Coronavirus: Track the virus' spread with this world map tool

The Johns Hopkins Center for Systems Science and Engineering (CSSE) created an online dashboard map that provides up-to-date data on reported cases and deaths worldwide.

Global visualization of reported Wuhan coronavirus cases

Current map of reported Wuhan coronavirus cases

Visualization: JHU CSSE
  • A new strain of coronavirus has spread from China to at least 19 countries, including the U.S. You can track the spread on this Johns Hopkins map.
  • It remains unclear how bad the outbreak will become, but the World Health Organization has stopped short of calling it a global health emergency. (Update Jan. 30 2020: The WHO has declared a global emergency)
  • The new coronavirus is less deadly but more contagious than SARS.


A new strain of coronavirus has killed more than 130 people and infected over 6,000 others as of January 29. So far, all deaths have occurred in mainland China, but the virus has spread to other countries, including the United States, Thailand, Germany, Canada, France, Singapore, South Korea, and Australia.

In dozens of nations, officials are taking precautionary measures to limit the spread of the virus, called 2019-nCoV, which is in the same family as the common cold and the SARS virus. It's currently unclear how bad the outbreak will become.

To track the spread of the virus, the The Johns Hopkins Center for Systems Science and Engineering (CSSE) created an online dashboard map that provides up-to-date data on reported cases and deaths worldwide. You can check it out here.

Map of Wuhan coronavirus cases in China

Visualization: JHU CSSE

"We built this dashboard because we think it is important for the public to have an understanding of the outbreak situation as it unfolds with transparent data sources," said Lauren Gardner, a civil engineering professor and CSSE's co-director. "For the research community, this data will become more valuable as we continue to collect it over time."

Gardener said it's "critical" to provide researchers with this data, which is being compiled from the World Health Organization, the Centers for Disease Control and Prevention, the National Health Commission of the People's Republic of China, and Dingxiangyuan, a social networking site for health-care professionals. The dashboard allows anyone to download a Google Sheet containing data on all reported cases, locations, and deaths.

​How bad will the outbreak be?

The answer depends largely on two factors: how deadly the virus is, and how easily it's transmitted from person to person.

Currently, the new strain of coronavirus has killed 2 to 3 percent of those infected, but that fatality rate is likely to change as the strain mutates. For comparison, the fatality rate for SARS was about 14 to 15 percent in 2003. But the new coronavirus seems to be more contagious than SARS. One reason is that infected people can go about 10 days without symptoms, making it easier for the virus to spread because infected people aren't aware they're contagious.

It's still the early stages of the outbreak, however, and the exact incubation period for 2019-nCoV remains unclear. Researchers are busy trying to determine how far, and how quickly, the virus might spread. That requires using a metric called the basic reproduction number, called "R naught" or R0.

This number represents how many people one infected individual is likely to get sick, and epidemiologists use it to estimate how contagious a virus is likely to be. So, for example, an R0 of 3 means each person with the virus infects about three other people. Higher R0s tend to mean worse outbreaks.

Wuhan University Sakura Castle

Wuhan, epicenter of the coronavirus outbreak

Howchou

But it's important to note that R0 is an average, meaning that some infected people might never spread the virus to a single person, while others might spread it to many. What's more, R0 depends on how susceptible an individual or population is to a virus, the nature of the virus, and the measures a community takes after an outbreak. Some people might become infected but remain perfectly healthy. In short, R0 is a useful but rough measure of the potential transmissibility of a virus.

The R0 of the new strain of coronavirus remains unclear, but estimates range from 1.4 to 5.5, and most fall between 2 and 3. So far, the World Health Organization has voted not to declare the outbreak a global health emergency, mainly because it hasn't significantly spread beyond China. But that could change if international cases keep popping up.

Some think it's past time to label this outbreak as an international emergency.

"The fact that there are cases now in so many countries and that it is spreading fast is of international concern," Peter Piot, director of the London School of Hygiene and Tropical Medicine, told the Financial Times. "I do not know what more they need."

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Gain-of-function mutation research may help predict the next pandemic — or, critics argue, cause one.

Credit: Guillermo Legaria via Getty Images
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This article was originally published on our sister site, Freethink.

"I was intrigued," says Ron Fouchier, in his rich, Dutch-accented English, "in how little things could kill large animals and humans."

It's late evening in Rotterdam as darkness slowly drapes our Skype conversation.

This fascination led the silver-haired virologist to venture into controversial gain-of-function mutation research — work by scientists that adds abilities to pathogens, including experiments that focus on SARS and MERS, the coronavirus cousins of the COVID-19 agent.

If we are to avoid another influenza pandemic, we will need to understand the kinds of flu viruses that could cause it. Gain-of-function mutation research can help us with that, says Fouchier, by telling us what kind of mutations might allow a virus to jump across species or evolve into more virulent strains. It could help us prepare and, in doing so, save lives.

Many of his scientific peers, however, disagree; they say his experiments are not worth the risks they pose to society.

A virus and a firestorm

The Dutch virologist, based at Erasmus Medical Center in Rotterdam, caused a firestorm of controversy about a decade ago, when he and Yoshihiro Kawaoka at the University of Wisconsin-Madison announced that they had successfully mutated H5N1, a strain of bird flu, to pass through the air between ferrets, in two separate experiments. Ferrets are considered the best flu models because their respiratory systems react to the flu much like humans.

The mutations that gave the virus its ability to be airborne transmissible are gain-of-function (GOF) mutations. GOF research is when scientists purposefully cause mutations that give viruses new abilities in an attempt to better understand the pathogen. In Fouchier's experiments, they wanted to see if it could be made airborne transmissible so that they could catch potentially dangerous strains early and develop new treatments and vaccines ahead of time.

The problem is: their mutated H5N1 could also cause a pandemic if it ever left the lab. In Science magazine, Fouchier himself called it "probably one of the most dangerous viruses you can make."

Just three special traits

Recreated 1918 influenza virionsCredit: Cynthia Goldsmith / CDC / Dr. Terrence Tumpey / Public domain via Wikipedia

For H5N1, Fouchier identified five mutations that could cause three special traits needed to trigger an avian flu to become airborne in mammals. Those traits are (1) the ability to attach to cells of the throat and nose, (2) the ability to survive the colder temperatures found in those places, and (3) the ability to survive in adverse environments.

A minimum of three mutations may be all that's needed for a virus in the wild to make the leap through the air in mammals. If it does, it could spread. Fast.

Fouchier calculates the odds of this happening to be fairly low, for any given virus. Each mutation has the potential to cripple the virus on its own. They need to be perfectly aligned for the flu to jump. But these mutations can — and do — happen.

"In 2013, a new virus popped up in China," says Fouchier. "H7N9."

H7N9 is another kind of avian flu, like H5N1. The CDC considers it the most likely flu strain to cause a pandemic. In the human outbreaks that occurred between 2013 and 2015, it killed a staggering 39% of known cases; if H7N9 were to have all five of the gain-of-function mutations Fouchier had identified in his work with H5N1, it could make COVID-19 look like a kitten in comparison.

H7N9 had three of those mutations in 2013.

Gain-of-function mutation: creating our fears to (possibly) prevent them

Flu viruses are basically eight pieces of RNA wrapped up in a ball. To create the gain-of-function mutations, the research used a DNA template for each piece, called a plasmid. Making a single mutation in the plasmid is easy, Fouchier says, and it's commonly done in genetics labs.

If you insert all eight plasmids into a mammalian cell, they hijack the cell's machinery to create flu virus RNA.

"Now you can start to assemble a new virus particle in that cell," Fouchier says.

One infected cell is enough to grow many new virus particles — from one to a thousand to a million; viruses are replication machines. And because they mutate so readily during their replication, the new viruses have to be checked to make sure it only has the mutations the lab caused.

The virus then goes into the ferrets, passing through them to generate new viruses until, on the 10th generation, it infected ferrets through the air. By analyzing the virus's genes in each generation, they can figure out what exact five mutations lead to H5N1 bird flu being airborne between ferrets.

And, potentially, people.

"This work should never have been done"

The potential for the modified H5N1 strain to cause a human pandemic if it ever slipped out of containment has sparked sharp criticism and no shortage of controversy. Rutgers molecular biologist Richard Ebright summed up the far end of the opposition when he told Science that the research "should never have been done."

"When I first heard about the experiments that make highly pathogenic avian influenza transmissible," says Philip Dormitzer, vice president and chief scientific officer of viral vaccines at Pfizer, "I was interested in the science but concerned about the risks of both the viruses themselves and of the consequences of the reaction to the experiments."

In 2014, in response to researchers' fears and some lab incidents, the federal government imposed a moratorium on all GOF research, freezing the work.

Some scientists believe gain-of-function mutation experiments could be extremely valuable in understanding the potential risks we face from wild influenza strains, but only if they are done right. Dormitzer says that a careful and thoughtful examination of the issue could lead to processes that make gain-of-function mutation research with viruses safer.

But in the meantime, the moratorium stifled some research into influenzas — and coronaviruses.

The National Academy of Science whipped up some new guidelines, and in December of 2017, the call went out: GOF studies could apply to be funded again. A panel formed by Health and Human Services (HHS) would review applications and make the decision of which studies to fund.

As of right now, only Kawaoka and Fouchier's studies have been approved, getting the green light last winter. They are resuming where they left off.

Pandora's locks: how to contain gain-of-function flu

Here's the thing: the work is indeed potentially dangerous. But there are layers upon layers of safety measures at both Fouchier's and Kawaoka's labs.

"You really need to think about it like an onion," says Rebecca Moritz of the University of Wisconsin-Madison. Moritz is the select agent responsible for Kawaoka's lab. Her job is to ensure that all safety standards are met and that protocols are created and drilled; basically, she's there to prevent viruses from escaping. And this virus has some extra-special considerations.

The specific H5N1 strain Kawaoka's lab uses is on a list called the Federal Select Agent Program. Pathogens on this list need to meet special safety considerations. The GOF experiments have even more stringent guidelines because the research is deemed "dual-use research of concern."

There was debate over whether Fouchier and Kawaoka's work should even be published.

"Dual-use research of concern is legitimate research that could potentially be used for nefarious purposes," Moritz says. At one time, there was debate over whether Fouchier and Kawaoka's work should even be published.

While the insights they found would help scientists, they could also be used to create bioweapons. The papers had to pass through a review by the U.S. National Science Board for Biosecurity, but they were eventually published.

Intentional biowarfare and terrorism aside, the gain-of-function mutation flu must be contained even from accidents. At Wisconsin, that begins with the building itself. The labs are specially designed to be able to contain pathogens (BSL-3 agricultural, for you Inside Baseball types).

They are essentially an airtight cement bunker, negatively pressurized so that air will only flow into the lab in case of any breach — keeping the viruses pushed in. And all air in and out of the lap passes through multiple HEPA filters.

Inside the lab, researchers wear special protective equipment, including respirators. Anyone coming or going into the lab must go through an intricate dance involving stripping and putting on various articles of clothing and passing through showers and decontamination.

And the most dangerous parts of the experiment are performed inside primary containment. For example, a biocontainment cabinet, which acts like an extra high-security box, inside the already highly-secure lab (kind of like the radiation glove box Homer Simpson is working in during the opening credits).

"Many people behind the institution are working to make sure this research can be done safely and securely." — REBECCA MORITZ

The Federal Select Agent program can come and inspect you at any time with no warning, Moritz says. At the bare minimum, the whole thing gets shaken down every three years.

There are numerous potential dangers — a vial of virus gets dropped; a needle prick; a ferret bite — but Moritz is confident that the safety measures and guidelines will prevent any catastrophe.

"The institution and many people behind the institution are working to make sure this research can be done safely and securely," Moritz says.

No human harm has come of the work yet, but the potential for it is real.

"Nature will continue to do this"

They were dead on the beaches.

In the spring of 2014, another type of bird flu, H10N7, swept through the harbor seal population of northern Europe. Starting in Sweden, the virus moved south and west, across Denmark, Germany, and the Netherlands. It is estimated that 10% of the entire seal population was killed.

The virus's evolution could be tracked through time and space, Fouchier says, as it progressed down the coast. Natural selection pushed through gain-of-function mutations in the seals, similarly to how H5N1 evolved to better jump between ferrets in his lab — his lab which, at the time, was shuttered.

"We did our work in the lab," Fouchier says, with a high level of safety and security. "But the same thing was happening on the beach here in the Netherlands. And so you can tell me to stop doing this research, but nature will continue to do this day in, day out."

Critics argue that the knowledge gained from the experiments is either non-existent or not worth the risk; Fouchier argues that GOF experiments are the only way to learn crucial information on what makes a flu virus a pandemic candidate.

"If these three traits could be caused by hundreds of combinations of five mutations, then that increases the risk of these things happening in nature immensely," Fouchier says.

"With something as crucial as flu, we need to investigate everything that we can," Fouchier says, hoping to find "a new Achilles' heel of the flu that we can use to stop the impact of it."

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