Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions
> Key findings:
> ● We estimate the basic reproduction number of the infection (𝑅𝑅0) to be significantly greater than one. We estimate it to be between 3.6 and 4.0, indicating that 72-75% of transmissions must be prevented by control measures for infections to stop increasing.
> ● We estimate that only 5.1% (95%CI, 4.8–5.5) of infections in Wuhan are identified, indicating a large number of infections in the community, and also reflecting the difficulty in detecting cases of this new disease. Surveillance for this novel pathogen has been launched very quickly by public health authorities in China, allowing for rapid assessment of the speed of increase of cases in Wuhan and other areas.
> ● If no change in control or transmission happens, then we expect further outbreaks to occur in other Chinese cities, and that infections will continue to be exported to international destinations at an increasing rate. In 14 days’ time (4 February 2020), our model predicts the number of infected people in Wuhan to be greater than 190 thousand (prediction interval, 132,751 to 273,649). We predict the cities with the largest outbreaks elsewhere in China to be Shanghai, Beijing, Guangzhou, Chongqing and Chengdu. We also predict that by 4 Feb 2020, the countries or special administrative regions at greatest risk of importing infections through air travel are Thailand, Japan, Taiwan, Hong Kong, and South Korea.
> ● Our model suggests that travel restrictions from and to Wuhan city are unlikely to be effective in halting transmission across China; with a 99% effective reduction in travel, the size of the epidemic outside of Wuhan may only be reduced by 24.9% on 4 February.
> ● There are important caveats to the reliability of our model predictions, based on the assumptions underpinning the model as well as the data used to fit the model. These should be considered when interpreting our findings.
From what I've read so far, it seems that hosts can infect healthy people 1-2 weeks before first symptoms. Something missing though is how long after the infection does the host become active in spreading the virus.
China has stated that they think it can be contagious before symptoms. The US has stated as of yesterday (Jan 27) that there is no evidence for that yet.
The German case confirms it is. A woman (from Shanghai, infected by her parents from Wuhan) gave a training seminar in Munich. She transmitted the virus to her German colleage (33 yr), but started to feel ill only on her flight back to China. (The man developed symptoms over the weekend, but his state improved, so he actually went to work on Monday, was hospitalized on Tuesday.)
> China has stated that they think it can be contagious before symptoms. The US has stated as of yesterday (Jan 27) that there is no evidence for that yet.
IIRC, the US hasn't seen the evidence for that yet, but they're also complaining that China's not sharing data with them. The CDC is getting its info from China from press briefings like everyone else.
Western news media are currently reporting ~100 dead and ~4,500 infected (though that number is surely much higher in reality). This is a ~2% mortality rate.
Can we naïvely extrapolate that we expect ~4,000 casualties from ~190,000 infections?
I'm not good at understanding numbers, but I'm sure someone here can chime in with a better way to read this.
You can naively extrapolate that, but it will be, well, a naive extrapolation. Not necessarily a bad thing, but it won't necessarily be accurate. If the virus does get into, say, the US, but it happens to only infect 20-40 year-olds through office transmission, it probably won't even be that fatal. If it happens to get into a senior home, it could be a great deal more deadly.
And that's before we consider the spoiler of mutations, which is the real problem. In the long term, it is evolutionarily advantageous for the virus to become less lethal and eventually fade into the background as just another cold, if it isn't wiped out by aggressive quarantining. However, in the short term, many of the same things that will make it more transmissible, such as more effectively converting host systems into virus factories, or contrariwise, being more effectively hidden while still being contagious, will also make it more dangerous to the host and/or society.
But for all that, there is a sense in which the "naive extrapolation" is also the best thing we have right now based on available data. It is, at least, data-driven.
I'm not qualified to have an opinion on the the virus, but the numbers could exhibit a selection bias: People with relatively mild symptoms and no death probably could be misdiagnosed as having a flu or proper influenza, which would imply that the mortality rate would actually be lower.
What about a 99.99% reduction in travel? Wuhan has 11 million and 1% of that is 100k, I'd imagine the quarantine is more successful than preventing 100k people from travelling.
As I said in a different comment, 5 million people leave Wuhan every year around this time, and the model that made this 99%/25% prediction is using data that already takes into account this mass-migration.
I think their point is that with such a high reproduction number, the impact of anyone slipping through is amplified so much that reduction in travel alone will not do much to stop the spread.
> reduction in travel alone will not do much to stop the spread.
This is exactly what you can't conclude from the analysis that was done, the numbers matter significantly.
If a 99% restriction locally gives a 25% reduction globally, that tells us very little about what happens with a 99.99% restriction, which is probably closer to what has been achieved.
It's not. The model used historical figures from Jan 2017 as its input data, so would also be taking into account these New Year's mass-migrations. Also, this year's stopped at a relative early stage.
Sure, if you want to get precise, you can model a 0% reduction in traffic for the first 10 days, then a subsequent reduction to 99.99%. The numbers will be completely different than modelling a reduction to 99% for the whole period.
Quoting numerical estimates without understanding how the underlying model compares to reality, is just stupid.
Figure 4 in the images from this tweet[1] (taken from the same paper above, page 8) show the effect of a 99% reduction in travel, over 65% of people in cities across China will become infected.
> Dr. Eric Feigl-Ding (Eric Ding) is a health economist, epidemiologist, and nutrition scientist at the Harvard Chan School of Public Health, and an expert advisor to the World Health Organization.
I'm not usually one for relying heavily on authority, but this guy[1] is likely to know when the R0 number looks very, very bad.
Literally thousands of other people have the same qualifications as him and are also not freaking out over Twitter. I'd say the data leans more heavily in the other direction.
One minor note is that the "real time" nature of this map is a bit deceiving at the moment, at least to me. While the specific figures imply that it's pulling data at a near real-time basis, it's still dependent on countries posting the latest figures in batch, and then being updated as last indicated in the top right. As of now, it seems verbal announcements precede the digital announcements and as such I've found journalist-maintained maps to be a bit more up to date with the latest announcements, such as the one maintained by the NYTimes. Although if this continues to spread to different demographics, this map will probably have much higher utility.
Absolutely. It's marketing bullshit. Nobody has current figures.
In fact, multiple specialist academics said ~3 days ago that only 5% of cases are confirmed, now may be less due to reports of equipment shortages, the additional time the virus has had to disperse geographically, and Chinese New Year. Therefore, we can multiply any official figures by 20x. Official figures are nearing 5,000 cases, which extrapolating from those estimates means we're at around 100,000 infections as of today.
Source: I wrote and am maintaining an animated map of the domestic spread (the one on Wikipedia), over here: https://github.com/globalcitizen/2019-wuhan-coronavirus-data... .. powered by two scrapers, main one is from DXY, which is ahead of this 'real time' map by many hours, judging by total figures.
Why are you assuming that epidemics only stop growing exponentially when they reach population saturation? That is not the case for all the recent respiratory epidemics.
Even if they do, why is 20 a "low" number? They are talking about estimating the current real figure, from the current laboratory-confirmed figure. 20 seems pretty reasonable if a little high, assuming the epidemic is indeed still in the exponential phase.
The realtime annotation is more because it's generic mapping software. All dashboards using this mapping software have that text.
The same site was handling fire information for the Australian bushfires and had the same text - although that was more "realtime" as the data source was being updated much more frequently.
Last updated: a few seconds ago
"As of Jan 27, 2020 8:30 pm EST".
The title of the page here on HN and also the last updated lines are kinda misleading.
As much as I believe in the Chinese gov fudging the numbers, there is no way for a line medical workers to know or even estimates the true numbers at the scale of ten thousands patients.
She said the R0 is 14? Seems very inconsistent with other sources(Chinese or otherwise[1]). We can take this video into consideration but there's no need to disregard other sources completely and only trust her.
Completely offtopic: I'm really impressed that I can get the basic mapping with all javascript turned off. Kudos for that. Half the pages you visit these days can't even show text or pictures without js.
Thanks! With this app, we just wanted to build something really basic that does its job with as little friction as possible, so glad you pointed that out.
Yep, seems you are correct, noscript shows it being blocked but I had the 3rd party scripts from https://cdn.jsdelivr.com/ whitelisted. Thought it might have simply been a splash page.
U.S. map looks off. The case you have near Washington D.C. should be in Snohomish county, Washington. You should have two cases in CA, one in Orange county and the other in Los Angeles county, not in San Joaquin.
Someone who is more versed in the usual statistics, how serious is it? Without domain knowledge, I have no idea if the few dozen deaths in this period at these locations is significant or not.
Deaths are mostly among immunocompromised, elderly or very young. Chances are you're going to be fine, if you get it, but it'll be a long and painful 2 weeks. The youngest adult that died was 34.
That said with a mortality rate of 2%, affecting a country like China with 1.4 billion people, even if half the people get infected, that's 14 million dead.
That was largely caused by high dose of hormone used during treatment. I can be wrong but hormone is no longer used that often/much in the current outbreak.
Also a question if it will be able to mutate in a larger population, given its long incubation period without symptoms it has more opportunity. I don't know how likely this is. Another question is how long will it continue to expand in reach in China and much affect it will have on the economy.
Summary: We know of deletion event in SARS Orf8, and amino acid change in ebola glycoprotein. In both cases, it decreased viral replication or virulence.
You say "even" as if it's a conservative estimate, but to me 50% of the country's population being infected by the same virus sounds extreme. Wouldn't this be on the extreme side?
If we assume that this virus is as infectious as the common cold, we can expect the infection rate within a household to be approximately 25% of contacts. That means that of the people you LIVE with, 25% will catch it from you.
50% infection rate in a large, distributed population like China would be very extreme.
Those colds that you’re seeing represent common symptoms of many viruses (metapneumovirus, paraflu, influenza, rhinovirus, RSV, etc, etc ... and many of these have multiple subtypes which can be concurrently circulating). In other words, you’re noticing common symptoms not necessarily the same virus.
Peak cold symptoms last about 3 days. I never said 50% of the population have the same cold at once. 50% catching it over a 6 month period is very reasonable.
> Chances are you're going to be fine, if you get it, but it'll be a long and painful 2 weeks.
They've reported that strong symptoms occur in only 25% of cases, so if you get it chances are you're just experiencing having a cold (which is caused by a coronavirus).
A relevant question is also, if most deaths really are among immunocompromised, elderly or very young, then how many of those 2% would have been killed by the flu or similar if coronavirus hadn't shown up? 14 million dead is terrible by any measure, but I'm wondering how much of a change over the norm it actually represents.
It's 3-4 orders of magnitude more deadly than the normal seasonal flu. The mortality rate is similar to SARS, but with far more infections.
The above comment saying that it "mostly" impacts elderly is a bit vague. The fact that within the first 100 deaths were multiple young healthy people means it is dangerous for the entire population. People in their 30s and 40s are not "old".
There was a single death of someone in their 30s out of 100+. And I don't even know if its been confirmed if they were immunocomprimised or not. Every other person to die was 47 or above, many of who had previous health issues. 1 out of 100 is is a pretty good indication that it mostly dangerous to the older population. The fact that no young children to have died yet, which also tend to be a vulnerable group for viruses like influenza and SARS is also worth noting.
Also, you should be more precise in your wording. 3-4 orders of magnitude worse than the flu is absolutely not true. The mortality rate for the flu is around 14.3 per 100,000. With this as a baseline, 4 orders of magnitude is 143%, which isn't actually possible unless you are aware of people being able to die more than once. Even 3 orders of magnitude is 14.3%, which is higher than SARS. The current estimate is around 2%, which is more like 2 orders of magnitude.
"50% of the deaths were under 47"... fixed that for you.
Also implying people over 47 are elderly and not worthy caring about? Most middle managers, craftsmen, ceo's, politicians, doctors, professors, military officers would disagree.
I guess it really depends on what share of the cases got reported.
Early disease death rates are always overestimated because people tend to report only the worst cases of it (even more if the usual symptoms look like a cold). But there is no way to know by how much we are overestimating it.
Yeah. I mean as a Plague, Inc. player I have to give kudos to this virus. Having the outbreak shortly before the spring festival is genius, the travel ban for Wuhan came so late that many people already traveled to all over the country to meet their families, greatly helping the spread.
Baidu's realtime map has a higher count this, though in Chinese. It seems to be more up to date, with detailed patient info sometimes included in the news tab.
Please don't use circle radius for indicating the number of observations. It is really easy to confuse the circle radius with the geographic extent of the observations, when in reality they are likely more tightly clustered.
Rather, consider using a heatmap to show the proportional density of observations in a way that better highlights their geographic distribution.
People who are actually concerned at this stage while ignoring the scientists who say there's no proof it's serious are prime examples of the types who get worked up by the media hypetrain and should be actively avoided. It's a harsh assessment but honestly think it's the case.
The media sell stories. People click on those stories, the stories that get clicked on most get other stories written on the topic. This is how the industry works. It's actually quite a simple model.
Human beings are fucking terrible at risk assessment. What do people here think the risk is for them of dying of coronavirus compared to say dying in a traffic accident? Which is more likely to happen to you by a few magnitudes?
If the 2% mortality rate is correct, then the risk of dying to the virus is significantly higher than my risk of dying in traffic. It is bad if such a potent virus were to spread everywhere.
That said, I don't trust the numbers so at this point it's hard to say. My gut says there are way more infected people than reported, but deaths are probably less likely to be underreported at that scale. Which means mortality rate would actually be significantly lower than 2%. On flip side, the chance of getting infected would be much higher.
China just shut down 15 cities and 2 provinces with nearly 80 million people and put men with guns in nbc suits at all the exits,shut down the internet,stop all travel and extend public holidays Im sure its perfectly harmless
Please cite the source of shutting down the internet. As a Chinese, as far as I read only physical movement are prohibited. Many people stay at home play online games now.
Regardless, let's turn that comment around: could it not similarly apply to hygiene and risk of infection? Just be an above-average smart citizen and you'll be fine, yes?
If these stats hold, the disease looks to have a mortality of around 2%.
Doesn't sound like a lot, but an R0 of >2 is concerning because of what it means for total infected. 2% of everyone within range of access to modern transportation is an awful lot of people.
The problem is not many patients who have contracted the virus have released from hospital yet. Any there are many serious cases. From many Chinese sources such as [1], Chinese gov's data shows there are 4515 confirmed cases, 106 deaths, 976 in critical conditions, recovered and discharged only 60 cases. So I'm not sure how we should calculate mortality rate right now.
But there are two few confirmed cases to understand the mortality rate. Might be there are additional factors unique to China that is causing a higher death rate.
It might mean, out of those patients being treated (i.e. already very ill with it), rather than total infected?
I was reading somewhere that the doubling in cases in China was mainly due to increasing capacity for hospitals to diagnose the infection rather than an actual measurement of the spread of the disease.
Isn't that too early since there are still thousands of new cases? The survival rate can improve. Most of those deaths are probably early patients who did not benefit from proper cares since at the time they did not know what it was.
I don't think there are enough cases outside China to perform that analysis yet. Of the 4474 cases, only 65 are outside China. My stats is rusty, but given that something like 2-3% of that 4474 in China have died, I think zero deaths from 65 cases outside China doesn't mean a ton.
I guess it is difficult to know if these are the right numbers. Elderly people, and people with a disposition (eg. COPD) are much more vulnerable to a corona virus infection.
I would wait before more people have gone through the disease before making a conclusion about statistics such as case fatality rates et cetera.
Unfortunately, none of the numbers are reliable at this point.
People are being turned away from hospitals. Dead patients are not being post-humously tested for coronavirus. Most patients hospitalized arent yet recovered (or dead) yet etc...
The only rate we know so far is the dead/hospitalized rate, which is around 13% - which comperable to SARS.
Terrible geocoding -- the one case in Sydney, state of NSW, is drawn as a dot in what is guess is the centroid of the state, hundreds of km away from anywhere.
almost 4% mortality rate in Hubei is pretty scary, I imagine a lot has to do with China not reporting real infection numbers which are rumoured to be much higher
@mods, there was the news the other day about Kobe's death. It got flagged, and for good reason.
Why is this coronavirus stuff not flagged also? There are currently 3 articles on the front page related to this. It just slipped or is there a reason for this?
It's related to aviation which always tends to make the front page. While this particular thread I think very much belongs here, there have been a bunch of links to nothing more than news articles over the last few days which are of little interest from a HN perspective.
https://www.medrxiv.org/content/10.1101/2020.01.23.20018549v...
Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions
> Key findings:
> ● We estimate the basic reproduction number of the infection (𝑅𝑅0) to be significantly greater than one. We estimate it to be between 3.6 and 4.0, indicating that 72-75% of transmissions must be prevented by control measures for infections to stop increasing.
> ● We estimate that only 5.1% (95%CI, 4.8–5.5) of infections in Wuhan are identified, indicating a large number of infections in the community, and also reflecting the difficulty in detecting cases of this new disease. Surveillance for this novel pathogen has been launched very quickly by public health authorities in China, allowing for rapid assessment of the speed of increase of cases in Wuhan and other areas.
> ● If no change in control or transmission happens, then we expect further outbreaks to occur in other Chinese cities, and that infections will continue to be exported to international destinations at an increasing rate. In 14 days’ time (4 February 2020), our model predicts the number of infected people in Wuhan to be greater than 190 thousand (prediction interval, 132,751 to 273,649). We predict the cities with the largest outbreaks elsewhere in China to be Shanghai, Beijing, Guangzhou, Chongqing and Chengdu. We also predict that by 4 Feb 2020, the countries or special administrative regions at greatest risk of importing infections through air travel are Thailand, Japan, Taiwan, Hong Kong, and South Korea.
> ● Our model suggests that travel restrictions from and to Wuhan city are unlikely to be effective in halting transmission across China; with a 99% effective reduction in travel, the size of the epidemic outside of Wuhan may only be reduced by 24.9% on 4 February.
> ● There are important caveats to the reliability of our model predictions, based on the assumptions underpinning the model as well as the data used to fit the model. These should be considered when interpreting our findings.
Source:
https://twitter.com/char_durand/status/1221997021663387649