High-throughput Testing in Indonesia

Ariel Pradipta from the Genomik Solidaritas Indonesia Lab (GSI Lab) spoke at the Nanopore Community Meeting 2021 on “The First 100 days of establishing nanopore-based sequencing for national SARS-CoV-2 surveillance.” Pradipta is a senior researcher fellow assisting in the national genomic efforts. They recognized a gap in rapid sequencing. To address this, they worked on improving the sample to sequence turnaround, which was at 160 days! They purchased a GridION sequencing instrument. Pradipta spoke about the challenges they encountered. The first one was discussions of undetected regions in sequencing. To improve this, they established CT-value thresholds. Another challenge was somewhat ironic: lack of samples even though there were high numbers of cases. To address this, they provided weekly SARS-CoV-2 variant reports. The team also. observed interest from healthcare systems in providing samples after the reports. The bioinformatics learning curve was steep. Pradipta noted that data management was logistically difficult. They established a bulk upload method and invested in a submission portal. Pradipta explained a frameshift warning issue they encountered and resolved. These improvements helped the team sequence more samples with a faster turnaround. I did not realize that Indonesia has over 17,000 islands! The GSI Lab wants to improve and invest in bioinformatics and high-throughput sequencing efforts.

High angle photo of beach
How can the ONT GridION and combined efforts of the wet lab and health care services work to improve turnaround of SARS-CoV-2 sequencing and variant reporting? Photo by Timur Kozmenko on Pexels.com