COVID-19 #11 (Still Optional)

BREAKING

"We now have a name for the #2019nCoV disease:

COVID-19.

I’ll spell it: C-O-V-I-D hyphen one nine – COVID-19"

-@DrTedros #COVID19 pic.twitter.com/Kh0wx2qfzk

— World Health Organization (WHO) (@WHO) February 11, 2020

COVID-19 #10 (Required Parts are Highlighted)

Some historical review …
Both in class, and in the media, we keep seeing analogies drawn between SARS and the new coronavirus, and also sometimes with MERS. Both SARS and MERS were once the “new coronaviruses”. Both are associated with human proximity to animal reservoirs, followed by human-to-human transmission.
SARS hit Hong Kong and surrounding areas in 2002-3. It then disappeared (probably evolving into something we don’t notice much). At that time, SARS was the biggest epidemic scare in decades. Ultimately there were about 8K cases, and 800 deaths, in about 30 countries. A 10% death rate is high for a coronavirus.
MERS is more chronic, and has been popping up since 2012, mostly in the Middle East, with a big cluster in South Korea related to travel from Saudi Arabia. MERS now seems more serious: while rare, it hasn’t gone away, and the fatality rate is about 35%. There have been about 2,500 cases over the last 8 years, hitting almost 30 countries.
For both of these, there is a strong possibility that the fatality rate is much lower. Since they have similar symptoms to a severe case of the common cold, it’s probable that there are a lot of people infected who don’t ever get tested.
Keep in mind that these things are not as common as seasonal influenza outbreaks, but are more deadly. In the U.S. alone, there have been 22 million cases of the flu so far this winter, but the fatality rate is about 0.05%.
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The new coronavirus is now much more widespread than either SARS or MERS, with about 40K confirmed cases. And it passed SARS death toll this past Saturday.
There are two new issues with the data.

• China has decided to change their counting rules. Now, if you test positive, but show no symptoms, you will not counted as a confirmed case. This is problematic, particularly in Hubei, where all hospital beds are full, and those without symptoms are being sent home.
• For several days now, new cases in China have been level at just over 3,000 per day, with about 10K new ones every 3 days. This is not mathematically consistent with growth through compounding (which is what infections do). There is a possibility that this means preventive measures are reducing infections. But, a much more likely explanation is that China has hit the limit of how many tests they can process per day.

Both of these will make the announced infection numbers trend upwards at a slower rate.
Also note that when China started recommending the widespread closing of factories and stores outside the quarantine area, they indicated February 9th as the likely day to re-open. Not many (including Apple’s Foxconn affiliate) are.
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This is a good time to start reviewing the economic impact of SARS. SARS was geographically focused like the new virus. MERS is less geographically focused, so we’re not sure how much damage it’s done.
There have been lots of casual estimates for the cost of SARS, but the scholarly gold standard is probably Lee and McKibbin [2004]. You don’t have to read this, but you should skim it and take a look at some of the tables (like Table 2.2) and charts (like Figure 2.4). In particular, pay attention to the language: things like negative shocks, and temporary vs. permanent shocks, are mainstays in macroeconomics that you’ll start learning about shortly.
Their conclusion is that the cost of SARS, mostly born by Hong Kong, is about $40B in current dollars at the time the paper was written. Data from FRED shows that Hong Kong’s GDP in current U.S. dollars was about $160B/yr at the time. Now, total costs of an epidemic are a stock variable, and GDP is a flow variable, so be careful about comparing those (for perspective, at roughly the same time, the damage from Hurricane Katrina was estimated at $400B).
Their Table 2.2 estimates the permanent effects on Hong Kong’s GDP at –3.2%, and on China’s at –2.3%. That’s a lot. The long-run effects on the U.S. economy from the 2007-9 recession are in that range.
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While browsing over the weekend, I came upon a version of the initial (in depth) article in The Wall Street Journal, entitled “New Virus Discovered by Chinese Scientists Investigating Pneumonia Outbreak” that trouble was brewing in China. Reading it is sobering: this was published less than 5 weeks ago:

Chinese scientists investigating a mystery illness that has sickened dozens in central China …

Yep … dozens.

The disease afflicting patients in Wuhan hasn’t been transmitted from human to human, and health-care workers have remained uninfected …

It is believed that something like 5 million people traveled through Wuhan in the days after this on their way to visit relatives for New Years celebrations. No quarantines were in place until 12 days after this article came out.

Health experts say one risk is that the disease could become a bigger threat as tens of millions of Chinese travel around the country during the Lunar New Year holidays …

Health authorities in Singapore and Hong Kong, cities that have direct flights from Wuhan, have issued alerts …

Similarities to other diseases were still speculative:

Researchers have determined that a large proportion of new infectious diseases in humans are transmitted via animals. Such illnesses are referred to as zoonoses. Two newer human coronaviruses, MERS-CoV and SARS-CoV, have been known to cause severe illness and death, according to the U.S. CDC.
The Wuhan strain is similar to bat coronaviruses that were a precursor to SARS …

K.Y. Yuen, chair professor of infectious diseases at the University of Hong Kong’s Faculty of Medicine said this:

Given the marked advances in hospital isolation facilities, infection-control training and laboratory diagnostic capabilities in the past two decades, it is unlikely that this outbreak will lead to a major 2003-like epidemic …

Of course, China has been pretty clear about this for a couple of weeks now: they have a large region in which healthcare facilities are overwhelmed.
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Estimates I mentioned in class last week of a total cost of $150B are based on extrapolating the 2-3% permanent effect of SARS to China’s contemporary $15,000B/yr economy. It now appears it’s going to be quite a bit larger than that.

COVID-19 #09 (Required Parts are Highlighted)

It’s early Friday evening. Four pieces came up that may interest you.
First, the beginning of the NPR show Planet Money was about the possible effects of the coronavirus outbreak on the U.S. economy. You can listen to it here, under the show's title “Uber’s Path to Profitability”.
Second, one of the things they mention in that piece is “black swan” event. This concept gained modern prominence from Nicholas Nassem Taleb’s book, that seemed to eerily predict the 2007-9 financial crisis, entitled The Black Swan. The name comes from the assertion amongst Europeans, going back about 2,000 years to the Romans, that all swans were white and therefore black ones were impossible. Until they were observed in Australia in the late 17th century that is. Taleb uses the black swan as a metaphor for macro-outcomes being influenced by events that could not be foreseen, and further seemed beyond the realm of possibility. The NPR show worries that the coronavirus epidemic may be a black swan.
This leads to the third item. The Federal Reserve released a semiannual report on Friday afternoon noting that:

… Possible spillovers from the effects of the coronavirus in China have presented a new risk to the outlook.

…

The recent emergence of the coronavirus could lead to disruptions in China that spill over to the rest of the global economy …

That does not sound like too big a deal, except that the Fed normally makes its semiannual reports in fairly dry and non-specific language, unlike these two instances.
Lastly, I missed a point that comes up in a lot of international comparisons involving health risks and deaths: doctors in different countries list causes of death differently. This is from the Reddit thread I linked to earlier:

It is true that the death rate reported by China is heavily misleading. But this is NOT due to an active cover-up. There are 2 main structural reasons:

1. This is primarily due to the structural method of how China records deaths on their certificate. It is established policy/practice in China to record the final cause of death, rather than all existing conditions and overlapping factors.

For example, if a (say 85 yo) patient in the US with diabetes and an existing heart condition gets nCoV, is admitted in the hospital, is confirmed with nCoV, then dies of heart failure, he is recorded as dying of nCoV AND heart failure with other complications. However if the same patient dies in China, he would only be recorded of dying by heart failure.
This is a well-known issue with China and co-morbid diseases. I don't agree with it, I wouldn't do it, but I don't run China. But this is not a new method they made up to try to hide deaths here, it's just the way it's done. This has led to jokes in the epidemiology community that "it's impossible to die of flu in China", because they basically don't record any deaths where the patient has flu. See here this recent article from the Global Times, which is one of China's state-sponsored newspapers.
This is not something even China is really trying to hide. They just tell us, sorry, our doctors just do things this way, we have no interest in changing it.

So, pretty much if this outbreak has started in the U.S. and followed the same course, death rates would have been much higher. Data weirdness like this is a regular part of doing cross-country comparisons on any subject.

COVID-19 #08 (Required Parts are Highlighted)

I emphasized in an earlier post that that projections of infections and deaths done for this virus are similar to those we’re going to learn this semester. For those just interested in thinking about how they measure an epidemic and what they look for in the numbers, check out this Reddit thread. This was the source of the comment I made the other day that the CDC stalled on believing Chinese authorities that the virus was being transmitted from person to person prior to the appearance of symptoms.
If you’re interested in openness of Chinese society, here’s a podcast interview with someone who monitors China’s social media. He asserts that what is coming out of China online is unprecedented (in a positive way).
I also talked to SUU alum RB, both of whose parents are doctors in Shanghai. Their view is that the epidemic if overhyped and will wind down shortly. (I don’t recommend reading too much in to that “shortly”, since most respiratory epidemics wind down as the weather starts to warm up).
China’s official numbers are showing a decline:

2. #2019nCoV: Does the shrinking of the size of the new cases mean anything real? Dunno. Could it be because their system is overwhelmed? Yes. Does it mean this outbreak is abating? I wouldn't bet on it based on 2 data points. Too soon to know how to interpret this.

— Helen Branswell (@HelenBranswell) February 7, 2020

The WHO’s top doctor on epidemics concurred with this. China may not be able to produce tests fast enough.
BTW: the CDC distributed test kits capable of making 140,000 diagnoses across the U.S. this week. That gives you some sense of what they think might be coming.

COVID-19 #07: Different Numbers (Required Parts are Highlighted)

The number of coronavirus cases has continued to rise. But, there are problems: 1) nothing goes in the official numbers unless there’s a test, 2) there are known shortages of tests, 3) there are suspicions that tests are not being provided, and 4) there are some areas without many labs (for example, lack of cases in Africa seems to result from a lack of labs).
The official numbers look currently are:

#2019nCoV update:

28,060 confirmed cases in China, & 564 deaths.

Outside China: 225 cases & 1 death.

Death rate: 1.9%

Don't panic.

SARS was defeated, this one will be defeated too. #CoronaVirusKenya

— Eric (@amerix) February 6, 2020

But there are now reports that Tencent has leaked alternative information. On 3 occasions over the last 2 weeks, internet glitches have revealed tables with rather different numbers, like these from last Saturday:

Left to right, those are “Nationally Confirmed Cases”, “Suspected Cases”, “Cured”, and “Deaths”.
There’s more:

Although some are chalking up the images to users tampering with their browsers, the 154,023 infections on Feb. 1 are remarkably close to the estimate predicted on that date by a scientific modeling study carried out by the University of Hong Kong (HKU) and published on the Lancet website. The study estimates the number of cases is much more given the 2.68 spread rate per case, the doubling of total infections every 6.4 days, and known travel patterns in China and worldwide.
…
As the report estimated over 75,000 cases on Jan. 25, and the Feb. 1 post was seven days later, the number of cases in Wuhan alone, according to the model, should have reached 150,000, uncannily close to the 154,023 listed for all of China on the Tencent page. With nearly 12 days having passed since the report was released, the model predicts the number of infections in Wuhan could now stand at 300,000.

Hard to know what to think about these numbers. Are they real numbers being leaked? Are they fake numbers meant to foment panic?
P.S.

34-yr-old Dr. Li Wenliang was jailed in #Wuhan after he posted a social media warning that patients he'd seen "looked like #SARS" on Dec30.
Once released, the heroic doctor came down w/#2019nCoV
Now, tragically, he has died.https://t.co/QFngp2paf9

— Laurie Garrett (@Laurie_Garrett) February 6, 2020

COVID-19 #06: A Debunking (Still Optional)

BD brought up conspiracy theories in class the other day. That’s a fine thing to bring up, but it’s my responsibility then to go out and fill in the blanks for you all.
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Here is a fact that makes that seem plausible to some posters on the internet:

… The location of China’s premier virology institute and only BSL-4 virology laboratory within 20 miles of the outbreak’s origin …

Now, do keep in mind that while this has been the subject of a lot of fictional video games, movies, and books (so many are primed to believe this). And, it has actually happened in the past (unintentionally here and intentionally here, although doubts remain about this one).
Having noted this, Twitter banned a well-known blogger/tweeter for doxing a scientist from that lab.  Keep in mind that the blogger/tweeter was banned for the doxing, not for their speculation about the origins of the virus. And, in his own defense, he wrote that it’s a funny definition of doxing that includes copying and pasting the personal information off the public website of that virology institute.
And, now we have this: that blogger/tweeter is now being commonly referred as “pro-Trump”. I view that as wishful thinking that probably ought to be penalized as well. But BuzzFeed went ahead and doxxed him, and no one is complaining much.
We live in pretty weird times …
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Part of this speculation is due to research published online prior to peer review, that many experts believe non-experts could have easily misinterpreted.

… Unique elements of the 2019-nCoV genome which noted some similarities to elements of the HIV genome. The authors seemed to suggest that these similarities couldn’t have arisen randomly, so people can be forgiven for jumping straight to “it’s a bioweapon” after reading it.

What non-experts do not generally know, and what makes this result problematic, is that most viruses have some similarities to HIV. Viruses trade genetic information with other viruses in the same host. That’s what they do. It’s how they evolve. It’s super-probable that the gene sequence the new virus shares with HIV aren’t original to either one of those, but were shared from other earlier viruses to both of them. It’s correlation not causation. Experts get that; non-experts … not so much.
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BUT, here’s what the serious people are actually looking at:

Take this to the bank: 2019-nCoV continues to give every appearance of being a wild coronavirus that jumped from bats to humans by way of an animal intermediary in the Huanan seafood market in Wuhan in late 2019. It is not an escaped bioweapon.

Or:

In responsible circles, the current theory about the virus’s origin is that it was very similar to the origin of SARS: an endemic coronavirus in bats spread through an intermediary wild animal sold as food in an exotic meat market in China. The initial cases of the Wuhan strain were all confined to vendors and customers from a small number of nearby stalls in the Huanan Seafood Market in Wuhan, where exotic meat was sold with few or no safety precautions.

And:

Brandon J. Brown, an associate professor at the University of California, Riverside, and a member of the Infectious Diseases Society of America, the International Society of Vaccines, and the Global Health Council, told BuzzFeed News it makes sense that the Wuhan Institute of Virology was researching the coronavirus in bats.
“One reason why this institute would be doing immune research would be to prevent what we are seeing right now with the novel coronavirus outbreak,” Brown said. “They have studied other coronaviruses at that site including SARS, where they discovered that it originated in bats.”
Brown also said that the entire idea of the coronavirus working as a bioweapon is pretty silly. “The fatality rate [of the coronavirus] is 200/10,000, which is currently lower compared to many other viruses including SARS, so if it was meant as a bioweapon, it is not a good one,” Brown said.

So, we’re still at 1) not as deadly as influenza, which we take for granted, but 2) easier to spread to others than influenza … it’s the common cold “on steroids”.
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Here’s one more analogy for students in Utah. The press continues to emphasize poor hygiene at the wet market in Wuhan. Maybe. Do consider that it may still have been better than typical hygiene during deer hunting season.

COVID-19 #05 (Still Optional)

It’s official. The Center for Disease Control’s (CDC’s) official Twitter feed (@CDCgov) states that:

The CDC, under statutory authority of the Health and Human Services (HHS) Secretary, has issued federal quarantine orders to all 195 United States citizens who repatriated to the U.S. on January 29, 2020. The quarantine will last 14 days from when the plane left Wuhan, China.

— CDC (@CDCgov) January 31, 2020

6. @CDCgov says last time quarantine was used in the US was in the 1960s and was related to smallpox. #2019nCoV

— Helen Branswell (@HelenBranswell) January 31, 2020