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

Lucky R. Runtuwene*, Nuankanya Sathirapongsasuti, Raweewan Srisawat, Narumon Komalamisra, Josef S.B. Tuda, Arthur E. Mongan, Gabriel O. Aboge, Victoria Shabardina, Wojciech Makalowski, Dela Ria Nesti, Wayan T. Artama, Lan Anh Nguyen-Thi, Kiew Lian Wan, Byoung Kuk Na, William Hall, Arnab Pain, Yuki Eshita, Ryuichiro Maeda, Junya Yamagishi, Yutaka Suzuki

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

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.

Original languageEnglish (US)
Article number44
JournalBMC Research Notes
Volume15
Issue number1
DOIs
StatePublished - Dec 2022

Bibliographical note

Funding Information:
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).

Publisher Copyright:
© 2022, The Author(s).

Keywords

  • Field sequencing
  • International collaboration
  • MinION
  • Portable sequencing

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology

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