Zika virus: Can a faster sequencing diagnostic tool help?

Since Brazil reported its first case of Zika virus disease back in 2015, the virus has rapidly advanced in Brazil and 22 other countries in the region. The virus is spread by mosquitos and is hard to detect or test. So far around 1.5 million people have been infected in the country. The disease has also been linked with microcephaly, the birth of babies with abnormally small heads. Now the World Health Organisation has set up an emergency committee to “ascertain whether the outbreak constitutes a Public Health Emergency of International Concern”.

One key method to prevent the spread of the Zika virus is to use tools that can detect and diagnose the disease early. But as reported by the Wall Street Journal, “today’s diagnostic tools can’t keep pace with outbreaks” like Ebola.

Dr Charles Chiu at the UCSF School of Medicine is currently researching the Zika virus in collaboration with British DNA sequencing company Oxford Nanopore Technologies. He hopes a faster, sequencing diagnostic tool will not only develop rapid diagnostics for the Zika virus but several other illnesses in tropical countries. 

“We are interested in focusing on the acute stage in patients either in the country where they contracted the disease or shortly upon their return. The idea here is that patients that present with symptoms can be rapidly screened by sequencing all of the DNA where we will be able to diagnose the disease,” Chiu explains overs the phone from California, US.

The non-FDA approved DNA sequencing device is called the MinION and is currently being developed for clinical use. Chiu says one of the main benefits of these instruments is that they are “portable” and believes that with better surveillance, will be vital in the “prompt identification of cases”.

“One aspect is so patients can get appropriate treatment but it's also for public health surveillance so the disease can be contained from spreading. Right now we really lack diagnostics especially in areas that are infected by the virus. We don’t really know the extent of the Zika virus infection in infected countries. Especially where you have millions of cases such as Brazil.”

Since the spread of the Zika virus in Brazil, the rate of microcephaly has increased massively. Microcephaly is serious because of its life-long repercussions. Babies born with it can suffer with difficulty walking, hearing loss and vision difficulties. But according to the Centers for Disease Control and Prevention a direct link has not been found between Microcephaly and the Zika virus, although research is being done into it. Chiu thinks that the reason for this is because microcephaly has largely been ignored over the last 40 years mainly because it’s been associated with a flu-like illness.

“People haven't really seen the need to do screening for Zika virus. Only recently have complications been prescribed such as genetic defects. One of the advantages of the kind of approach we are taking in terms of sequencing is that we are not targeting any one virus, we are simply looking for everything. No matter what the current outbreak happens to be from, whether its Zika virus or Ebola - this is a diagnostic test that can detect any of them,” Chiu tells me.

The diagnostic tool works like this: you draw blood from someone with an acute illness and then all of the DNA contained in the blood is sequenced. Millions of sequences are generated and the tool can then identify the few sequences that correspond to viruses.

“So let’s, say you came back from South America with an acute illness and I generate a million sequences from you and I find five out of the million for a virus. Those five are sufficient for us to actually diagnose you as having a virus.”

A major challenge for current diagnostic tools in the market is keeping up with the pace of the disease, whether it be Ebola or the Zika virus. But Chiu says he and his team have developed an algorithm called SURPI (Sequence-based ultra-rapid pathogen identification) that can “align and identify millions of reads within minutes to hours”. He says SURPI can be used on the laptop locally and in the cloud for “real-time sequencing”.

“We can actually process an Ebola sample within a few hours and once you start the sequencing we can detect Ebola virus in under ten minutes with real-time sequence analysis. So with this technology I am hoping to implement a test that could detect any disease within say six hours.”

Still, there are challenges. Chiu admits that this tool works like “any other direct detection method”. For instance, the Zika virus could be diagnosed within the first week or two but after a week the virus cannot be found in the blood. For that you have to look for antibodies. Plus, approval by the FDA poses another significant challenge as Chiu explains:

“This is a huge regulatory challenge because the detection is not just for one type of infection like a Zikka virus detector. This test is for any virus or any bacteria and the FDA is only now starting to develop guidelines on how to regulate a test this broad. I think this is part of the reason we have not seen it commercialised,” says Chiu.

At the moment the diagnostic tool is only being used in a research setting but Chiu hopes to have a clinical test available by March of this year. “The FDA approval will certainly take longer. There are a lot of questions we will be exploring within the next year,” Chiu concludes.


Related reading:

West Africa: Tech & the Big Ebola Picture

Africa: Looking at mHealth Initiatives Beyond Ebola

Sierra Leone: IBM’s New Ebola Insights


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Ayesha Salim

Ayesha Salim is Staff Writer at IDG Connect

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