Second Travel-Related Case of 2019 Novel Coronavirus Detected in United States | Hacker News Reader

Second Travel-Related Case of 2019 Novel Coronavirus Detected in United States

cdc.gov

150 pointslawrenceyan96 comments

If you are not a scientist this doesn't mean you can't help fighting this particular or any other infectious and non-infectious disease. It is easy - just help to improve the tools that scientists and laboratories use. For example, something like BioJulia[1][2] and BioPython[3][4] - both have some issues[5][6] that need help with or accepting donations[7]. There are many other tools that are used, feel free to list them in the comments.

[1] https://biojulia.net/

[2] https://github.com/BioJulia

[3] https://biopython.org/

[4] https://github.com/biopython/

[5] https://github.com/BioJulia/BioSequences.jl/issues

[6] https://github.com/biopython/biopython/issues?q=label%3A%22h...

[7] https://opencollective.com/biojulia#backer

Are these tools really used by disease labs?

Yes.

I run an infectious disease modeling lab - while I don't use these tools, I know people who do.

In my lab, we use R, Numpy, SciPy, StochPy, etc.

You could also just see about donating directly to a lab at a nearby university.

Scary username!

What are some of the R libraries that your team uses?

I wouldn't mind donating some time to help with bug fixes. I have no idea though which R libraries/projects are being used.

Lets see...

survival, parallel/snow, Amelia2, nlme,vioplot,ggplot2 and deSolve are the big ones.

In my anecdotal experience almost all new comp bio methods are implemented and used in R. Python is starting to become a bit more common but is still the minority. When performance matters people sometimes go for C/C++. I have never seen anyone actually using Julia but I guess there may be one or two.

Does anyone use Julia in production?

Yes.

Maybe you can elaborate on that?

And an interesting note of Biosequences versus the new Seq language: https://biojulia.net/post/seq-lang/

The market seems to be reacting to this. Hard to tell how serious it really is relative to the flu, but would not be surprised if China was underplaying the numbers, both infected and deaths.

I’ve been seeing containment numbers rising in the millions on the front page of NYTimes. In the morning it was 20 million. Then hours later it was mid 20s. It increased after that again. And now I’m reading 35 million. So, there’s a good possibility that China might be underplaying the infected and death numbers.

The numbers in the millions are the population affected by city-wide quarantines, where trains/long distance buses have been stopped from coming or leaving...

If the quarantine is indeed growing rapidly, that might suggest that Chinese officials are receiving updated information about the scope of the disease that prompts them to expand the quarantine.

A growing quarantine seems to suggest they believe the disease is not yet contained.

if you have even a modicum of knowledge of china, you will understand why certain cities were shutdown. saturday is new year's day in china, and thus, thursday and friday are the two busiest travel days of the year. it's like thanksgiving and the related travel in the u.s. but on a whole other level. since wuhan, where the outbreak originated, has a population of around 10 million, the city and two surrounding cities were closed down to prevent the, then upcoming, exodus and intake of millions of people, a percentage of which would be infected or would potentially become infected and then would return to their origin city, further spreading the virus.

Well jeez, excuse me for being wrong. Thank you for the correction.

sorry, i just like the word modicum. haha. didn't mean for it to sound so agressive.

I would not be surprised by that at all.

Every Asia-focused analyst will tell you that the only aspect of China's state-reported numbers you can assume with a high degree of confidence is that they're heavily massaged for PR purposes.

Official numbers yes, but sometimes behavior leaks. What are wealthy/well-connected Chinese businesspeople and officials doing? Maybe there's some insider trading or money moving that could shed light on the real situation?

IIRC people used to look at things like electricity and energy use to determine real Chinese GDP growth, but I would imagine this has become less useful as the Chinese economy transitions away from heavy polluting industry and towards higher energy efficiency.

That transition is still a ways off.

That is actually called the Li Keqiang index. Unfortunately, Li Keqiang has been mostly sidelined by Xi Jinping.

Sometimes it's also possible to draw inferences by observing how the numbers were massaged. For example if you look at the red graph of confirmed cases at [1], there's a very noticeable jump from 1-17 to 1-18. Coincidentally, the third session of the 13th Hubei Provincial People's Congress concluded on January 17. [2]

[1] https://3g.dxy.cn/newh5/view/pneumonia

[2] http://en.hubei.gov.cn/news/newslist/202001/t20200119_200642...

That jump was explained in details when it happened - test kits were made available shortly before that date. To be more specific, first batch of test kits were delivered to Wuhan on the 16th Jan [1].

[1] http://www.thepaper.cn/newsDetail_forward_5588213

That explains why the speed of diagnosis increased, thanks. Do you have a similarly good explanation for why the lab tests that, starting with 59 cases of unknown origin on January 5 [1], had confirmed 41 cases of coronavirus by January 11 [2] failed to detect any new cases until the better test kits arrived?

[1] http://wjw.wuhan.gov.cn/front/web/showDetail/2020010509020

[2] http://wjw.wuhan.gov.cn/front/web/showDetail/2020011109035

Even if the numbers are skewed it is already really bad imo. From my quick search at this point the virus seems to have a 4% mortality rate. The number of infections are low at this point and the spread is slow. But if my city of 35,000 people had this blast through the city and it got out of hand and only 1000 people caught it that is still 40 people statistically could die. 40 people suddenly dying in my small town would be a huge tragedy. The grief and loss would be immeasurable. I really hope this can be stopped quickly because I too question if the numbers are being downplayed and that would make the numbers even scarier.

the mortality rate is heavily skewed towards the elderly and/or already sick. from what i have read, it doesn't kill healthy young or middle aged adults.

What doesn’t kill you can still injure you for life, as I learned from a bout of pneumonia at age 34.

Both to those making claims or asking about the severity of the Wuhan coronavirus The Guardian offers a sober perspective of the current situation.

We don’t yet know how dangerous the new coronavirus is – and we won’t know until more data comes in. Twenty-six deaths out of 800 reported cases would mean a 3% mortality rate. However, this is likely to be a overestimate since there may be a far larger pool of people who have been infected by the virus but who have not suffered severe enough symptoms to attend hospital and so have not been counted in the data. For comparison, seasonal flu typically has a mortality rate below 1% and is thought to cause about 400,000 deaths each year globally. Another key unknown, of which scientists should get a clearer idea in the coming weeks, is how contagious the coronavirus is. A crucial difference is that unlike flu, there is no vaccine for the new coronavirus, which means it is more difficult for vulnerable members of the population – elderly people or those with existing respiratory or immune problems – to protect themselves. One sensible step to get the flu vaccine, which will reduce the burden on health services if the outbreak turns into a wider epidemic.

https://www.theguardian.com/science/2020/jan/24/what-is-the-...

No, the infections rose from like 650 to 1200 in the last 24 hours (at least, the published numbers did anyways). So almost half of the infections are less than 24 hours. Pneumonia can last for 1-2 weeks, so there's going to be a delay in calculating death rates.

Coronavirus is very bad news, especially if you are (a) older (<60), (b) male, (c) diabetic, or (d) have preexisting respiratory issues.[0-2]

Most people are aware that CoV can cause pneumonia, but what really makes it devastating is that it can also attack your immune system, bowel, or kidneys depending on what cell surface receptors the strain can latch onto.[3-4]

There are some treatment options. Steroids are given to tamp down inflammation and treat pneumonia in severe cases, but have a nasty side effect of osteonecrosis (bone death). Ribavirin with interferons may or may not be effective.[5-6]

[0] https://academic.oup.com/aje/article/159/3/229/79939

[1] https://www.ncbi.nlm.nih.gov/pubmed/16759303

[2] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5450662/

[3] https://www.ncbi.nlm.nih.gov/pubmed/24732781

[4] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4072739/

[5] https://www.ncbi.nlm.nih.gov/pubmed/24493194

[6] https://academic.oup.com/jac/article/71/12/3340/2631297

This also seems to paint it as not as bad as SARS or MERS: https://www.sciencenews.org/article/how-new-wuhan-coronaviru...

Hmm I wonder what hospital the patient is at. According to the email sent to the uchicago community from the provost, she's not at uchicago medical. I would guess northwestern or rush.

Honestly, most hospitals in the Chicago area with an ICU can handle this.

The problem is that you show up with minimal symptoms like someone who has a cold, to an ER where people have serious wounds and problems. You get triaged and end up sitting in the waiting room for hours, infecting potentially tens of other people, who may have weakened immune systems, etc. and it goes on to spread around the hospital.

What can the hospital even do to help you with this?

If you have travelled to the affected areas and have respiratory symptoms you DON'T just go to hospital. You call ahead and then do what you are told.

Only if you have the sense to do that. Have you met many Americans? I don't know why, but the ER has become the default destination for anything medical for many. There's no need to call ahead, they're open 24hrs! sigh

>Only if you have the sense to do that. Have you met many Americans?

I don't know why this kind of 'American stereotyping' is okay.

That aside, myself and my family ('Americans' in 'America') have physicians that we call when we have issues.

That physician is generally the one to tell us what to do.

Our situation isn't abnormal or unusual, either.

Do you have hmo coverage? I think what you describe is increasingly anachronistic and may vanish completely in coming years, for a majority of Americans at least, depending on certain political outcomes.

What do you do if you get sick on Christmas day?

Everywhere I've lived the family doctor should be first contact but everyone seems to get sick at 5:30pm on Friday...

It's backed up by the statistics, and if you go do some searches for "emergency room unnecesary" and the like, you'll find plenty of articles on the subject.

  Number of visits: 145.6 million
  Number of injury-related visits: 42.2 million
  Number of visits per 100 persons: 45.8
  Number of emergency department visits resulting in hospital admission: 12.6 million
  Number of emergency department visits resulting in admission to critical care unit: 2.2 million
  [0]

"71% of ED Visits Unnecessary, Avoidable" [1]

If you're not familiar with Americans going to ERs "just to be safe" for the most frivolous reasons, because their insurance will pay for it, we're not living in the same country.

With that sort of attitude being prevalent, it's easy to see how someone would go directly to the ER and spread something like this without giving it any thought.

[0] https://www.cdc.gov/nchs/fastats/emergency-department.htm

[1] https://www.beckershospitalreview.com/patient-flow/study-71-...

The major driver of overuse of the ER is EMTALA, which means you're going to be treated without regard for your ability to pay in an ER.

There's blame for that, but for many people with non-critical conditions in the ER, it's a rational choice.

The danger of intrahospital transmission was one of the WHO's key takeaways[1] from the SARS outbreak. Mitigation seems to depend on three pillars:

1. Identify infections quickly and isolate those patients as soon as possible

2. Aggressively trace and monitor anyone in contact with those patients, including hospital staff

3. Set a very low threshold for quarantine of any person suspected of infection

Thankfully the various governments involved seem to have already started running this playbook. There's also a fairly loud public education campaign[2] underway to make sure people know what to do (call the doctor, tell them what's happening, and follow their instructions) if they show symptoms.

Note: I'm not a doctor or epidemiologist, but I split my time between Hong Kong and Singapore so I've followed this situation relatively closely.

1. https://www.who.int/csr/sars/conference/june_2003/materials/...

2. https://www.moh.gov.sg/2019-ncov-wuhan

Triage should include a travel history. Additionally, especially during flu season, if you're presenting "like someone who has a cold" you should be wearing a mark.

In terms of what a hospital can do - if you get severe viral pneumonia, intensive care and supportive therapy is about all that can be done.

I've read rush. It was also the designated hospital for Ebola.

What is the best case scenario on how to get this under control?

The best case is hat it doesn't get worse because vaccine production and other treatments scale/improve faster than the virus spreads. It's still hard to predict the pace of either.

We also don't really know what the current scenario is. How bad is it already?

I read a vaccine takes at least a year, that's not a good outlook...

care to explain fellow down-voters?

on currently published numbers the death rate is around one death per 30 infections. (25th January, 41 people dead from 1287 infections). According to wikipedia the spanish flu had a death rate of 1 in 50 (although the numbers may not be that reliable), so until more is known about transmission it should prompt precautions.

We have no idea how many people have none to very light symptoms so these numbers are quite meaningless. I think we'll learn quite a lot more over the coming weeks from the cases in western countries. So far this doesn't seem too concerning but we'll see how it develops...

There's a delay from infection to death, it may take one to two weeks from showing symptoms to death. So it could be higher than 1 in 30. Still alarming either way.

Where on Wikipedia did you see 1 in 50 for Spanish Flu? I'm seeing a much higher number: "an estimated 10% to 20% of those who were infected died' [1]

[1] https://en.wikipedia.org/wiki/Spanish_flu#Around_the_globe

Exponential growth has a way of catching people off guard. Moore’s laws continually surprised business. Viral spread will catch society off guard. It is my opinion that we must, as a society, go to enormous lengths to stop this virus, beyond quarantining millions in Wuhan.

And what are you not-so-subtly suggesting?

Epidemiology, as a field, has a harder time in infectious diseases not representing things as exponential growth than it does being surprised by it.

Please explain more? What do they represent it as instead?

So the standard type of mathematical model that's used to describe early stage epidemics (such as this one) basically assume exponential growth.

It's hard to get the math to stop doing that when a disease reaches a non-exponential stage. That's why you got some bonkers predictions for Ebola - if you let an exponential model run for a year, it's always going to be bad.

Shutting down all transit and public gatherings for one of the biggest cities in China plus surrounding areas reaching 20M is quite a significant response, during the busiest and most important holiday of the year, is it not?

So is the entire biology community turning to face this or is that not a thing? Because it should be.

Encountering the problem that a new disease is threatening a sizeable portion of the world population?

Have every biologist looking at solving it. We have the technology. This requires a modern solution.

Most biologists are not virologists. Besides, HIV, Hep. C, and even the normal flus kill far more people, and threaten more of the world's population.

Can't we just stop that traveling nightmare? Now it's not only going to destroy our climate, but also bringing the Zombie Apocalypse.

> The global aviation industry produces around 2% of all human-induced carbon dioxide (CO2) emissions. Aviation is responsible for 12% of CO2 emissions from all transports sources, compared to 74% from road transport.

First result on Google...

The bigger problem with aviation is there's no known way to decarbonize it within the foreseeable future. Hopefully most people will be driving electric cars within the next few decades, but with airplanes that won't be possible absent a miraculous breakthrough.

The actual process already exists in electrofuels. [0] . If one has enough hear/electricity, they could generate fuel directly usable in existing jet engines with captured CO2, making overall process CO2-neutral

[0] https://karmaimpact.com/jet-engine-makers-cast-an-eye-on-nuc...

CO2 is fungible, so no problem just using regular fuel and sequestering an equivalent amount of CO2 from elsewhere in the atmosphere.

At $100/ton CO2 sequestration cost and 90kg CO2 per passenger-hour, that’s roughly $10/passenger-hour.

That is an important step, but unfortunately emissions at cruise altitude have a much higher impact than the CO2 at ground level you produce your fuel from.

> much higher

How much?

2-4 times

https://www.carbonindependent.org/22.html

Human breathing produces about 2.5 billion tons of CO2 per year. Aviation is just under 1 billion tons per year.

Aviation is one of the great wonders of the modern world. The carbon it produces is essentially inconsequential.

Compared to the wealth, knowledge, peace, and prosperity that international travel directly supports, calls to curtail plane travel in order to reduce CO2 IMO are seriously misguided.

The tons produced by aviation are produced in higher concentration in air, and produced nearer to the atmosphere at high altitude, making them more dangerous than the tons produced by human breathing. You can't just compare the total.

Wait, what? It all ends up dispersed the same way, doesn't it?

Yes, but one started in the atmosphere, was captured, and then released back into the atmosphere.

The other (fuel) started sequestered in the ground, was captured, and then released into the atmosphere.

> Human breathing produces about 2.5 billion tons of CO2 per year.

The carbon emitted in human breathing came from the food, and the carbon in the food came from the atmosphere. It's a closed cycle. It doesn't matter if it's a billion or two, an identical amount of carbon had to be captured first.

Well technically it’s all a closed cycle. Humans consume carbon sinks, whether it’s for glucose or joules, to survive.

The carbon sinks we consume to produce glucose do tend to be ones that pulled their carbon from to atmosphere in the last couple years, rather than millions of years ago.

And I agree, moving fresh carbon between atmosphere, organisms, and back into the atmosphere doesn’t have a net effect that builds up over time like burning fossil fuels. So it wasn’t a great comparison.

CO2 is plant food. All organic species are made out of substantial amounts of carbon. The mild warming has not killed anyone and no, droughts are not more common than they were 100 years ago. Only 11,000 people died from natural disasters and weather related phenomenon last year, down from over 1,000,000 per year, 100 years ago.

Comparing death rates per disaster, per capita, between now and 100 years ago, is wholly nonsensical. Biomedical technology is immensely more effective now, than 100 years ago. It is not a 1:1 comparison. What that curve looks like, I don't know, but it's not a fair comparison to draw ratios like that. Don't get me wrong, I'm not supporting the hysteria here, by any means, or at least, that is not my intent... but c'mon, let's be reasonable and think about this.

Diseases aside... to direct some attention to the other part of your message...

Yeah CO2 fuels photosynthesis, but when most of the light is blocked by smog and smoke, what then?

First of all, light is needed for photosynthesis, I'm sure we all can agree. But, when plants are in the dark, they actually release CO2. Actually, they release CO2 in the day time too, because plants also respire, they breathe oxygen, and release CO2, and when there is light, some of that CO2 can be used to make energy; they are efficient that way. Further, about half the CO2 that they consume during the day, is released at night, and the rest is converted to energy, or wasted, etc...

Just dumping more and more CO2 and acting like, fuck it, man, whatever, it's plant food... knowing these facts that I expressed above... Think.

CO2 is not visible. You cannot see CO2 (unless it's frozen as dry ice). Smog is caused by sulfates, not CO2. I'm all for clean burning fuel but not for smog-inducing pollution.

CO2 cannot trap or reflect visible light spectrum. It can only trap a very narrow band of infrared energy. That's what causes the minimal warming effect.

We're at less than 1K of warming today, but our emissions put us on a 3K+ path.

That's still cooler than temps experienced for the first part of civilization in the early Holocene (roughly 10k to 6K years ago). It was a boom time for humanity.

This chart here seems to contradict you.

https://en.wikipedia.org/wiki/Global_temperature_record#/med...

Am I misreading it?

Aviation has a relatively small global impact because almost nobody can afford to fly. For a typical person in a rich country, it is really easy to double your climate impact by taking a long distance flight per year, for example from Europe to SF.

Fuel price per mile is cheaper in economy than in a Prius. Most poor people don't drive the most efficient cars in market and surely do travel in cars much more than an exec.

Is it safe to assume that if people couldn't fly, they'd drive just as many miles instead? I don't think that's a safe assumption. I think people would visit family less often if it meant a 25 hour drive across the country. They'd probably not vacation on the other side of an ocean either.

this is a pneumonia infection, which usually infects three million Americans per year and kills sixty thousand. And if that is scary to you don't look up the damage influenza causes every year and has since time immemorial. I have absolutely no idea what's going on with the hysteria among the press or commenters, this is not a zombie virus.

Isn't this more infectious and potentially deadlier?

it may be possible that it is more infectious than ordinary pneumonia but it doesn't appear more deadly, in fact it appears to be less severe in the majority of patients. The mortality rate for hospitalized pneumonia patients, in general, is about 5%, for the coronavirus it appears to be about 3% right now but that number is likely too high because a lot of the less severe cases might not be diagnosed as such.

FYI, pneumonia is not a really a single infectious disease, it is a condition caused by a wide variety of infections (bacterial, viral and fungal) and non-infectious causes. The bacteria that most commonly causes pneumonia is generally benign in healthy individuals, it only causes pneumonia in a limited set of cases with predisposing factors.

but then compare the number of typical influenza dead to the year of the 2009 H1N1 pandemic

They were within ordinary ranges, though perhaps at the high end. The US has more flu deaths in a typical year than it had H1N1 deaths.

I was watching it obsessively early on, but it turned out to not be disastrous.

> The US has more flu deaths in a typical year than it had H1N1 deaths.

But far more infections from H1N1 (60+ million, whereas 45 million is the top estimated annual total flu infections from 2010 on): the 2009-2010 H1N1 pandemic flu turned out to be more infectious but less deadly (I wonder if this is in part because during the pandemic people reacted to potential flu symptoms more diligently) than typical seasonal flu, and there was very light seasonal flu activity.

"normal ranges"? https://d2vlcm61l7u1fs.cloudfront.net/media%2F6a3%2F6a3d1795...

That is not the total number of deaths for either the us or the world. Please compare total deaths.

Further, note that I said at the high end: many years were lower, but it didn’t exceed other non-pandemic years.

> this is a pneumonia infection, which usually infects three million Americans per year and kills sixty thousand. And if that is scary to you don't look up the damage influenza causes every year

A lot more infected, but still fewer killed by influenza in most years (since 2010, the range is 9 million to 45 million infected and 12,000-61,000 killed by influenza in the US, per CDC.)

https://www.cdc.gov/flu/about/burden/index.html

Travelling is vital for bringing poor people out of generational poverty. Without it, they'll be stuck in their economically depressed places of birth and the whole rest of the world will also be disadvantaged by not having their labor used productively. That could easily be worse than climate change and disease.

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