Covid-19: How it Spreads and How it can be Slowed

asicer said:
Looks like New Zealand got rid of it:
https://www.cbsnews.com/news/new-zealand-declares-end-coronavirus-prime-minister-jacinda-ardern/

BTW, how did Switzerland's strategy turn out?
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They had 16 new cases yesterday. Nationwide.

Switzerland_6_9_20.jpg
 
weilke said:
They had 16 new cases yesterday. Nationwide.
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Did they stick with keeping things open, shooting for herd immunity and isolating the vulnerable? Or did they do a course correction somewhere along the way?
 
asicer said:
Did they stick with keeping things open, shooting for herd immunity and isolating the vulnerable? Or did they do a course correction somewhere along the way?
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They partially shutdown, implemented massive testing and tracing, blocked pretty much everyone from entering the country back in February I believe.
And going on for about a month I believe, all new cases have had known transmission sources instead of general community spread.

Tim
 
asicer said:
Did they stick with keeping things open, shooting for herd immunity and isolating the vulnerable? Or did they do a course correction somewhere along the way?
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State of emergency with prohibition on public assemblies, closure of all retail (save for groceries), closure of schools, no religious services, no bars & restaurants etc. Once things started looking up at the end of april, they gradually reopened retail, restaurants and primary schools, allowed increasing numbers in groups etc. All the re-opening activities with common social distancing measures in place.
 
asicer said:
Did they stick with keeping things open, shooting for herd immunity and isolating the vulnerable? Or did they do a course correction somewhere along the way?
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Switzerland didn't keep things open, they locked down. You're probably thinking of Sweden who kept things open. Their per capita death rate is now higher than the US. The guy who designed their response has admitted he thinks they should have done more.
 
Juliet Hotel said:
Switzerland didn't keep things open, they locked down. You're probably thinking of Sweden who kept things open. Their per capita death rate is now higher than the US. The guy who designed their response has admitted he thinks they should have done more.
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The reason I asked is because I had this post in mind:

https://www.pilotsofamerica.com/com...-the-silver-lining.124889/page-3#post-2889261

tspear said:
Note: This following info is from a poster in Switzerland. So cannot verify the veracity, but does match the little press I have seen.
Switzerland is also taking a different approach. They are not shutting down, but isolating the vulnerable population (over 60, health concerns...). Schools stayed open, when closing, they are offering child care so grandparents do not watch the kids, restaurants, gatherings all continuing. Elderly expected to stay away, join family virtually... The idea is the health system has the capacity to handle the cases based on the lower rate you get with the younger population. This will then basically generate herd based immunity, and make it more manageable when it eventually gets to the vulnerable.
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steingar said:
Since it is common knowledge I'd say yes. You'll find Google very helpful in this regard.
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I wonder when the CDC will google to find your common knowledge.
 
SARS antibodies block coronavirus infections, study shows

https://www.sfchronicle.com/bayarea...ies-block-coronavirus-infections-15331566.php

Abstract

"SARS-CoV-2 is a newly emerged coronavirus responsible for the current COVID-19 pandemic that has resulted in more than 3.7 million infections and 260,000 deaths as of 6 May 20201,2. Vaccine and therapeutic discovery efforts are paramount to curb the pandemic spread of this zoonotic virus. The SARS-CoV-2 spike (S) glycoprotein promotes entry into host cells and is the main target of neutralizing antibodies. Here we describe multiple monoclonal antibodies targeting SARS-CoV-2 S identified from memory B cells of an individual who was infected with SARS-CoV in 2003. One antibody, named S309, potently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2 by engaging the S receptor-binding domain. Using cryo-electron microscopy and binding assays, we show that S309 recognizes a glycan-containing epitope that is conserved within the sarbecovirus subgenus, without competing with receptor attachment. Antibody cocktails including S309 along with other antibodies identified here further enhanced SARS-CoV-2 neutralization and may limit the emergence of neutralization-escape mutants. These results pave the way for using S309- and S309-containing antibody cocktails for prophylaxis in individuals at high risk of exposure or as a post-exposure therapy to limit or treat severe disease."​

The paper:

https://www.nature.com/articles/s41586-020-2349-y_reference.pdf

"This is a PDF file of a peer-reviewed paper that has been accepted for publication. Although unedited, the content has been subjected to preliminary formatting."​
 
Palmpilot said:
SARS antibodies block coronavirus infections, study shows

https://www.sfchronicle.com/bayarea...ies-block-coronavirus-infections-15331566.php

Abstract

"SARS-CoV-2 is a newly emerged coronavirus responsible for the current COVID-19 pandemic that has resulted in more than 3.7 million infections and 260,000 deaths as of 6 May 20201,2. Vaccine and therapeutic discovery efforts are paramount to curb the pandemic spread of this zoonotic virus. The SARS-CoV-2 spike (S) glycoprotein promotes entry into host cells and is the main target of neutralizing antibodies. Here we describe multiple monoclonal antibodies targeting SARS-CoV-2 S identified from memory B cells of an individual who was infected with SARS-CoV in 2003. One antibody, named S309, potently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2 by engaging the S receptor-binding domain. Using cryo-electron microscopy and binding assays, we show that S309 recognizes a glycan-containing epitope that is conserved within the sarbecovirus subgenus, without competing with receptor attachment. Antibody cocktails including S309 along with other antibodies identified here further enhanced SARS-CoV-2 neutralization and may limit the emergence of neutralization-escape mutants. These results pave the way for using S309- and S309-containing antibody cocktails for prophylaxis in individuals at high risk of exposure or as a post-exposure therapy to limit or treat severe disease."​

The paper:

https://www.nature.com/articles/s41586-020-2349-y_reference.pdf

"This is a PDF file of a peer-reviewed paper that has been accepted for publication. Although unedited, the content has been subjected to preliminary formatting."​
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Where can I get me some?
 
Palmpilot said:
I posted these links in a thread that is now closed. I was hoping that someone knowledgeable could comment on the methodology and/or conclusions:

Differential Effects of Intervention Timing on COVID-19 Spread in the United States

https://www.medrxiv.org/content/10.1101/2020.05.15.20103655v1.full.pdf
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On a first reading, here are the things that I would look into more deeply.

They do not appear to have compared the counties with and without coercive lockdown measures, which would have been interesting.

Their calculation of the effective Rt does strike me as about right.

They don’t mention the timing in that brief statement of the results but it does agree roughly with what I have observed as well. Social distancing started fairly early, likely based on news reports. There is a general trend toward decreased Rt a few days to weeks later (depends on the state when looked at that way).
 
bflynn said:
My read right now is that warmer weather is tamping this down, like it does with the common cold.
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Out of curiosity, what exactly are you reading to get that?

Certainly hasn’t been true for vast majority of southern states. Arizona is skyrocketing and temps have been around 110F.
 
bbchien said:
The reason for 3 weeks, is, sequestered in the house, one of transmission is covered....(roughly, 11 days x 2)
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Not sure 3 weeks is enough. USS KIDD was at least 14 days out of port when the first case showed up and then started spreading throughout the crew. At 3 weeks they still had plenty of active virus spreading.
 
Fearless Tower said:
Out of curiosity, what exactly are you reading to get that?

Certainly hasn’t been true for vast majority of southern states. Arizona is skyrocketing and temps have been around 110F.
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Yes, likely pretty hard to deconvolve the various factors right now and attribute to one cause or another.
 
Fearless Tower said:
Out of curiosity, what exactly are you reading to get that?
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a post from 3-4 weeks ago? Not a clue what I was specifically looking at. I suspect I was watching the graphs. In mid May, the numbers for Georgia were trending downward despite the state opening up. So businesses were opening and people were and are getting out, but the numbers weren’t really going up. May was about 10-15 degrees warmer, so it seems like a reasonable hypothesis.

Even now, despite so many people being out, the numbers are not even close to the highest numbers.
 
bflynn said:
a post from 3-4 weeks ago? Not a clue what I was specifically looking at. I suspect I was watching the graphs. In mid May, the numbers for Georgia were trending downward despite the state opening up. So businesses were opening and people were and are getting out, but the numbers weren’t really going up. May was about 10-15 degrees warmer, so it seems like a reasonable hypothesis.

Even now, despite so many people being out, the numbers are not even close to the highest numbers.
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While that appears to be true for Georgia, many of the warmer states appear to be making significant new highs in numbers of new cases.

https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html#states

(Scroll down about 1/6 of the way from the top.)
 
Yes, although some of these states, such as Arizona, didn’t ever really have a high to begin with. It’s likely the current spikes are due to people vacationing during Memorial Day as well as quarantine exhaustion.

You cannot confine healthy people indefinitely. Until this year “quarantine” always meant sick people for a reason.
 
Palmpilot said:
While that appears to be true for Georgia, many of the warmer states appear to be making significant new highs in numbers of new cases.

https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html#states

(Scroll down about 1/6 of the way from the top.)
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first, the data is very noisy.

second, increases in reported cases could be caused by increases in the number of test performed. When have the various States reached a point when there was no shortage of testing capacity available?
 
Bob Noel said:
first, the data is very noisy.

second, increases in reported cases could be caused by increases in the number of test performed. When have the various States reached a point when there was no shortage of testing capacity available?
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Bob,

Most of the states showing increases in cases are also getting increases in positivity rate. I do not follow the math well enough to explain it; but assuming I understand it the concepts:
1. If the case counts are increase just due to expanded testing the test positivity rate should be decreasing as you find it harder to find positive cases.
2. Higher positivity rates actually mean that the virus is actually spreading more unchecked and we have less of a handle on the actual cases, and are more likely to be under reporting cases.

Note: I did not check, but another poster posted charts for AZ which makes the situation in AZ look so bad. Case positivity rate, testing rates and case counts are all increasing. But not equally, the positivity rate went from roughly 7% to 40% based over a four week period. Per the poster, this means the number of cases is rapidly increasing.

Tim
 
tspear said:
Bob,

Most of the states showing increases in cases are also getting increases in positivity rate. I do not follow the math well enough to explain it; but assuming I understand it the concepts:
1. If the case counts are increase just due to expanded testing the test positivity rate should be decreasing as you find it harder to find positive cases.
2. Higher positivity rates actually mean that the virus is actually spreading more unchecked and we have less of a handle on the actual cases, and are more likely to be under reporting cases.

Note: I did not check, but another poster posted charts for AZ which makes the situation in AZ look so bad. Case positivity rate, testing rates and case counts are all increasing. But not equally, the positivity rate went from roughly 7% to 40% based over a four week period. Per the poster, this means the number of cases is rapidly increasing.

Tim
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1. What I meant by increased testing causing an increase includes consideration of the scenario of testing not being complete enough. Until there is a surplus of testing capacity, rationing testing will (possibly) miss a number of positive cases. Once there is sufficient testing capacity to test everyone that is showing symptoms and everyone who has been even minimally exposed to someone symptomatic (or positive), then testing beyond that would likely only being testing people who would be negative (unless there are a lot of asymtomatic people).

2. Sure, if the virus is spreading, then you would generally expect more positive results. However, increases in positive rates could simply be the result of better focused testing.

https://www.azdhs.gov/preparedness/...se-epidemiology/covid-19/dashboards/index.php

doesn't seem to indicate a positive rate going from 7% to 40%. The positive rate is noisy week to week. And isn't much higher than the positive rates of some weeks in April.

It looks like Arizona didn't really ramp up testing until May.
 
bflynn said:
Yes, although some of these states, such as Arizona, didn’t ever really have a high to begin with. It’s likely the current spikes are due to people vacationing during Memorial Day as well as quarantine exhaustion.

You cannot confine healthy people indefinitely. Until this year “quarantine” always meant sick people for a reason.
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I wasn't expressing an opinion on whether people should continue to be confined. I just think that's it's important to know what the data really are, however imperfect they may be.
 
Bob Noel said:
1. What I meant by increased testing causing an increase includes consideration of the scenario of testing not being complete enough. Until there is a surplus of testing capacity, rationing testing will (possibly) miss a number of positive cases. Once there is sufficient testing capacity to test everyone that is showing symptoms and everyone who has been even minimally exposed to someone symptomatic (or positive), then testing beyond that would likely only being testing people who would be negative (unless there are a lot of asymtomatic people).

2. Sure, if the virus is spreading, then you would generally expect more positive results. However, increases in positive rates could simply be the result of better focused testing.

https://www.azdhs.gov/preparedness/...se-epidemiology/covid-19/dashboards/index.php

doesn't seem to indicate a positive rate going from 7% to 40%. The positive rate is noisy week to week. And isn't much higher than the positive rates of some weeks in April.

It looks like Arizona didn't really ramp up testing until May.
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One other unknown is selection bias.

In the beginning, the only way a test was going to be administered was if one was sick enough they were going to be admitted to hospital.

Then it was open to all healthcare workers.

Then it became a "testing blitz" open to basically anyone that thought they were exposed(or just curious).

Then it became "Test everyone in Long term care facilities and prisons".

And about halfway through, "tests administered" and "Identified cases " started including not only PCR tests(for active cases) but also Serology tests(for anti bodies).

Timing of results has also changed. IIRC, in the beginning, results took more than a week to come back.

Now the data is annotated "Tests in the past seven days might not be included".

Trying to draw a pattern out of the data that has had all of the above(and more) variation in collecting and definition is not going to be very accurate.
 
'Cases' and 'positivity rate' are not great measures as they are so dependent on testing strategy and availability of tests. So while 'cases' are the earliest indicator, they are noisy and can be thrown off by changes in the testing strategy, testing market and variability in the turn-around times by different large commercial labs.

Patients get admitted to hospitals, admitted to ICUs and intubated based on somewhat stable criteria. The number of inpatient admissions, ICU admissions and intubated patients is not dependent on how many asymptomatic patients you pick up by widespread community testing. And looking at those numbers for AZ, things are not going the right direction:

AZ_inpatients_6_15.jpg


AZ_ICUadmits_6_15.jpg


AZ_ventilators_6_15.jpg
 
tspear said:
Bob,

Most of the states showing increases in cases are also getting increases in positivity rate. I do not follow the math well enough to explain it; but assuming I understand it the concepts:
1. If the case counts are increase just due to expanded testing the test positivity rate should be decreasing as you find it harder to find positive cases.
2. Higher positivity rates actually mean that the virus is actually spreading more unchecked and we have less of a handle on the actual cases, and are more likely to be under reporting cases.

Note: I did not check, but another poster posted charts for AZ which makes the situation in AZ look so bad. Case positivity rate, testing rates and case counts are all increasing. But not equally, the positivity rate went from roughly 7% to 40% based over a four week period. Per the poster, this means the number of cases is rapidly increasing.

Tim
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Only if all things are equal, which they aren't. It's complicated. Plus, early-on there was a lack of tests, so often people were told to just quarantine at home with no test administered. Add the hysteria from the media and every sniffle, in the middle of allergy season, was viewed as "OMG I'm going to die of COVID". Higher positive rates could be people finally realizing that they may have something other than COVID and not getting tested and those with more of the symptoms getting tested now as there are more test kits available.
 
Palmpilot said:
I wasn't expressing an opinion on whether people should continue to be confined. I just think that's it's important to know what the data really are, however imperfect they may be.
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you didn’t mean you specifically, it was a generalized term. I think many people are over with being confined and that is also making the rate go up.

Between vacations and less distancing/mask wear being influenced by warm weather, I don’t think it’s possible to ascertain the impact of temperature.
 
Bob Noel said:
1. What I meant by increased testing causing an increase includes consideration of the scenario of testing not being complete enough. Until there is a surplus of testing capacity, rationing testing will (possibly) miss a number of positive cases. Once there is sufficient testing capacity to test everyone that is showing symptoms and everyone who has been even minimally exposed to someone symptomatic (or positive), then testing beyond that would likely only being testing people who would be negative (unless there are a lot of asymtomatic people).
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Arkansas got Tyson Foods to test everyone at their meat processing plants. They found 200 infected, only one with symptoms. The other 199 had no symptoms; some may have been pre-symptomatic versus asymptomatic though.

NYC did a test last month and found 21.2% had antibodies. So, yes, many are asymptomatic.
 
I have been curious about the reported bump in cases recently, particularly in my state of AZ. So I just downloaded the case data (covidtracking.com) and re-computed the estimates of Rt, the estimated daily analog of R0 for the observed growth of cases in each state. The following is a graph of that estimate by calendar day for each state. AZ seems to have had a bump right around Memorial Day but is heading back down. And in none of the states are the values heading up toward the sort of large values we saw in some states in March and April. (Values above 1, the dotted line, correspond to growth of reported cases whereas values below are decreasing numbers of new cases.)

RtVsDate_June15.png
 
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Parts of Asia that relaxed restrictions without a resurgence in coronavirus cases did these three things

Key Points
  • South Korea and Hong Kong successfully relaxed pandemic restrictions without having another rise in cases by data sharing, using targeted testing and contact tracing.
  • The varying results of efforts across Asia to contain the virus and reopen society present policy options and perhaps lessons for countries behind on the outbreak’s timeline.
  • Public health specialists who spoke with CNBC said they’re not confident U.S. officials are taking note of what’s working and not working in Asia.
 
One doctor's summary of why face masks help, even home-made ones, with links to the evidence.

Excerpt:

"I’m not here to force you to wear a mask, or to call you stupid for not wearing one. I’m just here to show you the evidence that changed my mind. I hope you come to the same conclusion as I did: We don’t have to choose between killing the economy or killing people. With simple face masks in addition to hand washing we can eliminate the virus, reopen the economy, and save thousands of lives all at the same time."​

https://www.facebook.com/james.larson.md/posts/10221384253946100

(Yes, I know it's Facebook, but I take the view that whether a writer knows what he's talking about and presents supporting evidence are far more important than which communications medium he chooses.)

Edit: For reasons that make no sense to me, Facebook took down the post linked above. Fortunately, the author also posted it to his blog:

https://larsonsportsortho.com/are-masks-effective-against-the-coronavirus-disease/

He says that he will also be posting a new version with updated research on his Facebook page:

https://www.facebook.com/james.larson.md
 
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Greg Bockelman said:
That is all well and good but I would still like to know when we might be able to roam freely on the earth, so to say.
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I would like to know that too, but I'm resigned to the fact that it's unanswerable for now. It not only has to do with local or national (ours) regulations, but also regulations in places you might like to roam in the world. Of course there is sneaking out ;), but that's much easier within the country than outside of it.
 
The caveat in these studies is not all homemade masks are equal. Mrs. Steingar made one for me that's 3 layers of cloth and a coffee filter. I'd be surprised if it wasn't nearly as efficacious as an R95, and probably more so than a standard surgical mask. As far as when we'll be able to travel freely, no one really knows the future. Be thankful you're stuck in your home. An acquaintance is stuck in a small town in Brazil right now not knowing when he'll be able to get back.
 
Count me as someone else who won't cower in my home.
 
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