• Recently Browsing   0 members

    No registered users viewing this page.

Recommended Posts

My area of research isn't even tangential to COVID, I just like to read broadly and sometimes it comes in handy. The number of times I have surprised colleagues with "I remember reading something about [phenomenon] in [unrelated field] do you think that might apply here?" and had that end up being the solution isn't trivial. My recreational reading usually has nothing to do with my current area but it pays to be widely read.

  • Like 2

Share this post


Link to post
Share on other sites
3 hours ago, chemgeek said:

 

From several papers I have read, this being one (published in Allergy): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7300712/

 

Thank you, this looks interesting and I will read this later.

 

1 hour ago, analoggirl said:

Oh! And it might be that people with asthma and other respiratory illness/in the risk group (and their loved ones) are significantly more cautious than those that do not have such illnesses.

 

That would only impact the rate of asthmatics who are exposed/infected though, not how severe their symptoms are, no? And yes, everyone I know who has asthma, including myself, is absolutely paranoid about avoiding exposure.

  • Like 2

Share this post


Link to post
Share on other sites
5 hours ago, chemgeek said:

(3/275 hospitalized patients in the cited study vs 12-16% of general population -

 

SF, you are right, but that is how I read this comparison

 

1,09% of hospitalized patients are asthmatics

 

12-16% of the general population are asthmatics

 

If the amount of asthmatics exposed/infected is lower, it it follows that there are less that CAN get severe enough symptoms to be hospitalised

 

So we need numbers on how many *infected* asthmatics got hospitalised

 

But maybe I am reading that/thinking wrong?   

  • Like 3

Share this post


Link to post
Share on other sites

That's fair. & There are a few studies that suggest there's no difference between asthmatics & nonasthmatics in terms of hospitalization rate (though aside from the one I cited and a few out of China I have seen any suggesting the same about death rate, nor have I been able to find any stats on whether asthmatics as a group have a lower infection rate). The studies I have read do seem to suggest that of those with severe enough to be hospitalized covid-19, asthmatics are less likely to die if their airway obstruction is reversible (ie there's no permanent obstruction of their lungs.) and that asthmatics are overall less likely to be admitted for severe covid

 

But even that isn't certain enough that I want to stake my life on it.

  • Like 1
  • Thanks 1

Share this post


Link to post
Share on other sites

Glad to hear that my reasoning is fair. 

 

Either way, the positive interpretation of the studies are a lot better to think about IF you get infected, bc that helps with recovery right? :) 

 

Otherwise it is always better to just be safe always yeah haha

 

Also, 100% agree that broadening your horizon almost always helps you be better in your field

  • Like 1

Share this post


Link to post
Share on other sites

So unrelated to covid - anyone have XPs with pulled quads? 

 

I pulled a quad yesterday (ow) and it's not showing Big Scary signs of severe pull (no pop, can use the muscle, don't have an obvious lump or deformation of the muscle, etc). I am showing a few signs of a moderate pull (mild swelling, muscle weaknesses, spasms for about 1.5 hours after initial injury) Given I have pulled muscles before and know first aid for it and that COVID exists and I am avoiding doctor's offices on principle ATM, I am intending to self-treat at home unless it gets worse or isn't getting starting to get better in a week. That it's a quad is unfortunate because it's way harder to rest pulled leg muscles than a shoulder, pec, or bicep. 

 

Curious of your experience and what bad ideas an overly enthusiastic type like myself who tends to push too much too quick should avoid. I assume squats and star lunges are a no for a week ish for example. :P

Share this post


Link to post
Share on other sites

No quad experience, but as I said elsewhere, I usually find that the first day or two, there's a lot of trauma to the area that makes it all ambiguous, and the best approach is to just get the inflammation down with a ton of ice and rest for a day or two. Then you have a better idea what you're really dealing with.

  • Like 1

Share this post


Link to post
Share on other sites

Long time no post! Which is not bad of course. For me, it is business as usual, trying to keep everyone around me calm and feel supported, and give my common sense enough information to work with without making myself overanalyse everything...

 

However, I did want to share this information/open letter post, that seems properly sourced (except the links that give you a 404 error...? but it seems that the information can be found elsewhere from reliable sources, as far as I can judge?)

 

and worded in a balanced way:

 

https://docs4opendebate.be/en/open-letter/

 

I have found Reuters to be helpful with doing research on the "FB news", and so also in the claims that have been going around about what the maker of the PCR tests has said about them:

 

https://in.reuters.com/article/uk-factcheck-pcr/fact-check-inventor-of-method-used-to-test-for-covid-19-didnt-say-it-cant-be-used-in-virus-detection-idUSKBN24420X

 

Also, there is this related video that I don't know what to make of.

 

No idea if anyone else finds these useful in any way or if they are reliable though. I have no idea how to present such information/research in a better way :)

 

For me, it is simply useful for the sake of seeing people looking for/finding ways to keep the public debate as open as possible, assuming the letter is really from these medical professionals. (Oh and I have no direct source to know if there is really censorship going on where they work like the letter suggests. Ahhh so many disclaimers are necessary when you want to share something without making it sound you are making a claim :D ) Anyway, any thoughts from people that understand more than I do? 

 

EDIT:

 

Hmmm, I had not gotten to the part where they say that transfer of the virus via objects has not been scientifically proven.

 

I have been taught to wash my hands after touching cash all my life :D Except if a grown up has washed e.g. coins with soap well. Maybe they are afraid people will think the virus (an air way virus! not blood transferred that could enter through the blood stream when having a microtear in your skin or so) can enter your body via your skin.

 

After all, I recently learnt that people, when asked if the summer time/winter time switch would stop, they would want to go to a permanent Summer Time or Winter Time, 

 

they said things like "Oh Summer time, because then I would not have to wear jackets any more" or "summer time because we are happy people!" 

 

But there is some stuff to think about like case chemistry & the total health picture of people, however, I do think we should have always kept proper distance and hygene but that's my inner "personal space" and minor germophobia talking. Not opinion about what the government policy should be 🤔

 

EDIT2: I forgot to say I did find the signatories tab, with numbers which I assume are their numbers for the register of medical profs or so, and I also have noted there is a significant number of psychologists on the list :) Thanks Hatter!)

  • Like 1

Share this post


Link to post
Share on other sites
On 11/1/2020 at 9:50 AM, Aθena said:

No idea if anyone else finds these useful in any way or if they are reliable though. I have no idea how to present such information/research in a better way :)

 

For me, it is simply useful for the sake of seeing people looking for/finding ways to keep the public debate as open as possible, assuming the letter is really from these medical professionals. (Oh and I have no direct source to know if there is really censorship going on where they work like the letter suggests. Ahhh so many disclaimers are necessary when you want to share something without making it sound you are making a claim :D ) Anyway, any thoughts from people that understand more than I do? 

 

I am not an epidemiologist, but I am a molecular biologist who works with clinical labs that do COVID-19 testing. 

 

My personal take on the Open letter from medical doctors and health professionals to all Belgian authorities and all Belgian media is that they are ignoring the data that does not support their case. Several of their statements are outright lies.

  • They claim that COVID-19 is no worse than the seasonal flu with a death rate of 0.1-0.5%. Maybe that is true in Belgium, but it is not true in other places. In the US the death rate varies substantially by county. In my state the overall death rate is about 3%. My county is lower because we have the university medical school hospital and two other hospitals, and the local government has mandated masks and social distancing. Some of the highest death rates are in rural areas without access to hospital care. Death rates in major metropolitan areas vary. Chicago is running 2-3%. New York is 6-8%, while New Jersey is 7-11%. Even the lowest rates are 10x worse than the seasonal flu.                                                                          
  • They claim that there are good treatments for people who get sick. It is true that treatments have gotten better as doctors have compared notes on what works. That has clearly lowered the death rate from what it was last spring. It is not true that the treatments work for everyone, or that they prevent long term damage to the patient's body. I'm taking the US as a worst case scenario here. We are still seeing hospitals at or beyond capacity and hundreds of people dying every day.                                                                                                  
  • They imply that asymptomatic people are neither going to become sick nor infect others. Recent data does not support that assumption. See Asymptomatic SARS Coronavirus 2 infection: Invisible yet invincible at https://doi.org/10.1016/j.ijid.2020.08.076 for a current review. They look at data on virus levels in the nasal passages of asymptomatic and presymptomatic people. It is abundantly clear that people are contagious before they show symptoms. So far as we know now, people who do not go on to show obvious symptoms are also contagious. In my area, it looks like about 40% of people being tested have no symptoms (yet). We don't know how many of those people will get sick later.

How tests are done and what they show

 

There are many applications of the Polymerase Chain Reaction (PCR) that show different things and have different limitations. The classic PCR test is to show if a gene is present or not. Do you have the BRCA2 gene that is associated with breast cancer? That is a clear yes/no test.

 

Whose DNA is in this blood spot at a crime scene? The tests for forensic evidence look at several (16-25) regions of DNA that are highly variable between individuals. Genes are highly conserved between people, the other regions of the chromosome are more diverse. The more regions included in the test, the less chance that two people would randomly match. The challenge with forensic evidence is getting enough sample to get a full set of answers in the test. The answer is still yes or no, or maybe we just can't see enough to tell.

 

The criticism raised about PCR being a qualitative test is true. The scientific community recognized this 20 years ago, and developed quantitative PCR (qPCR) to meet the need for a test that measures not just what DNA is present, but also how much. The current tests for COVID-19 use RT-qPCR, not PCR.

 

The "RT" part of the test stands for Reverse Transcription. Some viruses are packaged DNA, others are packaged RNA. Corona viruses are made of RNA. When they get into cells the RNA can be immediately transcribed into proteins. One of those proteins is a reverse transcriptase that makes a DNA copy of the viral RNA, which acts as the template for making many more RNA copies. The RT used in RT-qPCR comes from a different virus (usually M-MLV), but it works the same way. The first step is to make a DNA copy of the RNA, which then is used as the template for a quantitative PCR reaction.

 

The detection step depends on having small pieces of DNA called primers that are an exact match for the target sequences in the virus. Good choice of primer sequences is crucial for the test being specific. Luckily, modern molecular biology has made finding the fully sequence of viruses very fast. The full sequence of COVID-19 was published in January. That allowed researchers to compare COVID-19 RNA sequences to other corona viruses and chose areas that are unique to use for testing. The test approved by the US Center for Disease Control looks for two different sections of the virus nucleocapsid gene (called N1 and N2 because scientists are busy). The test also includes a human gene that is the same for everyone as a reference control.

 

A person has to have a significant level of virus in their nose or saliva to give a positive test result. There could be some cross-reactivity if the person has a related SARS-type corona virus that cause SARS or MERS. No one is too worried about that because anyone who has those viruses should quarantine anyway.

 

A quibble to bash - the test is for viral RNA, not for intact infectious virus. It is relatively easy to test for viral RNA. Testing for infectious virus is another story. That requires cultured human cells and a level 3 biosafety set-up. People are certainly doing research on COVID-19 infectivity and drugs that can prevent it. That is different from clinical viral testing in patients. Right now we are assuming that anyone who has detectable levels of COVID-19 RNA in their mucus membranes has lots of virus in their body making that RNA. We are also assuming that a person who has enough virus in their mucus membranes to detect has enough to spread by breathing, talking, sneezing or coughing. 

 

I don't know what to make of the video about HIV and AIDS. There are plenty of studies from the 1990s where epidemiologists compared the health outcomes of people who had HIV and people who did not. There may not be one "eureka" paper, but there are plenty of papers about virus subtype and disease progression. My suspicion is that he is trying to discredit infectious disease research in general.

  • Thanks 3

Share this post


Link to post
Share on other sites

Aaaalright, I have just about enough about biology left in my brain to get the gist of what you said. I miss those classes.

 

Except for this bit, really went over my head completely:

 

8 hours ago, Mistr said:

It is relatively easy to test for viral RNA. Testing for infectious virus is another story. That requires cultured human cells and a level 3 biosafety set-up.

 

but you have written plenty. I am sure I can find a good explenation on it in my own time.

 

Also, yeah I think they were just focused on the Belgian health policy and what are proportional governmental measures there but the implication should have been more nuanced and clear in that sense... You would expect it from professionals?

 

8 hours ago, Mistr said:

A quibble to bash - the test is for viral RNA, not for intact infectious virus.

 

I feel frustration. This makes sense. It's so easy to make claims to people that do not have the full picture to evaluate those claims. So despite having that huge list of signatories, there's a reason why there are so many expertises. You cannot know everything.

 

And still, I also do not get why there is so much discussion about this:

 

8 hours ago, Mistr said:

They imply that asymptomatic people are neither going to become sick nor infect others.

 

So many medically educated people seem unclear about this that I started to doubt myself. Once upon a time, I learnt: there is an incubation time between the cause od disease entering a body and the first disease symptoms. During that time, you can infect others. Yes you do not cough or have a runny nose, but it is IN your body, it is multiplying, and we have spit, we have sneezing because of a dusty place, we have runny noses when going into the cold without beings sick etc (EDIT: I may be repeating myself, excuses)

 

Anyway, enough food for thought. Thank you for addressing those points! I We will get through this!

  • Like 1

Share this post


Link to post
Share on other sites
18 hours ago, Mistr said:
  • They claim that COVID-19 is no worse than the seasonal flu with a death rate of 0.1-0.5%. Maybe that is true in Belgium, but it is not true in other places. In the US the death rate varies substantially by county. In my state the overall death rate is about 3%. My county is lower because we have the university medical school hospital and two other hospitals, and the local government has mandated masks and social distancing. Some of the highest death rates are in rural areas without access to hospital care. Death rates in major metropolitan areas vary. Chicago is running 2-3%. New York is 6-8%, while New Jersey is 7-11%. Even the lowest rates are 10x worse than the seasonal flu.                                        

But are those US numbers for all people, including undetected cases, or only for people that have sought out medical attention (and is there a big group of people that won't get tested/treatment unless absolutely necessary)? Looking at Iceland for example the death rate is <0.5% and they've been testing extensively. Admittedly Iceland has an extremely healthy population, but that should at least provide an approximate upper bound in a healthy population, or do you not agree? Assuming ready access to a healthcare system that hasn't collapsed of course. Lots of assumptions I know!

 

Thanks for the write up, very interesting! (Though I'll admit my bio is not up to scratch. :D) It's nice hearing from a voice that's less tainted by politics.

 

On 11/1/2020 at 5:50 PM, Aθena said:

For me, it is simply useful for the sake of seeing people looking for/finding ways to keep the public debate as open as possible, assuming the letter is really from these medical professionals. (Oh and I have no direct source to know if there is really censorship going on where they work like the letter suggests. 

One thing to keep in mind is that medical professionals all have very different areas of knowledge which come with their own biases. E.g. I saw a number of psychologists on the list, who likely know very little about this topic from a physical health standpoint. However, they might be seeing an increased number of people with mental health issues on a daily basis which will obviously color their outlook.

 

I can't tell for sure about censorship globally, but at least in Sweden (maybe Europe) my gut feeling is that we're headed in the wrong direction. There are some topics that are simply not up for discussion. But that's getting quite off topic! 

  • Like 1

Share this post


Link to post
Share on other sites
51 minutes ago, Mad Hatter said:

Looking at Iceland for example the death rate is <0.5% and they've been testing extensively. Admittedly Iceland has an extremely healthy population, but that should at least provide an approximate upper bound in a healthy population, or do you not agree? Assuming ready access to a healthcare system that hasn't collapsed of course. Lots of assumptions I know!

 

Testing extensively has outcome benefits beyond simply gathering statistics. Early detection leads to early treatment, and also isolating behaviors that reduce the viral load the people around you are exposed to, and a decreased viral load seems to lead to a less severe case. So extensive testing in and of itself seems likely to statistically decrease the severity of individual cases of covid.

 

Ready access to healthcare is definitely a poor assumption in the US. I'm not sure the US even ranks among the developed nations on that front. On the testing front, it's still difficult to get tested in many places, and in places where tests are available, they're often expensive. So yes, there is a large group without good access to testing, whether the obstacle is logistic or economic.

 

Given that there are so many unknowns about the actual infection rate versus the official infection rate, the number that one is left with is "what percentage of the population actually died of this during a given time period". That can be statistically reconstructed after the fact, even without great testing data. In the US, that's 26-53k people per year for flu in 2018-2019. The official numbers for covid are projected to reach 500k for a 12 month period, and I suspect when they analyse death rates, they'll find, like the UK, that the unreported numbers might be up to double that. That tracks with Mistr's numbers, at the very best it's ten times as deadly as the flu, given the same population and time period. It doesn't tell you in either case what the theoretical virulence of an entirely uncontrolled disease is, but it does bound it and demonstrate concrete impact. Countries that controlled it better may get greater value out of projecting a death rate per positive case, because they didn't get spread that demonstrates the bounding. They're also likely to have better testing numbers. But given what we know about places where it wasn't well controlled, I'd be suspicious of numbers that don't project at least 10x the impact of the flu if left unchecked. (And, honestly, I suspect it's more on the order of 30x.)

 

What I'm increasingly concerned about is not the death rate, though that's bad. It's the lasting impact on the health of the survivors. The flu rarely leaves a large percentage of people with major permanent health problems, and it looks increasingly like covid does. A percentage have heart damage, a percentage have lung damage, a percentage have brain damage, a percentage have chronic fatigue, a percentage don't seem to recover from it at all. The rehabilitation and ongoing treatment of those issues is difficult and expensive, and some of those people will never work again. The ongoing cost to the health care system of treating covid survivors is not well known. When we say "not as bad as the flu", I usually want to ask "by what measure".

  • Like 4

Share this post


Link to post
Share on other sites

Quoting is not working right, but here are the answers to @Aθena's questions.

 

Viruses generally have an external coat that covers a central core of DNA or RNA. The coat usually has proteins that stick to some feature on the cell of the host. In the case of COVID-19, the protein on the surface is named "spike protein" because it looks like the spike on a crown in an electron micrograph image. The spike protein binds to the ACE2 receptor on human cells (https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1008762). There are more steps that happen after binding to let the virus enter the cell, unpack its RNA payload, and start making more virus. Antiviral drugs target some of those steps.

 

The distinction between detecting a whole virus or just its genetic material is moot if you want to see if someone is infected or not. Each virus has one copy of the RNA genome. It takes a lot of copies to show up in clinical RT-qPCR tests, so if a person tests positive that means they have a lot of virus in their nasal passages. Not just a few that they happened to inhale in a crowded room.

 

How much virus a person sheds into the air when they breathe or sneeze varies a lot. How much a person has to inhale to get infected varies a lot too. That is where testing the properties of the whole virus becomes important to researchers.

 

Another aspect of testing that is just starting to take off is wastewater testing. Epidemiologists have done wastewater testing for other pathogens for years. Now they are applying the same strategy to COVID-19 testing. The advantage of wastewater testing is that health officials can get population-wide data quickly from just a few samples. Getting people to go get tested is difficult. Some don't go because they feel fine, some don't go because they feel sick, some don't go because it takes too much time or they can't afford it. That means that many infected people don't get tested. Wastewater testing gets 100% compliance. People keep using the toilet regardless of how they feel. The information gathered is on a population scale, not for individuals or households. That still is helpful for health officials. Infection spikes show up in wastewater three days before hospital admission numbers start to climb. Universities have used this method to test wastewater from individual dormitories to control asymptomatic spread.

 

52 minutes ago, Mad Hatter said:

But are those US numbers for all people, including undetected cases, or only for people that have sought out medical attention (and is there a big group of people that won't get tested/treatment unless absolutely necessary)? Looking at Iceland for example the death rate is <0.5% and they've been testing extensively. Admittedly Iceland has an extremely healthy population, but that should at least provide an approximate upper bound in a healthy population, or do you not agree? Assuming ready access to a healthcare system that hasn't collapsed of course. Lots of assumptions I know!

 

The data are percent fatalities of total confirmed cases. It does not include people who never get tested. The total deaths from the pandemic can be determined in retrospect by looking at increase in death rate. That assumes that people die at a consistent rate from all other causes. Knowing that x number of people per 100,000 normally die each month, we can see how many died each month this year (call that x + C) and figure out the rate of death (C) from the pandemic.

 

Iceland has the advantage of being a small island. The authorities have complete control over everyone entering the country. They also have excellent health care. Last spring when the pandemic hit Europe there was a notably lower death rate in Germany than in the neighboring countries. Germany is still doing well with a rate of about 2%. Stockholm is currently over 6%. I think the current rates in Europe show what the current medical system can support. The death rate is going to be substantially lower in areas where the hospitals are not overwhelmed. See https://coronavirus.jhu.edu/map.html for current data.

  • Thanks 1

Share this post


Link to post
Share on other sites
23 minutes ago, sarakingdom said:

What I'm increasingly concerned about is not the death rate, though that's bad. It's the lasting impact on the health of the survivors. The flu rarely leaves a large percentage of people with major permanent health problems, and it looks increasingly like covid does. A percentage have heart damage, a percentage have lung damage, a percentage have brain damage, a percentage have chronic fatigue, a percentage don't seem to recover from it at all. The rehabilitation and ongoing treatment of those issues is difficult and expensive, and some of those people will never work again. The ongoing cost to the health care system of treating covid survivors is not well known. When we say "not as bad as the flu", I usually want to ask "by what measure".

 

And to make matters worse, this is a very large number of people with "a pre-existing condition" that will impact their future access to health care, at least in the USA.

  • Like 2

Share this post


Link to post
Share on other sites

Thank you both @sarakingdom and @Mistr for you answers! I've been struggling to reconcile the numbers in e.g. the US with the very low numbers in Finland where I live. It's just hard to get a clear picture of what's going on. Sure I can speculate and list a whole bunch of factors why there'd be differences, but it's still difficult to understand what's exaggerated or overblown and what's optimistic or careless. Your answers help.

  • Like 3

Share this post


Link to post
Share on other sites
21 hours ago, Mistr said:

The total deaths from the pandemic can be determined in retrospect by looking at increase in death rate. That assumes that people die at a consistent rate from all other causes.

 

This, by the way, is still going to cause an undercount of covid deaths, because lockdown is reducing traffic fatalities and flu deaths. I suspect that can be modeled statistically, by looking at the changes in known diagnoses and extrapolating the change in unknowns.

 

38 minutes ago, Mad Hatter said:

I've been struggling to reconcile the numbers in e.g. the US with the very low numbers in Finland where I live.

 

The basic answer is how quickly an organised response comes after the first cases. That's the difference between a thousand cases and a million cases.

  • Like 2

Share this post


Link to post
Share on other sites
15 minutes ago, sarakingdom said:

 

The basic answer is how quickly an organised response comes after the first cases. That's the difference between a thousand cases and a million cases.

Fundamentally I think this sums up why so many countries are able to keep things under control with relatively few restrictions - speed of your contract tracing and public health response is huge in limiting exponential growth.

 

(There's more factors obviously - frex extent of requires masking and compliance with public health recommendations - but agility of the public health services is huge)

  • Like 2

Share this post


Link to post
Share on other sites

I also want to express my gratitude. 

 

1 hour ago, Mad Hatter said:

Thank you both @sarakingdom and @Mistr 

 

1 hour ago, Mad Hatter said:

but it's still difficult to understand what's exaggerated or overblown and what's optimistic or careless. Your answers help.

^^^^

 

  • Like 1

Share this post


Link to post
Share on other sites
1 hour ago, sarakingdom said:

The basic answer is how quickly an organised response comes after the first cases. That's the difference between a thousand cases and a million cases.

Suddenly I feel oddly grateful to Russia for being an ever looming threat, making Finland surprisingly prepared for emergencies. :P 

 

Thanks again for being a sane voice of reason in this world. :) 

Share this post


Link to post
Share on other sites

Join the conversation

You can post now and register later. If you have an account, sign in now to post with your account.

Guest
Reply to this topic...

×   Pasted as rich text.   Paste as plain text instead

  Only 75 emoji are allowed.

×   Your link has been automatically embedded.   Display as a link instead

×   Your previous content has been restored.   Clear editor

×   You cannot paste images directly. Upload or insert images from URL.