Really believe that there's a gain of functional mutation in the east coast corona virus since it's primarily from Europe. New York approaching 10% mortality and other northeast states having high mortality despite loads of testing. All these European countries save Iceland and Germany getting their asses kicked.

If true, it would make an argument to just let the west coast open up everything, spread the less virulent more and see if that gives us immunity. I wonder if people are comparing the strains

I don't know how these things work.... but would an immunity to a strain on the West Coast be effective against a different, more virulent strain?

Would it be like the flu where being vaccinated against one strain make your symptoms less severe from another strain you weren't vaccinated for?

I don't know. New York and Connecticut definitely have high relative rates.

Yet, Washington's confirmed case fatality rate of 5.395% is slightly higher than New Jersey's of 5.145%.

Next door, Pennsylvannia's is 4.530%, which is just about where Colorado is at 4.443%.

(Per Worldometers, and yes, they're imperfect numbers due to lag in deaths, etc.)

Patentmike said:

---

BlackGoldAg2011 said:

---

yes, people are comparing strains
https://nextstrain.org/ncov/global

and no, there is no evidence yet to support a mutation to a less virulent strain

---

They are comparing the strains for people who get tested, and people are only getting tested when they show symptoms.

In other words, the way we're doing genomic testing and genome sampling would likely miss a less virulent strain.

---

which if you read what i read, I didn't say there was not a less virulent strain, i said there was not evidence to suggest that there was.

also, do you know for a fact these samples were only collected from symptomatic people? i don't see that stated anywhere. It is likely a fair assumption, but you are stating it like it is a known fact. besides, he didn't say an asymptomatic strain, he said less deadly. there strains causing symptoms and deaths are the ones being tracked in the numbers that are being used to compare the two areas, so they should be getting picked up in the genomic testing regardless.

BlackGoldAg2011 said:

---

Old Buffalo said:

---

...or NY is a corrupt cesspool and their numbers are bloated.

---

or Manhattan is the 8th most densely populated city in the world and they had their case load explode so their testing/infected ration is lower than other states inflating their CFR a bit above the rest. because evidence would suggest that if anything, their death numbers are being under reported.

---

Manhattan: 66,000 per sq. Mile.

Cool - we gonna act like there are not 4 other boroughs and Manhattan is the least impacted?

There are other densely populated cities in the world, too.

https://www1.nyc.gov/site/doh/covid/covid-19-data.page

OP may not be far off:

https://www.dailymail.co.uk/health/article-8237849/Coronavirus-mutated-Strains-evolved-far-deadlier-spread-Europe-New-York.html

BlackGoldAg2011 said:

---

Patentmike said:

---

BlackGoldAg2011 said:

---

yes, people are comparing strains
https://nextstrain.org/ncov/global

and no, there is no evidence yet to support a mutation to a less virulent strain

---

They are comparing the strains for people who get tested, and people are only getting tested when they show symptoms.

In other words, the way we're doing genomic testing and genome sampling would likely miss a less virulent strain.

---

which if you read what i read, I didn't say there was not a less virulent strain, i said there was not evidence to suggest that there was.

also, do you know for a fact these samples were only collected from symptomatic people? i don't see that stated anywhere. It is likely a fair assumption, but you are stating it like it is a known fact. besides, he didn't say an asymptomatic strain, he said less deadly. there strains causing symptoms and deaths are the ones being tracked in the numbers that are being used to compare the two areas, so they should be getting picked up in the genomic testing regardless.

---

Our disconnect appears to be over the word "evidence". There is very little experimental data on variants (one non peer reviewed report of variants being detected during cell culture passage from an infected patient). However, the serology tests suggesting infection rates 30-50 times the positive tests is circumstantial evidence that a less pathogenic variant may be prevalent in SoCal.

Put differently, do the serology results support spending more resources to look for variants in So Cal. If so, those results are "evidence" the variants exist...not proof, evidence.

On the source of sequenced samples, I am inferring from the shortage of tests that the sequenced samples are from symptomatic patients or those contact traced to symptomatic patients. That will change over time, but for now the inference is reasonable.

Density is just a convenient scapegoat for local, state, and national leaders.

TxAG#2011 said:

---

Old Buffalo said:

---

And I guess all the other densely populated cities handled it correctly?

Can this board just make up their mind?

Cases too low - We're not testing enough
Cases too high - We're wasting tests that can be used elsewhere
Deaths too low - We're not reporting enough
Deaths too high - We're not testing enough
Curve too steep - We've got to flatten it
Declining curve - We've got to wait until a vaccine

---

Have you ever considered we just haven't figured it out yet? Not everyone resorts to spouting nonsensical conspiracy theories when they don't understand something.

---

Crash the economy and destroy tens of millions of lives at all costs right? Maybe we have to come to the realization that we need to focus all of our efforts on the most vulnerable and let everyone else keep their livelihoods intact while the overwhelming majority keep the country going? This is a nightmare economic scenario that could change our country for the worse, forever. I just hope everyone, even those on the front lines, are truly factoring this in. I realize it's not the doctors jobs to focus on this right now, but goodness.

AgStuckinLBK said:

---

Really believe that there's a gain of functional mutation in the east coast corona virus since it's primarily from Europe. New York approaching 10% mortality and other northeast states having high mortality despite loads of testing. All these European countries save Iceland and Germany getting their asses kicked.

If true, it would make an argument to just let the west coast open up everything, spread the less virulent more and see if that gives us immunity. I wonder if people are comparing the strains

---

Hey Professor "Herd Immunity", tell us about the long term renal and cardiac effects for covid19 survivors. I'll hang up and listen.

Going to make me pull my hair out with the interchangeable usage of "strains" and "variants"....

There is only one strain of SARS-COV-2.

The virus has mutated over time (like all things and viruses) which has given way to all the different variants you can see plotted in phylogeny trees, etc that they have used to track where the virus that led to an infection in a certain geographical region came from.

I would typically call these variants or isolates. However they are being referred to in the media as strains which I think is confusing a lot of people in thinking they might have a different origin or different virulent properties.

To date, there is no evidence that these variants have different virulent properties. Their mutations most likely do not impact anything at all. Same can be said for vaccine development. The mutations most likely will not impact development of a global vaccine.


The only real change in virulence from a mutation I have seen is an isolate of the virus in Singapore that deleted a 382 bp region in ORF8. This is interesting because the original SARS also carries this deletion and it actually may make the virus less virulent. However there is nothing to suggest this variant has traveled outside Singapore and to my knowledge there hasn't been much study of this particular isolate, just speculation.

Far more likely it's still about viral load. NYC is most likely to have someone with the virus right next to you for long periods of time. Hence more infections and more importantly for the numbers, more severe infections.

jagvocate said:

---

AgStuckinLBK said:

---

Really believe that there's a gain of functional mutation in the east coast corona virus since it's primarily from Europe. New York approaching 10% mortality and other northeast states having high mortality despite loads of testing. All these European countries save Iceland and Germany getting their asses kicked.

If true, it would make an argument to just let the west coast open up everything, spread the less virulent more and see if that gives us immunity. I wonder if people are comparing the strains

---

Hey Professor "Herd Immunity", tell us about the long term renal and cardiac effects for covid19 survivors. I'll hang up and listen.

---

Does anyone know what the long-term effects are, considering the virus is so new nobody is in the long-term effect period?

People are only going to the hospital (and getting tested) in NY when they are gravely ill. I am pretty sure the reason for their higher cfr is not anymore complicated than that.

Patentmike said:

---

BlackGoldAg2011 said:

---

Patentmike said:

---

BlackGoldAg2011 said:

---

yes, people are comparing strains
https://nextstrain.org/ncov/global

and no, there is no evidence yet to support a mutation to a less virulent strain

---

They are comparing the strains for people who get tested, and people are only getting tested when they show symptoms.

In other words, the way we're doing genomic testing and genome sampling would likely miss a less virulent strain.

---

which if you read what i read, I didn't say there was not a less virulent strain, i said there was not evidence to suggest that there was.

also, do you know for a fact these samples were only collected from symptomatic people? i don't see that stated anywhere. It is likely a fair assumption, but you are stating it like it is a known fact. besides, he didn't say an asymptomatic strain, he said less deadly. there strains causing symptoms and deaths are the ones being tracked in the numbers that are being used to compare the two areas, so they should be getting picked up in the genomic testing regardless.

---

Our disconnect appears to be over the word "evidence". There is very little experimental data on variants (one non peer reviewed report of variants being detected during cell culture passage from an infected patient). However, the serology tests suggesting infection rates 30-50 times the positive tests is circumstantial evidence that a less pathogenic variant may be prevalent in SoCal.

Put differently, do the serology results support spending more resources to look for variants in So Cal. If so, those results are "evidence" the variants exist...not proof, evidence.

On the source of sequenced samples, I am inferring from the shortage of tests that the sequenced samples are from symptomatic patients or those contact traced to symptomatic patients. That will change over time, but for now the inference is reasonable.

---

The serology tests that suggest 30-50 times the positives has a huge problem with false positive serology. As in given the false positive rate of the serology, there is a high probability that every positive result they had could have been a false positive. Logically, one would assume that at least some are real, but you still can't assume a high rate of infection when your positive results could be dominated by false positives.

jagvocate said:

---

AgStuckinLBK said:

---

Really believe that there's a gain of functional mutation in the east coast corona virus since it's primarily from Europe. New York approaching 10% mortality and other northeast states having high mortality despite loads of testing. All these European countries save Iceland and Germany getting their asses kicked.

If true, it would make an argument to just let the west coast open up everything, spread the less virulent more and see if that gives us immunity. I wonder if people are comparing the strains

---

Hey Professor "Herd Immunity", tell us about the long term renal and cardiac effects for covid19 survivors. I'll hang up and listen.

---

So how long do you think we should wait in lockdown... until their is a vaccine? Because the only endpoint is herd immunity, either from people getting it or from a vaccine.

BiochemAg97 said:

---

Patentmike said:

---

BlackGoldAg2011 said:

---

Patentmike said:

---

BlackGoldAg2011 said:

---

yes, people are comparing strains
https://nextstrain.org/ncov/global

and no, there is no evidence yet to support a mutation to a less virulent strain

---

They are comparing the strains for people who get tested, and people are only getting tested when they show symptoms.

In other words, the way we're doing genomic testing and genome sampling would likely miss a less virulent strain.

---

which if you read what i read, I didn't say there was not a less virulent strain, i said there was not evidence to suggest that there was.

also, do you know for a fact these samples were only collected from symptomatic people? i don't see that stated anywhere. It is likely a fair assumption, but you are stating it like it is a known fact. besides, he didn't say an asymptomatic strain, he said less deadly. there strains causing symptoms and deaths are the ones being tracked in the numbers that are being used to compare the two areas, so they should be getting picked up in the genomic testing regardless.

---

Our disconnect appears to be over the word "evidence". There is very little experimental data on variants (one non peer reviewed report of variants being detected during cell culture passage from an infected patient). However, the serology tests suggesting infection rates 30-50 times the positive tests is circumstantial evidence that a less pathogenic variant may be prevalent in SoCal.

Put differently, do the serology results support spending more resources to look for variants in So Cal. If so, those results are "evidence" the variants exist...not proof, evidence.

On the source of sequenced samples, I am inferring from the shortage of tests that the sequenced samples are from symptomatic patients or those contact traced to symptomatic patients. That will change over time, but for now the inference is reasonable.

---

The serology tests that suggest 30-50 times the positives has a huge problem with false positive serology. As in given the false positive rate of the serology, there is a high probability that every positive result they had could have been a false positive. Logically, one would assume that at least some are real, but you still can't assume a high rate of infection when your positive results could be dominated by false positives.

---

Where did you find the false positive rate for the USC study?

Patentmike said:

---

BiochemAg97 said:

---

Patentmike said:

---

BlackGoldAg2011 said:

---

Patentmike said:

---

BlackGoldAg2011 said:

---

yes, people are comparing strains
https://nextstrain.org/ncov/global

and no, there is no evidence yet to support a mutation to a less virulent strain

---

They are comparing the strains for people who get tested, and people are only getting tested when they show symptoms.

In other words, the way we're doing genomic testing and genome sampling would likely miss a less virulent strain.

---

which if you read what i read, I didn't say there was not a less virulent strain, i said there was not evidence to suggest that there was.

also, do you know for a fact these samples were only collected from symptomatic people? i don't see that stated anywhere. It is likely a fair assumption, but you are stating it like it is a known fact. besides, he didn't say an asymptomatic strain, he said less deadly. there strains causing symptoms and deaths are the ones being tracked in the numbers that are being used to compare the two areas, so they should be getting picked up in the genomic testing regardless.

---

Our disconnect appears to be over the word "evidence". There is very little experimental data on variants (one non peer reviewed report of variants being detected during cell culture passage from an infected patient). However, the serology tests suggesting infection rates 30-50 times the positive tests is circumstantial evidence that a less pathogenic variant may be prevalent in SoCal.

Put differently, do the serology results support spending more resources to look for variants in So Cal. If so, those results are "evidence" the variants exist...not proof, evidence.

On the source of sequenced samples, I am inferring from the shortage of tests that the sequenced samples are from symptomatic patients or those contact traced to symptomatic patients. That will change over time, but for now the inference is reasonable.

---

The serology tests that suggest 30-50 times the positives has a huge problem with false positive serology. As in given the false positive rate of the serology, there is a high probability that every positive result they had could have been a false positive. Logically, one would assume that at least some are real, but you still can't assume a high rate of infection when your positive results could be dominated by false positives.

---

Where did you find the false positive rate for the USC study?

---

From their paper. They did a small test of pre-covid samples and found 30/30 negative (100% specificity... too small a sample size to get an accurate measure). They also looked at the test manufacture's data which had 369 negatives from 371 pre-covid samples (2 false positives in 371). The report a 95% CI of 98.1% - 99.9% specificity (or 0.01-1.9% f.p.). At the 95% CI, they should get between 3 and 36 false positives if no one in the county had antibodies to SARS-CoV2. They had 50 positives tests.

BiochemAg97 said:

---

Patentmike said:

---

BiochemAg97 said:

---

Patentmike said:

---

BlackGoldAg2011 said:

---

Patentmike said:

---

BlackGoldAg2011 said:

---

yes, people are comparing strains
https://nextstrain.org/ncov/global

and no, there is no evidence yet to support a mutation to a less virulent strain

---

They are comparing the strains for people who get tested, and people are only getting tested when they show symptoms.

In other words, the way we're doing genomic testing and genome sampling would likely miss a less virulent strain.

---

which if you read what i read, I didn't say there was not a less virulent strain, i said there was not evidence to suggest that there was.

also, do you know for a fact these samples were only collected from symptomatic people? i don't see that stated anywhere. It is likely a fair assumption, but you are stating it like it is a known fact. besides, he didn't say an asymptomatic strain, he said less deadly. there strains causing symptoms and deaths are the ones being tracked in the numbers that are being used to compare the two areas, so they should be getting picked up in the genomic testing regardless.

---

Our disconnect appears to be over the word "evidence". There is very little experimental data on variants (one non peer reviewed report of variants being detected during cell culture passage from an infected patient). However, the serology tests suggesting infection rates 30-50 times the positive tests is circumstantial evidence that a less pathogenic variant may be prevalent in SoCal.

Put differently, do the serology results support spending more resources to look for variants in So Cal. If so, those results are "evidence" the variants exist...not proof, evidence.

On the source of sequenced samples, I am inferring from the shortage of tests that the sequenced samples are from symptomatic patients or those contact traced to symptomatic patients. That will change over time, but for now the inference is reasonable.

---

The serology tests that suggest 30-50 times the positives has a huge problem with false positive serology. As in given the false positive rate of the serology, there is a high probability that every positive result they had could have been a false positive. Logically, one would assume that at least some are real, but you still can't assume a high rate of infection when your positive results could be dominated by false positives.

---

Where did you find the false positive rate for the USC study?

---

From their paper. They did a small test of pre-covid samples and found 30/30 negative (100% specificity... too small a sample size to get an accurate measure). They also looked at the test manufacture's data which had 369 negatives from 371 pre-covid samples (2 false positives in 371). The report a 95% CI of 98.1% - 99.9% specificity (or 0.01-1.9% f.p.). At the outside range (1.9% f.p.) they would get ~63 f.p. from the sample of 3330. They had 50 positives which is below the potential 63 f.p.

---

Gotcha. It's been awhile (25 years) since I reviewed a study like that and I missed those details.

Patentmike said:

---

BiochemAg97 said:

---

Patentmike said:

---

BiochemAg97 said:

---

Patentmike said:

---

BlackGoldAg2011 said:

---

Patentmike said:

---

BlackGoldAg2011 said:

---

yes, people are comparing strains
https://nextstrain.org/ncov/global

and no, there is no evidence yet to support a mutation to a less virulent strain

---

They are comparing the strains for people who get tested, and people are only getting tested when they show symptoms.

In other words, the way we're doing genomic testing and genome sampling would likely miss a less virulent strain.

---

which if you read what i read, I didn't say there was not a less virulent strain, i said there was not evidence to suggest that there was.

also, do you know for a fact these samples were only collected from symptomatic people? i don't see that stated anywhere. It is likely a fair assumption, but you are stating it like it is a known fact. besides, he didn't say an asymptomatic strain, he said less deadly. there strains causing symptoms and deaths are the ones being tracked in the numbers that are being used to compare the two areas, so they should be getting picked up in the genomic testing regardless.

---

Our disconnect appears to be over the word "evidence". There is very little experimental data on variants (one non peer reviewed report of variants being detected during cell culture passage from an infected patient). However, the serology tests suggesting infection rates 30-50 times the positive tests is circumstantial evidence that a less pathogenic variant may be prevalent in SoCal.

Put differently, do the serology results support spending more resources to look for variants in So Cal. If so, those results are "evidence" the variants exist...not proof, evidence.

On the source of sequenced samples, I am inferring from the shortage of tests that the sequenced samples are from symptomatic patients or those contact traced to symptomatic patients. That will change over time, but for now the inference is reasonable.

---

The serology tests that suggest 30-50 times the positives has a huge problem with false positive serology. As in given the false positive rate of the serology, there is a high probability that every positive result they had could have been a false positive. Logically, one would assume that at least some are real, but you still can't assume a high rate of infection when your positive results could be dominated by false positives.

---

Where did you find the false positive rate for the USC study?

---

From their paper. They did a small test of pre-covid samples and found 30/30 negative (100% specificity... too small a sample size to get an accurate measure). They also looked at the test manufacture's data which had 369 negatives from 371 pre-covid samples (2 false positives in 371). The report a 95% CI of 98.1% - 99.9% specificity (or 0.01-1.9% f.p.). At the outside range (1.9% f.p.) they would get ~63 f.p. from the sample of 3330. They had 50 positives which is below the potential 63 f.p.

---

Gotcha. It's been awhile (25 years) since I reviewed a study like that and I missed those details.

---

Been a while since I spent a lot of time reading papers too. I actually saw another analysis/review of the article that pointed it out, but I like to go back and do my own check. Hard to be sure who to trust with all this.

Patentmike said:

---

BlackGoldAg2011 said:

---

yes, people are comparing strains
https://nextstrain.org/ncov/global

and no, there is no evidence yet to support a mutation to a less virulent strain

---

They are comparing the strains for people who get tested, and people are only getting tested when they show symptoms.

In other words, the way we're doing genomic testing and genome sampling would likely miss a less virulent strain.

---

He didn't say there wasn't a less virulent strain, he said extensive testing has shown no evidence of that (which is true).