Mobile Malaria Sequencing

Tonight, I found the “Mobile Malaria Project” session from London Calling 2019. Jason Hendry from the University of Oxford in the UK presented their malaria work. Fifty percent of the population was at risk in 2017! In 2008, resistance to artemisinin was found in Cambodia. In 2014, resistance spread across Southeast Asia. Chloroquine was the frontline drug, and in 1957, resistance emerged. By 1982, it spread across the African continent. In 2014, molecular markers of artemisinin resistance were described. The research team applied for the Land Rover Bursary grant to convert a Land Rover into a mobile sequencing lab to perform surveillance of drug resistance and raise awareness. The core of the proposal had the MinION. The team had a workflow using the QIAGEN QIAamp DNA Investigator kit, whole genome amplification, PCR of antimalarial genes, barcode with EXP-NBD104/114, and sequence via ligation kit SQK-LSK109. The selective amplification enhances parasite detection.

The driving total was 7351 km! The Land Rover had battery power and a freezer. In the first run, they produced 20 Gbases of data! Hendry used the MinIT to remove and filter the adapter. Hendry shared plots of error rates. The deletions observed were in homopolymers. Downsampling, Hendry learned that with only 100 reads, resistance can be detected. The second experiment was in the field and focused on freshly collected mosquitoes. Twelve mosquitoes were pooled and used for extractions. The workflow was applied, and the team trained people to perform library preps. I was impressed that the team used barcoding by ligation in the field and obtained high throughput.
red Land Rover going over hill
How can a Land Rover be used as a mobile lab and training center for malaria resistance surveillance? Photo by ahmad syahrir on Pexels.com