Watching the virus mutate in real time

February 1, 2020 6:12 AM

When the story of the coronavirus (2019-nCOV) is finally written, it might well become a template for the utopian dream of open science. 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.

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.

posted by heatherlogan (15 comments total)

Related: it's worth revisiting China Syndrome, an account of SARS and its emergence. The author predicted a new spillover from conditions pretty much exactly like those in Wuhan - dense, messy, wild animal markets.
posted by j_curiouser at 9:27 AM on February 1, 2020

Really interesting, thanks! It's sad that it takes huge threats like this to break through the barriers preventing scientists from working together as closely as they might otherwise, but it's also hopeful to see that it's still possible.

I was fascinated to see how the New England Journal of Medicine has accelerated its peer-review process in response:

"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."

posted by adrianhon at 9:31 AM on February 1, 2020 [5 favorites]

It's not clear that the virus was transmitted from animals to humans at the wet market, but as a place where lots of people get together in a close space it's possible that it was just where the people who were infected in november went to, like, sell or buy food
posted by sukeban at 9:34 AM on February 1, 2020 [4 favorites]

Open science is a great way to debunk nonsense that could otherwise spread fast. A pre-print claiming that nCoV was engineered with pieces of HIV-1 genome inserted was repudiated quickly.
posted by They sucked his brains out! at 10:40 AM on February 1, 2020 [5 favorites]

Here's a Twitter thread where the inserts (mentioned above) are discussed in more technical detail.
posted by They sucked his brains out! at 12:48 PM on February 1, 2020

While I'm sure that the openness and speedy peer review helps, the most striking thing to me is how much faster and cheaper much of the relevant technology is compared to 2001 when SARS emerged. Sequencing is way faster, methods for analysis of sequence data are better. This drives everything to be faster and allows more sampling and more analysis.
posted by medusa at 1:44 PM on February 1, 2020 [4 favorites]

Nucleotide sequencing technology has come a huuuge way since 2001.

Not sure how much single-strand long-read technology was involved, but it trivializes genome assembly over traditional methods. Getting the full sequence of the virus really sped up being able to inexpensively and very rapidly interrogate and confirm with high reliability suspected cases.
posted by porpoise at 5:24 PM on February 1, 2020

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."

Fascinating, I do hope this becomes the norm.
posted by ellieBOA at 10:43 PM on February 1, 2020 [2 favorites]

The speed at which scientists are racing to understand the Wuhan Coronavirus, debunk myths about it, and provide ways of fighting it - are amazing to me (pretty much equally amazing as the ability of the virus to get itself so far and wide so fast). On the Brexit thread there is a recommendation for this speech by John le Carré. He says:

One day somebody will explain to me why it is that, at a time when science has never been wiser, or the truth more stark, or human knowledge more available, populists and liars are in such pressing demand.

So - sometimes it is worthwhile to appreciate the positive "wisdom and truth" side of that equation. While the old adage about the truth, lies and putting on boots, is accurate - scientific truth can move at a hell of a pace as well.
posted by rongorongo at 3:20 AM on February 2, 2020 [1 favorite]

Like most medical journals, the New England Journal of Medicine employs an embargo policy that prevents authors from discussing or publicizing their results prior to publication:

NEJM editors consider novelty when making manuscript decisions. If substantial publicity for a study occurs before or during the peer-review process, priority for publication could be affected. The more said in a press release prior to publication, the greater the negative impact may be on priority for publication.

The ultra-prestigious journals Science and Nature have historically had similar policies -- if you want the hottest results, you'd better pay for a subscription! So it's certainly not technology that's responsible for preventing scientists from working together as closely as they might otherwise.

A (very good) Washington Post article points out that:

When SARS began to spread [in late 2002/early 2003], the tools scientists needed were much less mature, including the basic infrastructure for sharing results rapidly so anyone could build on them. It wasn’t until 2013 that bioRxiv, a preprint server to share scientific papers, was created so scientists would have an easy way to widely share results before they had gone through the process of being vetted and accepted by scientific journals — a process that can take many months.

And yet high-energy physicists had been using the original arXiv preprint server since 1991, and it was already in near-universal use among theorists by 1993.

So while gene sequencing technology has certainly come a long way in the past 17 years, the basic infrastructure for sharing results was as fully mature in 2003 as it is today, it just hadn't been adopted by the biomedical sciences because of the patent-and-profit-driven culture of that discipline.

Capitalism spoils everything.
posted by heatherlogan at 9:10 AM on February 2, 2020 [2 favorites]

Capitalism spoils everything.

Yes, though other government ideologies have their own style of getting in the way of science: the cost of the initial stonewalling of Wuhan doctors who raised alerts in December is hard to estimate. (For opthalmologist Li Wenliang, in addition to official reprimand, it's also infection).
posted by progosk at 3:30 AM on February 4, 2020

Scientific American: How Coronaviruses Cause Infection—from Colds to Deadly Pneumonia, with some interesting stuff regarding bats.
posted by exogenous at 8:51 AM on February 5, 2020

(For opthalmologist Li Wenliang, in addition to official reprimand, it's also infection)

Worse: there are reports it's cost him his life.

.
posted by progosk at 7:03 AM on February 6, 2020

Another 14 million person city locked down. 400 million total according to report. That’s larger than the entire US population in lockdown.
posted by adamvasco at 12:41 PM on February 7, 2020

Mentour Pilot discusses how much at risk you are at of contracting Wuhan coronavirus on flight. Interesting generally, but particularly for his aside where he points out that there are currently 19 million people infected with the ordinary influenza virus, with 10,000 of them having died from it in the last year. In the US alone. Yes, the number who could die from a nasty new global pandemic is huge - but we rather overlook the number who get caught by more quotidian bugs.
posted by rongorongo at 10:57 AM on February 9, 2020