In this interview, we spoke to Physilia to understand the project further and her motivation in becoming an innovator. Physilia, how did it all start?
Well, it starts with three words: anything, anytime, anywhere. We are developing simple-to-use instructions for anyone interested in carrying out sequencing for malaria surveillance and biodiversity studies. With our project, anyone, anywhere will be able to sequence locally (almost) in real-time.
“Well, it starts with three words: anything, anytime, anywhere... With our project, anyone, anywhere will be able to sequence locally (almost) in real-time.”
Dr Physilia Chua
Welllcome Sanger Institute
The idea came up when talking to Mara Lawniczak, the Principal Investigator on the project. We work with partners all over the world, and we are planning on expanding collaborations. Challenges such as acquiring shipping permits in a timely manner for samples to be sent to Sanger for sequencing are a barrier for partners requiring real-time information. Hence, we need to develop new tools to help partners sequence locally, with their own equipment in the field, and thus become autonomous.
To do this, they need to be able to use Sanger-developed gene panels (an assembly of specific genes that are selected for a specific task, in this case for species identification) but at a local level. How? With ONT devices, which are relatively cheap and portable. We use a range of protocols at Sanger, some of which are high throughput, using an industrial scale set up with expensive machines and requiring significant expertise to run. But technology is advancing fast and now we have ONT MinIONs, which are thumbdrive-sized, portable, and affordable sequencing machines. We are translating our protocols so that they can be used with this technology. This will allow our partners to sequence their own DNA extract in real-time, thus bringing down the barrier to species monitoring locally worldwide.
So, which are the protocols you are looking into?
We are now working on guides for three protocols that we use here at Sanger: the Pf Amplicon Toolkit, ANOSPP, and BIOSCAN panels. The first set of easy-to-use guides that we’re working on is for the Pf Amplicon toolkit, which detects whether the parasite that causes malaria (Plasmodium falciparum) exhibits any drug resistance. Malaria is a deadly disease in many countries and knowing if a person has been infected with drug-resistant Plasmodium can help save lives. This toolkit will allow public health officials in countries affected by malaria to monitor drug resistance in real-time to make informed targeted treatments.
The second one, the ANOSPP panel, can tell us the species of any mosquito in the Anopheles genus, which is the family of mosquitoes that can transmit malaria, and also indicate if the mosquito might be infected with the Plasmodium parasite. This is vital in the fight against malaria and early detection is key to the successful surveillance of malaria prevalence and transmission.
The first two protocols are part of MalariaGEN, a global data-sharing network to support the effective control of malaria. The third one is the BIOSCAN panel, which will be able to identify insect species and reveal symbiotic interactions between insects and the environment. BIOSCAN is a new initiative launched by the International Barcode of Life (iBOL) to study species diversity and interactions at massive scales globally.