Global research alliance in infectious disease: a collaborative efort 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 countries, we aim to train the participants with Min‑ION’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 col‑lected 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 efort 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, specifcally the MinION platform, in a developing country.