Discussion thread IV - COVID-19 (new coronavirus)

[mscox]

An increasingly important statistic for monitoring countries and how they are handling the Covid-19 pandemic outbreak is the hospitalisation numbers, severity and duration of stay.

If severe and critical hospitalisations are on an exponential increase, along with confirmed cases, then inevitably the deaths will also begin to ramp up. Basically the aforementioned numbers and their rates of increase are the canary in the coal mine warning system.

It would be good if the Harvard Covid-19 dashboard could incorporate these stats.

 

[JJackson]

For those countries like the UK and US that seem to have largely skipped the testing and containment phase and consequently have little idea of the extent of community transmission the daily death figures are also useful. Pick a value for CFR and time from exposure to death (say 1% and 4 weeks - use whatever values you think likely) and 100 daily deaths. Then the implication is that 4 weeks ago 99*100 people were infected but did not die (or at least haven't yet) if you now look at the epidemic growth curve and see how much it has grown over the last 4 weeks in your country multiply this number by 9900 and you should get an approximate number for the new cases you should expect. While not a very statistically sound method what it does help with is reading the WHO sit-rep table data as for some countries the new deaths and new case numbers are proportionally very different. Why they are so different will depend on many factors but for countries at a similar stage of exponential growth they should be similar if the deaths are disproportionately high then there is likely to have been a lot of community transmission going on for a while which is not being counted. From today's sit-rep Germany (new cases 3140, new death 22), UK (1038, 56) the US failed to report any cases to WHO again yesterday so you would need to get data from another source.
If I get a high temp and dry cough here I am not asked to report it to anyone just self-isolate and then phone 111 only if I take a turn for the worse. Why I am not being asked to also fill in an on line form with DOB, basic symptoms, onset date and location I have no idea as this would be a valuable indicator of suspect cases and future hospital demand by area. Sadly my country is going to have a very hard time of it over the next month.

 

[mcphilbrick]

Facebook post -- Abnormal Symptoms: Loss of sense of taste and smell

https://bit.ly/3a96QvY

excerpt:

Thursday 3/19: Am I feeling better? Could it be? Just an early morning trick. Afternoon comes, more exhaustion, laid in a single position for like 5 hours playing a game on my phone. No appetite. No sense of smell or taste. No fever, no cough.

Friday 3/20: More energy than I’ve had all week. Still no appetite. Am down 6 pounds, trying foods just to see if I can taste anything. But otherwise, spirits are ok. Then I get the call about 6:30pm to let me know I have tested positive.

Why do I share this information… I never had a fever, I never had a cough, my shortness of breath was so hard to detect it felt like I was inventing it at times. My hallmark symptoms were fatigue, EXTREME fatigue, some congestion, body aches, and a headache. A random bout of diarrhea and vomiting on one of the days. On those little “Covid v Flu v Cold v Allergies” I basically flunked every single category. The identifiable symptoms are things I never experienced, but I tested positive. I’m so sorry there isn’t mass testing available. It sucks.

I am thankful for the people who have known they are positive and talked about their symptoms, because it’s really the only way I was able to pay any attention to mine.

 

[cartski]

“EXTREME fatigue, some congestion, body aches, and a headache. A random bout of diarrhea and vomiting on one of the days. On those little “Covid v Flu v Cold v Allergies” I basically flunked every single category. The identifiable symptoms are things I never experienced,”

Note sure I’d agree that there were no definitive symptoms of COVID from that quote.

But more importantly, IMO, is to re-write the differential self-diagnosis algorithm for “COVID v Flu v Cold v Allergies” And put that into an accessible online tool.

Many with a non-COVID virus are not self isolating. If that is a false negative self diagnosis....

 

[flatlander]

Anyone see any data yet on accuracy of the testing outside of China? I know there seems to be several different types of tests, but is there a standard so they can make sure it is as accurate as possible?

-I ask because in looking at the data output of the state lab in AZ it looks like 87-90% of those tested are testing negative and it would be nice to take that data and maybe look at other options that might help places that run into testing issues, etc.
-I started looking at the numbers because even with the opening up of testing from private labs the state lab has still been pushing for only testing cases that present at the- hospitals, so basically the more severe showing definite symptoms, etc.
-In AZ several commercial labs have stepped in and testing is ramped up and will ramp more next week. Reports of 2 day turn around and all doctors can send in samples to be tested at these labs. (this information is all based on news reports coming out of doctors as well as the ADHS reps.)

So when you look at the numbers and take what the state lab is reporting (which thankfully they report ruled out cases, positive cases, pending cases, and the number tested. When I look at the completed tests (ruled out and positives) you see that the negative cases range from 87-90% over the past week, so positives are 10-13%.

Two things I was wondering others opinions on. One there must be something else running around that is giving symptoms that isn't picked up in flu testing, etc. Ronan indicated maybe adenoviruses & rhinoviruses that I believe he said could be tested for. If that is easily tested for and already available couldn't that also be screened and just maybe it would alleviate testing capacity for COVID 19 (although increasing through put is the best answer, but if you can't do that ruling out everything else would be another alternative). If you say 85% of the tests are negative due to virus not present, test inaccuracies, etc. that is a lot of throughput that could be saved for actual cases right? My fear is that you use up all the resources and then you don't have any for real cases as well as monitoring those cases to closure (at some point you have to continue to monitor the positive cases until they test negative correct? and I believe it has been seen in many patients that this monitoring can take some time, over a month?)

My second thought is using these numbers to understand number of test being done in the commercial/private labs. Using AZ again, currently they don't report number tested, etc. However could you take the numbers from the state lab and extrapolate what the throughput has been on the commercial labs (I know tons of assumptions here but maybe get a rough number)? Of course the best would be actual numbers but if I did the back of the envelope calculation using AZ numbers from 3/14-3/21 the commercial positives were 72. If I use a positive percentage of 13% then it would show the labs have run 554 test in that time. Now go out to todays number total positives from commercial labs is 194. If I use that with the 13% it would be 1492 tests run. So in two days they jumped to a 939 tests performed. Do you think that is a fair extrapolation of the data, again realizing that there are many unknowns in the data.

Thoughts?

​

 

[longshots]

https://www.ncdhhs.gov/covid-19-case-count-nc

gotta say I have had some similar thoughts... NC only has 3.5% positive (297 out of 8438) --- so either folks are calling in to doctors and lying about their symptoms because the want to have a test, or something else is going around... of course right now most everyone in NC has a cough as the pollen is VERY HIGH...

one other thing is I believe we have made too big a deal out of testing at this point - if we had a massive amount of tests that could be quickly run it would make a difference in tracking and containment, but now that we are just about past the containment we might as well only test those who are so serious that they need hospitalization as it lets the doctors know they are not a flu or other respiratory disease candidate --- it is funny that reporters ask, "when can everyone get a test and then we know who is sick and can have them stay home"... uh... except for the person who is still incubating and will test negative for a few days more before developing COVID-19 --- so we need to test everyone, everyday for at least 14 days (if not more) ... hmmmmm.... 332 million Americans by 14 days... about 4.6 billion tests...

 

[flatlander]

A note on the smell symptom. They talked about this today in the WHO call. Seems they are working with people around the world to note symptoms, etc. The smell one was brought up specifically.

 

[Steffi]

40 mutations of COVID-19 found in Iceland (original Icelandic mutations) - and the virus has been imported from more counties than originally thought. One person was diagnosed with 2 types of virus, one original and a mutation, the subsequent transmissions were the mutated virus.

Austra, Italy, USA, Netherlands and now UK.

7 persons cought the virus on a football camp in UK

https://www.ruv.is/frett/tvenns-kona...t-i-sama-manni
https://www.information.dk/indland/2...nd?lst_artfrnt

The Lancet has asked deCode for an article, I would expect that before the weekend.
Shortage of sticks in Iceland now so testing is limited to "must know" for the moment.

 

[cartski]

Form MMWR on March 23rd: (can’t get link to work)

” SARS-CoV-2 RNA was identified on a variety of surfaces in cabins of both symptomatic and asymptomatic infected passengers up to 17 days after cabins were vacated on the Diamond Princess but before disinfection procedures had been conducted (Takuya Yamagishi, National Institute of Infectious Diseases, personal communication, 2020). Although these data cannot be used to determine whether transmission occurred from contaminated surfaces, further study of fomite transmission of SARS-CoV-2 aboard cruise ships is warranted.”

This is much different that the NEJM findings on fomite and aerosol.

Begs the question on what’s actually going on in other confined vehicle spaces with high usage and re-circulating air, like busses, trains, cars, mini-vans, etc.

 

[JimO]

One source indicated that the rtPCR test has a false negative rate of about 30%. Going forward they will start testing for antibodies to see what percentage of a given population has been exposed, but that is hindsight and won't help with preventing transmission.

 

[longshots]

https://www.cdc.gov/mmwr/volumes/69/wr/mm6912e3.htm?s_cid=mm6912e3_w

 

[sharon sanders]

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Craig Spencer MD MPH
@Craig_A_Spencer
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9h
Before you leave, you wipe EVERYTHING down. Your phone. Your badge. Your wallet. Your coffee mug. All of it. Drown it in bleach. Everything in a bag. Take no chances. Sure you got it all??? Wipe is down again. Can't be too careful.
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Craig Spencer MD MPH
@Craig_A_Spencer
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You walk out and take off your mask. You feel naked and exposed. It's still raining, but you want to walk home. Feels safer than the subway or bus, plus you need to decompress. The streets are empty. This feels nothing like what is happening inside. Maybe people don't know???
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Craig Spencer MD MPH
@Craig_A_Spencer
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You get home. You strip in the hallway (it's ok, your neighbors know what you do). Everything in a bag. Your wife tries to keep your toddler away, but she hasn't seen you in days, so it's really hard. Run to the shower. Rinse it all away. Never happier. Time for family.
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Craig Spencer MD MPH
@Craig_A_Spencer
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You reflect on the fact that it's really hard to understand how bad this is - and how bad its going to be - if all you see are empty streets. Hospitals are nearing capacity. We are running out of ventilators. Ambulance sirens don't stop.
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Craig Spencer MD MPH
@Craig_A_Spencer
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Everyone we see today was infected a week ago, or more. The numbers will undoubtedly skyrocket overnight, as they have every night the past few days. More will come to the ER. More will be stat notifications. More will be put on a ventilator.
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Craig Spencer MD MPH
@Craig_A_Spencer
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We were too late to stop this virus. Full stop. But we can slow it's spread. The virus can't infect those it never meets. Stay inside. Social distancing is the only thing that will save us now. I don't care as much about the economic impact as I do about our ability to save lives
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Craig Spencer MD MPH
@Craig_A_Spencer
You might hear people saying it isn't real. It is. You might hear people saying it isn't bad. It is. You might hear people saying it can't take you down. It can. I survived Ebola. I fear #COVIDー19. Do your part. Stay home. Stay safe. And every day I'll come to work for you
12:09 AM ? Mar 24, 2020?Twitter Web App
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[flatlander]

Hum, I was hoping that since there were tests being developed independently outside of China that the 30% would be lower(different eyes on the test, different pressures, etc.). I agree on the antibody testing, but they have been doing that study in China for a month now and still no data out of them. I think that will be important for a couple of reasons. It will show true spread, it will show if antibodies are developed in patients with known infections (all of them), and they can monitor and see if they last to prevent future reinfection. I don't remember seeing anything yet about a study around that and I believe there were several cases where they thought people had been reinfected.
We also have not seen any data on all of the treatment studies either. WHO said they were conducting over 200 treatment studies yet no data on any of it? I know they launched further studies through the solidarity trials, but there had to have been something that at least eliminates possibilities right?

This is where I remind myself that the virus has only been known to everyone for a couple of months now. But I see so much potential that could really help many around the world.

 

[flatlander]

I agree that testing everyone at this point is not the answer unless they can utilize the systems they have and increase throughput. Find better test methods, etc. Then they should be able to do more and ramp down as people are cleared out. It looks like there is a lot of development going on to update the test which is a good thing if the accuracy is not up there (which I fear).
I do however think that in many areas contact tracing, isolating, etc. is still a viable option. I only believe this because one of the WHO doctors shared a story about an outbreak in the Congo where they were doing 25,000 contact traces per day. If they can do that many a day North America and Europe could surely do even more. I fear however the medical leaders decided back in Jan. that this virus was like the flu and there was no use trying to contain it so they never pushed the set up and start of a system of tracing.
I also think they really should have set up centers for those who tested positive to be monitored more closely. This helps for several reasons. If the patient starts to get worse they can implement additional treatment right away and try and hold off or stop the escalation of the illness. In addition it also helps in keeping down the opportunities for it to spread further in households and communities. Unfortunately that doesn't even seem to be on the radar in the US and I assume it isn't in other countries either.

 

[flatlander]

Very concerning regardless of how the passengers got the virus. I would be curious however if the temp. control of the cabins was maintained once they were vacated and what temp they would have been at? If they were stagnant at a low temp then I would assume (I know not good science) that the virus would last longer. Especially if there was no cleaning going on.

Just a thought for future transportation solutions, maybe looking into UV-C lighting? I don't know a whole lot about the technology but the little I have read it seems like a solution they are using in hospitals to help cut down on virus spreading.

 

[sharon sanders]

Good morning everyone.

You know what to do now to keep everyone safe.

If you are evacuating out of the US tri-state area please self quarantine for 14 days at your new place.

Sign up for benefits. Call landlord/mortgage co.

Watch your local news & public health dept.

--------------------------------------------------


FluTrackers.com
@FluTrackers
If you guys find any typos in my tweets, please let me know.

I am on the east coast of the U.S. and as the night wears on......

Thanks to all of our followers!

We are all a team....ya know....

 

[sharon sanders]

I wanted to make a statement about our email policy.

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This is still our policy. In fact, we are known for our discretion. We protect our sources 150%.

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We are going through some hard times and just know that your FluTrackers team is here.

We aren't going anywhere.

Take care.

 

[Shiloh]

Doctors And Nurses Say More People Are Dying Of COVID-19 In The US Than We Know: https://www.buzzfeednews.com/article/nidhiprakash/coronavirus-update-dead-covid19-doctors-hospitals

...two of the hardest-hit areas in the nation — New York City and Los Angeles County — released guidance earlier this week encouraging doctors not to test patients unless they think the test will significantly change their course of treatment. That means that potentially more people in both places could be admitted to hospitals with severe respiratory symptoms and recover — or die — and not be registered as a coronavirus case...

...Doctors and nurses working in several hospitals around the country, who spoke with BuzzFeed News on the condition of not being named out of fear of repercussions, said that the official counts of COVID-19 related deaths are not comprehensive for three main reasons: a lack of tests and protective equipment means not everyone who contracted or dies of COVID-19 is diagnosed; overwhelmed hospitals may be running behind on reporting the numbers to state and county authorities; and some hospitals reporting their totals on a daily basis say they’re not being reflected promptly in county and state reports....

...What it does mean is that we don’t have a fully accurate picture of how widespread COVID-19 deaths are, or where they’re happening at the highest rates. While staff at hospitals prioritize treating patients and saving lives — testing doesn’t usually change the course of treatment for COVID-19 — the lack of reliable numbers becomes a real problem when it comes to understanding the true scope of the crisis, and where resources are most urgently needed, according to doctors and disaster response experts...

 

[Gert van der Hoek]

Devi Sridhar@devisridhar

We will be stuck in an endless cycle of lockdown/release for next 18 months, if we do not start mass testing, tracing, & isolating those who are carriers of the virus while pursuing rapid research for antiviral treatment or vaccine. This is the message the public needs to hear.


Professor & Chair of Global Public Health,
@EdinburghUni
Medical School. Director of
@GlobalHealthGP
. Health governance, financing, policy, systems & security.

Devi Lalita Sridhar (born 1984) is a Professor and Chair of Global Public Health at the University of Edinburgh. Her research considers the effectiveness of public health interventions and how to improve developmental assistance for health.

 

[gsgs]

they reported ~300 weekly extra deaths from all causes in Bergamo-city (pop=122K). Assume just 6 weeks at this level and 1.6% of the entire
population died. Now they have 45 weekly deaths normally --> 2% of the population dying per year vs. 1% in USA, so presumably
many old or sick people, so divide by 2 --> still 2.5M deaths from this wave in USA (all causes, if it goes as in Bergamo).
https://www.ecodibergamo.it/stories...leco-lancia-unindagine-nei-comuni_1346651_11/