When an outbreak of a deadly virus hits, the usual course of action is to interview the infected and gather clinical data to establish a timeline for the pathogen's spread. Who shook hands or made out with whom, where, and when? This method works well enough in most cases, but scientists believe genetic analysis can make tracking a deadly outbreak even more accurate.
This is what researchers at the University of British Columbia were thinking when they decided to trace an outbreak of measles that occurred in BC in 2010, after the Olympic Games came to Vancouver. The measles virus was once thought to be more or less defeated in developed nations, but has experienced a roaring comeback thanks to the anti-vaccination movement.
"Nobody gave a shit about measles back then"
The team started their work a few months after the outbreak, but working in fits and starts led to the results being published just this week in the Journal of Infectious Diseases. "Nobody gave a shit about measles back then," said Jennifer Gardy, the paper's lead author.
According to the paper, sequencing the whole genome of the virus in samples collected from infected people allowed the researchers to trace the outbreak to two separate visitors carrying separate strains of the measles virus, likely from two different parts of the world. This last conclusion was drawn because the 2010 BC outbreak actually consisted of two strains of measles: one of which was recently isolated in China, and the other in Italy, India, and the US, according to the paper.
"This whole genome sequencing technique, reading the whole genome of a pathogen, and reading it for each pathogen you take from each person—this is a really new way to look at outbreaks," said Gardy. "Before, we used interview based techniques. It gives us a best guess as to whom infected whom, but we could never know for certain."
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The idea behind sequencing the genome of a virus or bacteria to trace its spread is deceptively simple: instead of tracking the movements of infected people, you look at the genetic similarities in the virus found inside them. If a strain of measles found in one person has a 100 percent genetic match to that found in another—as was the case in the BC researchers' study—then it's highly likely that the virus was transferred between them.
Matching these findings up with epidemiological data—the where and when—can confirm these results, leading to a more authoritative timeline of the virus' spread.
Whole genome sequencing for epidemiological purposes is a relatively new practice, having popped up just in the last decade as the technology to sequence genes becomes ever cheaper, faster, and more available. "I used to explain it like the shift from VHS to DVD, but it's almost more profound," Gardy said of rapidly improving genomics tech. "It's like we went right from VHS tapes to streaming on the internet."
"This is a really new way to look at outbreaks"
The same technique was used by Gardy and her colleagues in 2011 to track the spread of a tuberculosis outbreak in BC that lasted for three years. Other researchers have sequenced the genomes of bacteria and viruses to track a whole host of nasty things including salmonella, staph, pneumonia, and, yes, measles.
Canada has experienced numerous measles outbreaks since 2010, the most recent of which occurred in March of 2015 and led to more than 100 confirmed cases in Quebec. According to Gardy, genetic sequencing could be used to trace the spread of these ongoing outbreaks.
Before we get to the point of enlisting advanced genetic sequencing tech to trace measles, however, perhaps the best course of action is to simply get vaccinated—despite what your weird aunt posts on Facebook.