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

Abstract
ObjectiveTo 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.ResultsOne 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.

Citation
Runtuwene, L. R., Sathirapongsasuti, N., Srisawat, R., Komalamisra, N., Tuda, J. S. B., Mongan, A. E., Aboge, G. O., Shabardina, V., Makalowski, W., Nesti, D. R., Artama, W. T., Nguyen-Thi, L. A., Wan, K.-L., Na, B.-K., Hall, W., Pain, A., Eshita, Y., Maeda, R., Yamagishi, J., & Suzuki, Y. (2022). Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing. BMC Research Notes, 15(1). https://doi.org/10.1186/s13104-022-05927-2

Acknowledgements
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
Springer Science and Business Media LLC

Journal
BMC research notes

DOI
10.1186/s13104-022-05927-2

PubMed ID
35151353

Additional Links
https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-022-05927-2

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