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Portable genetic sequencing technology helps track malaria

Portable genetic sequencing technology helps track malaria
15 Jan
The recipient of the 2018 Land Rover bursary, supported by the RGS-IBG, has been awarded extra funding to continue its work

In 2018, the Mobile Malaria project, led by George Busby, Jason Hendry and Isaac Ghinai was awarded the Land Rover Bursary – an award run by the Royal Geographical Society (with IBG) on behalf of Jaguar Land Rover. The bursary offers £30,000 and the use of a vehicle to make a challenging journey that promotes a wider understanding or enjoyment of geography.

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The team returned from its first expedition in June 2019, having worked in partnership with scientists based at the National Malaria Elimination Centre in Zambia. The project has now been awarded further funding by the Bill and Melinda Gates Foundation to expand on its work.

The key aim of the first round of the project was to work with local scientists in Namibia, Zambia and Kenya to test the feasibility of mobile genetic sequencing technology. This meant using the Land Rover to transport a genetic sequencing machine that could be run off the back of the truck to sequence the genes of mosquitoes and malaria parasites. The project showed that it was possible to generate DNA data on genes involved in resistance to antimalarial drugs using this very small, portable piece of equipment. 

20190428 Kenya EzraByrne 1The team work from the back of the Land Rover

The second phase of the project seeks to extend this. ‘The purpose is to do three things,’ Busby explains. ‘The first is to optimise the price and the ease of use of this genetic-sequencing technology. The machines are very small and portable, and you can use them to sequence mosquitoes and parasites. We want to make it as easy as possible to use so that they can be deployed at scale.’

Using the machine involves collecting small blood samples from people infected with malaria. Lab tests can then extract and amplify the DNA of any malaria parasites present. From there, specific genes within the DNA can be cut out and placed into the machines for analysis. The second goal involves building the capacity to analyse these genetic data. ‘In order to analyse this sort of data, you need computational skills and coding skills that are just not routinely taught in Africa. They’re barely routinely taught here, [in the UK],’ says Busby. ‘So we’re trying to develop a suite of training products that can train people to analyse the data that comes off this machine.’

Much of this resulting data is related to drug resistance in parasites. Specific genes already known to be related to drug resistance are chosen. ‘You can then analyse the data in a way that allows you to predict whether or not a parasite is resistant to a drug,’ says Busby. ‘If it contains certain mutations, then we can predict with quite high confidence that it’s likely to be resistant.’

LR RGS Bursary Mobile Malaria 210919 09 GeorgeBusbyEmployees at the National Malaria Elimination Centre

Other genes can also be examined, including those that help scientists infer how many different parasites there might be in a sample – this can indicate how much malaria is present in a particular area – and those that are involved with rapid diagnostic tests. These tests are commonly used across Africa and work by detecting a certain protein in the blood that is produced by parasites. Some parasites now have the ability to ‘hide’ from these tests by no longer producing the protein. Genetic testing can help identify how many parasites have this gene and how effective tests might therefore be. 

The final step of the project is to make sure these data are used. ‘The third goal, which is a bit more aspirational at the moment, is to try to think about ways in which we can communicate the data that you get off these machines to policymakers in Zambia,’ explains Busby. Making use of the data in this way could help determine which drugs to use, where to carry out certain tests, or to assess how well drugs and tests are working.

20190428 Kenya GeorgeBusby 12The technology is small and portable allowing it to be transported easily

For project scientist Mulenga Mwenda-Chimfwembe, based in Zambia, the project has opened up new possibilities. ‘In the very short time that I’ve been able to do this sequencing, I’ve also been able to train others,’ she says. ‘Our lab space is pretty small. It allows us to see the endless possibilities that we can do in a resource-limited setting, in a very small space, with our climatic conditions.’

As with so many projects this year, for the time being, things are progressing a little differently. Project scientists in Zambia are currently using the machines to try to sequence Covid-19 samples. ‘One of the things we’re trying to support at the moment is using genomic information to work out where the Covid infections are coming from, how they’re being imported, what’s the likely passage of entry into Zambia,’ says Busby. ‘That has really important implications.’

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