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

Runtuwene LR 1 , Sathirapongsasuti N 2 , Srisawat R 3 , Komalamisra N 3 , Tuda JSB 4 , Mongan AE 4 Show all authors , Aboge GO 5 , Shabardina V 6 , Makalowski W 7 , Nesti DR 8 , Artama WT 9 , Nguyen-Thi LA 10 , Wan KL 11 , Na BK 12 , Hall W 13 , Pain A 14 , Eshita Y 15 , Maeda R 16 , Yamagishi J 15 , Suzuki Y 17

Affiliations 

  • 1 Division 1, AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan. luckyron@niid.go.jp
  • 2 Section of Translational Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
  • 3 Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
  • 4 Faculty of Medicine, Sam Ratulangi University, Manado, Indonesia
  • 5 Department of Public Health, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
  • 6 Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
  • 7 Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Muenster, Germany
  • 8 Department of Bioresources Technology and Veterinary, Vocational College, Universitas Gadjah Mada, Yogyakarta, Indonesia
  • 9 Department of Biochemistry, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
  • 10 Center of Biomedical Research, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
  • 11 Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
  • 12 Department of Parasitology and Tropical Medicine, College of Medicine, Gyeongsang National University, Jinju, South Korea
  • 13 Centre for Research in Infectious Diseases, University College Dublin, Dublin, Ireland
  • 14 Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
  • 15 Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
  • 16 Division of Biomedical Science, Department of Basic Veterinary Medicine, Obihiro University of Agriculture and Veterinary, Obihiro, Japan
  • 17 Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
BMC Res Notes, 2022 Feb 12;15(1):44.
PMID: 35151353 DOI: 10.1186/s13104-022-05927-2

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.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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