Can genomics help prevent epidemics?

By Nurfilzah Rohaidi

Interview with Dr Swaine Chen, Senior Research Scientist, Genome Institute of Singapore.

Last year, Singapore saw hundreds of local cases of Zika. Genomics helped researchers rule out any links to the Zika strain that originated in Brazil, where it is known to cause birth defects - and this went a long way towards informing response efforts.

Genomics is “a kind of fingerprinting, very similar to how we might find the fingerprints of a culprit at the scene of the crime”, Dr Swaine Chen, Senior Research Scientist at the Genome Institute of Singapore, tells GovInsider. “If we can identify bad guys specifically, we can identify that outbreak.”

It is emerging as a useful tool to tackle epidemics, he adds. When the adversary is too small to see, the ability to peer into its DNA could help healthcare authorities to turn the tide on epidemics - and potentially save lives.

Fingerprinting bacteria

Dengue fever is a perennial problem in tropical Singapore, and in 2006, the country implemented a national dengue monitoring regime. Every non-residential building in Singapore is inspected every three months, adding up to over a million inspections a year.

Having these steps already in place helped Singapore to quickly test for Zika virus last year, as it is spread by the same kind of mosquito that causes dengue. “The infrastructure was already there to track fevers and patients and tests for dengue,” says Chen.

Genomics was also integral to how investigators identified the cause of a 2015 Group B streptococcus (GBS) outbreak in Singapore, the largest of its kind at the time. “We were able to show that the GBS-causing infections in human patients was the exact same as the GBS we isolated from raw fish samples from the stalls they ate at,” Chen says.

Doctors at the hospital identified that the patients all had a common history of eating a raw fish dish. Chen’s lab provided concrete proof that it was indeed the fish: they sequenced bacteria from the blood of 70 infected patients, along with 10 fish samples, and the genetic ‘fingerprints’ were exactly the same across the board. It proved for the first time that GBS infections could spread through food consumption, Chen noted.

This also led to public agencies tightening controls on the handling of raw fish, and advising food stalls to stop selling the dish.

Sequencing in the cloud

Lessons from Singapore’s experience with GBS could inform future dengue response, Chen says. “Could we detect the outbreaks earlier? Could we forecast transmission? Could we use that to target interventions to stop these outbreaks sooner and do public communications?”
”Could we use genomics to target interventions to stop these outbreaks sooner?”
It currently costs up to S$150 (US$110) to sequence an entire genome - but sequencing is becoming cheaper, says Chen. In years to come, genome sequencing could be cheap enough for it to make a difference in the field, or at point of care.

How will this look? Chen envisions “genomic data streams” coming in from all over Singapore, helping to provide real-time insights as an outbreak develops.

While sequencing is currently only possible through a lab, in the future, individual mosquito traps could be equipped with sequencing devices. “Could we upgrade this outstanding infrastructure, take it up another level, and add genomics to make them a million genomics inspections?”

And as soon as a sick patient enters a hospital, staff will be able to take their blood or a bacterial sample, and sequence it to rapidly identify what exactly they are dealing with. “This is going to be reasonable, not today - maybe in five years,” Chen predicts.

Ubiquitous genomics

One challenge is that genomics requires immense computing power to process millions of data streams. The genomics institute is working with Amazon Web Services to cut time taken to analyse a single person’s genome from six hours to 15 minutes, and save 95% of the cost along the way, Chen explains. “We really see a vision where we can have genomic devices collecting data throughout the city, scattered throughout the environment, uploading data to the cloud.”

Singapore’s robust dengue infrastructure, coupled with genomics capabilities, cheaper sequencing and a vast IoT network will be crucial to manage and possibly even prevent future epidemics, he believes. “The data will be collected in the field, and analysed in the cloud. You can have a lot of central integration of that to do forecasting; the weather report is a very nice analogy for that,” Chen says.
“We really see a vision where we can have genomic devices collecting data throughout the city.”
It is clear that genomics can play a “huge” role in disease prevention, he says. Just as genomics can help to identify infectious disease outbreaks, it can give patients greater insights into their individual disease risk.

“Can we predict risk for mental neurological diseases, or heart disease, or cancer, or diabetes?” Chen wonders. “You don’t have to ‘fix’ the DNA, but if we know that you’re at risk for many of these things, we can try to do something early.”

Bacteria and viruses can spread quickly, sight unseen, and wreak havoc on lives and communities. As genomics advances, it can help healthcare systems become more prepared to face these threats as they come.

Dr Chen was a speaker at the AWS Public Sector Summit in Washington, DC on 20 and 21 June 2018.