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Tracking the coronavirus epidemic from Wuhan to the world

Scientists and public health officials worldwide collaborate to understand COVID-19 and slow its spread
people walk around on a street wearing surgical masks over their noses and mouths
Residents wear surgical masks as they cross a street in a shopping district on Jan. 31, 2020 in Hong Kong, China, amid the coronavirus crisis. Scientists around the world are racing to understand the new virus, SARS-CoV-2, which originated in Wuhan, China late last year. Photo by Anthony Kwan / Getty Images

Editor’s note: We’ve updated this story since its original publication on Jan. 31, and may make further updates as the situation progresses.

With more than 46,000 confirmed cases in China and more than 400 elsewhere in the world, according to the World Health Organization, the viral disease known as COVID-19 has killed more than 1,300 people, disrupted global travel and forced governments and other organizations to take extreme measures to limit its global spread, from evacuations to mass quarantines.

The novel coronavirus behind COVID-19, which is  is not currently spreading within the U.S. beyond people in close contact with returned travelers from Wuhan, said the Centers for Disease Control and Prevention.

Scientists are racing to understand this new threat, including how the virus is evolving and passing from person to person, to inform ongoing public health efforts, including the possible development of a vaccine.

Among the scientists on the front lines of that research effort are infectious-disease experts at Fred Hutchinson Cancer Research Center, such as Dr. Trevor Bedford. Bedford, a computational biologist who studies how viruses evolve and spread, is gaining insights about COVID-19 (formerly known as 2019-nCoV and also called SARS-CoV-2) that he hopes will help save lives from this new viral respiratory illness.

headshot of Dr. Trevor Bedford
Dr. Trevor Bedford is a computational biologist at Fred Hutch who is tracking the evolution and spread of the new coronavirus. Photo by Robert Hood / Fred Hutch News Service

As he has been analyzing the spreading virus, Bedford has been sharing what he’s learned so far with the public via media interviews, his team’s open-source platform for real-time tracking of viral evolution — Nextstrain.org — and his Twitter feed (follow Bedford at @trvrb).

COVID-19 questions and answers

The U.S. Centers for Disease Control and Prevention and the World Health Organization have up-to-date information and resources on a variety of questions related to the novel coronavirus, including:

On Feb. 13, Bedford told a gathering of international science reporters at the annual meeting of the American Association for the Advancement of Science in Seattle that his latest calculations show that by Feb. 8 as many as 200,000 people may have been infected, with about 15% of them experiencing severe symptoms.

An expert in building family trees of virus evolution, Bedford said that models that use genome sequencing to build family trees of the new virus are consistent with models developed by Imperial College London and others mapping the current scope of the outbreak. That model estimates that the case fatality of COVID-19 is about 1%. (Note that only a subset of infected people will be considered a “case.”)

“The thing that is scary about this is that it does seem to be transmissible, and it does seem to be severe,” he said.

Here are more highlights of what he and other experts have learned so far — and the critical questions they’re still pursuing:

When did the virus emerge and how is it spreading?

Analyses by Bedford and others of the genetic sequences of some of the first human cases showed that the virus had remarkable lack of genetic diversity from person to person after it first emerged.

At first, there was not enough data to clarify what this meant — was the virus jumping repeatedly to humans from animals or, more dangerously, spreading rapidly between people after an initial jump from animals? “The DNA can’t distinguish those two scenarios. Only epidemiological data or DNA from the reservoir animal can,” Bedford told WIRED on Jan. 22. Figuring this out “would be the big epidemiological goal for everyone at the moment,” he told the journal Nature the same week.

“If it’s not contained shortly, I think we are looking at a pandemic,” Bedford told STAT News on Jan. 27 — although he cautioned that it was impossible to say how serious a COVID-19 pandemic would be.

This research by Bedford and other virus-trackers is possible because of rapid genetic sequencing of infected people — unfeasible or even impossible not too many years ago — and a global commitment to sharing these genetic data freely with the worldwide research community. On Feb. 13 at the AAAS annual meeting, Bedford said Nextstrain already had 84 novel coronavirus genomes.    

Typically, scientists “don't really talk externally that much because you're trying to get your best science so it can't be scooped,” Bedford told the CBC, Canada’s national public broadcaster, on Feb. 1. “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.”

He outlined the speed at which genomic information has been flowing:

“Basically, a week after registering that there’s this new thing, the amazing scientists in China have a genome for the novel virus that had never been seen before. Then, after the first genome was released on a Friday afternoon, we had five more Sunday morning. And now, nine days later, we’re up to 24,” Bedford explained on the public radio show Science Friday on Jan. 24. “That first genome has been amazing for people developing rapid tests to be able to actually confirm cases, and these subsequent genomes are being very useful to understand basic epidemiological questions.”

Because of the rapidly emerging nature of the disease, “adding a few key samples can change the story significantly,” Bedford told the journal Nature on Jan. 28.

That is, in fact, what happened. With access to additional genetic sequences from more infected people, Bedford and Nextstrain teammates wrote on a report on their site on Jan. 30 that the disease’s low mutation rate is the result of person-to-person spread since its initial jump, or jumps, from unknown animals to people in November or early December 2019.

In their Jan. 30 report, the team also wrote:

  • While the virus has started to pick up mutations as it spreads between people — as this type of virus naturally does — these mutations don’t appear to be linked with changes in the virus’ behavior.
  • Although data are too preliminary for firm conclusions, the new virus appears to be less likely to kill those with confirmed cases than its coronavirus cousin, SARS.
screenshot from Nextstrain.org showing a world map with colored dots of different sizes. The largest dots are in China; smaller dots of other colors appear in North America and elsewhere.
In this Jan. 30 report on Nextstrain.org (click to view online), Bedford and teammates describe their latest data on the spread and evolution of SARS-CoV-2 across the world. The map shows the number and location of viral sequences they analyze from cases around the world as the virus traveled out of China. Genomic analysis of nCoV spread. Situation report 2020-01-30. Author: Trevor Bedford, Richard Neher, James Hadfield, Emma Hodcroft, Misja Ilcisin, Nicola Müller. https://nextstrain.org/narratives/ncov/sit-rep/2020-01-30

Meanwhile, a new analysis of the first 425 people with the virus, published on Jan. 29 in the New England Journal of Medicine by a China-based research team, concluded that it takes about five days for a person who is ultimately diagnosed with the illness to develop symptoms after their initial infection with the virus.

Bedford wrote on Twitter on Jan. 30 that the key question at that point for understanding the disease’s transmission is how many people get infected with the virus without getting diagnosable symptoms of the disease.

Screenshot of a Tweet from Trevor Bedford (@trvrb) send at 11:01 a.m. on Jan. 30. The Tweet reads: "These numbers should be caveated that they are looking at _cases_ and not at _infections_. There is a big question now about the # of mild or asymptomatic infections relative to the # of cases who meet case definition (fever & symptoms of lower respiratory tract infection). 3/3"
(Click to view on Twitter)

This story in Science from Jan. 31 looks in depth at work by Bedford and other scientists to uncover the novel virus’ origins by mapping coronavirus genomes.

Who is most at risk of COVID-19?

So far, people who have been coming down with the most severe cases of COVID-19, the illness caused by COVID-19, are almost always older people and people with underlying health conditions, according to the CDC’s Jan. 30 media briefing.

Is there a vaccine or other treatment?

There is no vaccine, but researchers are already developing candidates, the Washington Post reported on Jan. 30. It’s unclear whether one can be developed before the virus runs its course.

Although there are no drugs specifically for COVID-19, the WHO advises that patients who are hospitalized with confirmed cases of infection be treated with therapies to overcome particular symptoms of illness.

Could the novel coronavirus have been genetically engineered in a lab?

At the AAAS annual meeting on Feb. 13, Bedford fielded a number of questions from the international press corps about stories circulating that COVID-19 might have been genetically engineered. “If you look for evidence of genetic engineering, you can find none whatsoever. It is completely consistent with natural evolution,” Bedford said.

Fred Hutch News Service writer Sabin Russell contributed reporting for this story.

Susan Keown, a staff writer at Fred Hutchinson Cancer Research Center, has written about health and research topics for a variety of research institutions, including the National Institutes of Health and the Centers for Disease Control and Prevention. Reach her at skeown@fredhutch.org or on Twitter @sejkeown.

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Last Modified, February 20, 2020