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

• Published in: BMC research notes 2022-02, Vol.15 (1), p.44-44, Article 44
• Main 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
• Language: English
• Subjects: Animals; Care and treatment; Cattle; Collaboration; Communicable Diseases; Conserved sequence; Consortia; Dengue fever; Developing countries; Diagnosis; DNA sequencing; Drug resistance; Ebola virus; Epidemics; Field sequencing; Genome; Genomes; High-Throughput Nucleotide Sequencing; Infectious diseases; International collaboration; LDCs; Malaria; Metagenomics; MinION; Nucleotide sequence; Nucleotide sequencing; Parasites; Pathogens; Portable computers; Portable sequencing; Research Note; Sequence Analysis, DNA; Software; Viruses
• ISSN: 1756-0500; 1756-0500
• DOI: 10.1186/s13104-022-05927-2

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. 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.