PlagueWatch 2020-23 - Coronavirus

[Bob Green]

Saturday morning numbers reflect 562 new confirmed cases in Virginia. Death toll increased by 27 to 258. In my opinion, the numbers have yet to peak here. Social distancing and partial lockdown measures need to continue.

[CDu]

A report from the Boston Globe regarding Chelsea which seems to be a hot bed of infection.

https://www.bostonglobe.com/2020/04/...e-coronavirus/

This report found that 32% of people who had not tested positive for COVID 19 had antibodies.

The pilot study was done by MGH researchers who set up shop in a town square in Chelsea and took samples from 200 "random"? people on the street. Those who had tested positive using the swab technique were excluded.

"The 200 participants generally appeared healthy, but about half told the doctors they had had at least one symptom of COVID-19 in the past four weeks. Public health experts already knew Chelsea had the state’s highest rate of confirmed COVID-19 cases and that the actual rate was probably higher. At least 39 residents have died from the virus, and 712 had tested positive as of Tuesday, a rate of about 1,900 cases per 100,000 residents, or almost 2 percent."

I doubt this is reflective of other areas in the country, but 32% is way closer to herd immunity (>70%) than other reports. Trying to look at the positives here.

Yeah there are almost certainly some communities where 25% or more of the population have been infected. But it is almost certainly not true nationally, as Chelsea is apparently one of the most heavily infected places in the country.

[CDu]

To expand on that MGH Chelsea study:

Chelsea has 2% of its population confirmed infected. Previous research suggests that the true infection rate is 2 to 10 times higher than the confirmed cases. That would suggest their true infection rate is anywhere from 4-20%. A true 33% population infection rate based on the 200-person sample would be outside the 95% confidence interval.

So let’s take a look at that study. They excluded people who tested positive with a swab. That is good, but it highlights a question. It is unclear whether they excluded any contacts of those positive tests. If I test positive, my wife is more likely to have antibodies than someone in the general population (family members of infected people are way more likely to have previously been infected and more likely to get infected if they haven’t been, by virtue of contact patterns). I would hope that they only allowed tests of one person per residence, and excluded all residences for whom one tested positive on the swab test. But I don’t know that (BostonDevil, do you know?). And if not, that would overestimate things.

Even if the 32% is correct, that would be potentially good news for Chelsea depending upon duration of immunity. But it also would still suggest the case fatality rate is still over 0.3% (and counting) based on Chelsea’s current COVID death data. If the data are an overestimate based on any bias in the sample, it suggests Chelsea still is further from herd immunity and that the case fatality rate is even higher.

From a broader perspective, even if we assume the 33% is correct and take the ratio of expected cases to confirmed, we get about 16.5. Taking that nationally, we would have over 11 million cases in the US, or about 3.5% of the population. And the case fatality rate would be about 0.32%.

[MChambers]

Here's an interesting article from The Atlantic about what life may look like after social distancing, It's written by a former DHS official.

Over the past week, I’ve been informally contacting friends and colleagues in a variety of fields—sports, travel, architecture, entertainment, arts, the clergy, and more—to ask them how their world might look after social distancing. The answer: It looks weird.

We will get used to seeing temperature-screening stations at public venues. If America’s testing capacity improves and results come back quickly, don’t be surprised to see nose swabs at airports. Airlines may contemplate whether flights can be reserved for different groups of passengers—either high- or low-risk. Mass-transit systems will set new rules; don’t be surprised if they mandate masks too.

https://www.theatlantic.com/ideas/ar...awaits/610090/

[MChambers]

The Atlantic is on a roll the last couple of days. Here's a very thoughtful article by Ed Yong, one of my favorite science writers, about what life after social distancing may look like. In short, it won't be simple and things won't be getting back to normal anytime soon.

the only viable endgame is to play whack-a-mole with the coronavirus, suppressing it until a vaccine can be produced. With luck, that will take 18 to 24 months. During that time, new outbreaks will probably arise. Much about that period is unclear, but the dozens of experts whom I have interviewed agree that life as most people knew it cannot fully return. “I think people haven’t understood that this isn’t about the next couple of weeks,” said Michael Osterholm, an infectious-disease epidemiologist at the University of Minnesota. “This is about the next two years.”

https://www.theatlantic.com/health/a...normal/609940/

[Bostondevil]

To expand on that MGH Chelsea study:

Chelsea has 2% of its population confirmed infected. Previous research suggests that the true infection rate is 2 to 10 times higher than the confirmed cases. That would suggest their true infection rate is anywhere from 4-20%. A true 33% population infection rate based on the 200-person sample would be outside the 95% confidence interval.

So let’s take a look at that study. They excluded people who tested positive with a swab. That is good, but it highlights a question. It is unclear whether they excluded any contacts of those positive tests. If I test positive, my wife is more likely to have antibodies than someone in the general population (family members of infected people are way more likely to have previously been infected and more likely to get infected if they haven’t been, by virtue of contact patterns). I would hope that they only allowed tests of one person per residence, and excluded all residences for whom one tested positive on the swab test. But I don’t know that (BostonDevil, do you know?). And if not, that would overestimate things.

Even if the 32% is correct, that would be potentially good news for Chelsea depending upon duration of immunity. But it also would still suggest the case fatality rate is still over 0.3% (and counting) based on Chelsea’s current COVID death data. If the data are an overestimate based on any bias in the sample, it suggests Chelsea still is further from herd immunity and that the case fatality rate is even higher.

From a broader perspective, even if we assume the 33% is correct and take the ratio of expected cases to confirmed, we get about 16.5. Taking that nationally, we would have over 11 million cases in the US, or about 3.5% of the population. And the case fatality rate would be about 0.32%.

I do not. I am aware of but not acquainted with the lead investigator. I do know that MGH through the local health center has long had a research presence in Chelsea (I've analyzed some of their data ) , so, I would be interested to see how many of the people willing to participate are already patients at the MGH-Chelsea Health Center. BD's a priori belief? A lot, more than would be predicted by chance. Not saying that would necessarily affect the percentages, but I would be interested in that data. Given the assurances of anonymity and HIPAA rules, they probably didn't collect it though.

[CDu]

I do not. I am aware of but not acquainted with the lead investigator. I do know that MGH through the local health center has long had a research presence in Chelsea (I've analyzed some of their data ) , so, I would be interested to see how many of the people willing to participate are already patients at the MGH-Chelsea Health Center. BD's a priori belief? A lot, more than would be predicted by chance. Not saying that would necessarily affect the percentages, but I would be interested in that data. Given the assurances of anonymity and HIPAA rules, they probably didn't collect it though.

Yeah, that gets at a second question, which is the randomness of the sample in general. I hadn’t thought about the “former/current MGH patient participants biasing the sample” possibility. If participants were more likely than average to be recent MGH patients, that would probably bias the sample upwards in terms of risk as well (greater risk of getting infected if going to the hospital). Obviously we don’t know if that is the case here.

[Bostondevil]

Yeah, that gets at a second question, which is the randomness of the sample in general. I hadn’t thought about the “former/current MGH patient participants biasing the sample” possibility. If participants were more likely than average to be recent MGH patients, that would probably bias the sample upwards in terms of risk as well (greater risk of getting infected if going to the hospital). Obviously we don’t know if that is the case here.

The MGH-Chelsea is an outpatient clinic. They recruit there for all sorts of studies. I just think a willingness to participate may be affected by having done it before and found out that nothing bad happens when you do. Chelsea is 2/3rds hispanic with large numbers of recent immigrants.

[Bostondevil]

We know that blacks and hispanics are making up a larger portion of the confirmed cases of Covid 19 than would be predicted by a random sample, but I'm not buying that race matters until I see rates adjusted for SEC and other factors, which we won't get for awhile.

[CDu]

The MGH-Chelsea is an outpatient clinic. They recruit there for all sorts of studies. I just think a willingness to participate may be affected by having done it before and found out that nothing bad happens when you do. Chelsea is 2/3rds hispanic with large numbers of recent immigrants.

Thanks for the clarification. The question remains though that if regular visitors to that clinic are more likely to participate, the risk of bias is higher. But if it is just “previous study participants are more likely to participate” then I agree it would be unclear if any bias related to that issue is present.

[Acymetric]

We know that blacks and hispanics are making up a larger portion of the confirmed cases of Covid 19 than would be predicted by a random sample, but I'm not buying that race matters until I see rates adjusted for SEC and other factors, which we won't get for awhile.

Maybe a stupid question, but what does SEC stand for here?

[JasonEvans]

The pilot study was done by MGH researchers who set up shop in a town square in Chelsea and took samples from 200 "random"? people on the street.

One important note about this study -- by setting up shop "in a town square" you are inherently sampling a group that is more at risk for catching COVID. You are sampling people who go outside and go into a public place like a town square. There are many, many people who are staying indoors virtually all the time or who only go to the market or some other necessary place when they come out. So, I am not surprised that we found a high incidence of infection in a place where there is a lot of COVID and a survey group that is almost exclusively risk-taking people who are not practicing the same level of social distancing as the rest of us.

[JasonEvans]

Maybe a stupid question, but what does SEC stand for here?

I believe it is secondary containment... either that or Socio-Economic Classification

[MChambers]

I believe it is secondary containment... either that or Socio-Economic Classification

Not Southeastern Coronavirus?

[rsvman]

A report from the Boston Globe regarding Chelsea which seems to be a hot bed of infection.

https://www.bostonglobe.com/2020/04/...e-coronavirus/

This report found that 32% of people who had not tested positive for COVID 19 had antibodies.

The pilot study was done by MGH researchers who set up shop in a town square in Chelsea and took samples from 200 "random"? people on the street. Those who had tested positive using the swab technique were excluded.

"The 200 participants generally appeared healthy, but about half told the doctors they had had at least one symptom of COVID-19 in the past four weeks. Public health experts already knew Chelsea had the state’s highest rate of confirmed COVID-19 cases and that the actual rate was probably higher. At least 39 residents have died from the virus, and 712 had tested positive as of Tuesday, a rate of about 1,900 cases per 100,000 residents, or almost 2 percent."

I doubt this is reflective of other areas in the country, but 32% is way closer to herd immunity (>70%) than other reports. Trying to look at the positives here.

I just found out yesterday that some companies were apparently just "re-branding" general coronavirus serology tests as "covid-19" serology tests. In other words, these so-called COVID-19 antibody tests were actually not specific for SARS-CoV-2, and could be tripped positive by infection with any of the random circulating coronaviruses. At least one of these manufacturers is actually being charged with wrongdoing over this.

It's a big problem because I happen to know that this year was a pretty big year for the garden-variety coronaviruses that circulate every year and that, by some estimations, are the second most common cause of "common cold." I have seen lots of kids with one of these other coronaviruses this season; about a month and a half ago I took care of a kid that had TWO of them at the same time.

Any "COVID-19 antibody test" that is not specific for SARS-CoV-2 is worthless, and will overestimate SARS-CoV-2 infection rate by a LONG way.



On a more personal note, I think I had a moderate-risk exposure yesterday afternoon. The patient I was helping to care for had previously tested negative, so was not on contact precautions or in any kind of special isolation. As the days wore on, his disease more and more resembled COVID-19, but everybody was reassured by the negative testing. Because he has mental deficiencies, he does not even try to cover his cough. When I saw him yesterday I was wearing a cheap, poorly fitted mask that I had already been wearing for four days (probably better than nothing, but it was leaking like crazy because I could see my breath fog up on my glasses). While I looking at him he had a coughing fit pretty much in my face (I was a few feet away). I had no eye protection.

At that point I moved to the side of the room AWAY from the direction he was coughing and continued speaking with his mother. During the rest of the time I was in there he had three or four more marked coughing spells (again not covering his mouth in any way).
Overnight between yesterday and today he spiked a fever to 40.6. I also found out that whoever did the swab for his original SARS-CoV-2 testing did it wrong. Our test only works with nasopharyngeal swabbing. Mom said whoever did the test only swabbed the front of the nose.

I suspect he had COVID-19 all along. We will not know until Monday afternoon. In the meantime, I am now doing twice daily body temperatures and symptom monitoring, and may have to be quarantined if his test comes back positive.

This illustrates some of the problems we are facing on the front lines. I guess I should've known better than to trust that the test was properly performed.

Time will tell. Maybe he has something else. We are testing for other respiratory viruses in the meantime. I am highly suspicious that he has COVID-19, though. The only thing that calms my mind a bit is a report from the MMWR I read yesterday morning about a patient admitted to an adult hospital with symptoms not suspected to be COVID-19 who was later found out to have it and was transferred to another hospital. They did an investigation at the original hospital among all the people who provided care to that patient and found that only one of the providers who had "moderate risk exposure" became infected. Risk factors for infection in caregivers were presence during aerosol-generating procedures and amount of time spent in close contact. A lot of the providers never even wore masks at all and did not become infected. So, I am holding out hope that: a) he will turn out to have something else, and, if not, that b) my contact, being only a few minutes and with me wearing at least a cheap surgical mask, will not be enough to get me infected.

[sagegrouse]

We know that blacks and hispanics are making up a larger portion of the confirmed cases of Covid 19 than would be predicted by a random sample, but I'm not buying that race matters until I see rates adjusted for SEC and other factors, which we won't get for awhile.

Yes, controlling somehow for socioeconomic status would be an important step. Lower SE status seems to present several concerns (I am making this up on the spot):

• Crowding, leading to higher infection rates with more people living in close proximity.
• Poor health factors, such as obesity, diabetes and hyper-tension. When we get to a point where we can evaluate those who became seriously ill or died, we will understand better how many normally health adults have had serious cases. Some have -- such as essentially heart attacks among people in their 30s and 40s in Italy.
• Access to health care, somewhat related to the point above.
• Knowledge (and acceptance) of what must be done to minimize the spread of COVID-19.

[MChambers]

I just found out yesterday that some companies were apparently just "re-branding" general coronavirus serology tests as "covid-19" serology tests. In other words, these so-called COVID-19 antibody tests were actually not specific for SARS-CoV-2, and could be tripped positive by infection with any of the random circulating coronaviruses. At least one of these manufacturers is actually being charged with wrongdoing over this.

It's a big problem because I happen to know that this year was a pretty big year for the garden-variety coronaviruses that circulate every year and that, by some estimations, are the second most common cause of "common cold." I have seen lots of kids with one of these other coronaviruses this season; about a month and a half ago I took care of a kid that had TWO of them at the same time.

Any "COVID-19 antibody test" that is not specific for SARS-CoV-2 is worthless, and will overestimate SARS-CoV-2 infection rate by a LONG way.



On a more personal note, I think I had a moderate-risk exposure yesterday afternoon. The patient I was helping to care for had previously tested negative, so was not on contact precautions or in any kind of special isolation. As the days wore on, his disease more and more resembled COVID-19, but everybody was reassured by the negative testing. Because he has mental deficiencies, he does not even try to cover his cough. When I saw him yesterday I was wearing a cheap, poorly fitted mask that I had already been wearing for four days (probably better than nothing, but it was leaking like crazy because I could see my breath fog up on my glasses). While I looking at him he had a coughing fit pretty much in my face (I was a few feet away). I had no eye protection.

At that point I moved to the side of the room AWAY from the direction he was coughing and continued speaking with his mother. During the rest of the time I was in there he had three or four more marked coughing spells (again not covering his mouth in any way).
Overnight between yesterday and today he spiked a fever to 40.6. I also found out that whoever did the swab for his original SARS-CoV-2 testing did it wrong. Our test only works with nasopharyngeal swabbing. Mom said whoever did the test only swabbed the front of the nose.

I suspect he had COVID-19 all along. We will not know until Monday afternoon. In the meantime, I am now doing twice daily body temperatures and symptom monitoring, and may have to be quarantined if his test comes back positive.

This illustrates some of the problems we are facing on the front lines. I guess I should've known better than to trust that the test was properly performed.

Time will tell. Maybe he has something else. We are testing for other respiratory viruses in the meantime. I am highly suspicious that he has COVID-19, though. The only thing that calms my mind a bit is a report from the MMWR I read yesterday morning about a patient admitted to an adult hospital with symptoms not suspected to be COVID-19 who was later found out to have it and was transferred to another hospital. They did an investigation at the original hospital among all the people who provided care to that patient and found that only one of the providers who had "moderate risk exposure" became infected. Risk factors for infection in caregivers were presence during aerosol-generating procedures and amount of time spent in close contact. A lot of the providers never even wore masks at all and did not become infected. So, I am holding out hope that: a) he will turn out to have something else, and, if not, that b) my contact, being only a few minutes and with me wearing at least a cheap surgical mask, will not be enough to get me infected.

The serology tests certainly don't seem to very accurate yet, even the ones that are specific to the novel coronavirus.

Very sorry to hear about your potential exposure. Will be thinking of you.

[budwom]

Here's an interesting article from The Atlantic about what life may look like after social distancing, It's written by a former DHS official.

Over the past week, I’ve been informally contacting friends and colleagues in a variety of fields—sports, travel, architecture, entertainment, arts, the clergy, and more—to ask them how their world might look after social distancing. The answer: It looks weird.

We will get used to seeing temperature-screening stations at public venues. If America’s testing capacity improves and results come back quickly, don’t be surprised to see nose swabs at airports. Airlines may contemplate whether flights can be reserved for different groups of passengers—either high- or low-risk. Mass-transit systems will set new rules; don’t be surprised if they mandate masks too.

https://www.theatlantic.com/ideas/ar...awaits/610090/

But given the (evident) fact that asymptomatic people can spread the virus, and there are assumed to be quite a few of these people, what exactly does taking temperatures accomplish? Better than nothing, I guess, but hardly reassuring in any meaningful way, right?

[MChambers]

But given the (evident) fact that asymptomatic people can spread the virus, and there are assumed to be quite a few of these people, what exactly does taking temperatures accomplish? Better than nothing, I guess, but hardly reassuring in any meaningful way, right?

Yes, I agree. But I think we see temperature stations, sensible or not. The article is worth your time.

[CDu]

I believe it is secondary containment... either that or Socio-Economic Classification

Socioeconomics is correct.