2019-nCoV / Corona virus Pt 2

[Skeptic Ginger]

In all seriousness, we ought to all be wearing masks when we're out, even if they aren't high quality, hospital grade, masks. After reading, I'm convinced they protect the wearer a little bit, and the people near the wearer a lot.

The shortage of masks led the public health to lie about this instead of explaining it to people.

It's like Fauci today telling people testing would be nice but we don't need it. What a Trump apologist. Guess it makes Fauci feel better to pretend 'we got this'.

 

[Skeptic Ginger]

The thing is he isn't. He is not a virologist, he is not a medic. He is a scientist who does research on the genetics of antibiotic resistance in bacteria. That he happens to have the title of assistant professor in Epidemiology does not make him an expert on human infectious disease epidemiology and outbreak control nor the mathematical modelling thereof.

Sounds like an epidemiologist to me.

 

[Skeptic Ginger]

Don't jinx us!

ETA: We just had our first case of probable community spread, though, its a tour guide at Kualoa Ranch would would be in close and often confined contact with tourists from all over especially Japan and China since this all began

My cousin who lives in Waikiki said testing was almost nonexistent last week. IMO, you guys are like we are in WA, it's there but no one is looking.

 

[JeanTate]

A good source is here.
https://cmmid.github.io/topics/covid19/
This is the Centre for Mathematical Modelling of Infectious Diseases from The London School of Hygiene and Tropical Medicine (familiarly known as the trop shop). You can download their code if you want.

Thanks.

 

[Planigale]

Quoting the BBC:

"The modelling projected that if the UK did nothing, 81% of people would be infected and 510,000 would die from coronavirus by August.

The mitigation strategy is better, but would still result in about 250,000 deaths and completely overwhelm intensive care in the NHS.

The experience of Italy, and the first cases in the UK, led to this dawning realisation."

And: "The government has always said it is following the science and the science has changed profoundly."

Am I the only one to find this hard to accept?

Did those who built the models not even try to learn from China's experience? They had to wait for hundreds of deaths in Italy before they twigged to the fact that the UK was going to be in for a very rough ride?

Actually as someone who has been looking at the models for the UK as they have come out, this is true. We were looking at trying to drop the R₀ to about 1.5 which we thought should blunt the peak (actually giving a biphasic peak). But more recent data suggested this would not be successful. Instead we maybe looking at periodic tightening and loosening social isolation allowing a drip feed of infection. The real danger is just releasing the lock down and then getting exactly the same outcome but just delayed. The problem is what is the exit strategy? Do we wait for a vaccine which is months away at best or hope that effective treatment is found and we can mass produce it for the world?

(and if you want to be really scared what are the chances of MERS CoV and SARS CoV 2 transferring some genetic material if someone in the middle east gets co-infected, and ending up with increased human to human transmissibility of MERS CoV or increased mortality from SARS CoV 2)

 

[Skeptic Ginger]

He is actually an Associate Professor (meaning he obtained tenure, not easy to do) of Epidemiology in the Department of Epidemiology, and a faculty member in the Center for Communicable Disease Dynamics at Harvard. He doesn't just happen to hold a title in a department of epidemiology: he is a hard core epidemiologist with extensive training and research in that area. One major focus of his work is on the spread of antibody resistance in bacterial infections of human populations. Another is the dynamics/distributions/changes/spread in the serotypes of different pathogenic bacteria in humans and the consequences of this in regard to immunity and vaccination.

He has already published over 140 publications in these and closely related fields. He is both very successful as a scientist and his expertise is highly relevant to the coronavirus epidemic. He is very much an expert in precisely those fields you dismiss. The fact he studies spread of infectious bacteria versus infectious virus means virtually nothing in terms of the direct relevance of his work for understanding epidemics.

 

[JeanTate]

Thanks.

just a caution: most of the manuscripts listed are "in progress" or "under review." These are either incomplete or not yet vetted by peer reviewed.

Noted.

I skimmed one or two, and they seem what I'd expect: enough for you to be able to independently and objectively validate* the conclusions (one could obtain the same input data independently - dataset downloads - and build the same models oneself). YMMV of course.

This is in contrast to what the UK government seems to have done: the models on which its conclusions depend are not in the public domain; there seems no obvious way anyone could do independent and objective validation*.

*YMMV; for you "verify" may be a more appropriate word

 

[Planigale]

Are you teasing me? Probably more than 90 to 95% are highly relevant.

First, are we literally on the same page? Perhaps you are looking at a non-representative part of his publication list. Here is a list in reverse chronological order that shows off his most recent work first, although the relevance of his pubs stretches back to the very start of hist career some 15 years ago:
https://www.ncbi.nlm.nih.gov/pubmed/?term=Hanage

Or perhaps you may not recognize how his dissections of the genetics of different isolates of pathogens in different people represent the cutting edge of epidemiology? These methods, and their contributions to the modeling of the spread of bacteria and viruses, have revolutionized epidemiology at all levels (from the spread of an antibiotic resistant bacterium in a hospital to a worldwide epidemic.

If you don't believe me or a more detailed consideration of his publications yourself, you may wish to consider why he was hired and obtained tenure in a department of epidemiology and membership in a center for communicable disease dynamics. You can even go on line and see how these programs define their areas of study and expertise.

I have no doubt he is an excellent scientist. I have no doubt that understanding antibiotic resistance is very important for the future of health care. But just as I would not expect my friend who models infectious disease outbreaks to get down and dirty in a lab looking a gene transmission in pneumococci, I have no confidence that a laboratory based geneticist is well placed to look at the behaviour of infectious disease in a human population, and the best public health interventions to disrupt an outbreak.

 

[Dr.Sid]

Grim numbers (taken from WHO daily situation reports), cumulative reported Covid-19 deaths:

Hubei province: 3085 (15 March) (population ~59 million)
Italy: 1809 (16 March) (population ~60 million)

China: 3218 (16 March) (population ~1.43 billion)
USA: 41 (16 March) (population ~0.33 billion)

Italy's reported cumulative deaths will likely exceed Hubei's by ~this weekend (21/22 March)

The US' will exceed China's ... when?
The answer to that question depends on many things, not least the possibility of a second Covid-19 epidemic in China.

You should not take China as 1.43 billion people. Hubei province with 59 million people is responsible for 67790 cases. The second most affected province has 1356 cases.
So the situation in Italy is actually not so different from China, I mean Hubei.

 

[JeanTate]

Thanks.

Actually as someone who has been looking at the models for the UK as they have come out, this is true. We were looking at trying to drop the R₀ to about 1.5 which we thought should blunt the peak (actually giving a biphasic peak). But more recent data suggested this would not be successful. Instead we maybe looking at periodic tightening and loosening social isolation allowing a drip feed of infection. The real danger is just releasing the lock down and then getting exactly the same outcome but just delayed. The problem is what is the exit strategy? Do we wait for a vaccine which is months away at best or hope that effective treatment is found and we can mass produce it for the world?

Yeah, I'm ignorant ... how were these models informed by data from China?

Oh, and is "biphasic" the same as, or similar, to bimodal?

(and if you want to be really scared what are the chances of MERS CoV and SARS CoV 2 transferring some genetic material if someone in the middle east gets co-infected, and ending up with increased human to human transmissibility of MERS CoV or increased mortality from SARS CoV 2)

That's something I wondered about a while ago, and even wrote a post here about that, but referring to influenza instead of a coronavirus.

 

[eeyore1954]

They made up for it in today's numbers, with a 25% increase.

We'll see that kind of anomaly - Italy did the same a few days back.



Your numbers just aren't adding up - you should be in the position Washington State is, but you're not.

I wish I could figure it out, and I bet lots of scientists do too.

Japan is still a huge anomaly as well. I must eat more fish.

Japan also has one of the oldest populations too. At least according to Wikipedia it is second to Monaco.

When I was young my next door neighbor was of Japanese decent and born in Hawaii. If he was still alive he would have had full immunity.

 

[Planigale]

Thanks.


Noted.

I skimmed one or two, and they seem what I'd expect: enough for you to be able to independently and objectively validate* the conclusions (one could obtain the same input data independently - dataset downloads - and build the same models oneself). YMMV of course.

This is in contrast to what the UK government seems to have done: the models on which its conclusions depend are not in the public domain; there seems no obvious way anyone could do independent and objective validation*.

*YMMV; for you "verify" may be a more appropriate word

But who do you think is doing HMG's modelling? Also see here for contribution to UK model.

https://www.medrxiv.org/content/10.1101/2020.02.12.20022566v1

 

[The Great Zaganza]

Japan also has one of the oldest populations too. At least according to Wikipedia it is second to Monaco.

People in Monaco will all have fled to sea on their yachts.

 

[pipelineaudio]

T
Your numbers just aren't adding up - you should be in the position Washington State is, but you're not.

Its been pouring for days now. That will stick the tourists inside, not sure if its really any colder, who knows what effect it will have

 

[pipelineaudio]

My cousin who lives in Waikiki said testing was almost nonexistent last week. IMO, you guys are like we are in WA, it's there but no one is looking.

The state health department was actively opposing testing and absolutely refused testing to confirm the Feb 1st cases

Now we have companies competing with each other to do testing including walgreens. We shall see. I thought that those could actually spread it since they arent going to be changing suits for every test

 

[JeanTate]

Thanks.

You should not take China as 1.43 billion people. Hubei province with 59 million people is responsible for 67790 cases. The second most affected province has 1356 cases.
So the situation in Italy is actually not so different from China, I mean Hubei.

There are, of course, swings and round-abouts. For example, Taiwan, Hong Kong, and Macau are included in China, yet the various Chinese agencies have ~zero ability to directly affect public health policy (etc) in Taiwan, and not much in Macau or Hong Kong either. Together, though, the populations of these three places is tiny compared with that of the 31 (?) provinces under direct control of the government in Beijing.

So: the US Federal government has direct control over public health policy for ~330 million people, as the Italian government has for ~60 million people.

Yes, there are also swings and roundabouts, including:
- US States and Territories (e.g. Guam) may have more control than Italian provinces
- Italy as an EU member (and one of the 26 Schengen countries) may be more limited in what it can do than either the US or China

 

[casebro]

Denial is truly not just a river in Egypt.

And Dude Albie is just a Dude. Which has nothing to do with the discussion.

No denial on my behalf, I was merely looking ahead to how it is going to end. You seem to be in denial, like it is never going to end? I proposed a scenario, what is yours?

NOTHING going on now is thought to prevent the eventual exposure of us all, it is all just to delay the swamping of the resources. So let's move the discussion forward to how is it going to taper off? Or are we all going to stay in our bomb shelters for ever?

 

[Trebuchet]

You know, there's being cautious and then there's just being silly.
I had to go into town to pick up prescriptions, so I did some minor shopping (cat litter was on a good sale) as well. When I parked at the supermarket there was a lady nearby with a heavily loaded cart. She was in the process of spraying some sort of sanitizer on her rubber boots.,
When I came out half an hour or so later, she was still there, taking items out of her shopping one by one, wiping them down, and putting them in a different bag. She was of course wearing gloves.
I noticed four dozen eggs in her car.

 

[casebro]

Didn't I read that the CDC test is also a SARS test? How many died of sars, difference?

 

[JeanTate]

Thanks.

But who do you think is doing HMG's modelling? Also see here for contribution to UK model.

https://www.medrxiv.org/content/10.1101/2020.02.12.20022566v1

Somewhat orthogonal.

I am not aware of any definitive statements by HMG as to the actual models (including input parameter values) used to reach HMG's publicly stated conclusions that have been discussed these last page or three of this thread.

I'd love to be made aware of any such definitive statements.