Coronavirus Discussion

[trystan]

4 minutes ago, Lagie said:

This is a very interesting read -

https://www.ctvnews.ca/mobile/health/great-medical-mystery-as-covid-19-long-haulers-complain-of-months-long-symptoms-1.4981669

yeah, i've seen articles like that too.  scary stuff.

 

but maybe my brother randomly had the flu? dunno.

[Astreya]

47 minutes ago, trystan said:

 just last week, we went to the doctor for an antibody test.... and it was negative!  i mean, it's good he didn't have it, but what the heck was that at the end of march??

There are quite some problems with antibody tests. Not all of them are really specific and/or sensitive enough. Here's an article that details the problems a bit: https://www.businessinsider.com/equation-shows-risk-of-coronavirus-antibody-testing-sensitivity-specificity-2020-5?r=DE&IR=T

 

Edited June 18, 2020 by Astreya

[trystan]

so maybe he did have it and the test didn't catch it?

 

i can't read the article - says my ad blockers are blocking it, and i know they're not. *sigh*

[Astreya]

@trystan

Spoiler

Some back-of-the-envelope math reveals the risk in relying on even the best antibody tests to tell us who's had the coronavirus
Andy Kiersz and Blake Dodge May 14, 2020, 6:32 PM

• Tests for diseases, like the serological tests for antibodies to the novel coronavirus, aren't perfect.
• They can create false positives or negatives, and their predictive value is tied to the broader population.
• Even tests with good sensitivity scores can make mistakes 50% of the time or more.

Medical tests, like the blood tests that look for antibodies to the novel coronavirus, aren't perfect.

 

Sometimes, you end up with a false negative: You actually did have the coronavirus and your immune system developed antibodies to the virus, but the test says you don't have those antibodies. Other times, you end up with a false positive: The test results say you have antibodies to the coronavirus, but you don't actually have them.

 

Those false positives can be particularly dangerous if you're relying on the presence of antibodies to hopefully have some protection from the coronavirus and resume normal life. Scientists are still uncertain about how much protection against future infection people with antibodies have, or how long that protection lasts for.

 

Still, some countries have floated the idea of an "immunity passport" for people who have already gone through the coronavirus and presumably have some protection against reinfection, at least temporarily. In other places such as New York, government officials are using antibody tests to get a sense of how many people have had the coronavirus.

 

In either case, if there are a lot of false positives, you could end up with misleading results.

 

While each test has its own performance characteristics, some simple math can help reveal how accurate it is when used in a big population of people.

 

The positive predictive value of a medical test, like the blood tests for antibodies to the novel coronavirus, tells you the probability of actually having a disease (or antibodies) if you test positive for it.

 

'It's not like something you can take to the bank'

 

Even with a test that correctly identifies antibodies in coronavirus-positive people more than 90% of the time, and no antibodies in coronavirus-negative people just as often, if you have a population where the actual prevalence of the disease is very low, the test can produce false results for half of those who take it, according to Dr. Andrew Noymer, a public health associate professor at the University of California Irvine.

 

"Even when you log on to your healthcare portal, and it says, 'Congratulations, you are positive for Covid antibodies,' meaning you ostensibly have some immunity, it's not like something you can take to the bank," Noymer said in an interview.

 

One way to increase the chance of accurate results is to make use of multiple tests or pieces of information. For instance, if an individual who previously tested positive for the coronavirus itself later gets an antibody test, you'd expect that test to show that they have antibodies. If it doesn't, you're likely to be suspicious of the results.

 

But if the antibody tests are used to screen large groups of people, we won't have other pieces of information to use in many cases.

 

Calculating how often a test gives you accurate results

 

To calculate the positive predictive value, we need three pieces of information: the true positive rate, or the probability the test will correctly say that you have antibodies if you actually do (a metric called "sensitivity"); the true negative rate, or the probability that the test will correctly say that you don't have antibodies if you haven't been infected (called "specificity"); and the underlying share of people in the population that actually have the disease.

 

The positive predictive value is, at its heart, just the share of people who who have coronavirus antibodies and test positive, out of everyone who tested positive.

 

The total number of people who have tested positive can be broken down into people who really have antibodies (true positives), and people who don't (false positives).

 

We can figure out the number of true positives and false positives based on our knowledge of the performance of the test, along with the number of people who actually have the disease.

 

This means that the usefulness of our test in figuring out how many people have antibodies depends on two things: how good the test is, and how many people in the population actually have antibodies.

 

If the underlying condition—in this case, antibodies—is rare in the population, even a very good test can lead to lots of false positives, as the number of people who don't have the disease could far outweigh the number of people who do.

 

"If I have high sensitivity and high specificity, my positive predictive value is still going to be lower when the prevalence for that disease is low in the population," said Dr. Puneet Souda, managing director of life science tools and diagnostics at SVB Leerink, in an interview. "But if the prevalence is high, then my positive predictive value is going to be higher, as long as my sensitivities and specificities are high."

 

Underlying prevalence matters

 

Suppose that we have 1,000 people in a town, and an 8% prevalence rate. That means, of the 1,000 people, 80 have been infected by the coronavirus and developed antibodies.

 

Let's also suppose that our hypothetical test has both a sensitivity and specificity of 95%, which sounds pretty good.

That is, in 95% of patients who have antibodies, it'll detect them, and in 95% of patients who don't have antibodies, it'll correctly say they haven't been exposed.

 

Let's say we test everyone in our town, and calculate the number of true positives and false positives. Our 95% sensitivity means that 95% of the 80 people who actually have antibodies will come back as true positives, giving us 76 positive results from that group.

But our 95% specificity means that we'll have a 5% false positive rate. In other words, 5% of the people in our town who don't have antibodies will wrongly be told that they in fact do have them.

 

Since only 80 people actually do have antibodies in our town, we know that the other 920 all don't.

 

But our 5% false positive rate means that 46 people out of that group of 920 will be wrongly told that they have antibodies.

Putting together our 76 true positives and our 46 false positives, we have a total of 122 positive results. But this means that we end up with a positive predictive value of just 76/122, or 62%.

 

A bit better than a coin toss

 

So if you're a citizen of our town, and the test says that you have antibodies, the chance that you really do is just 62%. 

That's a bit better than a coin toss, but not by much.

 

And if you're relying on a positive test for reassurance that you're safe from infection and can return to work, it may not give quite the level of security you're hoping for.

 

Of course, these numbers are just hypothetical, and one big unanswered question is how many people have actually had the coronavirus.

An early survey of New York City residents in April suggested that around 20% of the population had been infected and developed antibodies, according to Gov. Andrew Cuomo.

 

If we do a similar calculation as above, with a hypothetical test that has a 95% sensitivity and specificity, but assume a 20% prevalence rate, the positive predictive value jumps to a much better 83%. Still far from perfect, but a big step up from our near coin-toss. 

New York is using a test from BioReference with a listed sensitivity of 91.2% and specificity of 97.3% for some of the screenings.

 

To see the relationship between sensitivity, specificity, and prevalence, this chart illustrates what positive predictive value you get at different underlying shares of the population who actually have coronavirus antibodies for the above hypothetical test, and for two actually available tests.

 

One test, from BioReference, has a listed sensitivity of 91.2% and specificity of 97.3%, and a test from Abbott Laboratories has a sensitivity of 100% and a specificity of 99%. Even the very low false positive rate of 1% for the latter still means that a positive test isn't a slam dunk if the underlying prevalence is very low.

 

Source: https://www.businessinsider.com/equation-shows-risk-of-coronavirus-antibody-testing-sensitivity-specificity-2020-5?r=DE&IR=T

 

[trystan]

thanks @Astreya! interesting!

  

the thing is, my brother and his son didn't get tested, but they did check in with their state health department every few days or so with updates. SO - they could have had it, but they didn't get tested.  there's just too many variables there.  i'm going to go with "who knows?" at this point.  they're healthy now, so that's a win in my book.

[b64277]

8 hours ago, casprrr said:

Already got my results, negative for COVID-19. 😀

YAY thats great to hear!!!  

[olympe]

14 hours ago, casprrr said:

Already got my results, negative for COVID-19. 😀

Congrats!  

[Astreya]

Daily update for Oberhausen, NRW, Germany:

 

As of today, Thursday, June 18, 08:00 GMT+2,  my home town (population 211 000) has 5 active cases, while 253 people have recovered. All in all there have been 269 people who suffered from Covid-19 since the beginning of the pandemic. The number of newly infected people per 100 000 citizens in the last 7 days is 0.0.

 

Currently 3 persons are treated in hospitals, none of them in intensive care. 11 persons sadly died. 19 persons are currently quarantined. All in all there have been 12 095 Covid-19 tests in Oberhausen so far.

 

Source: https://www.oberhausen.de/de/index/rathaus/verwaltung/umwelt-gesundheit-und-mobilitat/gesundheit/aktuelle_informationen/informationen_zum_coronavirus/aktuelle_meldungen.php

 

That means for two days we had no additional Covid-19 infection. Astonishing, considering that the overall numbers for daily infections in Germany are rising again.

[purplehaze]

Recovering from Covid-19 can be an extended process. Some facilities are opening new rehab units just for these patients, others are handling them along with regular rehab. The following article paints a pretty scary picture of what recovery is like. This disease is not over when you can breathe on your own again and are clear of the virus. I did not copy the entire article, as it is long, but just some of the highlights. The article itself describes the actual experience of a couple of Covid-19 patients, which are interesting to read if you have the time.

...For patients, rehab can be grueling, physically and emotionally, but it rebuilds skills and confidence to manage the recovery from the coronavirus on their own.

“We really saw that it was a huge need for patients that needed intensive, interdisciplinary care in order to improve their endurance, improve their swallowing, improve their cognition, improve their ability to take care of themselves — dress themselves, bathe themselves — and return home,” said Lori Patria, director of therapy services at the University of Maryland Rehabilitation and Orthopedic Institute. “That’s where we all want to go. That’s always the gold standard: returning home.”

COVID-19 does its worst damage on aging patients and those with underlying conditions. They already may take longer to recover from illnesses.

“It’s a false narrative to assume that people can leave the hospital … and they can go back home and have a quick and successful recovery,” said Dana Bradley, dean of the Erikson School for Aging Studies at the University of Maryland, Baltimore County. “That’s why rehab centers play such an important role in the treatment plan and getting people that have had COVID back to normal. … Sometimes, this recovery can take a long time.”

Rehabbing COVID patients isn’t so different from rehabbing patients with, say, acute respiratory distress syndrome, according to Dr. Michael Dimyan, director of spasticity management and neurorehabilitation practice for the University of Maryland’s rehabilitation institute.

Both illnesses debilitate lungs and can weaken people “physically, emotionally, cognitively, and also create depression and post-traumatic stress.”

The difference, he said, “is that it usually doesn’t affect large populations all at once, and usually people are hospitalized for maybe a week at a time and their level of disability is not as severe.”

“Now we have this sudden situation where a large number of people are affected and they’re affected more severely because they’re being hospitalized for two, three weeks at a time, intubated and sedated … so they’re much more impaired.”

At his center, 134 rehabilitation beds are divided into four units. Staff converted the stroke unit for COVID rehab.

Those patients could have respiratory problems, swallowing deficits because of intubation, cognitive issues because of lack of oxygen early on, plus general weakness, Patria said. Leaders there saw a match for their team of attending physicians, rehab nurses, occupational therapists, speech therapists, physical therapists and recreational therapists to fill an unmet need.

https://www.baltimoresun.com/coronavirus/bs-md-coronavirus-rehab-20200618-n2ft3tiukffkjb3j35ue73pufa-story.html

[olympe]

Another one of my hometown's nursery homes got hit by covid. It's part of a bigger complex (including several separate nursing homes - one for people with dementia (Haus Eiche/house oak), one for people needing intensive care including people on ventilators (Haus Ahorn = house maple), one for general care, but also palliative care (Haus Buche = house beech) and another one that is more like a shared house for (mostly fit) senior citizens (Haus Magnolie = house magnolia). On the same grounds you can find our local hospital that specializes mostly on pulmonology where all local covid-tests are taken. And, yes, there's also a nursing school that, until last year, solely specialized on nursing for the elderly.

 

Of course, it had to be house maple (intensive care, care for people needing oxygen, people in persistent vegetative state) that got hit - which is probably the worst case scenario. Like, seriously. It's where the most vulnerable people are. Heck, I even learned together with some people who work in that house. And from the things they used to tell, people in that house take hygiene really, really seriously (as they should). So that's likely not what's to blame for the outbreak.

[Lagie]

2 hours ago, AngelsSin said:

It's looking bad for Florida, numbers keep rising in my state. In just one day we have over 3,200 new cases. They are saying we may be the next epicenter. In my county just last week we only saw 10-12 new cases less than a week later we are now at 100 new cases a day and I know other counties goes have it much worse. It doesn't help that our governor continues to be stupid. He won't even consider slowing things down. He just wants to push through it. And I have to get back into the workforce during this spike. 😲 

Source: https://www.usatoday.com/story/news/nation/2020/06/17/florida-governor-ron-desantis-keeping-state-open-coronavirus-cases-rises/3210417001/

 

Also less than 25% of ICU beds available.

Source: https://www.newsweek.com/multiple-florida-hospitals-run-out-icu-beds-coronavirus-cases-spike-1511934

 

You have a group of 16 friends who decide to for the first time to go out to a bar to celebrate a b-day and every single one of them end up with COVID.

Source: https://www.ajc.com/news/friends-florida-bar-and-all-later-test-positive-for-covid/Vmj5SxFOiR6KWfyEFhJNEM/

 

At least make masks mandatory in public. I mean really this is ridiculous.

Wow, that IS scary.

I saw that about the friends - and a bunch of the bar staff have it, too.

"We opened too soon," they say. Ya, think?

 

I had a near scuffle with two customers today who tried to come into my shop maskless. It is LAW here that you wear a mask if you are not in your house, or in your car, so we stuck to our guns. One lady begrudgingly donned hers, but said four doctors say masks don't do any good. The other lady swore she didn't have one, then spent the next fifteen minutes or so loudly denouncing the whole mask thing and us and the law and anything else that came to  mind. It's exhausting, having to keep track of so many things (masks, numbers in the shop, social distancing) for a full four hours.

[Classycal]

Sounds like they were covidiots Lagie.

[Astreya]

Daily update for Oberhausen, NRW, Germany:

 

As of today, Friday, June 19, 08:00 GMT+2,  my home town (population 211 000) has 5 active cases, while 254 people have recovered. All in all there have been 270 people who suffered from Covid-19 since the beginning of the pandemic. The number of newly infected people per 100 000 citizens in the last 7 days is 0.5.

 

Currently 3 persons are treated in hospitals, none of them in intensive care. 11 persons sadly died. 25 persons are currently quarantined. All in all there have been 12 251 Covid-19 tests in Oberhausen so far.

 

Source: https://www.oberhausen.de/de/index/rathaus/verwaltung/umwelt-gesundheit-und-mobilitat/gesundheit/aktuelle_informationen/informationen_zum_coronavirus/aktuelle_meldungen.php

 

Today we got one new infection again. The fact that there have been three persons in hospital without any change for quite a while now shows how long Covid-19 obviously can take for some persons (unless one person got out and another one in, of course).

[Lagie]

7 hours ago, Classycal said:

Sounds like they were covidiots Lagie.

Indeed!

 

3 hours ago, Astreya said:

Today we got one new infection again. The fact that there have been three persons in hospital without any change for quite a while now shows how long Covid-19 obviously can take for some persons (unless one person got out and another one in, of course).

It does seem to take a long time. One fellow on the news a week or so ago had been in hospital for 76 days. 

Interesting that your area and our country have the same number of deaths (ours is high for our case count but has remained stable since April).

[Astreya]

@Lagie

How many people live in the area for which your Covid-19 infections and deaths are counted? My numbers always refer to my home town, which is an independent municipality (="kreisfreie Stadt") with an own Gesundheitsamt (local health office) within the state Northrhine-Westfalia (NRW), which is the most populous state of Germany with about 18 million citizens.

 

By the way, out of curiosity I calculated the average age of the people who died from/with Covid-19 in Oberhausen - here the youngest casualty was 81 years of age and the oldest 93 with an average of 88.6 years. The city officials point out that the RKI does not discern whether the fatalities were actually caused by SARS-CoV-2 or if the persons died from other causes while simultaneously being infected with the virus.

[olympe]

Well, it certainly looks like Germany is getting hit by a 2nd wave starting this week. It was to be expected.  Too much too soon.

 

That being said, today Brazil surpassed 1 million cases. And yesterday, they broke the record for "most new cases per day per country", and today they broke it again. They're close to 50 k new cases today, and will probably surpass that particular benchmark before tomorrow.

[Astreya]

@olympe

The big problem are the areas where people have the opportunity to gather in masses - and I fear with Summer hitting big from Monday on. more people will flock to leisure areas in masses while completely ignoring all safety measures like distancing and wearing masks.

 

On the other hand, I'm a bit astonished that in my area people really diligently wear masks while shopping (at least in the places where I went). The town always reports how many cases there are when the police or "Ordnungamt" (a civilian regulatory agency that supports the police, but has less authorities) have to warn and/or fine people for violating the corona measures, and it seems there are extremely few cases here: https://www.oberhausen.de/de/index/rathaus/verwaltung/umwelt-gesundheit-und-mobilitat/gesundheit/aktuelle_informationen/informationen_zum_coronavirus/aktuelle_meldungen.php

 

In another area in NRW (Rheda-Wiedenbrück in the Gütersloh area), there has been a large outbreak in the huge Tönnies meat plant where by now about 803 people have been tested positive for Covid-19. As a result, NRW Prime Minister Armin Laschet threatens a new lockdown. Additionally, all workers in all meat plants in the whole state NRW will be tested again.

Source: https://www.ruhr24.de/nrw/coronavirus-aktuell-nrw-ticker-heute-corona-app-toennies-guetersloh-laschet-live-infektionen-zr-13798124.html

 

Edited June 19, 2020 by Astreya

[Lagie]

11 hours ago, Astreya said:

@Lagie

How many people live in the area for which your Covid-19 infections and deaths are counted? My numbers always refer to my home town, which is an independent municipality (="kreisfreie Stadt") with an own Gesundheitsamt (local health office) within the state Northrhine-Westfalia (NRW), which is the most populous state of Germany with about 18 million citizens.

 

By the way, out of curiosity I calculated the average age of the people who died from/with Covid-19 in Oberhausen - here the youngest casualty was 81 years of age and the oldest 93 with an average of 88.6 years. The city officials point out that the RKI does not discern whether the fatalities were actually caused by SARS-CoV-2 or if the persons died from other causes while simultaneously being infected with the virus.

This is for our entire country. We have 400,000 people in total in the entire country.

 

2 hours ago, olympe said:

Well, it certainly looks like Germany is getting hit by a 2nd wave starting this week. It was to be expected.  Too much too soon.

 

That being said, today Brazil surpassed 1 million cases. And yesterday, they broke the record for "most new cases per day per country", and today they broke it again. They're close to 50 k new cases today, and will probably surpass that particular benchmark before tomorrow.

So sorry to hear that about Germany. My brother and his family live outside Frankfurt.

And wow, to Brazil.

 

Then there's this scary info:

Five workers at the National Oceanic and Atmospheric Administration’s “Hurricane Hunter” airbase in Lakeland have come down with the virus, just as an especially active storm season is kicking off in Florida.

Source: https://newrepublic.com/article/158215/florida-coronavirus-cases-ron-desantis-leads-state-morgue

Edited June 20, 2020 by Lagie

[Astreya]

18 minutes ago, Lagie said:

This is for our entire country. We have 400,000 people in total in the entire country.

Ah, thank you! I wasn't sure whether it was maybe for the main island or stuff, but entire country sure makes the most sense when your population is around that number.

[olympe]

So, Brazil's numbers got "corrected" - the new cases for the day before yesterday are (roughly) halved now. Not gonna lie, this doesn't exactly incrrease their credibility.

[Astreya]

@olympe

One scientist in Florida was fired for refusing to manipulate the Covid-19 case numbers, too. At least she set up a site with the proper numbers herself:https://www.theguardian.com/us-news/2020/jun/15/florida-coronavirus-cases-counter-rebekah-jones-fired-scientist

 

While I'm at it...

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

Daily update for Oberhausen, NRW, Germany:

 

As of today, Saturday, June 20, 09:00 GMT+2,  my home town (population 211 000) has 8 active cases, while 254 people have recovered. All in all there have been 273 people who suffered from Covid-19 since the beginning of the pandemic. The number of newly infected people per 100 000 citizens in the last 7 days is 1.9.

 

Currently 2 persons are treated in hospitals, none of them in intensive care. 11 persons sadly died. 30 persons are currently quarantined. All in all there have been 12 400 Covid-19 tests in Oberhausen so far.

 

Source: https://www.oberhausen.de/de/index/rathaus/verwaltung/umwelt-gesundheit-und-mobilitat/gesundheit/aktuelle_informationen/informationen_zum_coronavirus/aktuelle_meldungen.php

 

Edited June 20, 2020 by Astreya

[Awdz]

16 minutes ago, Astreya said:

@olympe

One scientist in Florida was fired for refusing to manipulate the Covid-19 case numbers, too. At least she set up a site with the proper numbers herself:https://www.theguardian.com/us-news/2020/jun/15/florida-coronavirus-cases-counter-rebekah-jones-fired-scientist

 

 

That kind of thing makes me grateful for the transparency & data-driven approach our governor took. So proud that the curve for NYS reversed - and even more glad that the monitoring continues to limit recurrence of a surge rather than assuming once & done. I wish everywhere had as reasoned an approach, as it is heartbreaking to see reports of the pandemic worsening in so many places. So many deaths could have been prevented...*prays for those who lost loved ones to pandemic*

[Daydreamer09]

@Astreya

You mentioned that new drug that's showing promising results, well Sci Show on YouTube actually put out a video with more info on it out. I haven't watched the whole thing yet myself. This channels been really good about scientific updates on covid19 research.

 

 

[Astreya]

@Daydreamer09

Thanks for linking this!

 

For those who can understand German, here are extensive 1 hour long interviews (including transcripts and links to the studies) with the leading German virologist Prof.Dr.Christian Drosten from the Charité in Berlin (he was in the team that developed the first working Covid-19 PCR test in Mid-January) as podcasts. He's talking about the most recent studies, bleeding edge research, and answers questions from the  public every Tuesday in the NDR:  

https://www.ndr.de/nachrichten/info/Corona-Podcast-Alle-Folgen-in-der-Uebersicht,podcastcoronavirus134.html

 

Edited June 20, 2020 by Astreya

[trystan]

9 hours ago, olympe said:

So, Brazil's numbers got "corrected" - the new cases for the day before yesterday are (roughly) halved now. Not gonna lie, this doesn't exactly incrrease their credibility.

welcome to a country run by another science-denier.  i'm sure the US's numbers are way more than they really are.  it's kinda scary.

 

i also saw it's such a very American thing - we're so over it, we're tired of lockdown, so covid is over now too, right? just because we're "done with it" doesn't mean it's done with us.