A new and portable device speeds up dengue virus identification
A team led by a professor from the University of Tokyo has devised a fast and cost-effective method of determining dengue fever virus types using a portable DNA sequencer.
Use of the palm-sized device will hopefully be able to speed up diagnosis at hospitals in developing countries and also help trace the path of infection.
There are four types of the virus that causes dengue fever, a mosquito-borne tropical disease. A patient with a history of infection from one type can develop severe symptoms if infected with another.
The team led by Yutaka Suzuki, a professor at the University of Tokyo, as well as Hokkaido University in northern Japan, has taken MinION, a next-generation nanopore DNA sequencer developed by Oxford Nanopore Technologies in the U.K., and applied it to the identification of the virus types.
The process starts with serum being separated from a blood sample taken from an infected patient. Ribonucleic acid in the serum carrying the genetic information of the virus is then detected and converted to DNA fragments which are amplified for sequencing.
The DNA sequencer can now read the DNA information and a computer linked to the device converts it into nucleotide sequence data. This can now be cross-referenced with a database of genetic information to determine which type of virus the patient is infected with.
In partnership with local hospitals, the project studied viruses from infected patients and discovered that the DENV-1 type of the virus was dominant in Indonesia, while the DENV-3 type was more common in Vietnam.
The prevalence of virus types in different regions could help identify infection routes.
Until now, identification has relied on conventional methods of amplifying DNA using a polymerase chain reaction or large, advanced genetic sequencers, which typically fall well outside health care budgets in the developing world.
Using the MinION will only require the device, a computer and the appropriate chemical agents to convert RNA to DNA.
The project foresees the identification method being put to widespread use as soon as licenses for the data sequencer can be obtained.
The team also intends to take the study further so that the method can be used for a wider range of viruses, including malaria and mycobacterium tuberculosis, by selecting chemicals for the DNA conversion relevant to specific diseases.
Understanding the genetic information of a virus can also help identify its tolerance to specific drugs. Suzuki hopes the new method will allow viral diseases to be diagnosed at the local-hospital level.