'We're opening everything': Scientists share coronavirus data in unprecedented way to contain, treat disease

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When the story of the coronavirus (2019-nCOV) is finally written, it might well become a template for the utopian dream of open science — where research data is shared freely, unrestrained by competition, paywalls and patents. 

Already the world knows more about the early days of this outbreak than it did when SARS first appeared in China in 2002, as scientists unite in unprecedented scientific collaboration aimed at containing and treating this disease.

As detailed accounts of the first cases have been published in prominent medical journals, it's clear that scientists were among the first responders at hospitals in Wuhan, China, the epicentre of the outbreak. 

One patient, a 49-year-old woman, was a merchant at the Huanan Seafood Wholesale Market. In late December, she developed a fever and a cough and had an uncomfortable sensation in her chest. After four days, the cough became serious enough that she went to the hospital where a CT scan revealed she had pneumonia.

The same day that she was admitted to a Wuhan hospital, a 61-year-old man arrived with similar symptoms. He was a frequent visitor to the Huanan market and had been suffering from a fever and a cough for a week before showing up at the hospital. He was so sick that he needed mechanical ventilation to breathe. 

As doctors struggled to treat what was still an unknown illness, a team of scientists arrived from the Chinese Centre for Disease Control and Prevention.

They collected fluid from deep in the patients' lungs and carefully placed them in sterile cups to begin the process of isolating the unknown virus believed to be causing this atypical pneumonia. 

The woman survived, and she has been released from hospital. The man died. But their lung samples provided some of the earliest glimpses of a new and deadly human pathogen. 

Within days, those scientists and several others had sequenced the viral genome, deciphering the virus's genetic code — a vital key to diagnosing and ultimately treating the disease. They immediately shared that critical genetic roadmap with researchers all over the world.

That early collaboration allowed doctors in other countries to be ready when the first cases appeared outside China. 

Watching the virus mutate in real time 

Because the viral genomes had been publicly released, when a  65-year-old man and his 27-year-old son were admitted to a hospital in Vietnam on Jan. 22, doctors there were able to identify the virus, isolate the patients, backtrack their travel history and monitor 28 close contacts, none of whom have developed symptoms.

By then evolutionary biologist Trevor Bedford had already used the growing database of viral genomes to conclude this virus made the leap from animals to humans sometime in mid-November, an astonishingly precise estimate that helped scientists understand how long the virus had been infecting people. 

"In looking at the genomes that were coming in from Wuhan, we could see that there was very little genetic diversity," said Bedford, at the Fred Hutchinson Cancer Research Center and the University of Washington in Seattle, Wash.

The low number of mutations not only told him the virus was new in humans, it also corrected an early misunderstanding and revealed that the virus was spreading easily between humans. 

"As soon as the first genomes were coming in, it became clear that there's lots of human-to-human spread," he said.

The availability of having a full genome sequence of a novel virus available to the public to be able to develop diagnostics, to be able to diagnose patients in other countries is unprecedented.- Maria Van Kerkhove, WHO infectious disease epidemiologist

The genome data also allowed some groups to quickly zero in on the animal source, by using the genetic data to link this virus to one found in Chinese horseshoe bats.

Just three weeks after the first viral sequence was published, more than 42 different genomes are available on Nextstrain, an open source viral genome database that continues to grow as scientists diagnose patients and publish the viral genomes in just a few days. 

That data is allowing Bedford to watch the virus mutate in real time, making it possible to identify how people became infected and which cases are linked. It also provides critical data to allow other scientists to estimate the size of the epidemic.

Other groups are using the genetic data to develop rapid diagnostic tests and begin working on antiviral drugs. And already at least five different groups have started working on a possible vaccine, including one from Saskatchewan. 

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"The availability of having a full genome sequence of a novel virus available to the public to be able to develop diagnostics, to be able to diagnose patients in other countries is unprecedented," said Maria Van Kerkhove, an infectious disease epidemiologist at the World Health Organization (WHO) news conference on Wednesday. 

Sharing virus samples 'essential': WHO

On Tuesday, Australia announced that its scientists are the first outside China to grow the novel virus and will share it with the world.

"It is essential that viruses are shared so that the further development of diagnostics and serologic assays — so that the further development of vaccines — can continue," said Van Kerkhove.

To keep on top of the rapidly breaking science, medical and scientific journals agreed to send copies of coronavirus papers to WHO before publication, with the authors' permission. WHO announced this development in a tweet with the headline, "Great news!"

"That is a little different," said Edward Campion, executive editor of the New England Journal of Medicine. "The WHO wants to know what's going on in China and have asked us to help in getting information."

The journal also announced that it is speeding up its peer review. 

 "Some of these articles have been reviewed and edited and revised in 48 or even 24 hours, including working overnight and weekends but still going through rigorous peer review to meet the standards that we think are important," said Campion. "We have some peer reviewers who've agreed to work overtime."

On Friday, 67 leading research organizations and scientific journal publishers from around the world announced an agreement to make relevant coronavirus research immediately available and free.

Bedford said the current climate of sharing is unusual for scientists.

"You don't really talk externally that much because you're trying to get your best science so it can't be scooped," he said.

"You only really talk about things once it's all been published. This is flipping that around entirely where people are just being completely open with what they know." 

It's a temporary glimpse of a world where science is openly shared. But the measures also raise questions about the way science-as-usual is practised.

Vincent Larivière is an information scientist and professor at the University of Montreal, who studies the way science is disseminated. He said the move to speed up publication and share research is a tacit admission that business-as-usual in research slows down science.

"[They say] we're opening everything because it's important that we advance things fast. Well, the flip side of this argument is that your normal behaviour is to put barriers to science."

"This virus is dangerous and deadly, but there's lots of other diseases that are dangerous and deadly, and for which opening could save lives. So if you really want to go in that direction, just open everything." 

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