Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing

[Objective] To disseminate the portable sequencer MinION in developing countries for the main purpose of battling infectious diseases, we found a consortium called Global Research Alliance in Infectious Diseases (GRAID). By holding and inviting researchers both from developed and developing countrie...

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Authors: Runtuwene, Lucky R., Sathirapongsasuti, Nuankanya, Srisawat, Raweewan, Komalamisra, Narumon, Tuda, Josef S. B., Mongan, Arthur E., Aboge, Gabriel O., Shabardina, Victoria, Makalowski, Wojciech, Nesti, Dela Ria, Artama, Wayan T., Nguyen-Thi, Lan Anh, Wan, Kiew-Lian, Na, Byoung-Kuk, Hall, William, Pain, Arnab, Eshita, Yuki, Maeda, Ryuichiro, Yamagishi, Junya, Suzuki, Yutaka
Format: article
Status:Published version
Publication Date:2022
Country:España
Institution:Consejo Superior de Investigaciones Científicas (CSIC)
Repository:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/272290
Online Access:http://hdl.handle.net/10261/272290
Access Level:Open access
Keyword:International collaboration
Portable sequencing
Field sequencing
MinION
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spelling Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencingRuntuwene, Lucky R.Sathirapongsasuti, NuankanyaSrisawat, RaweewanKomalamisra, NarumonTuda, Josef S. B.Mongan, Arthur E.Aboge, Gabriel O.Shabardina, VictoriaMakalowski, WojciechNesti, Dela RiaArtama, Wayan T.Nguyen-Thi, Lan AnhWan, Kiew-LianNa, Byoung-KukHall, WilliamPain, ArnabEshita, YukiMaeda, RyuichiroYamagishi, JunyaSuzuki, YutakaInternational collaborationPortable sequencingField sequencingMinION[Objective] To disseminate the portable sequencer MinION in developing countries for the main purpose of battling infectious diseases, we found a consortium called Global Research Alliance in Infectious Diseases (GRAID). By holding and inviting researchers both from developed and developing countries, we aim to train the participants with MinION’s operations and foster a collaboration in infectious diseases researches. As a real-life example in which resources are limited, we describe here a result from a training course, a metagenomics analysis from two blood samples collected from a routine cattle surveillance in Kulan Progo District, Yogyakarta Province, Indonesia in 2019.[Results] One of the samples was successfully sequenced with enough sequencing yield for further analysis. After depleting the reads mapped to host DNA, the remaining reads were shown to map to Theileria orientalis using BLAST and OneCodex. Although the reads were also mapped to Clostridium botulinum, those were found to be artifacts derived from the cow genome. An effort to construct a consensus sequence was successful using a reference-based approach with Pomoxis. Hence, we concluded that the asymptomatic cow might be infected with T. orientalis and showed the usefulness of sequencing technology, specifically the MinION platform, in a developing country.This project is supported by a grant from The Japan Society for the Promotion of Science Core-to-Core Program, B. Asia-Africa Science Platforms (id. JPJSCCB20190006).Peer reviewedBioMed CentralJapan Society for the Promotion of ScienceConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202220222022info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/272290reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésThe underlying dataset has been published as supplementary material of the article in the publisher platform at 10.1186/s13104-022-05927-2https://doi.org/10.1186/s13104-022-05927-2Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2722902026-05-22T06:33:51Z
dc.title.none.fl_str_mv Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing
title Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing
spellingShingle Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing
Runtuwene, Lucky R.
International collaboration
Portable sequencing
Field sequencing
MinION
title_short Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing
title_full Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing
title_fullStr Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing
title_full_unstemmed Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing
title_sort Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing
dc.creator.none.fl_str_mv Runtuwene, Lucky R.
Sathirapongsasuti, Nuankanya
Srisawat, Raweewan
Komalamisra, Narumon
Tuda, Josef S. B.
Mongan, Arthur E.
Aboge, Gabriel O.
Shabardina, Victoria
Makalowski, Wojciech
Nesti, Dela Ria
Artama, Wayan T.
Nguyen-Thi, Lan Anh
Wan, Kiew-Lian
Na, Byoung-Kuk
Hall, William
Pain, Arnab
Eshita, Yuki
Maeda, Ryuichiro
Yamagishi, Junya
Suzuki, Yutaka
author Runtuwene, Lucky R.
author_facet Runtuwene, Lucky R.
Sathirapongsasuti, Nuankanya
Srisawat, Raweewan
Komalamisra, Narumon
Tuda, Josef S. B.
Mongan, Arthur E.
Aboge, Gabriel O.
Shabardina, Victoria
Makalowski, Wojciech
Nesti, Dela Ria
Artama, Wayan T.
Nguyen-Thi, Lan Anh
Wan, Kiew-Lian
Na, Byoung-Kuk
Hall, William
Pain, Arnab
Eshita, Yuki
Maeda, Ryuichiro
Yamagishi, Junya
Suzuki, Yutaka
author_role author
author2 Sathirapongsasuti, Nuankanya
Srisawat, Raweewan
Komalamisra, Narumon
Tuda, Josef S. B.
Mongan, Arthur E.
Aboge, Gabriel O.
Shabardina, Victoria
Makalowski, Wojciech
Nesti, Dela Ria
Artama, Wayan T.
Nguyen-Thi, Lan Anh
Wan, Kiew-Lian
Na, Byoung-Kuk
Hall, William
Pain, Arnab
Eshita, Yuki
Maeda, Ryuichiro
Yamagishi, Junya
Suzuki, Yutaka
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Japan Society for the Promotion of Science
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv International collaboration
Portable sequencing
Field sequencing
MinION
topic International collaboration
Portable sequencing
Field sequencing
MinION
description [Objective] To disseminate the portable sequencer MinION in developing countries for the main purpose of battling infectious diseases, we found a consortium called Global Research Alliance in Infectious Diseases (GRAID). By holding and inviting researchers both from developed and developing countries, we aim to train the participants with MinION’s operations and foster a collaboration in infectious diseases researches. As a real-life example in which resources are limited, we describe here a result from a training course, a metagenomics analysis from two blood samples collected from a routine cattle surveillance in Kulan Progo District, Yogyakarta Province, Indonesia in 2019.
publishDate 2022
dc.date.none.fl_str_mv 2022
2022
2022
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/272290
url http://hdl.handle.net/10261/272290
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv The underlying dataset has been published as supplementary material of the article in the publisher platform at 10.1186/s13104-022-05927-2
https://doi.org/10.1186/s13104-022-05927-2
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869405999344910336
score 15,811543

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