagnosis and genotyping of chikungunya virus using a dried reverse transcription loop-mediated isothermal amplification (LAMP) assay and MinION sequencing. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
Detection and sequencing of chikungunya virus (CHIKV) genome was performed using a combination of a modified reverse transcription loop-mediated isothermal amplification (RT-LAMP) method and a MinION sequencer. We developed the protocol for drying all the reagents for the RT-LAMP in a single reaction tube. Using this system, the CHIKV genome was effectively amplified under isothermal conditions, and used as a template for MinION sequencing with a laptop computer. Our in-house RT-LAMP method and MinION sequencing system were also validated with RNAs and serum samples from recent outbreaks of CHIKV patients in Brazil. The obtained sequence data confirmed the CHIKV outbreaks and identified the genotype. In summary, our established inexpensive on-site genome detection and sequencing system is applicable for both diagnosis of CHIKV infected patients and genotyping of the CHIKV virus in future outbreak in remote areas. |
format |
Article in Journal/Newspaper |
author |
Kyoko Hayashida Yasuko Orba Patricia C Sequeira Chihiro Sugimoto William W Hall Yuki Eshita Yutaka Suzuki Lucky Runtuwene Patricia Brasil Guilherme Calvet Cintia D S Rodrigues Carolina C Dos Santos Maria A M Mares-Guia Junya Yamagishi Ana M B de Filippis Hirofumi Sawa |
author_facet |
Kyoko Hayashida Yasuko Orba Patricia C Sequeira Chihiro Sugimoto William W Hall Yuki Eshita Yutaka Suzuki Lucky Runtuwene Patricia Brasil Guilherme Calvet Cintia D S Rodrigues Carolina C Dos Santos Maria A M Mares-Guia Junya Yamagishi Ana M B de Filippis Hirofumi Sawa |
author_sort |
Kyoko Hayashida |
title |
Field diagnosis and genotyping of chikungunya virus using a dried reverse transcription loop-mediated isothermal amplification (LAMP) assay and MinION sequencing. |
title_short |
Field diagnosis and genotyping of chikungunya virus using a dried reverse transcription loop-mediated isothermal amplification (LAMP) assay and MinION sequencing. |
title_full |
Field diagnosis and genotyping of chikungunya virus using a dried reverse transcription loop-mediated isothermal amplification (LAMP) assay and MinION sequencing. |
title_fullStr |
Field diagnosis and genotyping of chikungunya virus using a dried reverse transcription loop-mediated isothermal amplification (LAMP) assay and MinION sequencing. |
title_full_unstemmed |
Field diagnosis and genotyping of chikungunya virus using a dried reverse transcription loop-mediated isothermal amplification (LAMP) assay and MinION sequencing. |
title_sort |
field diagnosis and genotyping of chikungunya virus using a dried reverse transcription loop-mediated isothermal amplification (lamp) assay and minion sequencing. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2019 |
url |
https://doi.org/10.1371/journal.pntd.0007480 https://doaj.org/article/8d2ec082313445329eb6a430de2c153d |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 13, Iss 6, p e0007480 (2019) |
op_relation |
https://doi.org/10.1371/journal.pntd.0007480 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0007480 https://doaj.org/article/8d2ec082313445329eb6a430de2c153d |
op_doi |
https://doi.org/10.1371/journal.pntd.0007480 |
container_title |
PLOS Neglected Tropical Diseases |
container_volume |
13 |
container_issue |
6 |
container_start_page |
e0007480 |
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1766336342172631040 |