When people who have travelled overseas are admitted to hospitals with unexplained fevers in tropical areas like Cairns and Darwin, doctors are keenly aware that the patients could be carrying exotic infectious diseases, such as Zika or Chikungunya.
The laboratory tests cannot detect unknown new diseases. Not only can this result in delays or incorrect treatment for patients, but there is a risk of exotic or new diseases spreading across the country.
Now Dr Paul Horwood, senior research fellow at the Australian Institute of Tropical Health and Medicine (AITHM), is testing whether
‘The advantage of using sequencing is that you can test for everything at once,’ says Dr Horwood. ‘Using a bioinformatics approach, if there is some new virus or unexpected virus, there is the potential we could pick them up. Whereas using a targeted [conventional laboratory] approach would mean a lot of work to try to determine if there is a new pathogen there.’
The research project is one of more than 50 being funded by the Hot North study. The results could be a key step in taking genomic sequencing for infectious diseases out of the laboratory and into everyday hospital practice in Australia and neighbouring developing countries.
He is working in collaboration with Professor John McBride of the JCU Clinical School at Cairns Hospital; Dr Ella Meumann, an infectious diseases physician at Darwin Hospital and Dr Matt Field, an AITHM bioinformatician. The first 15 patients enrolled in the Hot North study have been diagnosed with a range of diseases, including malaria, dengue fever and melioidosis.
Blood samples from each patient will be sequenced using Illumina HiSeq technology. Dr Field will be ‘blinded’ to the diagnosis and original laboratory tests results and have to work out the pathogen causing the disease from the sequencing results alone. The results will be used to improve the sequencing pipeline, so tropical diseases can be more rapidly and accurately diagnosed.
Dr Horwood previously researched emerging diseases in tropical developing countries, including investigating outbreaks of chikungunya and other diseases in Papua New Guinea. He says using funding from other sources, they are working with the PNG Institute of Medical Research to see if portable hand-held MinION sequencing device can be used for sequencing of diseases within the country. It would involve biomedical and technical support as well as training from Australia.
‘Where there are outbreaks of disease this could be particularly important,’ says Dr Horwood. With the MinION approach, researchers could produce sequencing results ‘in country’ without the logistical problems of sending samples to external reference centres.
Dr Horwood says: ‘It could greatly increase the capacity in countries like Papua New Guinea and enable them to more quickly discover the causes of disease outbreaks, leading to improved outbreak response and treatment for patients.’
Dr Paul Horwood
Phone: +617 4232 1684