Covid 19 virus

[Weston]

Universities in the USA started moving to online instruction last Wednesday. Today they started announcing that undergrads should not come back to campus after spring break, possibly not returning until next fall. I know that MIT, Stanford, and Harvard have implemented these policies, I assume other schools are also doing so.

Not that I really interact with the undergrads, but campus is going to be pretty quiet for the next few months and its going to be basically impossible for any lab or project based classes to be offered.

Given that this looks like its going to lead into an economic recession its a pretty good time to be a grad student. Guaranteed job security!

[whalphen]

At the end of last month I took a look at the US case count to try to get an idea of how quickly this disease would be spreading.  I just wanted to be able to make some plans regarding travel.  So, I watched the numbers from the worldometer website.  I found that the US case count doubled on a very regular pace.  From March 1 I started recording the number each day and plotting it.  It's amazing how predictible it has been.  Since March 1 in the US it has been very tightly tracking an exponential growth pattern.  The number of cases is doubling every 2.4 days.  On this growth path, the number of US cases will reach over 420,000 by the end of March.  However, in the US , bureaucratic and financial hurdles are resulting in very little testing being done.  So the actual number of cases is likely much higher than the available numbers.  If more extensive testing is done it will likely drive the numbers to go above the projection.  If significant actions are taken to slow the spread, the data will track below the curve.  So far, neither of these are seen in the data.

So, when will we see an inflection in the curve -- at the latest?  Epidemiologists are saying to expect 60% to 80% infection rate before herd immunity takes effect.  On the current growth path for the US, that will occur between April 21 and April 23.  But, considering that the case count is likely higher than we know and that fear will probably grip the population and policy leaders before that prompting them to take some actions to slow the spread, I suspect we'll see an inflection point in the US in mid April.  Unfortunately the inflection point will not be the peak.  I think it's safe to say this epidemic will be with us for more than the next couple of months.

[edy]

PANDEMIC!

Yes WHO finally shifted their stance from epidemic to pandemic. There were various reasons they held back but it is clearly a matter of mindset, political, social and economic strategies that motivated their decision along with the facts on the ground. Bottom line is, they don't want people to give up fighting since there was still "hope" when it was being treated as an epidemic. At this point, you might think resistance if futile, but even as a pandemic (which everyone already knew was where it was going), it is still good to fight it like an epidemic to slow down it's progression. This will be difficult in many liberal democracies but it may eventually come down to Italian-like lockdowns (I doubt we will ever allow Chinese-like lockdowns) which is going to be devastating either way.

[Simon]

i have food for a month. They have been compelled to change their stance as governments have an eye and a half on their corporate bosses and the stock market and not enough on the pandemic.

[Cerebus]

PANDEMIC!

Yes WHO finally shifted their stance from epidemic to pandemic. There were various reasons they held back but it is clearly a matter of mindset, political, social and economic strategies that motivated their decision along with the facts on the ground. Bottom line is, they don't want people to give up fighting since there was still "hope" when it was being treated as an epidemic. At this point, you might think resistance if futile, but even as a pandemic (which everyone already knew was where it was going), it is still good to fight it like an epidemic to slow down it's progression. This will be difficult in many liberal democracies but it may eventually come down to Italian-like lockdowns (I doubt we will ever allow Chinese-like lockdowns) which is going to be devastating either way.

The prior H1N1 outbreak was officially classified as a pandemic by the WHO. Just because it has met the criteria to be labelled a pandemic rather than an epidemic means only one thing, that much/most of the world is involved. Being a 'pandemic' is not a necessarily a question of seriousness or scale, just of geographical spread. I'm being pernickety precisely because the word 'pandemic' makes people use 18pt type, exclamation marks and start running around in circles panicking. By definition, all of you (unless we have some 11 year old members) lived through the 2009 H1N1 influenza pandemic, and you're still here.

There were various reasons they held back but it is clearly a matter of mindset, political, social and economic strategies that motivated their decision along with the facts on the ground.

Much more likely is that they have a set of formal criteria that have to be met before something moves along the scale of nomenclature from outbreak=>epidemic=>pandemic.

[Simon]

It's now quite widespread around the world. We got to this stage because we all went on holiday. I have a colleague that still expects to go to Austria at the end of the month 

[edy]

I'm being pernickety precisely because the word 'pandemic' makes people use 18pt type, exclamation marks and start running around in circles panicking. By definition, all of you (unless we have some 11 year old members) lived through the 2009 H1N1 influenza pandemic, and you're still here.

Yes agreed. My understanding is that the classification change also affects how governments treat the outbreak, how funding is distributed, how they mobilize their health systems. It can change their policies toward travel, focusing their help internationally or bunkering down domestically, and so on. So now as we shift towards pandemic-management there will be different strategies employed, none of which involve stockpiling of toilet paper (I hope). 

All reports seem to indicate that like H1N1, it will probably end up infecting 70% of the population and that the vast majority (80%) of people will experience mild to moderate cold-like symptoms which eventually they recover from, with the remaining 20% having severe symptoms possibly requiring hospitalization. In this smaller subset of people, mostly immunologically fragile or breathing-compromised, we will see the possibly 2-3% of pneumonia-related deaths. While H1N1 had a purported death rate of 0.5%, most countries are already experiencing near-capacity health-care system utilization with many under-funded... so it will breach capacity unless things are slowed down.

So no need to panic but this is going to stress out hospitals for sure. Being in Canada and seeing how stressed to the brink our government-run health care system already is, and having quite a number of doctor and nurse friends, I am hearing from them what nightmare we might expect in the coming months if things keep "tragectorying" the way they have been so far. Nothing to do but wait and watch. 

[Simon]

The Uk will do badly once it spreads. accident and emmergency are always on the backfoot.

[not1xor1]

Well N10  have used war like language but the actual action has not been that forthcoming. It would appear that they are still hedging their bets that it won't happen but that will make it happen. My sister is due to have a baby in May, I am not happy, last thing she needs is a Covid-19 ridden hospital to give birth in because we lost control of it.

Both young women and babies (10 years and less) are low risk categories and by May it the virus should be much weaker.

COVID-19 is just a (one of the largest) bunch of RNA code enclosed in a protein shell.
It requires the host cell machinery to reproduce and doesn't live long outside a host. The hotter and wetter (RH) is the air the shorter is its life (in the air or on various surfaces).

[not1xor1]

I expect to see acceleration in China in the next few days while people start migrating again.

China continues to report unrealistically low numbers of new daily cases. Just 4 today.

given the harsh measures taken those are not unrealistic
I rather expect lots of unreported cases in the US (and even worse in Russia)

[DBecker]

All of the roadside births I've heard about at the hands of cabbies or police officers have all had happy endings.

Selection bias.  Quick births at full term are usually healthy mothers and babies.  Multiple days of pre-labor and labor is correlated with problems.

Similarly planned home births in areas with good health care tend to have good outcomes because people with higher risk don't select that option.  Home births with no other options have worse statistics  because there are usually no good fall-back plans.

The statistics for Covid-19 are uncertain because we can't separate the selection effects.  Perhaps we have 10x symptom-free cases for every serious case.

[iMo]

https://www.reddit.com/r/medicine/comments/ff8hns/testimony_of_a_surgeon_working_in_bergamo_in_the/?utm_source=share&utm_medium=ios_app&utm_name=iossmf

[edy]

https://www.reddit.com/r/medicine/comments/ff8hns/testimony_of_a_surgeon_working_in_bergamo_in_the/?utm_source=share&utm_medium=ios_app&utm_name=iossmf

Long testimony, scary to read but perhaps a glimpse into what awaits us. Let's hope we have the fortitude and foresight to delay or stop this tidal wave before it gets to that point.

Just as an aside... I am in the health professions and ordered (along with a bunch of unrelated medical supplies) some masks from a medical supply company to health professionals/private clinics. I received everything BUT the masks order which are indefinite back-order. I have a doctor friend of ours that is in a private multi-doctor clinic and she had to drive 1 hour away to buy a box of masks.

So you need to prioritize masks going to people in the community who have high "Bacon numbers"... i.e. people who are potentially in contact with many other people throughout the day and in close proximity (dentists, doctors, etc), as they would be a "node" with high connectivity of potential transmission. Having said that, a lawyer in New York apparently is being implicated as being such a "node" with multiple cases being tracked back to that office. Blocking as many of these high-connectivity nodes would be more effective I would think. Computer-modelling this may gain useful insight into the best places to distribute such equipment and the best strategies for containment when limited supplies are available.

[metrologist]

Selection bias.

My comment was merely a statement of my experience, nothing more. I've never seen a person with purple skin is not the same as saying there are no people with purple skin. But I actually saw a guy on TV that did have purple skin, or maybe it was more of a blue. Maybe if I'd never seen the segment I truly would not believe people could have purple skin. Maybe the media is biased and does not report of botched curbside births. 

I'd not want to have a pregnant sister in the same situation right now either.

[donotdespisethesnake]

by May it the virus should be much weaker.

Snopes rates that as "unproven". https://www.snopes.com/fact-check/coronavirus-warm-weather/

[Nusa]

However, the areas that got it first are going to recover first. So China is going to be back to work sooner than the US, which is just starting to react, despite Trumps assurances that everything will be ok.

(I have food for maybe three months, although the last month won't have much variety.)

[iMo]

German Chancellor Merkel on Covid:
https://berlinspectator.com/2020/03/11/merkel-on-coronavirus-we-need-to-pass-the-test/
"Therefore 60 to 70 percent of all people in Germany could be infected."
aka "What Doesn't Kill You Makes You Stronger"

[Cerebus]

by May it the virus should be much weaker.

Snopes rates that as "unproven". https://www.snopes.com/fact-check/coronavirus-warm-weather/

"The virus should be much weaker" and 'the virus is less likely to be transmitted in warmer weather' - the latter being what Snopes considers - are not the same thing.

There's a real possibility that the virus in circulation may be less virulent by May by a combination of two reasons: (1) Coronaviruses are highly mutable, there's a very high probability of new variants emerging during a pandemic, (2) viruses/bacteria/parasites that kill their hosts are less likely to spread than less lethal variants. This was actually seen, and confirmed, during one of the earlier flu pandemics (I don't offhand remember which one) where later in the pandemic the original flu variant died off and a mutated, less virulent, variant continued to spread - the death rate fell while infection rates continued at the same level. Although this is a real possibility, it's not a effect that any plan to control the disease ought to rely on.

[iMo]

The virus is more prone to a damage with higher temperature, lower humidity and more ultraviolet exposure.
Therefore we have flu epidemics in the northern hemisphere usually in winter (and also the human immune system is at lowest level in winter/spring).

[iMo]

The cloudy vs. sunny days in the spring may represent days vs. hours of the virus activity on a surface.

PS: Italy closes all stores except pharmacies and food outlets

[VK3DRB]

People should learn their history and not be as ignorant as the morons in Thailand wearing the swastika.

The 1919 Spanish 'flu (actually it started in the USA) came in three waves. It was the third wave that wiped out most of the victims. The Chinese communist party is beating its chest about how great totalitarian rule is, but at least another wave will very likely follow, much worse than the first one. How these serial liars are going to face up to the Chinese people if and when it happens will be interesting.

The WHO just announced the pandemic. Monday might be a good time to buy stocks with a long term view.

[hamster_nz]

Because I found it very thought provoking, here is the RNA for one of the Australian samples :

https://www.ncbi.nlm.nih.gov/nuccore/MT007544

At ~30,000 bases, that's about at most 8 kilobytes of information, that can kill thousands (maybe soon millions?) of people, and billions of $.

PS. If felling uber-geeky you can also cut and paste part of the sequence (a line or two) into BLAST (see link on top right) and see what else matches...

[Kjelt]

The virus is more prone to a damage with higher temperature, lower humidity and more ultraviolet exposure.
Therefore we have flu epidemics in the northern hemisphere usually in winter (and also the human immune system is at lowest level in winter/spring).

Higher humidity. With lower humidity as in the winter the nasaldrops loose their moist content faster and the particles travel larger distances. That is why you should keep a further distance with lower humidity than high humidity where the heavier particles will drop sooner and travel a shorter distance.

[Sredni]

PS: Italy closes all stores except pharmacies and food outlets

In the rest of Europe they are still at stage 1: don't worry, 80% only show mild symptoms.
Don't forget to wash your hands, and no, masks are not needed (don't but them, we need them)

EDIT: Apparently, other parts of the world are still at stage 0: "lalalalalala it's just the flu, I don't want to look at numbers".

P.S.
Dave, "Amid growing suggestions that ministers have acted too slowly in seeking to combat the virus – the editor of the Lancet medical journal accused them of “playing roulette” with people’s lives"
https://www.independent.co.uk/news/health/coronavirus-news-live-uk-cases-trump-us-travel-ban-europe-pandemic-delay-phase-a9396186.html
You might want to try to delete that, as well.

[vad]

At the end of last month I took a look at the US case count to try to get an idea of how quickly this disease would be spreading.  I just wanted to be able to make some plans regarding travel.  So, I watched the numbers from the worldometer website.  I found that the US case count doubled on a very regular pace.  From March 1 I started recording the number each day and plotting it.  It's amazing how predictible it has been.  Since March 1 in the US it has been very tightly tracking an exponential growth pattern.  The number of cases is doubling every 2.4 days.  On this growth path, the number of US cases will reach over 420,000 by the end of March.  However, in the US , bureaucratic and financial hurdles are resulting in very little testing being done.  So the actual number of cases is likely much higher than the available numbers.  If more extensive testing is done it will likely drive the numbers to go above the projection.  If significant actions are taken to slow the spread, the data will track below the curve.  So far, neither of these are seen in the data.

So, when will we see an inflection in the curve -- at the latest?  Epidemiologists are saying to expect 60% to 80% infection rate before herd immunity takes effect.  On the current growth path for the US, that will occur between April 21 and April 23.  But, considering that the case count is likely higher than we know and that fear will probably grip the population and policy leaders before that prompting them to take some actions to slow the spread, I suspect we'll see an inflection point in the US in mid April.  Unfortunately the inflection point will not be the peak.  I think it's safe to say this epidemic will be with us for more than the next couple of months.

The epidemic (or pandemic) is already out of control. It is spreading in communities at exponential rate. Such exponential spread can only stop when majority of the population (on the order of magnitude of 50%) gets immunity either through contracting the disease or through vaccination. The latter is out of the question (vaccine is at least 12-18 month behind). So the actual spread will continue until most people get infected.

As for tracking test results... In open countries, like the US, there is the limit on how many positive tests the country can report each day (determined by the number of available test kits, lab throughput, qualification criteria determined by bureaucrats, etc.).

For example, 2 weeks before now the US had limited ability to perform tests:  January through end of February they performed only ~1,500 tests in total in few CDC labs across the country, and that yielded few dozens domestic positive tests. Once million test kits were provide to health authorities of 50 states over the past few weeks, the number of positive tests in the US started climbing exponentially. This does not mean that there was no exponential community spread before the test kits were provide to states. The system was simply not able to gauge that spread with 1,500 tests they performed in 2 month.

Sooner or later the speed of the spread will outpace the current testing capacity in the US. The statistics will start flattening out in the US, but the exponential spread will continue.

As for authoritarian regimes - you simply cannot trust the numbers they produce. Recent figures from China are laughable, and they cannot be rationally explained. Another example is Russia. Russia has long history of manipulating its numbers. For example, in 2017 Russia reported 432 mortality case from flu and common cold. In the same year, CDC estimated mortality rate of 61,000 (95% CI 46K-95K) from flu in the US. Either vodka and cabbage are efficacious measured against flu, or Russian state-owned statistics agency spread misinformation. And, surprise surprise, the same agency reports laughable numbers of Covid-2019 cases in Russia now...