OtherGround Forums OG doc. AMA on COVID-19

9/12/20 2:30 PM
2/4/09
Posts: 14333
arc123 -
NoNeed4aScreenName -
arc123 -

No other docs taking over the reigns? 
 

Still nobody dying. Sweden still there (and with lower fatalities YTD than 2018). PCR test still being used at 40x amplification. 

It's not 40x it's an exponential amount of gamification. Its 40 cycles of amplification. 

 

In theory you should be able to detect 1 copy of the virus in the cells with enough cycles. In practice that's not quite realistic but you can quantify viral RNA based and infer # of viruses present but it will still just he an estimate. An educated estimate 

Genuine question - how would you compare your knowledge / experience in this field to Carl Heneghan (Head of Evidence Based medicine at Oxford Uni). 
 

im not going to be deceitful - I am expert in some areas, but this is not one of them. I am heavily influenced in my opinions by him and a building number if similar view points.  I cannot debate with you directly so I’d like it if you could help me with understanding the differences in these view points, as they obviously cannot both be correct. 

I think you could be misrepresenting what he is saying. I havent read it but PCR works in cycles. Every cycle your target doubles (in theory) so if you have 1 copy after a second cycle you have 2, then 4, then 8, then 16..etc.

 

The CT value is only when the signal starts to go into exponential phase and rises above background noise. 

 

You also need to understand though in these experiments they are using very low starting material with viral RNA. 

 

When you amplify your target you need to create primers. These primers will flank your target sequence or the gene you are interested in. 

 

For COVID its novel so theres something different from all other coronviruses. The primers should flank this novel sequence which, in theory, would then exclude all other viruses except Covid 19

 

Is it making sense how I am explaining it?

9/12/20 2:54 PM
7/28/08
Posts: 2060
NoNeed4aScreenName -
arc123 -
NoNeed4aScreenName -
arc123 -

No other docs taking over the reigns? 
 

Still nobody dying. Sweden still there (and with lower fatalities YTD than 2018). PCR test still being used at 40x amplification. 

It's not 40x it's an exponential amount of gamification. Its 40 cycles of amplification. 

 

In theory you should be able to detect 1 copy of the virus in the cells with enough cycles. In practice that's not quite realistic but you can quantify viral RNA based and infer # of viruses present but it will still just he an estimate. An educated estimate 

Genuine question - how would you compare your knowledge / experience in this field to Carl Heneghan (Head of Evidence Based medicine at Oxford Uni). 
 

im not going to be deceitful - I am expert in some areas, but this is not one of them. I am heavily influenced in my opinions by him and a building number if similar view points.  I cannot debate with you directly so I’d like it if you could help me with understanding the differences in these view points, as they obviously cannot both be correct. 

I think you could be misrepresenting what he is saying. I havent read it but PCR works in cycles. Every cycle your target doubles (in theory) so if you have 1 copy after a second cycle you have 2, then 4, then 8, then 16..etc.

 

The CT value is only when the signal starts to go into exponential phase and rises above background noise. 

 

You also need to understand though in these experiments they are using very low starting material with viral RNA. 

 

When you amplify your target you need to create primers. These primers will flank your target sequence or the gene you are interested in. 

 

For COVID its novel so theres something different from all other coronviruses. The primers should flank this novel sequence which, in theory, would then exclude all other viruses except Covid 19

 

Is it making sense how I am explaining it?

Hey - I do get what you’re saying, thanks.

 

Heneghan is debating the validity of using the PCR at at the ‘level’ or cycle count - clearly stating that 30 would be high, but acceptable, and stating out right that at 45 (which is U.K. level) will show false positives and such low levels that it shouldn’t be as a ‘case’.


is this not correct logic in your view? 

 

9/12/20 3:04 PM
7/28/08
Posts: 2061

https://jamanetwork.com/journals/jama/fullarticle/2770758

 

"Substantial data now demonstrate the presence of preexisting T-cell immunity to SARS-CoV-2 in blood donors either prior to the COVID-19 pandemic or more recently among those without infection."

9/12/20 3:06 PM
7/28/08
Posts: 2062

Does it feel to you that our DNA is being collected for some reason? 100,000s tests taken daily, and this written into law yesterday with (again) no parliamentary oversight.

 

https://www.legislation.gov.uk/uksi/2020/973/made?view=plain

9/18/20 4:31 PM
7/28/08
Posts: 2072

Hey OG Doc(s) - the curve has been pretty fucking flat for the last 4 months, so the only sensible course of action is surely another lockdown.

 

where you at mataleo? I’m surprised this thread has died so quickly, it was a firm favourite whilst you were spreading your wares. 

9/21/20 1:57 PM
7/28/08
Posts: 2084

TTT

9/22/20 1:47 PM
1/11/17
Posts: 1189

Really interested to hear some (professional) opinions on why lockdowns would be initiated when deaths are at as low as 0.01% of the peak. (UK)

9/22/20 1:55 PM
2/4/09
Posts: 14644
Left_Hook_Cemetery -

Really interested to hear some (professional) opinions on why lockdowns would be initiated when deaths are at as low as 0.01% of the peak. (UK)

Arent they calling for 6 MONTHS

9/22/20 6:04 PM
7/28/08
Posts: 2086
NoNeed4aScreenName -
Left_Hook_Cemetery -

Really interested to hear some (professional) opinions on why lockdowns would be initiated when deaths are at as low as 0.01% of the peak. (UK)

Arent they calling for 6 MONTHS

Yup. 

Edited: 9/23/20 3:13 AM
10/23/05
Posts: 4364
<blockquote>Left_Hook_Cemetery - <span id='userPost66719524' class='User-369174'><p>Really interested to hear some (professional) opinions on why lockdowns would be initiated when deaths are at as low as 0.01% of the peak. (UK)</p></span></blockquote><br />Honestly, none of the proposed measures make much sense.<br /><br />-Yes we are seeing a second wave in many countries, including Canada, France, Spain, Netherlands, etc...<br /><br />-Yes, cases are going up and it's not simply because of more testing or because of different definitions or what is a positive.<br /><br />However, and this is the biggest argument, people are not getting sick right now. This isn't like last April. Severe cases (those going to hospitals, those needing a ventilator, those dying, and those having sequelae) are not exploding, only minor spikes everywhere.<br /><br />It really does seem (as of now) that the virus has much less virulence (more transmissible but milder form). Maybe that will change. But until then, I don't get why these lockdown measures are being instituted. Some places are still being hit pretty hard (Iran, Turkey, South America, some places in the USA), but this is just isn't the cast elsewhere.
9/23/20 7:17 AM
11/24/09
Posts: 2574

https://www.cbc.ca/news/canada/british-columbia/symptoms-removed-student-health-checklist-covid-bc-1.5731432

 

any thoughts on that ? kinda weird to just removes symptoms like that 

9/23/20 10:23 AM
1/11/17
Posts: 1191
mataleo1 - <blockquote>Left_Hook_Cemetery - <span id='userPost66719524' class='User-369174'><p>Really interested to hear some (professional) opinions on why lockdowns would be initiated when deaths are at as low as 0.01% of the peak. (UK)</p></span></blockquote><br />Honestly, none of the proposed measures make much sense.<br /><br />-Yes we are seeing a second wave in many countries, including Canada, France, Spain, Netherlands, etc...<br /><br />-Yes, cases are going up and it's not simply because of more testing or because of different definitions or what is a positive.<br /><br />However, and this is the biggest argument, people are not getting sick right now. This isn't like last April. Severe cases (those going to hospitals, those needing a ventilator, those dying, and those having sequelae) are not exploding, only minor spikes everywhere.<br /><br />It really does seem (as of now) that the virus has much less virulence (more transmissible but milder form). Maybe that will change. But until then, I don't get why these lockdown measures are being instituted. Some places are still being hit pretty hard (Iran, Turkey, South America, some places in the USA), but this is just isn't the cast elsewhere.

Much appreciated.

It's also a little weird that no one is really questioning it in any mainstream media.

Maybe govs are concerned about what will happen when winter hits. Maybe they just want the most reckless among practice a little caution until we are truly out of the woods.

9/23/20 10:36 AM
10/23/05
Posts: 4365
What's going on with the site Kirik? :)

If hospitalizations or deaths increase significantly, governments can adjust and propose measures. Until then, we're essentially treating a "number" i.e. COVID cases. Some are doing a better job than others at interpreting data (in my opinion). For example, the Netherlands are doing right. Minimal measures, contact tracing. Cases are way up but I don't care too much about that metric, as mentioned.
9/23/20 10:40 AM
2/11/03
Posts: 41181
mataleo1 - What's going on with the site Kirik? :)

If hospitalizations or deaths increase significantly, governments can adjust and propose measures. Until then, we're essentially treating a "number" i.e. COVID cases. Some are doing a better job than others at interpreting data (in my opinion). For example, the Netherlands are doing right. Minimal measures, contact tracing. Cases are way up but I don't care too much about that metric, as mentioned.

Why is the number of cases the metric here? I dont get it, is it a media thing? Personally I would think the positivity rate is more important. The number of cases vs the number of people tested.
9/23/20 10:52 AM
10/23/05
Posts: 4366
Isaac298 - 
mataleo1 - What's going on with the site Kirik? :)

If hospitalizations or deaths increase significantly, governments can adjust and propose measures. Until then, we're essentially treating a "number" i.e. COVID cases. Some are doing a better job than others at interpreting data (in my opinion). For example, the Netherlands are doing right. Minimal measures, contact tracing. Cases are way up but I don't care too much about that metric, as mentioned.

Why is the number of cases the metric here? I dont get it, is it a media thing? Personally I would think the positivity rate is more important. The number of cases vs the number of people tested.

In epidemiology, we focus on "Patient important outcomes" aka PIOs.

If the worst that happens is that you need to be in bed a couple days, then it's not concerning. Even if positivity rate is up, I'm not sure this has much consequence if it doesn't result in hospitalizations, intubation, sequelae, death. We've seen tons of cases of late, but the majority have minor symptoms. Very different from March to May.

Again, this may change quickly.
9/23/20 11:01 AM
3/23/07
Posts: 61170

you might have to log out and back in, but you now have a gray name mataleo1

9/23/20 11:03 AM
10/23/05
Posts: 4367
saglv - 

you might have to log out and back in, but you now have a gray name mataleo1


Awesome! Do I get an OG t-shirt too?

9/23/20 12:25 PM
1/1/01
Posts: 66754
Looks good on ya!
9/23/20 12:33 PM
8/18/13
Posts: 10638
mataleo1 -
saglv - 

you might have to log out and back in, but you now have a gray name mataleo1


Awesome! Do I get an OG t-shirt too?

Good to see you still posting in here despite the tidal wave of idiots that attempted to sabotage the thread Doc! 

This thread epitomises why I keep coming here and wading through the bullshit. Glad they grey’d you! 

9/23/20 12:42 PM
10/23/05
Posts: 4368
Dreville79 - 
mataleo1 -
saglv - 

you might have to log out and back in, but you now have a gray name mataleo1


Awesome! Do I get an OG t-shirt too?

Good to see you still posting in here despite the tidal wave of idiots that attempted to sabotage the thread Doc! 

This thread epitomises why I keep coming here and wading through the bullshit. Glad they grey’d you! 


Thx man. I was swamped with deadlines, but am finally getting a respite. I will be a little more selective on which questions I answer though.

9/24/20 2:50 AM
7/28/08
Posts: 2088
mataleo1 -
Dreville79 - 
mataleo1 -
saglv - 

you might have to log out and back in, but you now have a gray name mataleo1


Awesome! Do I get an OG t-shirt too?

Good to see you still posting in here despite the tidal wave of idiots that attempted to sabotage the thread Doc! 

This thread epitomises why I keep coming here and wading through the bullshit. Glad they grey’d you! 


Thx man. I was swamped with deadlines, but am finally getting a respite. I will be a little more selective on which questions I answer though.

Sounds a bit like the BBC

9/24/20 7:59 AM
1/12/07
Posts: 23358

things are getting interesting, where do you currently stand Mat?

9/24/20 8:24 AM
10/23/05
Posts: 4371
SpunQ - 

things are getting interesting, where do you currently stand Mat?


Not my field of expertise, but I've always contended that T-cell immunity was likely in COVID, and could perhaps help explain why we're seeing less severe infections on the second wave.

If there are microbiologists/immunologists on the board, i'd love to have their opinion.

9/24/20 8:25 AM
7/28/08
Posts: 2089
mataleo1 -
SpunQ - 

things are getting interesting, where do you currently stand Mat?


Not my field of expertise, but I've always contended that T-cell immunity was likely in COVID, and could perhaps help explain why we're seeing less severe infections on the second wave.

If there are microbiologists/immunologists on the board, i'd love to have their opinion.

You definitely see this as a second wave Doc?

9/24/20 9:11 AM
10/23/05
Posts: 4372
arc123 - 
mataleo1 -
SpunQ - 

things are getting interesting, where do you currently stand Mat?


Not my field of expertise, but I've always contended that T-cell immunity was likely in COVID, and could perhaps help explain why we're seeing less severe infections on the second wave.

If there are microbiologists/immunologists on the board, i'd love to have their opinion.

You definitely see this as a second wave Doc?


What does a second wave mean? It just means an identifiable second bump in infections. And that bump isn't solely explained by variable definitions of positivity or by increased testing.

However, I again stand by my prior assertion that this bump has been very benign so far. The increase in hospitalization, deaths and sequelae is very minor. Which is why I don't really understand the measures being implemented right now.