3Blue1Brown: Exponential growth and epidemics

Video 'splainer:

https://invidio.us/watch?v=Kas0tIxDvrg

#covid19 #covid-10 #coronavirus #ncov2019 #exponentialGrowth #video

COVID-19 A Laycat's US Outbreak Model

This is a non-expert's simple extrapolation of the past 11 days' COVID-19 experience within the US, projecting both further likely spread of the COVID-19 outbreak and the possible actual extent of infected individuals based on a presumed testing lag.

As with my earlier China extrapolation: The real message here is how quickly experience deviates below the projection here, suggesting containment efforts are effective. In the case of China, that began about two weeks after my initial post. I am a space alien cat on the Internet, not an expert.

I've probably fucked up all kinds of things. Cluebats welcomed.

How this model works

I'm using a simple exponential growth formula, and basing the expected number of cases (and deaths) from the 5 March 2020 case and death counts, based on what appears to be native community spread rates through the US from 20 February 2020 through 5 March (the period of visible community spread). This is a short window though one showing rapid growth.

It is overwhelmingly evident that the US does NOT have a solid handle on monitoring, and likely won't for at least another week, possible several. This both makes the data presented and model based on them more uncertain, and means that as monitoring improves, apparent case counts will likely increase rapidly. Again, this reflects experience in China.

Virus behaviour, population behaviour, public health measures, weather changes, sunspots, and timelords could all change things markedly.

Exponential growth function

The fomula for exponential growth is:

y(t) = a * e^(k * t)

See: https://www.mathsisfun.com/algebra/exponential-growth.html

Where:

• y(t): quantity at time t
• a: initial quantity
• e: the natural log constant, about 2.7183
• k: the grow rate per period.
• t: the number of periods.

"Period" here is "days".

We can solve for k:

k = ln(y(t)/a)/t

This gives us the growth rate given two measurements t periods apart.

We can solve for t:

t = ln(y(t)/a)/k

In particular, if we solve for y(t) = 2 and a = 1, we get the doubling time.

I've written a simple gawk script which computes for k and doubling rate, and also projects the weekly (7 day) and fortnightly (14 day) growth rates.

Detection lag

A huge problem within the US is that confirmed cases are lagging actual infection dates by a substantial amount. How long that is is ... not entirely clear, though I'm going to assume a 14 day (two week) lag based on:

• Initial infection is followed by a non-symptomatic period of about a week on average.
• Seeking medical assistance has seen a further lag of several days in getting an appointment / performing a test.
• Test results themselves take 4 days based on information I've seen.

The total lag is about 2 weeks.

I'd suggested that this could lead to as much as a 100-fold understatement of actual cases. Based on current data, that seems pessimistic: it's "only" about 47x greater than the published confirmed cases count -- a number that's moved around considerably, by the way, so don't put too much faith in that either. But it gives an indication.

We also get a doubling time of about 2.2 days, which means that however bad the situation is now, it's going to be twice as bad in a little over 48 hours. When you hear statements that the situation is "rapidly evolving" this is what is being referenced. Things are changing very quickly. Locations which may have low risk today may have a high risk in a day or two.

You should be finalising preparations and supplies runs about now, if not already.

Again: non-expert extrapolation based on early data, a simple model, and many uncertainties. I expect we'll likely see following trend, if not overshooting it, for a week or two, mostly as monitoring catches up to reality. I'm very much hoping we'll start to see a low-side numbers starting about two weeks out (18-22 March), as containment efforts begin to be effective. The caveat is that I don't see effective containment measures being enacted, certainly not on the scale that China performed starting ~22 January. In which case the projection here could well fit actual experience for longer.

As before, I'm posting this as a line in the sand of what my projection was. I hope and expect to be proved wrong on this within a couple of weeks. I'm dying to see how well this matches reality.

The professionals are apparently doing this as well

Dr. Messonier of the CDC mentioned 5 March in an NPR interview that there were numerous groups doing epidemic modelling to try to estimate the actual spread of SARS-CoV-2 within the US, though she pointedly refused to give any numbers herself. I have yet to find any published projections, but would be interested in seeing any.

The script

Hardcoded in (edit to modify) are the initial and current case counts. You'll need to supply days between these measures as well. Data are taken from Wikipedia's 2020 Coronavirus Outbreak in the United States article.

The script calcuates the growth rate, with an arbitrary high and low bound (basically assuming one day more or less error in the reported range -- it's kind of weak sauce but gives some idea of sensitivity), the doubling time, the weekly growth rate, and the 14-day growth rate.

It then produces two reports, one every day for 29 days, the other every seven days for 200 days. Both cut off if the infected population exceeds total US population, given as 330.4 million. Shown are projected deaths, cases, cases at a low or high growth rate, and as "w/ 14 day lag" the possible ground truth of total cases from which confirmed cases are drawn. I'll note that this presently exceeds 10,000 cases, and ... doubles ever 2.2 days or so. A rate which will hit 1,000,000 by 18 March.

By April 25, if present rates continue, the entire US is infected. At the WHO's 3.4% fatality rate, 11.2 million die, and given economic modelling, your retirement fund is trash.

(And then the disease may return in the fall....)

For Rest-of-world, you can substitute in values for that outbreak for a simiilar model. (I've got a separate script for this.) As values are hardcoded, it's a tad inflexible.

## Program Output

Minor reformatting aside, this is output as currently stands.

COVID-19 US Outbreak Model

Assumptions:
- init cases (2020-4-26): 14
- cases (2020-3-5): 175
- deaths (2020-3-5): 11
- daily growth rate: 1.316
- doubling time (days): 2.195
- 7 day growth: 6.83x
- 14 day growth/mon. lag: 46.59x

day	date	deaths	cases	@ lo dbl	@ hi dbl	w/ 14d lag
1	Mar 06, 2020	14	230	224	238	10,726
2	Mar 07, 2020	19	302	287	324	14,113
3	Mar 08, 2020	25	398	367	440	18,569
4	Mar 09, 2020	32	524	470	600	24,431
5	Mar 10, 2020	43	689	602	816	32,145
6	Mar 11, 2020	57	907	771	1,111	42,294
7	Mar 12, 2020	75	1,194	988	1,512	55,647
8	Mar 13, 2020	98	1,571	1,266	2,057	73,216
9	Mar 14, 2020	129	2,067	1,621	2,800	96,331
10	Mar 15, 2020	171	2,720	2,076	3,811	126,744
11	Mar 16, 2020	224	3,579	2,659	5,186	166,760
12	Mar 17, 2020	296	4,709	3,405	7,057	219,409
13	Mar 18, 2020	389	6,196	4,360	9,603	288,680
14	Mar 19, 2020	512	8,152	5,584	13,068	379,821
15	Mar 20, 2020	674	10,726	7,151	17,784	499,736
16	Mar 21, 2020	887	14,113	9,159	24,201	657,511
17	Mar 22, 2020	1,167	18,569	11,729	32,933	865,098
18	Mar 23, 2020	1,535	24,431	15,021	44,816	1,138,224
19	Mar 24, 2020	2,020	32,145	19,236	60,987	1,497,580
20	Mar 25, 2020	2,658	42,294	24,635	82,992	1,970,390
21	Mar 26, 2020	3,497	55,647	31,548	112,938	2,592,474
22	Mar 27, 2020	4,602	73,216	40,402	153,688	3,410,959
23	Mar 28, 2020	6,055	96,331	51,740	209,142	4,487,854
24	Mar 29, 2020	7,966	126,744	66,261	284,604	5,904,742
25	Mar 30, 2020	10,482	166,760	84,856	387,295	7,768,965
26	Mar 31, 2020	13,791	219,409	108,670	527,038	10,221,752
27	Apr 01, 2020	18,145	288,680	139,167	717,203	13,448,923
28	Apr 02, 2020	23,874	379,821	178,222	975,983	17,694,965
29	Apr 03, 2020	31,412	499,736	228,238	1,328,136	23,281,550

day	date	deaths	cases	@ lo dbl	@ hi dbl	w/ 14d lag
1	Mar 06, 2020	14	230	224	238	10,726
8	Mar 13, 2020	98	1,571	1,266	2,057	73,216
15	Mar 20, 2020	674	10,726	7,151	17,784	499,736
22	Mar 27, 2020	4,602	73,216	40,402	153,688	3,410,959
29	Apr 03, 2020	31,412	499,736	228,238	1,328,136	23,281,550
36	Apr 10, 2020	214,403	3,410,959	1,289,346	11,477,413	158,908,518
43	Apr 17, 2020	1,463,411	23,281,550	7,283,681	99,184,812	1,084,632,112
50	Apr 24, 2020	9,988,535	158,908,518	41,146,424	857,129,291	7,403,170,243

Source Code

https://pastebin.com/raw/Sn2jrG5f

Please note any observed errors / corrections.

Earlier

• March 3: "COVID-19: A Laycat’s guide to what to consider / watch for" https://joindiaspora.com/posts/3abaa5e03fca0138fcb6002590d8e506
• February 28: "A Laycat’s COVID-19 / Coronavirus Updates – February 28, 2020" https://joindiaspora.com/posts/bc04cb503c840138f4b8002590d8e506
• ~ January 22: "The Wuhan 2019nCoV Coronavirus Epidemic is growing by a factor of ten a week" https://joindiaspora.com/posts/6eab7f50245f0138ba5f002590d8e506

#coronavirus #covid-19 #covid19 #ncov2019 #epidemiology #epidemics #exponentialGrowth #IHopeIAmWrong #awk

COVID-19: A Laycat's guide to what to consider / watch for

Sources of information are sufficiently easy to find, and developments fast enough, that I"m not going to keep up with all developments. I cannot. See my comprehensive post from 4 days ago for sources.

Items covered here:

• What to consider.
• What to expect and look for.
• Basic safety tips.

What to consider

Again: China appears to be containing the epidemic. Growth is now several times larger outside China than in.

Outside of China, COVID-19 seems to be entering its epidemic / growth phase. Testing and monitoring have been insufficient, widely criticised, and are likely to continue to be in many regions.

Writing of Iran two days ago, I suggested that the case count given death rate looked too low. That hunch was rapidly corroborated by experts, and Iran's case counts have since climbed into plausible territory for surveillance, but likely represent the ground truth of two weeks ago. Spread both within and outside Iran based on travellers monitored elsewhere suggests a current widespread epidemic.

Similar logic holds true epecially for Egypt which likewise has a low official case count but numerous travellers passing through Egypt testing positive for SARS-CoV-2.

In South Korea, by contrast, the total tests administered are high in number, the possible cases fairly large, but the death count low. Many tests are returning negative, suggesting that test coverage is wider than the epidemic's reach, a good thing. The corresponding mortality rate is also low, suggesting marginal cases are being detected.

In both cases, the key information is that incomplete reporting and monitoring may be identified by comparing the high-severity case count and deaths to the expected averages. That's about five perecent severe cases, and a total case fatality rate (CFR) of 3.4%. (Revised upwards in the past day.)

The U.S. has recently eased limits on who is tested and taken measures for more test kits to be produced. Expect total case counts to rise, quite possibly by large amounts. Key is to look at the case-mix: mild, moderate, severe, deaths, and recovered cases. More mild and moderate cases relatively is a good sign and indicates more complete monitoring.

U.S. leadership of the COVID-19 effort, particularly at the White House, leaves much to be desired. This is unfortunate, but a reality. I'd prefer not to focus discussion on the who, though the what should be done is open for discussion.

Characteristics of COVID-19 other than its raw transmissibility are major considerations. The long asymptomatic-but-infectious period, relative ease of spread through droplets, possible airborne or other transmissions (the Diamond Princess spread raises questions of how 600+ members of the 3,500 passengers and crew were infected), possibly re-infection or re-emergence, and a fairly high 3.4% CFR, nondistinct early symptoms, faulty test protocols, limited test kits, long lag between infection and test reports (2 weeks), rapid growth rate, and institutional and governmental denial, all increase the risks posed by this epidemic.

There's a very long lag between an infection occurring and it being counted, about two weeks. This means that all available infection count data in growth regions is a look into the past, and actual _current infections are likely as much as 100x greater. This fact has been missed in virtually all mainstream coverage I've seen, though some medical sources are discussing this. The problem is that we simply don't have current confirmed measurements to tell us how bad things are, we have to extrapolate based on existing measurements and models of epidemic spread and growth.

If you're in the U.S., stop thinking in terms of "the outbreak in Washington State". That outbreak has already been detected in North Carolina, and has all but certainly spread elsewhere. Given test protocols, we won't know, probably for another few days. Hopefully in less than a week or two.

What to expect and look for

There are an increasing number of event cancellations, largely voluntary. Google, Facebook, Adobe, and numerous other tech companies have either cancelled conferences or moved them online-only. There are several notable holdouts, most particularly the 2020 Summer Olympics scheduled for June in Tokyo. In Europe there are mandatory cancellations of events and performances as well as school closures. Anticipate further cancellations and the possibility of widespread mandatory cancellations of large gatherings. I would see these as a sign of taking the epidemic seriously and a rational response.

Travel restrictions are also likely to broaden. Outside of China, these have largely involved international travel. WIth a case of the Kirkland, Washington, strain of SARS-CoV-2 appearing in North Carolina, internal spread within countries is a growing issue. Anticipate possible internal travel restrictions within Europe and the United States as well as elsewhere. Again, an inconvenient measure, but one not unwarranted or unreasonable.

Product rationing and supply-chain disruptions are likely. Logistics pipelines tend to lag by 2-8 weeks minimum for products arriving from China to elsewhere (which is to say most products). The late-January shutdown in China, somewhat muted by the anticipated closure due to holidays, is likely to start impacting European and American retailers and manufacturers by now. Disruptions within local ports and distribution networks will further snarl distribution, and it's likely that it will take several weeks to start things up again on the other side, when that happens. Logistics tend to be fairly robust, but they've not been tested against shocks like this since major globalised trade began. Exacerbations by panic buying and similar behaviour are also likely.

Financial markets will likely continue to reflect lowered outlooks. If you have no need to sell assets, you're likely ultimately better off not doing so. If you may need to sell to cover obligations ... phasing an asset reallocation over time is less risky than attempting to time the market in one big move. Either way, be prepared for a rocky year.

Again: second-order effects are likely to be the biggest impacts of this outbreak. Worst-case estimates of deaths could number in the tens of thousand to possibly millions, which remains a small fraction of the global population. But disruptions simply to avoid or slow that possibility are likely to have major impacts on local and global economies. Forecasts currently are for growth to halve for 2020, and it's possible that is an optimistic viewpoint. Monetary policy alone can ensure available cash, but won't address supply shortages if those exist of key commodities.

Look for local announcements by state and local health authorities. These should include measures along the lines outlined above, including requests, or requirements, for public-facing institutions and stores to make use of disinfectent and hand gels. Request your local agencies provide this information.

Measures that help the poor and underserved help all. This means sick leave (so your meal or groceries aren't being prepared or stocked by someone who's infected), free coverage for testing and quarantine treatment, healthcare for all, and public health monitoring and preventive measures. Press for these from your representatives and officials.

Keep an eye out for school and work closures. Talk to your manager / employer about policies. Again: request state and local authorities create policies on these points. Sick leave, work-from-home, and other measures should be among those discussed.

Basic safety tips

If you're NOT already sick, MASKS ARE WORSE THAN USELESS. The wrong masks, maks worn or used incorrectly, or when simply not needed, don't help and may increase your risk of disease. Medical personnel are trained in correct use, are at greatest risk, and must be healthy to be able to serve the public. Hoarding masks only limits their access.

If you ARE sick and are travelling among others, a mask may help avoid infecting healthy individuals. It won't help all that much, but even modest protections help reduce spread.

WASH YOUR HANDS. 20 seconds, with soap and water. The virus has a lipid sheath -- a fat-based membrane -- and just soap or detergent alone will break that down and destroy the virus. Warm or hot water is not necessary.

Alcohol-based hand sanitiser is useful when you cannot wash your hands. Barrier protection (gloves) can be used where you must touch public surfaces (transit, elevators, shopping).

See Laurie Garrett's reccomendations on these and additional points in Foreign Policy magazine.

#covid-19 #ncov2019 #coronavirus #epidemic

COVID-19 Iran: Backing out possible cases by deaths data

This is personal speculation not grounded in any sources. Treat accordingly.

The observed case fatality rate (CFR) for COVID-19 has been about 2-3%, based on Chinese data. There is some reason to believe middle-east susceptibility based on genetic factors is lower than in China, a fact which will actually amplify my conclusions.

Given limited testing and disclosures, coming up with numbers for actual cases in various countries and regions is difficult. Iran quite particularly so, though one could make an argument for the U.S. as well.

Iran officially reports 54 deaths from COVID-19 (Reuters, 2020-03-01), and 978 infected.

This gives a CFR of 5.5%, which is more than double the Chinese rate. That is much higher than expected.

At a 2% CFR, we'd expect the actual basis to be 2,700 cases. At 3%, 1,800.

The baseline would be the case count two weeks ago, with a weekly growth rate of about 10x (see the cases & deaths chart from my earlier summary), which would put actual current infections at 180,000 - 270,000, if containment has been ineffective.

There are reasons to believe Iran's reporting of deaths has itself been downplayed.

On February 28, the BBC reported Iranian coronavirus deaths as high as 210. This gives a range for 7,000 - 10,500 cases, again, two weeks ago, or 100x that now, at 700,000 - 1,050,000.

There are reasons to suspect that number is inflated (it's the bad news the British might be keen to hear). So take it with a grain of salt.

But we end up with a range of possible current infections within Iran between 180,000 and over 1 million.

Which would be a pretty serious situation.

Again, this is speculation, and it's unconfirmed by any reputable sources of which I'm aware. Consider it a possible bounds check on Iranian cases, and any corroborating or debunking sources are strongly appreciated.

#iran #covid-19 #ncov2019 #coronavirus #epidemic #speculation

COVID-19 "Spreading stealthily through Pacific Northwest" for up to six weeks

STAT is an exemplary source according to science journalist Laurie Garrett, though they bury the lede here:

This weekend, as it became clearer and clearer that Covid-19 has been spreading stealthily through the Pacific Northwest, the task facing health officials has become more and more monumental. To try to stop the virus’ transmission and restrain the outbreak, they need to identify every single person with whom patients have come into contact, isolate those at risk of harboring the illness, and monitor the entire network of people for symptoms....

On Friday night, there were reports of four people — two in California, one in Oregon, and one in Washington State — who’d tested positive for the virus but had neither a known history of traveling outside the U.S. nor any identified contact with previously diagnosed patients. By Saturday afternoon, officials reported an outbreak of the virus in a long-term care facility outside of Seattle as well as the first death in the U.S. due to the illness — but it wasn’t clear whether those two events were related.

“That’s the kind of thing that we’re trying to answer now,” said Jeffrey Duchin, health officer for public health for Seattle and King County in a Saturday press briefing. “We’re doing an investigation as we speak to try and understand all the potential exposures that that patient may have had and if there’s any potential commonalities … but at this point we don’t have links.”

By Saturday night virologists had sequenced samples from one of the mysteriously acquired Covid-19 cases in Washington State, and found that the pathogen looked like a descendent of the virus swabbed from the first reported case in the U.S., identified way back on January 16. But there was no known contact between the two patients.

“There are some enormous implications here,” tweeted Trevor Bedford, a researcher at Fred Hutchinson Cancer Research Center in Seattle, who studies how viruses evolve and spread. “This strongly suggests there has been cryptic transmission in Washington State for the past 6 weeks.”

(Emphasis added.)

https://www.statnews.com/2020/03/01/speed-is-critical-as-coronavirus-spreads-in-u-s-officials-face-daunting-task-of-tracing-case-contacts/

My suspicion is that Seattle is not the only region within the US that the virus is spreading, and that the US are well behind the curve in addressing an ongoing outbreak.

#covid-19 #ncov2019 #coronavirus #seattle

COVID-19: Florida is the new Iran. Pandemic meets Spring Break

Unpardonable malpractice and incompetence by local, state, and federal officials threaten to trigger widespread distribution of COVID-19 through the US by way of a treasured college tradition: spring break.

Florida officials are not releasing testing results. Spring break is effectively now (Feburuary 29 - March 7).

As of 2015, half of all college students plan some kind of spring-break vacation or travel.

There's been news coverage of this. On February 25, the Chicago Tribune carried a story "Spring break is coming and the coronavirus is spreading. Here’s what to know before you go.", predicated on the information that:

The head of the World Health Organization said Monday the virus has “pandemic potential" but is not spreading uncontained across the globe “for the moment.”

What a difference four days makes.

At present, there are in fact multiple instances of community transmission within the US, though the CDC COVID-19 status page (archive) claims otherwise:

At this time, this virus is NOT currently spreading in the community in the United States.

Further, there are imediments on testing (insufficient materials, inappropriate protocols, official refusal to grant testing permission, as at UC Davis Medical Center), and confusion at the national and state levels in how to address the disease.

We know that cruise ships are about the worst possible place to be.

And we're about to see roughly ten million young people (half of the nineteen million college students in the US go out, get their mental states altered, congregate, exercise poor judgement, and then return to the campuses from which they came, all over the country, largely through the air travel network.

Remember that COVID-19 broke out in China just as its major travel event, Chinese New Year, hit. This helped spread the disease throughout the country.

The US are about to run the same experiment.

"Insanity is doing the same thing over and over again and expecting different results"

#covid19 #ncov2019 #coronavirus #florida #springBreak #epidemic #pandemic #cruiseShips #tourism

On the Media: Black Swans

The One News Programme I Can Stand^TM^ covers Coronavirus (and is ... alarmed), prediction, and race.

Excellent as always.

https://www.wnycstudios.org/podcasts/otm/episodes/on-the-media-black-swans
(Transcript in a few days.)

Audio: https://www.podtrac.com/pts/redirect.mp3/audio.wnyc.org/otm/otm022820_cms997580_pod.mp3

#OnTheMedia #Covid19 #ncov2019 #forecasting #race #LaurieGarrett #FarhadManjoo #IbramXKendi #podcasts

A Laycat's COVID-19 / Coronavirus Updates -- February 28, 2020

With events of the past several days, I'm revising my views considerably. As the U.S. Centers for Disease Control (US CDC) says, "the Global Novel Coronavirus situation is rapidly evolving and expanding". The World Health Organisation (WHO): "No country will be spared, warn experts, as fight against coronavirus ramps up" (Reuters).

Global cases now exceed 83,000, deaths 2,800, still principally in China, though with outbreaks elsewhere this is likely to change.

Putting it mildly, all hell broke loose on February 24. I'm no longer able to keep up with developments, this piece has been in process for 4 days.

As usual: I'm a space alien cat on the Internets. I claim no expertise in public health, infectious disease, or epidemiology. I read widely and think too much. I synthesize information from numerous sources. This update is offered in that light. Sources are provided (I may have missed a few), and where information is uncertain I note this. I strongly recommend you verify this information and vet my sources. Questions welcomed, answers possible.

A terminology note: For the outbreak I'll be referring to the now-accepted name "COVID-19" rather than "2019-nCoV" or "coronavirus" largely going forward, and using the hashtags #covid19 and #sarscov2 rather than #ncov2019 in general going forward. The virus is now being referred to as SARS-CoV-2. Experts are describing the naming practice as "chaotic".

The term "community transmission" is also used, see below for definition and implications.

The hero images here show case and mortality, principally by age, and the latest global spread chart from Wikipedia.

General Advice

COVID-19 is now at community outbreak status in numerous countries and regions: China, South Korea, Japan, Hong Kong, Iran, Italy, Singapore, Taiwan, Thailand, Germany, the United States, Holland. There are occurrences in other countries though largely of known origin. This does not necessarily mean the disease is widespread, but it means sources aren't specifically known.

• Stay informed on outbreak status. See "Sources" section.

• There are few medical treatments or preventives: no vaccine, no medications.

• Avoidance is the best practice. Practice basic hygiene: Wash your hands, cover your cough, stay home.

• Prepare for several weeks of limited external contact, as well as closures of schools, businesses, and public event cancellations.

• Secondary impacts will likely be widespread. You may have noticed financial markets declining. Expect more, as well as other effects.

Sources

• Wikipedia's 2019-20 Coronavirus Outbreak article remains an excellent current summary of current state of knowledge of the outbreak. This has now spawned several related pages, including a page specific to the disease itself, Coronavirus Disease 2019, a timeline through January 2020 and February 2020 timeline, as well as outbreaks by country and territory.

• World Health Organisation COVID-19 page

• US CDC's COVID-19 page

• European Commission Public Health COVID-19 page

• Johns Hopkins Geographic Spread Interactive Map. Shows countries / regions with reported cases, deaths, and recoveries. Note that the indicated location may be approximate for all cases within a country, and not indicate actual location of known case(s).

I've tried to rely on medical journals or mainstream centrist news sources where possible. In cases, late-breaking news or developments are principally available from social media and informal sources. Where these seem reasonably credible and plausible, I've included several.

Overview

• The situation in China is largely improving, though remains quite serious.
• Outbreaks outside China are the biggest new development, and the most concerning. New cases outside China now represent the majority of new cases. Global spread to all countries is now a near certainty.
• US CDC's clinicians expect a community outbreak within the U.S., "a matter of when, not if". OK, it's now "when".
• Detection, surveillance, and monitoring capabilities and protocols are limited and strongly affect perceptions and responses to the outbreak.
• As yet, there is no vaccine and there are no medications approved to treat COVID-19.
• Mortality data are becoming clearer, especially by age, based on Chinese experience. This increases from age 50+, markedly at 60+, 70+, and 80+. Infants and children do not appear at significant risk. Men are more susceptible than women.
• Viability in warm and humid climates is ... unclear, but seems low.
• Genetic variations may affect susceptibility, highest for native Japanese, lowest in the Gulf / Middle East region, moderate for most people of European ancestry, based on ACE-2 receptor prevalence.
• Public-health and "non-pharmaceutical interventions" (US CDC's language) are standard. Wash your hands, cover your cough, stay home.
• Public health institutions: national, WHO, US CDC, and others.
• Second-order effects, initially principally to financial markets and the economy, are likely the largest immediate impacts. More may follow.
• There are several documents giving public advice and policy guidance. Breaking transmission chains is key through hygiene, sanitation, and avoidance measures.

More notably: My previous estimates of total case counts and mortality now appear to be low. I'd suggested ~100k cases and ~1,000 deaths. With broader spread these are likely to be much higher, possibly by 10x - 100x, perhaps more.

I'll discuss each of these at more length below.

China Containment

Reporting 78,824 cases, 2,788 deaths, and community transmission.

U.S. State Deparment travel advisory level 1 "Avoid non-essential travel".

Starting with the good news: It appears that China's efforts at containment are largely succeeding. Both cases and deaths are trending sharply downwards --- that is, there are fewer new cases and deaths with additional days. Whilst the disease has spread throughout the country the overwhelming majority of cases have been in Wuhan city and Hubei province.

China's intervention, largely widespread travel restrictions, had visible and pronounced effects by late January, virtually halting spread outside Hubei province, based on available data. This should be the model elsewhere.

Though there've been persistent questions about the accuracy and completeness of China's disclosures of data. Even without misreporting, there are strong clinical reasons to believe the total case-count understates total infections, but for the most part this does not matter as it is trends rather than absolute numbers which are most revealing, and data on deaths is more reliable and confirms, with a ~2 week lag, incidence data. That is: infected dead bodies are hard to hide, and trends in mortality data very strongly confirm a net reduction in new infections over recent weeks.

The shadow over Chinese response is possible outbreaks in prison and other institutional populations, which are large within China. This may lead to re-emergences, transmissions to the general population, and/or stubborn reservoirs of outbreak. As with many countries, services, and in particular medical and health care, to prison populations is not prioritised. This is reflected in other regions outside China as well.

My assessment is that China COVID-19 data are generally credible presently. The case counts themselves are likely low, deaths are a more reliable, though lagging indicator, but behaviour and correspondence seem generally sensible. Information outside China, particularly from neighbouring regions such as South Korea and Japan can also verify Chinese experience.

Outbreaks outside of China

As of 25 February 2020 there are more new daily reported cases outside of China than inside China.

This has been the most notable change in the past week, with known cases growing rapidly in Iran, Italy, South Korea, and Japan. There are further outbreaks, though fairly contained, in Hong Kong, Singapore, Korea, Taiwan, and Thailand.

By the US CDC's estimate, 2 of the 3 requirements for declaring a global pandemic have been met. The third is community transmission in multiple countries.

The specific histories and dynamics of various country's experiences, transmission, and responses to COVID-19 are also instructive. In particular, information access, trust, institutional competence, and infrastructure are all extremely significant in effective responses.

Given current trends, cases outside of China will top 10,000 within a few days, and could exceed 100,000 within a week or two. Limiting growth beyond those levels depends on containment efforts implemented immediately.

Iran

Reporting 388 cases, 34 deaths, and community transmission.

U.S. State Deparment travel advisory level 2: "Practice Enhanced Precautions".

Though not the largest outbreak, quite possibly the most troubling known one in that government competence, credibility, capability, and trust are all low. Iran's deputy health minister, after mocking concerns of an outbreak and declaring that "quarantines belong to the Stone Age", is infected with the virus, and self-quarantining at home. "Iran says official who played down virus fears is infected" (AP).

In particular, the high death rate (10% of cases) suggests a substantial undercount of actual infections, as this is well above the ~3% rate which seems typical elsewhere. Note that other middle-eastern countries with lower ACE-2 genetic markers might suggest Iran's overall susceptibility is lower than populations further east. The high spread and deaths are concerning.

Twitter stream to follow: Farnaz Fahishi: https://twitter.com/farnazfassihi "Journalist nytimes Former WSJ | War Correspondent | Mideast & Iran Expert Author book on Iraq war Ellis Island Medal of Honor Columbia & Harvard Alum"

South Korea

Reporting 2,377 cases, 16 deaths, and community transmission.

U.S. State Deparment travel advisory level 2: "Avoid non-essential travel".

The largest outbreak outside China. There's been a major increase in cases, most notably emerging from a conservative Christian church: Secretive Church Sect At The Center Of South Korea's Coronavirus Outbreak (NPR) 2020-02-24

Critics say the disease may have spread within the church quickly because of the way that it worships. "Shincheonji followers hold services sitting on the floor, without any chairs," packed together "like bean sprouts," says Shin Hyun-uk, director of the Guri Cult Counseling Center, an organization in Gyeonggi province that works to extract members from the church.... A petition on the presidential website, which has garnered more than half a million signatures, calls on the government to forcibly disband the group.

Italy

Reporting 655 cases, 17 deaths, and community transmission.

U.S. State Deparment travel advisory level 2: "Practice Enhanced Precautions".

The largest community outbreak in Europe. Two Chinese tourists tested positive in Rome on 31 January. An outbreak was detected in Lombardy (northern Italy, bordering Switzerland) on 21 February, now numbering over 400 cases, and confirmed or suspected cases throughout the country.

Japan

Reporting 228 cases, 5 deaths, and community transmission.

U.S. State Deparment travel advisory level 2: "Practice Enhanced Precautions".

PM Abe asks all of Japan schools to close over coronavirus (Reuters) 2020-02-27

Japan’s entire school system, from elementary to high schools, will be asked to close from Monday until spring break late in March to help contain the coronavirus outbreak, Prime Minister Shinzo Abe said on Thursday.

Philippines

Reporting 3 cases, 1 death. Possibly community transmission.

No travel advisory.

After initial cases, no further spread that I've noted.

On February 7, WHO-Philippines suggested that COVID-19 could spread in warm, humid climates. Since then it has not, which is reassuring.

As with other regions, testing and detection capabilities may be limited, so reassuringly low case counts may be misleading. So far, the information is encouraging.

North Korea

Reporting 0 cases, 0 deaths. Data generally considered implausible.

Though the country reports no cases officially, this is increasingly implausible given experiences in China and other neighbouring countries. As China's initial response showed, efforts to conceal potentially embarrassing or negative information from both international and domestic view can sharply limit initial awareness and communications. North Korea's extreme totalitarian dictatorship is not amenable to free-flowing information, most especially of bad news. The country's institutions and means for effective epidemic response are quite limited, based on past experiences.

There are unofficial reports of outbreaks, though these also may reflect politically motivated messengers or audiences. The unfortunate truth is that the state of information is simply unreliable. Though I find the likelihood of at least some and possibly serious outbreak high.

Among news items questioning the PRK situation:

• "Could North Korea handle a Covid-19 outbreak?" (BBC) 2020-02-26. "North Korea is seen as highly vulnerable to infectious diseases, and its healthcare system ill-equipped to deal with them. So far, the country claims to have no cases of Covid-19 - but some observers are questioning whether that can be true. Experts say an outbreak in North Korea would be devastating for a population already suffering from malnourishment and poor health...."

• "North Korea reportedly quarantines 380 foreigners in bid to prevent coronavirus outbreak" (CNBC) 2020-02-24. "North Korea has reportedly quarantined 380 foreigners as part of efforts to prevent the coronavirus outbreak. The majority of those quarantined are thought to be diplomats stationed in the capital city of Pyongyang, Yonhap news agency reported Monday, citing state media in North Korea.... The isolated regime has repeatedly denied any confirmed cases of the coronavirus. That's despite concerns North Korea would be vulnerable to an outbreak given it shares a long and porous border with China and lacks vital medical supplies and infrastructure to cope with a fast-spreading virus...."

• "Coronavirus: North Korea quarantines foreigners" (BBC) 2020-02-24. "...North Korea has not confirmed any cases but the country shares a long and often porous border with China. There are concerns that North Korea, which is subject to international sanctions, lacks the health infrastructure to test and treat those infected and that any outbreak could quickly spread unchecked...."

• "North Korea: Kim Jong-un makes first public appearance in 22 days amid coronavirus outbreak (SCMP) 2020-02-16. "...North Korea has not confirmed any cases of the new coronavirus, but state media said the government was extending to 30 days the quarantine period for people showing symptoms, and all government institutions and foreigners living in the country were expected to comply 'unconditionally'...."

• "All of its neighbors have it, so why hasn't North Korea reported any coronavirus cases?" (CNN) 2020-02-07. "...One of the world's poorest countries has, according to its public statements, managed to avoid the virus despite the fact that in neighboring mainland China, it has killed more than 600 people and infected more than 31,000. More than 300 people have tested positive for the virus in over 25 places around the world -- including the other two countries that share a land border with North Korea, Russia and South Korea. In fact, every country and territory within a 1,500-mile radius of North Korea, except for sparsely populated Mongolia, has confirmed a case...."

Other Europe

Numerous cases in various countries. No additional travel advisories at this time.

• Holland reports its first case (Reuters) 2020-02-27
• Germany reports 20 cases and start of epidemic (Reuters) 2020-02-27
• Further cases in France, the UK, Switzerland, Sweden, and quite possibly elsewhere.

Community transmission is generally probable, if not extant.

United States

Reporting 60 cases, 0 deaths, 6 recoveries. One case of community transmission detected.

Most U.S. coronavirus cases remain associated with the Diamond Princess cruise ship outbreak, with 54 of the 634 confirmed cases aboard the ship being Americans, now repatriated and quarantined in the U.S. Another 14 cases are travel related (2 by person-to-person transmission), and one community-transmitted case, in Northern California, involving a Solono County resident now treated at UC Davis Medical Center in Sacramento, CA.

There have been concerns voiced over politicisation of the outbreak in the U.S., of political rather than clinical leadership of the outbreak, and of attempts to limit or contain both announcements and testing of suspected COVID-19 cases. All of these are errors which were widely criticised in China's early response. I'm very much hoping the U.S. does not repeat these mistakes for long.

The long erosion in the U.S. of political and institutional trust, as well as governmental competence, is worrying.

US CDC Update,

On Tuesday 25 February 2020 the CDC held a press conference with an Update on COVID-19 (audio). This was the original inspiration for this post, as noted, events are overtaking me me.

Summarising:

• The Global Novel Coronavirus situation is rapidly evolving and expanding
• Community spread is defined as cases without any known source of exposure
• Hong Kong, Iran, Italy, Japan, Singapore, South Korea, Taiwan, and Thailand are affected.
• 2 of 3 definitions of pandemic have been met. The third is worldwide spread.
• U.S. control especially at points of entry.
• Monitoring and travel advisories are being issued by the U.S. State Department.
• Quarantines, cooperation with HHS / DHS to repatriate individuals
• Very few cases in U.S., no spread in community as of 25 February. (NOTE: This is no longer true.)
• Ultimately we expect we will see community spread in this country. It's not so much a question of if this will happen any more, but rather more a question of exactly when this will happen, and how many people in this country will have severe illness.
• At this time there is no vaccine to protect against this new virus, and no medications approved to treat it.
• Non-pharmaceutical interventions (NPIs) will be the most important tool in our response to this virus. The specific interventions will vary by community and conditions.
• Specific recommendations made in document mentioned last Friday
• "Community mitigation guidelines to prevent pandemic influenza", United States, 2017, drawing on ~200 journal articles written 1990 - 2016. Provides a framework on response strategy.
• 14 cases picked up through the public health system.
• 42 cases repatriated from the Princess cruise liner.

Medical Characteristics

There's more information about the specific medical behaviour and characteristics of SARS-nCoV-2, the virus and disease behind COVID-19. Some of this is reassuring, some less so.

• The long incubation period, infectiousness before symptoms present, and possible reinfection of "recovered" cases, all lead to an increased likelihood of spread. We don't know where this is until well after it's already there.
• Availability of test kits, testing protocols, and healthcare insurance coverage and costs may all exacerbate spread of the disease.
• Transmission continues to appear to be via droplets. This is not "airborne transmission", as such droplets fall rapidly to the ground, but can result in transmission especially via coughing or sneezing.
• Hand-to-face transmission from surfaces is also common.
• Both infectiona and mortality increase sharply with age, most espeically at ages 60+. Infants and childre appear at very low risk.
• Co-morbidities of being a present or past smoker, and having cardiovascular disease, asthma, or diabetes, seem to greatly increase risk, especially of death.
• There is a possible genetic component varying widely by region.
• No drugs are currently approved for use, though several are being studied.

Case mortality by age

This is one of the two images I've attached to this post.

As noted above: there is a very low risk for infants and children, and modest risk through about age 50, increasing by about 2-3x for each 10 year span above that age, based on Chinese data. Experiences elsewhere may differ from this.

Pre-existing conditions show a strong influence, particularly smoking or previous smoking history.

From: "The Epidemiological Characteristics of an Outbreak of 2019 Novel Coronavirus Diseases (COVID-19) — China, 2020" (China CDC).

Partially reproduced as a table:

Age	Cases	Deaths	CFR%	Mort/10 PD
0-9	416	0	--	--
10-19	549	1	0.2	0.002
20-29	3,619	7	0.2	0.001
30-39	7,600	18	0.2	0.002
40-49	8,571	38	0.4	0.003
50-59	10,008	130	1.3	0.009
60-69	8,583	309	3.6	0.024
70-79	3,918	312	8.0	0.056
80+	1,408	208	14.8	0.111

• "CFR" is case fatality rate
• "PD" is patient-days

Mortality for men has been ~2x for women, possibly reflecting smoking rates.

Detection, monitoring, surveillance, and reporting

This all but certainly will have the biggest impact on containment efforts. COVID-19 is undetectable for a considerable period after infection, during which patients are infectious.

• COVID-19 is asymptomatic well after contracting the disease and without symptoms being present. Latent cases within a community are highly likely. Detection lags infection by days or weeks.
• Suspected and known cases lag actual infections.
• Test kits are not widely available. Use is targeted to most likely cases, based on screening protocols. Testing has been specifically denied of suspected cases (e.g., California UC Davis Medical Center) on the basis of not meeting established protocols.
• Protocols may themselves lag ground truth, particularly where screening by suspect countries of origin is concerned.
• Testing may be prioritised toward medical personnel and first responders.
• Regional and national variations in detection and disclosure are high.
• "No reported cases" may not be good news --- this might be because of no cases, of no testing, or of barriers to reporting.
• See especially: North Korea. At risk: any country with limited medical and/or public-health infrastructure, or a strongly privatised healthcare system.

Expanding "suspected case" clinical diagnosis criteria, increasing availability of test kits, allowing use of locally-sourced or locally-produced test-kits, and expanding testing protocol criteria, are all critical.

Most troubling has been the U.S. response after similar issues were widely criticised in China, of denying testing of a suspected patient over the objections of local doctors:

Diagnosis Of Coronavirus Patient In California Was Delayed For Days (NPR) 2020-02-27

The first suspected U.S. case of a patient getting the new coronavirus through "community spread" — with no history of travel to affected areas or exposure to someone known to have the COVID-19 illness — was left undiagnosed for days because a request for testing wasn't initially granted, according to officials at UC Davis Medical Center in Sacramento, Calif.... UC Davis included more details about the case in its own statement, drawing on an email sent to staff at its medical center. It said the CDC initially ruled out a test for the coronavirus because the patient's case didn't match its criteria....

"Upon admission, our team asked public health officials if this case could be COVID-19," the hospital said. "We requested COVID-19 testing by the CDC, since neither Sacramento County nor CDPH [California Department of Public Health] is doing testing for coronavirus at this time. Since the patient did not fit the existing CDC criteria for COVID-19, a test was not immediately administered. UC Davis Health does not control the testing process."

(Emphasis added.)

UC Davis Medical Center went to the unusual step of issuing its own letter on the incident.

Testing also requires individuals not face large financial costs or other penalties for coming forward. From Miami, FL: "Novel coronavirus test for Miami man leads to $3,275 bill:

Osmel Martinez Azcue ... went to Jackson Memorial Hospital ... [and was told] he’d need a CT scan to screen for coronavirus, but asked for a flu test first. “This will be out of my pocket"... [T]wo weeks later, [He got an insurance] claim for $3,270.

Healthcare is not a private concern. It is a concern of the common weal.

Remember, in the U.S., 40% of households cannot cover an unexpected $400 expense. Inequality is a public health issue.

Viability in warm and/or humid climates and seasonality

An early speculation was that SARS-CoV-2 would not survive well outside of cool and dry environments, typical of higher-latitude winters. Whilst the US CDC's 24 Feb press conference reiterated this, WHO-Philippine in a February 7, 2020 tweet s have suggested this may not be the case. Actual case count (3), mortality (1), and recovery (2) data for the Philippines, from Wikipedia, don't seem to indicate this.

"Warm and humid" also applies to spring and summer seasonal conditions in most places. There are hopes (again mentioned by US CDC).

Stay tuned.

Known-source vs. Community Transmission

"Community transmission" as defined in the US CDC's 24 February press conference means cases with no known source --- a disease is circulating within a community.

Epidemiologically, this means that efforts to trace contacts and restrict further exposures are limited, and instead general preventive measures must be implemented. My understanding is that community transmission does not necessarily mean cases are widespread, though it may. It does mean that specifically-targeted isolation and vector-disruption methods cannot be applied, and that general, community-wide measures must be relied on: hygiene, sanitation, reduced contacts, travel limitations, limiting large gatherings, quarantine.

Potential for Re-infection After Release

There've been Chinese reports of re-emergence of COVID-19 in individuals post-release (SCMP). This is now confirmed in Japan:

"Japanes Woman Confirmed as Coronavirus Case for Second Time Weeks After Initial Recovery":

A woman working as a tour bus guide was reinfected with the coronavirus, testing positive after having recovered from an earlier infection, Osaka’s prefectural government said. Her case, the first known of in Japan, highlighted how much is still unknown about the virus even as concerns grow about its global spread.

ACE-2 as infection route and genotypic variances

This is prelimiary information and may not be confirmed.

SARS-COV-2 may infect through a receptor known as ACE-2, principally through the lungs. Research suggests the genetic marker for that receptor is highly prevalent in Japan, much less so in the Middle East, and moderately prevalent in Western and Northern Europe.

https://www.researchgate.net/figure/ACE-II-genotype-frequency-in-different-populations-countries_tbl2_5642354

Personal and Community Responses

Again: there is no medical treatment. Breaking (or avoiding) transmission chains is most critical. At the personal level, this means basic hygiene and avoidance. At community and government levels, this means quarantines, travel restrictions, detection, monitoring, and effective response. These are decidely low-tech but effective.

Trust and competence by public health institutions and leaders are critical.

Adapted from: https://www.ready.gov/pandemic:

Before a Pandemic

• Store a two week supply of water and food.
• Periodically check your regular prescription drugs to ensure a continuous supply in your home.
• Have any nonprescription drugs and other health supplies on hand, including pain relievers, stomach remedies, cough and cold medicines, anti-diarrhoeal medication, fluids with electrolytes, and vitamins.
• Get copies and maintain electronic versions of health records from doctors, hospitals, pharmacies and other sources and store them, for personal reference.
• Talk with family members, loved ones, neighbours, co-workers, and other frequent contacts, about how they would be cared for if they got sick, or what will be needed to care for them in your home.

During a Pandemic

Limit the Spread of Germs and Prevent Infection.

• Avoid close contact with people who are sick.
• When you are sick, keep your distance from others to protect them from getting sick too.
• Cover your mouth and nose with a tissue when coughing or sneezing. It may prevent those around you from getting sick.
• Wash your hands frequently to help protect you from germs.
• Avoid touching your eyes, nose or mouth.
• Practice other good health habits. Get plenty of sleep, be physically active, manage your stress, drink plenty of fluids, and eat nutritious food.

Zynep Tufekci's Scientific American article makes the case for "Preparing for Coronavirus to Strike the U.S.":

We should prepare, not because we may feel personally at risk, but so that we can help lessen the risk for everyone. We should prepare not because we are facing a doomsday scenario out of our control, but because we can alter every aspect of this risk we face as a society.

That’s right, you should prepare because your neighbors need you to prepare—especially your elderly neighbors, your neighbors who work at hospitals, your neighbors with chronic illnesses, and your neighbors who may not have the means or the time to prepare because of lack of resources or time.

Public Health Institutions

There are numerous institutions involved in the COVID-19 outbreak response, ranging from international and large-national centres to smaller national governments, as well as regional (state / province / prefecture) and local (city / county / metropolitan region). Names may be similar, and capabilities and authority, as well as independence and trust, vary widely.

Among these:

• The World Health Organisation (WHO): "WHO works worldwide to promote health, keep the world safe, and serve the vulnerable." Roles are limited to advising and information sharing, with no policy and very limited operational capabilities within countries.
• European Commission Public Health: " The EU's role is to complement national policies by helping them achieve shared objectives, generating economies of scale, pooling resources, and helping countries tackle common challenges such as antimicrobial resistance, pandemics, chronic diseases or the impact of increased life expectancies on healthcare systems."
• The United States Centers for Disease Control and Prevention (US CDC): "CDC increases the health security of our nation. As the nation’s health protection agency, CDC saves lives and protects people from health threats." Serves policy, informational, and operational roles within the U.S., often engages in international crises. May be called "the CDC", a practice I'll strive to avoid as this creates confusion with similarly-named agencies, many modelled on it, in other countries.
• Other national CDCs: Notably China. Where referenced I'll note national affiliation, e.g., "China CDC" or "Japan CDC".

Second-order Effects

For all the concerns raised, the largest impacts of COVID-19 have not been to biological health but economic, financial, social, and commerce effects. In some places longer-term institutional and political impacts may result. For the most part, these are the consequence of preventive measures, most especially on travel, transport, and social aggregation, including schools, work, and other group activities.

Travel and association restrictions are effective at halting epidemics, but are disruptive to human economic and social activity. If your area becomes impacted, consider that these are issues you'll have to deal with, including loss of income, children out of school, and workplace disruptions. Those exposed to financial markets can also be affected.

Cultural and sport events may also be affected. "Olympic official: Tokyo is 'looking at a cancellation' if coronavirus not contained by late May" (Axios). "In light of global precautions being announced to combat the coronavirus outbreak, we’ve decided to postpone DEF CON China 2.0." (defcon) The UAE cycling tour has been cancelled (Reuters). Numerous others have now been reported.

Information, Misinformation, and Disinformation

Epidemics of rumour, misinformation, and disinformation follow epidemics of disease, and for virtually the same reasons. Both are information (one, words, ideas, and fears, the other DNA and lifeforms) spreading through a suceptible population via vectors and amplification mechanisms to create dysfunctional effects. Adam Kucharski's new book [The Rules of Contagion: Why things spread and how they stop](200~https://www.theguardian.com/commentisfree/2020/feb/08/misinformation-coronavirus-contagious-infections?CMP=fb_cif) is preternaturally timed with this current epidemic.

It's been noted that the aproaches of China and Russia (source eludes me) are both harmful to effective response in their own ways. China's early attempts to halt information or discussion delayed an early effective response. In Russia, apparent intentional sowing of disinformation is blunting containment efforts and spreading panic.

Authoritative information is concerning enough. I've pointedly avoided mentioning or linking rumours, few of which have any relevance to addressing the epidemic. Practice good information hygiene as well as epidemiological hygiene, and for the same reasons.

Epidemics attack trust: we're uncertain who is or isn't safe or a risk. Trust in institutions, tests, providers, responses, and response protocols all matter. Trust in supply chains, advice on what and what not to stockpile, as well.

"Coronavirus "infodemic" threatens world's health institutions":

Why it matters: The tide of bad information is undermining trust in governments, global health organizations, nonprofits and scientists — the very institutions that many believe are needed to organize a global response to what may be turning into a pandemic.

Informational Resources

Again, major public health organisations:

• The World Health Organisation COVID-19 Outbreak
• European Commission Public Health COVID-19
• The United States Centers for Disease Control and Prevention COVID-19

Specific guidance on response, both individual and organisational / community:

• U.S. Department of Homeland Security "Ready: Pandemic" public response advice, addresses both before and during recommendations.
• "Community mitigation guidelines to prevent pandemic influenza", United States, 2017, Draws on ~200 journal articles written 1990 - 2016. Provides a framework on response strategy to COVID-19.
• US CDC medical travel advisories.

Be safe.

Wash your hands.

#covid19 #ncov2019 #coronavirus #epidemic #publicHealth #HealthcareForAll

COVID-19 / Coronavirus update in progress

TL;DR: Things are getting far more serious, mostly outside of China.

The US CDC yesterday stated that community transmission -- cases with no determinable source emerging in the US -- is a practical certainty, a matter of when and not if.

Response is "nonpharmaceutical interventions" (NPI), boiling down to:

• Wash your hands.
• Cover your cough.
• Stay home if infected, or outbreak occurs locally.

There are presently no vaccine or medications approved for treatment.

If you're below age 50, risk is fairly minor. Infants and children are particularly not at risk based on China data. For the decades of the 50s, 60s, 70s, and 80+, mortality increases about 2-3x for each ten-year jump, to about 14% for 80+.

There's a bunch more. China is looking relatively good, its interventions have worked. Don't panic. Do pick up a few bottles of alcohol-based hand sanitizer and keep them on you (purse, jacket pocket, backpack, etc.) at all times. Masks really are not effective to prevent getting infected, though if you're infected, it's a very good idea to wear them to help prevent spread to others when you must travel.

Expect more disruptions through travel restrictions, quarantine, event cancellations (Olympics and multiple conferences are discussing this), work and school closings, etc.

Wikipedia's 2019-20 Coronavirus Outbreak article is an excellent source generally. I'll be adding others in my update.

Terminology is also changing, as will be my hashtags.

#covid19 #ncov2019 #coronavirus #sarsncov2

U.S. Centers for Disease Control (CDC) COVID-19 Update, 25 February 2020

"Ultimately, we do expect we will see community spread in this country [the US]. It's not a question of if this will happen any more, but a question of exactly when this will happen, and how many people in this country will have severe illness.... Non-pharmaceutical interventions will be the most important tools in our response."

• Stay home if you're sick.
• Cover your cough.
• Wash your hands.
• Frequently clean surfaces at home, work, school, and elsewhere.

Maximum benefit comes from layered actions.

https://www.cdc.gov/media/releases/2020/t0225-cdc-telebriefing-covid-19-update.mp3

Audio only for now, transcript forthcoming.

#covid19 #coronavirus #cdc #pandemic #epidemic #ncov2019

(Note I'm now using the "covid19" hashtag for ongoing coverage.)

Concerns over possible North Korean 2019-nCoV cases

The critical region to my mind in the 2019-2020 Coronavirus outbreak is North Korea, as previously mentioned.

It's adjacent to and has strong commercial and tourism ties with China. It is an authoritarian regime with poor internal communications, freedom of speech, or tolerance for views divergent with the administration. It has few resources and a poor history of dealing with epidemics. And its climate and current weather conditions are highly favourable to Coronavirus which thrives in cold and dry conditions.

And it's been claiming no cases of 2019-nCoV, which seems increasingly unlikely.

There are unofficial reports that there have been cases, though this is also problematic: dissidents inside and outside North Korea have a tendency to tell sources what they want to believe. Unfortunately this is a case of low-trust communications all around.

And now, via NPR, indications that my fears seem shared:

...North Korea's track record of fighting epidemics does not bode well for its handling of the coronavirus outbreak, other experts warn. Other communicable diseases are widespread in the country, which has one of the world's highest rates of tuberculosis and an estimated 15% of the population is infected with Hepatitis B.

"Past epidemics that originated in China have always spread to North Korea, and vice versa," says Choi Jung-hoon, a North Korean neurologist who defected to South Korea in 2012. During the 2003 SARS epidemic and other disease outbreaks, he says, cases in North Korea often went unreported or under-reported....

#ncov2019 #coronavirus #wuhan #northKorea #epidemics #china

https://www.npr.org/sections/goatsandsoda/2020/02/20/807027901/north-korea-claims-zero-cases-of-coronavirus-infection-but-experts-are-skeptical

Wuhan Coronavirus: Case classification standards change causing reported-cases spike

A key issue in any observation-based data is changes to the criteria for observation. That's coming to play in the 2019-nCoV outbreak numbers today, with Reuters and other sources reporting "Coronavirus death toll leaps in China's Hubei province":

[T]he 2,015 new confirmed cases reported in mainland China on Wednesday were dwarfed by the 14,840 new cases reported in Hubei alone on Thursday, after provincial officials started using computerized tomography (CT) scans to look for infections.

Hubei had previously only allowed infections to be confirmed by RNA tests, which can take days to process and delay treatment. RNA, or ribonucleic acid, carries genetic information allowing for identification of organisms like viruses.

The current reports stand at 60,330 confirmed cases and 1,369 official deaths, according to current data at Wikipedia. I'll note that fifteen days ago based on then-current trends, projection without epidemiological containment was for 200,000 cases, 10,000 deaths. Thankfully, even with a broader inclusion criteria, we're well below those values. Containment does largely appear to be working, and the epidemic may be further self limiting. (More below.) My existing projections are based on the earlier criteria and should not be applied to the broader clinical-diagnosis numbers.

Numbers reported depend on observational criteria. In general, my recommendation is to look to the case count as a trend indicator, across successive periods with consistent criteria, and for deaths as a far stronger magnitude indicator.

That is: we know that the cases were underreported. That's been widely criticised, and I suspect you'll see reports now of a sudden explosion in cases as Another Dire Sign. It's ... more complicated than that. Case reports to date have largely been a function of:

1. Limited numbers of virus test kits sensitive to the 2019-nCoV specific RNA (viruses don't have DNA, so this is the equivalent).
2. Testing of severe cases only. For non-severe cases (the majority), home isolation and care are largely sufficient.
3. Accepting most cases as "suspected" rather than confirmed.

The new numbers should be compared against earlier "suspected" cases, not "confirmed" cases. What are now being included are clinically diagnosed cases, based not on a definitive RNA test, but on symptoms as presented at a clinic, largely CT scans of lungs, among other measurements. This is actually very common in medical practice, and many conditions are diagnosed based on symptoms rather than a definitive test, often because symtoms are far more accessible (a case of availability heuristic), faster, cheaper, and in virtually all cases, sufficient. It's nice to have a definitive diagnosis, but not necessary. My understanding is that test kits have often been reserved for medical personnel themselves, many of whom have been infected with 2019-nCoV.

As before, epidemiological and public health responses are most important. If you are in an outbreak area (China, generally), rather than rushing out to buy masks (of marginal use), make sure you have and are using cleaning supplies, and minimise hand-to-face transmission. Wash surfaces, door handles, light switches, bannisters, and other contacted surfaces. Disinfect (spray bleach) around bath and toilet facilities. Use alcohol-based hand-sanitisers. (Again, antibacterial treatments do not work for viruses, that's wasted money.) Wash your hands frequently. Avoid crowded public spaces. Wipe down shopping trolly handles and other surfaces if possible. Be aware of what you're touching (elevator controls, any public touch-screen devices, keyboards, etc.). If you are infected and must go out, wear a mask but primarily to protect others --- you're limiting spread of droplets from your mouth and nose. (It's possible that applying table salt to the masks may increase their anti-viral properties, possibly by spraying with a saline solution.)

Expect to see travel bans and restrictions in place both within and transiting China for another few weeks, possibly months.

The real risk with 2019-nCoV is that it escapes containment and becomes a recurring annual disease much as the current common cold and influenza, though with far greater impacts. Given its high mortality rates, this could have severe impacts worldwide (deaths in the 10s to 100s of millions), though it's likely that this would eventually moderate. That's the scenario people are hoping to avoid.

Risks remain high, the containment trends still look very positive. Coronavirus fares poorly at higher temperatures and humidities -- odds of it spreading especially within the subtropical and tropical regions, and particularly in summer months, are fairly low. This means that China and neighbouring countries (again, notably North Korea with limited public health and public information resources and practices), Europe, and North America are probably most at risk. Community transmission elsewhere has remained low (cruise ships being a notable exception), and deaths outside China are also extremely rare: 2 (Hong Kong and Japan) despite 9,525 cases outside of China.

Fingers crossed.

The other notable news is that the Chinese Communist Party chiefs of Wuhan City and Hubei Province have both been sacked for their mishandling and information suppression of the 2019-nCoV initial outbreak. Again, China and the world could have had an additional 4-6 weeks' prior notice of the disease had initial reports not been covered up, before the mass internal migration of Chinese New Year celebrations. That was extreme misgovernance, and I expect to see more heads fall, possibly higher up, as well as further political reforms toward free speech within China.

https://www.reuters.com/article/us-china-health/coronavirus-death-toll-leaps-in-chinas-hubei-province-idUSKBN207025

#nCoV2019 #coronavirus #china #wuhan #hubei #epidemics

Mostly uniformed notes on Coronavirus, Wuhan, China, and the online response

I'm not a sinologist, sinophile, nor antisionist. I'm not an expert on China, or epidemics, or eastern-region politics. But I watch and observe, and occasionally comment. This story is an interesting one, but my observations are largely speculation, exceptions generally being cited or referenced.

There are two elements of this story I'm finding fascinating, both involving viral propogation. One is biological, the other epistemic.

The Plague

It's been about nine days since I posted my exponential growth 2019 nCoV observation, followed (in comments) by predictions that containment efforts begun arond 22 Jan would start showing clear evidence in new case data by early February, and that mortality should start falling by the 15th - 22nd, another 2-3 weeks out.

The first is bearing out, the second may be beating my initial projection. Both of these trends are encouraging.

I'll emphasise: I'm not a medical professional or epidemiologist. I read and study a lot, I've watched earlier outbreaks, and I've a fairly strong stats and data background which informs views of data. But really: I'm just some guy in a cat mask making guesses on the Internet.

That said:

• Signs are encouraging.
• The risk remains very real. We'll likely see somewhere in the neighbourhood of 100,000 cases (plus or minus a factor of 2) and 1,000 or so deaths (same). I think it's unlikley we'll see grossly more, say 10x, that.
• Quarantine, containment, education, public awareness, travel and commerce restrictions, and (within pandemic regions) frequent decontamination, are very much the order of the day.
• Effective treatments are few and will probably not emerge before the epidemic peaks or subsides. Mostly health professionals are limited to treating symptoms and secondary infections, with mixed effectiveness.
• There may be some nontraditional treatments or precautions which prove effective. No, I'm not talking crystals or Goop, but potential practices to reduce particle spread or make the virus less comfortable within hosts. Salt-impregnated masks have been mentioned favourably. I could think of other possible approaches, I won't bother mentioning them simply as rumour and misinformation spreading is already more than problematic.
• Given limited treatment, beds, an diagnostic kits, I'd argue that conclusively testing every presenting case is not a useful use of resources. Confirming infections among medical personnel is, but otherwise, triaging serious cases in to care, and directing less-serious cases to self-quarantine seems reasonable. We're talking city-wide, province-wide, and country-wide control where populations number to 10 million, 100 million, and 1 billion, respectively. This is a very large-scale problem. The goal is containment and management, not acute treatment of every individual case.
• Limitations on public knowledge of disease, germ theory, medical capabilities and limitations, and public health methods, is a challenge here. China's large population includes a very large undereducated population. (Though its educated population dwarfs that of any other country on Earth, possibly excepting India.)
• Failure to continue effective management could change all of this. The goal is to work effectively.

Media and Politics

The media and online response is ... interesting.

I've seen several long YouTube monologues, the first I believe by the individual known as "Brother Mask", another by a civil rights attorney, giving first-hand reports from within Wuhan itself. Many of the reports of conditions seem accurate. Some of the criticisms arising from them ... possibly less so. There have also been numerous posts in various places -- Mastodon and Diaspora, though of course many on Twitter, Reddit and elsewhere.

It's clear that many are seeing this as a propaganda opportunity to be used against the Chinese government. And there are certainly numerous criticisms which are valid.

Given the flood of online propaganda aimed at Western states in recent years, notably by Russia, but also China, generally following a "torrent of distraction" rather than "hose of reality distortion" favoured by Moscow. Seeing this now turned at China is ... interesting and ironic.

I don't consider myself a supporter of China, though I am impressed by the progress it's made most especially in recent decades. China is simply huge, and operates at scales the rest of the world fails to comprehend -- Wuhan is the city of 11 million you'd never heard of until two weeks ago. The country has faced, and does face immense challenges, and whilst not executing perfectly, has succeeded in many ways that deserve recognition. As do its failures. I'm often critical of elements of China's behaviours, both domestically and abroad (Uyghers, Tibet, and elsewhere). China is much like the proverbial Chinese symbol for crisis: opportunity and threat.

The main reason ideologically-driven discussions, debates, or (far more often) screaming matches are so boring is that they're simply so uninformative. The positions are well-established, the participants rarely principled or in good faith, and quite often themselves blinded to realities they'd prefer not to confront.

It's abundantly clear that China grossly mishandled the outbreak of 2019-nCoV, much as it did SARS in 2003, though not managing to cover up the epidemic as long in this instance. The death, or is it martyrdom, of Li Wenliang, is portentious. Unconfirmed reports of 800 million Weibo posts within 2.5 hours of its annoucement. It seems at least possible that changes to central control over information flows may occur, though the legacy of Tienanmen Square still looms large, and information regarding it remains tightly controlled. Chinese partisans have been engaged in petty battles over map definitions within the 2019-2020 Wuhan Coronavirus Outbreak Wikipedia page, as evidenced by the Talk page. Yes, Wikipedia has its conflicts and attempts at manipulation, but they occur in public and are often countered.

China's own meddling with both independent Taiwan and Hong Kong appear to be backfiring badly in terms of trust in the CCP and central government. That seems somewhat just desserts, though not always epistemically valid information.

At the same time, there's what seems strongly to be hay-making by opponents of the government, quite possibly even factions within the CCP battling against each other (my speculation), and quite likely entities or factions within Taiwan and Hong Kong, as well as the usual rabble-rousers, xenophobes, ecouragers of chaos (viz: Stephen Bannon), and general whackadoodles worldwide.

The interesting situation is that China seems to be approaching a point at which neither a closed-down media system, nor a wide open one, is risk-free. The first, had it persisted only a few weeks longer, could have had us talking a bound an epidemic ranging into the millions of cases and tens or hundreds of thousands of deaths, as well as global economic disruptions lasting months (and a likely risk-based reduced exposure to China). The second, while guarding against the "tell the emperor what pleases him" failures of rigid control, also enables the enemies of the emperor to speak freely. It seems all but certain that China will have to move out of its comfort zone here.

Or ... and if this path is chosen, all but certainly with the assistance of all the usual Silicon Valley suspects we've come to know and love ... institute an even more pervasive, flexible, and effective set of internal and external informational firewalls which permit the flow of critically important information whilst somehow managing to disrupt attempts at political opposition.

I don't find the second possibility overly likely from a technical standpoint, but Orwell and Huxley seem to have been winning the War for the Internet so far, and it seems unwise to not give them their nod.

Norbert Wiener, the father of Cybernetics, had a strong experience with information controls during World War II, as he worked on numerous research projects for the US government and military. After the war, his assessment was that the security restrictions on communications hurt the Allied forces more than they helped. For the most part, the enemy was already aware of the research projects, so the spread of information to the enemy was not meaningfully curtailed. But the Allies, working with limited technical and intellectual personnel resources, were hurt more by the duplicate, slowed, and inefficient progress made on the projects due to the communications restrictions.

Whether Wiener's view was accurate or merely his own personal bias, I'm not sure. But China is likely to be debating the same question, if not now, then soon.

#china #coronavirus #ncov2019 #wuhan #LiWenliang #propaganda #media #epidemics #tienamen #uygher

The Wuhan 2019nCoV Coronavirus Epidemic is growing by a factor of ten a week

A semi-log plot at Wikipedia shows the exponential growth of this epidemic over the past two weeks. On such a plot, a straight line corresponds to an exponential growth in linear scale.

This trend need not continue, but if it does, the implications are ... severe. And efforts at containment will be measured against any reduction from this trend. Keep in mind also that this tracks confirmed cases, which is a subset of total actual infections.

As of two days ago, January 26, 2020, total cases stood at about 2,000, and deaths at 100. If trends continue we'll see, in very rough numbers:

• In 1 week: 20,000 cases, 1,000 deaths.
• In 2 weeks: 200,000 cases, 10,000 deaths.
• In 3 weeks: 2,000,000 cases, 100,000 deaths.
• In 4 weeks: 20,000,000 cases, 1,000,000 deaths.

Again, this is not certain to happen, but is projection based on current trend.

An epidemic is comprised of an infectious agent, a host population, susceptible individuals, vectors of transmission, and susceptibility or immunity to infection. Incubation period, time between infection and symptoms, infectiousness before onset of symptoms, and ease of transmission are all factors affecting spread.

In an epidemic, particularly against a virus with no known curative treatement, the way you attack spread is by vector control. You want to stop the spread of the viral particles themselves.

Within a given region, this means isolating known infectious individuals, minimising the amount and degree of contact between them and others, and between asymptomatic individuals, is key. Note that those not showing symptoms may or may not have the virus.

This means, for the most part, the measures applied so far: masks (of limited use), handwashing (very important), general isolation -- not going out and about, meaning limited school, work, and social activities, and limiting of long-distance travel, especially any transportation which completes journies within the incubation period.

Airplanes are epidemic engines. This was notably observed by British journalist and documentarian James Burke, when he revisiited his 1980s series Connections, and was asked how he might continue the series. His answer: to look at the concluding inventions and consider their further implications, for example, air travel and its role in epidemics.

So yes: curtailing air transport out of regions in which the virus is known to be pandemic (spread through the general population) is an extremely advisable measure. Should have been done weeks ago, but now is better than never. Expect to see further transport restrictions, and possible quarantines, particularly of evacuated individuals.

If you're in a region at risk of outbreak (presently: China), rather than buying masks, you should be stocking up on nonperishable food such that you have several weeks supply and can further minimise exposure though shopping, as well as hand sanitiser (alcohol should work, antibiotic is useless against viruses). Shopping-cart handles and other surfaces are prime transmission vectors: elevators, public transport, doors, light switches, etc. Regular cleaning and sanitisation of these is helpful.

Workplaces should require any infected individuals take sick leave, regardless of cause. (This is just common sense, unfortunately as always, uncommon.)

Immunisation against other diseases (e.g., standard influenza) won't protect you from 2019nCoV, but it will reduce the odds of confusing symptoms of unrelated conditions with those of the coronavirus which is helpful to both individuals, their contacts/families, and healthcare systems. Get your flu shot and insist on those around you getting theirs as well.

We've also seen secondary transmission to individuals never having visited China, in both Germany and Japan. Which means the disease is absolutely human-to-human transmissible.

Normally in major epidemics my concern is on global poor megacities, which have vast populations but poor public health infrastructure. That's likely a risk here, but North Korea seems another potentially volatile location given:

• Proximity and relations with China.
• Generally poor infrastructure.
• An informational structure much given to revealing what it's believed the recipient wants to hear, rather than the truth.
• Wintry climate, generally favouring viral transmission.
• Often poor and crowded living conditions, particularly within military, work, and prison camps.

Whilst PRK has limited ties with the rest of the world, some do exist, and the elite are possibly more likely to be able and inclined to flee elsewhere, possibly taking the disease with them.

PRK have already been taking measures to limit border crossings. This is politically feasible (the benefits of absolute rule), but the actual effectiveness may fall short of requried levels.

https://en.wikipedia.org/wiki/2019–20_Wuhan_coronavirus_outbreak

#coronavirus #wuhan #ncov2019 #china #epidemic #prk #northkorea #publichealth