The measles outbreak in Canada's largest city was already a minor epidemiological puzzle when scientists discovered something that deepened the mystery.
Of the 11 Greater Toronto Area patients diagnosed with the highly contagious illness since the end of January, none are connected to each other in any way that public health staff could discover through interviews with the patients or their parents. None had recently travelled outside Canada to a place where they might have caught the measles.
Public health officials had hoped that genetic analysis of the measles viruses in these cases might shed light on where the Toronto outbreak came from.
Instead, scientists found something new: The version of the measles virus circulating in Ontario is a variant that has never before been reported to the World Health Organization database that contains descriptions of more than 22,000 slightly different viral sequences of the measles virus found across the globe.
The measles virus is constantly mutating, meaning subtly distinct versions are regularly added to the global storehouse, said Matthew Gilmour, the new scientific director general who oversees Canada's National Microbiology Laboratory (NML) in Winnipeg, where the genetic sequencing was done.
"It's new to us now, but as other countries uncover this virus as well, they'll have a chance to put it in the same database," Dr. Gilmour said. "The puzzle will start to become clear then as to what the actual origin of this strain is."
So far, solving the measles puzzle in Toronto has not been as simple as in some other Canadian outbreaks.
Consider what happened in Quebec recently, where 10 cases of the measles were diagnosed in the Lanaudière region near Montreal.
When public health officials announced the cases Feb. 11, they had already concluded the unvaccinated patients were from two families; at least one of the 10 had visited Disneyland in California, the epicentre of an ongoing measles outbreak in the United States.
NML scientists analyzed samples from five of the Quebec patients and found the virus to be a spot-on match for the virus circulating in the Disneyland outbreak. Case closed.
In the Greater Toronto Area, officials are still hunting for any connections at all between their patients, nine of whom were diagnosed in the city proper and two of whom were diagnosed in nearby suburbs.
"I would agree that this is unusual," said Michael Finkelstein, Toronto's associate medical officer of health. "They [the patients] don't have any travel history, which adds to our information or knowledge about the cases."
As a general rule, Canada's national lab does not sequence the entire genome of a single sample of the measles virus because the process would cost several thousand dollars, take two to three weeks and is usually not necessary. Instead, scientists start by sequencing a small fragment of the genome, part of the N-gene, because it is the most variable part of the virus and therefore the likeliest to offer clues about whether measles cases are connected.
By looking at the exact sequence of the past 450 nucleotides, or building blocks, of the virus's N-gene, scientists can determine the "sequence variant" or version of the measles they are dealing with. Because the measles virus mutates slowly – much more slowly than influenza, for example – cases in the same chain of transmission usually have identical N-450 sequences, as they are called.
A matching N-450 sequence is not definitive proof that cases are connected. But if two patients have two different versions of the virus, you can say for certain the cases are not connected. So despite the fact the N-450 sequence in the Ontario cases has yet to be identified anywhere in the world, it still offers some useful clues about the Toronto outbreak.
The Toronto cases are not connected to the Disneyland outbreak. There was a possibility that a missed patient from that outbreak might have unwittingly imported measles to the province, but the genetic analysis ruled that out. The genetic analysis also suggests – but does not prove – that the cases that have been analyzed so far are the result of a single yet-to-be-identified patient importing the virus to the province.
Dr. Gilmour said the national lab has so far sequenced eight cases from Ontario. At least one of the cases is from the Niagara Region, according to Valerie Jaeger, the region's medical officer of health. (Six cases have been diagnosed in the Niagara Region so far, all of them linked to each other through old-fashioned contact tracing, unlike the GTA cases.)
The eight Ontario cases analyzed by the national lab all had the newly identified N-450 sequence, which is similar to a version of the virus that has been circulating recently in Europe, Dr. Gilmour said.
When the scientists dug deeper into the genomes by sequencing another gene called the H-gene, they found minor differences in two of the eight cases, Dr. Gilmour added. That means there is an infinitesimal chance that more than one person brought the same version of the measles to Ontario around the same time.
"I think that would be unlikely," said Jonathan Gubbay, a medical microbiologist with Public Health Ontario. "What's the chance of it arriving here in two separate ways? No one else in the world has reported it."
Dr. Gilmour agreed, saying the national laboratory is operating on the theory that one person brought the measles to Ontario.
One thing is for certain: The virus came here from abroad. Measles was officially eliminated in Canada in the late 1990s, which means that all new cases that pop up here were originally imported.
Figuring out where the Ontario cases came from could take some time, especially considering the WHO Measles Nucleotide Surveillance system, or MeaNS for short, is far from a complete repository of every circulating version of the virus.
Many poor countries where measles is endemic do not have the lab capacity or money to sequence parts of the virus, meaning the database is "not complete by far," said Miguel Mulders, co-ordinator of the WHO's global measles and rubella laboratory network.
"But we are trying to make the database as comprehensive as possible."