[Mick]

When the all of the failings of the federal government are tallied, I hope the incredibly restrictive approach to testing gets the attention it deserves.

It's good that the coronavirus happened on Trump's watch. I doubt any other politician would have handled in a significantly different way, but Trump will receive all the blame and it will hit him in November.  It's important to keep up the full court press criticism on Trump, so that low-information voters can be motivated to do the right thing.

[Mick]

When the all of the failings of the federal government are tallied, I hope the incredibly restrictive approach to testing gets the attention it deserves.

It's good that the coronavirus happened on Trump's watch. I doubt any other politician would have handled in a significantly different way, but Trump will receive all the blame and it will hit him in November.  It's important to keep up the full court press criticism on Trump, so that low-information voters can be motivated to do the right thing.

[stupac2]

I doubt any other politician would have handled in a significantly different way

...Why? There are multiple examples across the political spectrum of politicians who handled it better (given their decreased power) in the US alone, never mind those leaders abroad who have done far better. What rationale do you have for this?

[stupac2]

I doubt any other politician would have handled in a significantly different way

...Why? There are multiple examples across the political spectrum of politicians who handled it better (given their decreased power) in the US alone, never mind those leaders abroad who have done far better. What rationale do you have for this?

[BostonCard]

When the all of the failings of the federal government are tallied, I hope the incredibly restrictive approach to testing gets the attention it deserves.

It's good that the coronavirus happened on Trump's watch. I doubt any other politician would have handled in a significantly different way, but Trump will receive all the blame and it will hit him in November.  It's important to keep up the full court press criticism on Trump, so that low-information voters can be motivated to do the right thing.

Well, I just came back from Universe 2, where Hillary won the 2016 election.  The bad news is that instead of COVID-19, that universe was dealing with Armaggedon.  Fortunately one of our nukes hit the Wuhan seafood market and that pretty much ended the chain of transmission.

But it does show that a different politician would have handled it differently.

BC

[BostonCard]

When the all of the failings of the federal government are tallied, I hope the incredibly restrictive approach to testing gets the attention it deserves.

It's good that the coronavirus happened on Trump's watch. I doubt any other politician would have handled in a significantly different way, but Trump will receive all the blame and it will hit him in November.  It's important to keep up the full court press criticism on Trump, so that low-information voters can be motivated to do the right thing.

Well, I just came back from Universe 2, where Hillary won the 2016 election.  The bad news is that instead of COVID-19, that universe was dealing with Armaggedon.  Fortunately one of our nukes hit the Wuhan seafood market and that pretty much ended the chain of transmission.

But it does show that a different politician would have handled it differently.

BC

[Mick]

BC, question for you re: the title of this thread.  You convinced me that the coronavirus didn't show up early in the SF Bay Area a few threads back.  I'd mentioned that about 1/2 dozen people I'm close to had symptoms similar to COVID-19, myself included.

Based upon the lack of antibodies in the Stanford survey and the fact that they didn't show up until the third week of February, your conclusion -- and my conclusion -- was that the coronavirus had not showed up early in the SF Bay Area.  Now I read that, not only was the first American COVID death on Feb 6, but that person had no connections with China, and in fact was considered a community transmission.  And there was another COVID death on Feb 17, same circumstances.

https://www.nytimes.com/2020/04/22/us/sa...death.html

Based on that new evidence, would you revise your opinion?  Do you think the coronavirus was circulating in Santa Clara County sometime in January, or even earlier?

[Mick]

BC, question for you re: the title of this thread.  You convinced me that the coronavirus didn't show up early in the SF Bay Area a few threads back.  I'd mentioned that about 1/2 dozen people I'm close to had symptoms similar to COVID-19, myself included.

Based upon the lack of antibodies in the Stanford survey and the fact that they didn't show up until the third week of February, your conclusion -- and my conclusion -- was that the coronavirus had not showed up early in the SF Bay Area.  Now I read that, not only was the first American COVID death on Feb 6, but that person had no connections with China, and in fact was considered a community transmission.  And there was another COVID death on Feb 17, same circumstances.

https://www.nytimes.com/2020/04/22/us/sa...death.html

Based on that new evidence, would you revise your opinion?  Do you think the coronavirus was circulating in Santa Clara County sometime in January, or even earlier?

[dabigv13]

Not BC but I'll take the question. If we presume the "Stanford antibody study" is close to correct, the upper bound of prior exposure was about 1 out of 25 people. And that's from March. In January there may have been a few cases, but the odds it was you or someone you know is very slim. Like one in a million. Plenty more vanilla flu or other URI viruses than this.

[dabigv13]

Not BC but I'll take the question. If we presume the "Stanford antibody study" is close to correct, the upper bound of prior exposure was about 1 out of 25 people. And that's from March. In January there may have been a few cases, but the odds it was you or someone you know is very slim. Like one in a million. Plenty more vanilla flu or other URI viruses than this.

[BostonCard]

I think he's referring to a different Stanford study (note, it didn't measure antibodies, it was a PCR study of stored respiratory samples that were negative for other pathogens.

https://jamanetwork.com/journals/jama/fu...ultClick=1

They sampled ~3000 respiratory samples (nasopharyngeal and bronch) between Jan 1 and Feb 29, and found only two positive samples, both in the second to last week of February.

Obviously now we have at least one case that dates back to Feb 6 (and probably means she was infected in late January).

So how to reconcile the two sets of facts.  One possibility is sampling.  Stanford was collecting 300 - 500 samples a week during that period of time.  Getting zero positive tests would mean the confidence interval around the proportion is 0 to 0.9%.  Assuming the population reflects individuals in the Bay Area that display flu-like symptoms, it would be easy to envision a rate within that interval producing no positives in the study, but that still leaving many people out in the community, of which only one might have died.

Second possibility is that at the time it was a very localized cluster that wouldn't have normally gone to Stanford hospital for testing.  Same county, but there are a lot of hospitals in San Jose closer than Stanford, and if the cluster hadn't yet spread more widely, Stanford wouldn't see it.

The third possibility is that there is a methodological flaw in the Stanford study.  In order to cut down on their PCR kits, the Stanford researchers pooled samples together (and if any of the pools was positive, evaluated the individual samples).  If the pooling diluted the samples and decreased the sensitivity, it is possible that they would have missed cases.


Apparently California is relaxing restrictions for COVID testing, so if you do get serology, please do report your results (if you are ok doing so on a semi-anonymous forum).  Curious minds want to know!

BC

[BostonCard]

I think he's referring to a different Stanford study (note, it didn't measure antibodies, it was a PCR study of stored respiratory samples that were negative for other pathogens.

https://jamanetwork.com/journals/jama/fu...ultClick=1

They sampled ~3000 respiratory samples (nasopharyngeal and bronch) between Jan 1 and Feb 29, and found only two positive samples, both in the second to last week of February.

Obviously now we have at least one case that dates back to Feb 6 (and probably means she was infected in late January).

So how to reconcile the two sets of facts.  One possibility is sampling.  Stanford was collecting 300 - 500 samples a week during that period of time.  Getting zero positive tests would mean the confidence interval around the proportion is 0 to 0.9%.  Assuming the population reflects individuals in the Bay Area that display flu-like symptoms, it would be easy to envision a rate within that interval producing no positives in the study, but that still leaving many people out in the community, of which only one might have died.

Second possibility is that at the time it was a very localized cluster that wouldn't have normally gone to Stanford hospital for testing.  Same county, but there are a lot of hospitals in San Jose closer than Stanford, and if the cluster hadn't yet spread more widely, Stanford wouldn't see it.

The third possibility is that there is a methodological flaw in the Stanford study.  In order to cut down on their PCR kits, the Stanford researchers pooled samples together (and if any of the pools was positive, evaluated the individual samples).  If the pooling diluted the samples and decreased the sensitivity, it is possible that they would have missed cases.


Apparently California is relaxing restrictions for COVID testing, so if you do get serology, please do report your results (if you are ok doing so on a semi-anonymous forum).  Curious minds want to know!

BC

[Mick]

I think he's referring to a different Stanford study (note, it didn't measure antibodies, it was a PCR study of stored respiratory samples that were negative for other pathogens.

https://jamanetwork.com/journals/jama/fu...ultClick=1

They sampled ~3000 respiratory samples (nasopharyngeal and bronch) between Jan 1 and Feb 29, and found only two positive samples, both in the second to last week of February.

Obviously now we have at least one case that dates back to Feb 6 (and probably means she was infected in late January).

So how to reconcile the two sets of facts.  One possibility is sampling.  Stanford was collecting 300 - 500 samples a week during that period of time.  Getting zero positive tests would mean the confidence interval around the proportion is 0 to 0.9%.  Assuming the population reflects individuals in the Bay Area that display flu-like symptoms, it would be easy to envision a rate within that interval producing no positives in the study, but that still leaving many people out in the community, of which only one might have died.

Second possibility is that at the time it was a very localized cluster that wouldn't have normally gone to Stanford hospital for testing.  Same county, but there are a lot of hospitals in San Jose closer than Stanford, and if the cluster hadn't yet spread more widely, Stanford wouldn't see it.

The third possibility is that there is a methodological flaw in the Stanford study.  In order to cut down on their PCR kits, the Stanford researchers pooled samples together (and if any of the pools was positive, evaluated the individual samples).  If the pooling diluted the samples and decreased the sensitivity, it is possible that they would have missed cases.


Apparently California is relaxing restrictions for COVID testing, so if you do get serology, please do report your results (if you are ok doing so on a semi-anonymous forum).  Curious minds want to know!

BC

OK, I'll get a referral from my PCP and share the results.

[Mick]

I think he's referring to a different Stanford study (note, it didn't measure antibodies, it was a PCR study of stored respiratory samples that were negative for other pathogens.

https://jamanetwork.com/journals/jama/fu...ultClick=1

They sampled ~3000 respiratory samples (nasopharyngeal and bronch) between Jan 1 and Feb 29, and found only two positive samples, both in the second to last week of February.

Obviously now we have at least one case that dates back to Feb 6 (and probably means she was infected in late January).

So how to reconcile the two sets of facts.  One possibility is sampling.  Stanford was collecting 300 - 500 samples a week during that period of time.  Getting zero positive tests would mean the confidence interval around the proportion is 0 to 0.9%.  Assuming the population reflects individuals in the Bay Area that display flu-like symptoms, it would be easy to envision a rate within that interval producing no positives in the study, but that still leaving many people out in the community, of which only one might have died.

Second possibility is that at the time it was a very localized cluster that wouldn't have normally gone to Stanford hospital for testing.  Same county, but there are a lot of hospitals in San Jose closer than Stanford, and if the cluster hadn't yet spread more widely, Stanford wouldn't see it.

The third possibility is that there is a methodological flaw in the Stanford study.  In order to cut down on their PCR kits, the Stanford researchers pooled samples together (and if any of the pools was positive, evaluated the individual samples).  If the pooling diluted the samples and decreased the sensitivity, it is possible that they would have missed cases.


Apparently California is relaxing restrictions for COVID testing, so if you do get serology, please do report your results (if you are ok doing so on a semi-anonymous forum).  Curious minds want to know!

BC

OK, I'll get a referral from my PCP and share the results.

[M T]

The very first death known to date, and we don't know who (or where) she got it from.
Is this a cautionary tale that test & trace is going to be harder than imagined?  It may be the only tool we have, but it may be dull & leaky.

The only cases that initiate a chain of testing & tracing are symptomatic cases.
So person A shows up with symptoms.  I'd bet a lot of the 80% mild symptomatic cases don't go to their doctor for a few days. 
For tracking, you need to look backward in time for all contacts over two weeks before symptoms start - perhaps that's 18 days (you have to figure out who they are, find them, and get them to be tested). 

Test all of them, right?
First, how many people do you think you are near in any 2 or 3 week period?   How long would it take to contact them?  How much expense is it for them to interrupt what they're doing and go get tested?  How much will the testing cost (and who pays it)?    (By the way, Dignity Health in the Bay Area is offering 15 minute results for COVID-19.  SCC has just gotten under 2 days for the average time for results.)


But based on PCR tests on symptomatic patients, PCR tests on an infected case are going to be negative 20% of the time after a week, 50% of the time after two weeks, 70% at 18 days.  I'd have to guess you'd get negatives more often on any truly asymptomatic case.

The quality of the antibody tests is in flux and I hesitate to quote any numbers.  I believe they also have trouble detecting the antibodies in the mild cases.

In short, I believe the tracking is going to be challenged by false negatives.

You might be thinking that maybe false negatives really just indicate that person wasn't very infectious anyway.  They may not be infections AT THE TIME OF THE TEST.  But they may have infected others previously.  But, because they test negative now, the search stops.

The search may stop but any asymptomatic spread continues until one of them is symptomatic.  When another symptomatic case pops up, we play Whack-a-Mole again.

[M T]

The very first death known to date, and we don't know who (or where) she got it from.
Is this a cautionary tale that test & trace is going to be harder than imagined?  It may be the only tool we have, but it may be dull & leaky.

The only cases that initiate a chain of testing & tracing are symptomatic cases.
So person A shows up with symptoms.  I'd bet a lot of the 80% mild symptomatic cases don't go to their doctor for a few days. 
For tracking, you need to look backward in time for all contacts over two weeks before symptoms start - perhaps that's 18 days (you have to figure out who they are, find them, and get them to be tested). 

Test all of them, right?
First, how many people do you think you are near in any 2 or 3 week period?   How long would it take to contact them?  How much expense is it for them to interrupt what they're doing and go get tested?  How much will the testing cost (and who pays it)?    (By the way, Dignity Health in the Bay Area is offering 15 minute results for COVID-19.  SCC has just gotten under 2 days for the average time for results.)


But based on PCR tests on symptomatic patients, PCR tests on an infected case are going to be negative 20% of the time after a week, 50% of the time after two weeks, 70% at 18 days.  I'd have to guess you'd get negatives more often on any truly asymptomatic case.

The quality of the antibody tests is in flux and I hesitate to quote any numbers.  I believe they also have trouble detecting the antibodies in the mild cases.

In short, I believe the tracking is going to be challenged by false negatives.

You might be thinking that maybe false negatives really just indicate that person wasn't very infectious anyway.  They may not be infections AT THE TIME OF THE TEST.  But they may have infected others previously.  But, because they test negative now, the search stops.

The search may stop but any asymptomatic spread continues until one of them is symptomatic.  When another symptomatic case pops up, we play Whack-a-Mole again.

[oldalum]

I think you are right, you can't trace casual contacts (like sharing an elevator, being in the same store). So I think we are going to continue to have to do social distancing at least for casual contacts, and have a policy of wearing masks outside of the house, and businesses will have to be like grocery stores are now, to cut down on that asymptomatic transmission as much as possible. Higher-risk contact tracing (e.g., haircuts, dentists and dental hygienists, meeting in person with business people like real estate agents or bankers) will continue to be possible because people will remember those contacts and the workers will need to keep logs of their clients; workers with constant exposure to the public may need to be surveillance tested regularly (like sex workers!).

[oldalum]

I think you are right, you can't trace casual contacts (like sharing an elevator, being in the same store). So I think we are going to continue to have to do social distancing at least for casual contacts, and have a policy of wearing masks outside of the house, and businesses will have to be like grocery stores are now, to cut down on that asymptomatic transmission as much as possible. Higher-risk contact tracing (e.g., haircuts, dentists and dental hygienists, meeting in person with business people like real estate agents or bankers) will continue to be possible because people will remember those contacts and the workers will need to keep logs of their clients; workers with constant exposure to the public may need to be surveillance tested regularly (like sex workers!).

[magnus]

I think you are right, you can't trace casual contacts (like sharing an elevator, being in the same store). So I think we are going to continue to have to do social distancing at least for casual contacts, and have a policy of wearing masks outside of the house, and businesses will have to be like grocery stores are now, to cut down on that asymptomatic transmission as much as possible. Higher-risk contact tracing (e.g., haircuts, dentists and dental hygienists, meeting in person with business people like real estate agents or bankers) will continue to be possible because people will remember those contacts and the workers will need to keep logs of their clients; workers with constant exposure to the public may need to be surveillance tested regularly (like sex workers!).

The only case I've heard about for US contact tracing was the 1st patient in WA.  They contacted and sampled 60 "close contacts" (defined by anyone who interacted with him for more than 10 minutes).  But that didn't find a single positive connection and unfortunately did not break the transmission chain.

[magnus]

I think you are right, you can't trace casual contacts (like sharing an elevator, being in the same store). So I think we are going to continue to have to do social distancing at least for casual contacts, and have a policy of wearing masks outside of the house, and businesses will have to be like grocery stores are now, to cut down on that asymptomatic transmission as much as possible. Higher-risk contact tracing (e.g., haircuts, dentists and dental hygienists, meeting in person with business people like real estate agents or bankers) will continue to be possible because people will remember those contacts and the workers will need to keep logs of their clients; workers with constant exposure to the public may need to be surveillance tested regularly (like sex workers!).

The only case I've heard about for US contact tracing was the 1st patient in WA.  They contacted and sampled 60 "close contacts" (defined by anyone who interacted with him for more than 10 minutes).  But that didn't find a single positive connection and unfortunately did not break the transmission chain.

[BostonCard]

Testing and tracing doesn't have to be perfect, they just have to be good enough to reduce R(t) to below 1.  Suppose the baseline R0 is 2.5 (a reasonable estimate for COVID-19).  That means that absent any intervention, every infected patient transmits the infection to 2.5 other people.  You don't have to intercept all of those chains of transmission to keep the infection stable; you just have to intercept 1.5 of those transmission chains so that the R(t) gets down to 1, in which case each infected patient will infect only one other patient and the infection rate remains stable.  If you can drive R(t) to slightly below 1 the infection rate will decline over time.

BC

[BostonCard]

Testing and tracing doesn't have to be perfect, they just have to be good enough to reduce R(t) to below 1.  Suppose the baseline R0 is 2.5 (a reasonable estimate for COVID-19).  That means that absent any intervention, every infected patient transmits the infection to 2.5 other people.  You don't have to intercept all of those chains of transmission to keep the infection stable; you just have to intercept 1.5 of those transmission chains so that the R(t) gets down to 1, in which case each infected patient will infect only one other patient and the infection rate remains stable.  If you can drive R(t) to slightly below 1 the infection rate will decline over time.

BC

[magnus]

More on the first case, a 57 year old woman from San Jose.

https://www.mercurynews.com/2020/04/23/s...-19-death/
(sorry, paywall)

It mentions that her most recent travel was to Oregon in January, but that her closest contacts have no clue where/when she could have contracted the virus.  

Wonder if they'll find any splash pattern near her home/work (Fremont).

[magnus]

More on the first case, a 57 year old woman from San Jose.

https://www.mercurynews.com/2020/04/23/s...-19-death/
(sorry, paywall)

It mentions that her most recent travel was to Oregon in January, but that her closest contacts have no clue where/when she could have contracted the virus.  

Wonder if they'll find any splash pattern near her home/work (Fremont).