COVID COVID-19 Coronavirus Containment Efforts

[Jarvis323]

Earlier in the thread a paper was mentioned that made some comparison with HIV, but I think the resemblence is superficial since SARS-CoV-2 doesn't seem to replicate in the immune cells.

I cited that paper. It's an accepted Nature paper, but it turned out to be controversial. There has been a lot of criticism of it on reddit and twitter as far as I could tell. I don't know what to make of it at this point.

The news article that reported it also made a lot of claims based on anonymous sources.

I guess I shouldn't have been so quick to post it.

Side rant: This crisis is a major awakening for many people to the scientific research process. News articles typically treat hearsay as fact, let alone un-peer reviewed publications. It may come as a shock also to many that even accepted peer reviewed papers could have flaws, or even have false conclusions without technical flaws, and that even mainstream theories (e.g. big bang) are not matters of fact.

Even most Journalists claiming to be fact checking and combating misinformation are blatantly doing the opposite (likely without even realizing it).

Lack of critical thinking skills is showing to be a major world crisis, that is negatively affecting all areas from research, to public policy and action, politics, and public belief/opinion. I mean, I'm no exception. We just really need to do a better job in the future teaching people how to think critically.

In my opinion, current culture and systems thrive/operate way too much based on manipulation, and incentivize dumbing down, and mis/under-informing the general population. I think this will lead our species and planet to ruin in the long run if we aren't careful.

 

[atyy]

Different from what, exactly? The fact that I've seen little or no discussion of mandatory contact tracing by either the federal government or companies that are capable of doing it tells me the stomach for it is very, very low.

Different from if Apple & Google decided to just make it a mandatory update on their OS?

Hmm...I stated in several previous posts that Singapore needed to be excluded from country data because it is more a city-state than a country. That's not meant as an insult, just as a description of the reality that the rules of science that apply to China, South Korea or the USA don't necessarily apply well to Singapore. Indeed, it seems like what is happening there now is not unlike the second-wave outbreak in small, isolated towns discussed yesterday.
https://www.bloomberg.com/news/arti...re-flipped-from-virus-hero-to-cautionary-tale

Yes, I agree, Singapore's experience is not generalizable (or at least not obviously). And don't worry, I've never understood any of your statements to be an insult, but thanks for the note on that. Even what is happening here now is not generalizable - I doubt it is like a second-wave outbreak that some worry about for small towns in the US. The huge spike in Singapore now is among construction workers living in quite densely packed dorms (10 people in a room), so that is totally unlike a small town in the US. These workers are now being moved to temporary housing which is less dense, and the government and various organizations are trying to make sure their welfare is taken care of despite having to suddenly live in new temporary housing. So far (fingers crossed) there hasn't been an increase in ICU cases, possibly because construction workers are usually fit and have only a mild illness. But one can't take that for granted, as we had a construction worker who got COVID-19 several months ago, before this spike in cases, and it took 2 months in ICU before he was well enough to be moved out.

 

[atyy]

What is a contact tracing app/what would it even look like/do? You guys are aware that Google and Apple already track your every move as an integral part of the phone OS, right? All they have to do is provide that data to the government, and then the government can do whatever it wants to track you -- no app needed. The only real value of an app is to provide you with a user experience, which obviously isn't required. In South Korea for example, the government tracks phone locations, credit card data and does facial recognition. And citizens get push-notifications of contact and get fined/punished if found outside without their phones. Avoidance has been a problem (link below), so in order to defeat people leaving their phones at home, they've added tracking bracelets for certain grouops.

Yes, in principle location information can already be pulled from your phone service provider (eg. to help emergency services locate a caller).

But the current apps envisaged by Apple and Google are use a different idea and hope it works on voluntary basis. The idea is that if two people have the app and allow its use, their phone will use bluetooth to figure out when they are close contacts (eg. when they are less than 6 ft apart for 10 minutes), and the app logs these close contact incidents. When one of the people is confirmed and enters it into the system, the app will inform close contacts, who can then self-isolate and get tested.
https://www.theverge.com/interface/...-coronavirus-api-public-health-app-challenges

 

[DennisN]

I don't enjoy sharing these gloomy news articles, but I thought these worries concerning the near future was too important not to mention:

• CDC chief warns of 'even more difficult' wave of Coronavirus next winter (The Guardian, 21 april 2020)
• Fears of prolonged Coronavirus downturn and second wave of US cases (The Guardian, 22 april 2020)
  And I guess the possibility of a second wave accompanied by a flu season applies to more countries than US.
• Coronavirus pandemic 'will cause famine of biblical proportions' (The Guardian, 21 april 2020)
  Maybe the title is worded a bit too definitive, but here's a quote:
  

  More than 30 countries in the developing world could experience widespread famine, says David Beasley, chief of the UN’s food relief agency.

 

[russ_watters]

Yes, in principle location information can already be pulled from your phone service provider (eg. to help emergency services locate a caller).

But the current apps envisaged by Apple and Google are use a different idea and hope it works on voluntary basis. The idea is that if two people have the app and allow its use, their phone will use bluetooth to figure out when they are close contacts (eg. when they are less than 6 ft apart for 10 minutes), and the app logs these close contact incidents. When one of the people is confirmed and enters it into the system, the app will inform close contacts, who can then self-isolate and get tested.

Right, so that requires that a substantial fraction of people who get sick voluntarily report it to the app, in a timely fashion. Otherwise, it won't work. And I think it's highly unlikely happen. In other countries that have successfully implemented contact tracing, that feature isn't part of the app and isn't optional; the government provides the test results directly to the phone/software companies. That "user experience" feature (self-reporting) doesn't exist because it's a very ineffective way to get the key data.

Think about a counterexample: navigation and traffic. Nobody downloaded an app or consciously opted-in to be tracked for it. It works so well precisely because it doesn't require the user to opt-in (they're just in).

 

[peanut]

This World Earth Day, let's remember that the story of SARSCoV2 COVID19 is the story of SARS, MERS, etc. All are zoonotic diseases: they come from other species. As humans continue to encroach on animal habitats, more such diseases are likely to emerge.

 

[Astronuc]

LA Times reports, "Autopsies reveal first confirmed U.S. Coronavirus deaths occurred in Bay Area in February," which is repeated by other media, e.g., Yahoo, Washington Post, NBC, . . . .

Officials previously had said the first Silicon Valley death was March 9. But the Santa Clara County medical examiner revealed Tuesday that people who died Feb. 6, Feb. 17 and March 6 also died of COVID-19.

"These three individuals died at home during a time when very limited testing was available only through the [U.S. Centers for Disease Control and Prevention]. Testing criteria set by the CDC at the time restricted testing to only individuals with a known travel history and who sought medical care for specific symptoms,"

Santa Clara County press release - https://www.sccgov.org/sites/covid19/Pages/press-release-04-21-20-early.aspx

The Medical Examiner-Coroner performed autopsies on two individuals who died at home on February 6, 2020 and February 17, 2020. Samples from the two individuals were sent to the Centers for Disease Control and Prevention. Today, the Medical Examiner-Coroner received confirmation from the CDC that tissue samples from both cases are positive for SARS-CoV-2 (the virus that causes COVID-19).

The victims were tested posthumously, and the results returned 75 days and 64 days, respectively, after death! Date of autopsy (specimen collection) is not mentioned.

Clearly early detection (and testing) is necessary.

"The County of Santa Clara is reporting a total of 1,922 cases and 83 deaths." on April 20.
https://www.sccgov.org/sites/covid19/Pages/press-release-04-20-2020-dashboard-cases-reporting-process-update.aspx

"Santa Clara County has so far reported 88 coronavirus-related deaths, including five new deaths reported Tuesday. The county now has 1,948 confirmed cases."
https://www.mercurynews.com/2020/04...s-in-bay-area-occurred-in-february-not-march/

Also, I read a brief headline that the government of Wuhan had revised their number up by the end of last week.

 

[Astronuc]

Fortunately (?) these towns tend to be lower income and very low mobility, so the likelihood of someone returning from Italy to start a cluster of infections is really low. See: "Allentown".

Interesting example. I had a colleague who lived and worked in Allentown (PPL), and he used to travel frequently to Europe for work (supplier audit). If that was still happening, he could potentially bring Coronavirus into the community. Certainly, the more remote a town (Mauch Chunk, Mahanoy City, Hazelton, or Sayre), the less likely of exposure, but it could happen.

Lehigh County reports 2295 confirmed cases and 49 deaths.
https://www.health.pa.gov/topics/disease/coronavirus/Pages/Cases.aspx

In the near future and longer term, it would be useful to understand how different areas of the nation/economy are affected by mobility.

There is only one county in Washington state that reports 0 cases, and it is the least populated county. One adjacent county has at least one case, and two other adjacent counties have 13 and 14 cases.

 

[atyy]

Right, so that requires that a substantial fraction of people who get sick voluntarily report it to the app, in a timely fashion. Otherwise, it won't work. And I think it's highly unlikely happen. In other countries that have successfully implemented contact tracing, that feature isn't part of the app and isn't optional; the government provides the test results directly to the phone/software companies. That "user experience" part doesn't exist because it's a very ineffective way to implement the key feature.

Think about a counterexample: navigation and traffic. Nobody downloaded an app or consciously opted-in to be tracked for it. It works so well precisely because it doesn't require the user to opt-in (they're just in).

So just to make sure I understand you - you wouldn't mind if the South Korean contact tracing system could be implemented in the US (say if Congress legislated it and the President approved)?

 

[gmax137]

Also, what if the federal government mandated that they be able to access information from your phone for contact tracing, say location information?

I would turn my phone off. And maybe remove the SIM card when not in use.

 

[kyphysics]

https://www.bloomberg.com/news/arti...weeks-earlier-than-first-thought?srnd=premium

The U.S.’s first deaths from the new Coronavirus came weeks earlier than was previously known, suggesting the virus may have long been spreading outside of health officials’ attempts to contain it earlier this year.

Two residents of Santa Clara County, California, who died at home on Feb. 6 and Feb. 17 were infected with the virus, according to a https://www.sccgov.org/sites/covid19/Pages/press-release-04-21-20-early.aspx by the county’s public health department.

The first death is 20 days earlier than what was previously thought to be the first U.S. fatality, and about three weeks before health officials identified the first Covid-19 infection without a known tie to other cases. The deaths were also weeks before cities and states began implementing widespread social-distancing measures.

 

[bhobba]

Just an interesting aside. Everyone this year, correctly, is getting a strengthened Flu jab, so much so it is in short supply, but the government is ensuring everyone who wants it (and as I said that is everyone this year) will get it May at the latest. But doctors have noticed with the Coronovirus measures the Flu has plummeted to a trickle even though not everyone has been vaccinated yet. Just imagine how much better Flu season would be in a normal year if everyone got the Flu jab and did simple measures like washing hands and basic social distancing.

Thanks
Bill

 

[DennisN]

Good news from Germany:

Germany approves first human trials for vaccine

A clinical test of a Covid-19 vaccine has been approved in Germany, the country’s Federal Institute for Vaccines has said. In the first part of the trial, 200 healthy people between 18 and 55 will receive several variants of the vaccine. The vaccine candidate was produced by biotech firm BioNTech, and is an RNA vaccine.

Source: The Guardian live update (22 april 2020)

 

[russ_watters]

So just to make sure I understand you - you wouldn't mind if the South Korean contact tracing system could be implemented in the US (say if Congress legislated it and the President approved)?

Yes.

I don't think the contact-trace-and-quarantine technique can succeed without it, and it can only be implemented on a national/federal government level (I'm not sure how, legislatively). My concern/expectation/prediction is that after we lift mandatory social distancing, we'll just get another spike/wave. Perhaps after a second wave, people/government will decide it's important to do.

 

[hmmm27]

IMnsHO, opt-in.

I normally go out of my way not to give Google/M$/Apple/etc. the time of day - mostly because they don't ask and are pretty weaselly in general but, if they're doing it strictly for "we're all in this together" publicity, dump the data at the end, and I won't find myself on the arse end of a spam flood in perpetua, then "I hereby give permission..." is forthcoming.

 

[russ_watters]

Interesting example. I had a colleague who lived and worked in Allentown (PPL), and he used to travel frequently to Europe for work (supplier audit). If that was still happening, he could potentially bring Coronavirus into the community. Certainly, the more remote a town (Mauch Chunk, Mahanoy City, Hazelton, or Sayre), the less likely of exposure, but it could happen.

I was born in Allentown; my dad worked for Air Products and both parents for Bethlehem Steel, and that was a reference to the Billy Joel song (circa 1982). The song accurately describes much of my extended family. It may not apply as well anymore, as Allentown seems to have become something of a suburb of Philadelphia.

 

[russ_watters]

I would turn my phone off. And maybe remove the SIM card when not in use.

What if you would be fined $8,000 or arrested and given a non-removable tracking bracelet for turning your phone off to break a curfew?
https://www.businessinsider.com/sou...irus-catch-people-dodging-tracking-app-2020-4

 

[Astronuc]

I was born in Allentown; my dad worked for Air Products and both parents for Bethlehem Steel, and that was a reference to the Billy Joel song (circa 1982). The song accurately describes much of my extended family. It may not apply as well anymore, as Allentown seems to have become something of a suburb of Philadelphia.

I've been through Allendown many times, and I've seen it change (like many other places) since the 1980s. I've met folks from Lehigh University in Bethlehem, and I interacted with a well-known professor of materials science and engineering about 3 decades ago. For me, it's a sentimental and historic place because of the LVRR and other connections.

 

[kadiot]

New Zealand is flattening the curve. R0 less than 1. Disease will eventually die out.

 

[Astronuc]

Regarding the spread, USA Today reports on an investigation of the meat packing industry in which dozens of facilities report outbreaks of Coronavirus and cases of COVID-19, e.g., Smithfield plant in SD and Tyson plants in several states.
https://www.usatoday.com/in-depth/n...y-force-choice-worker-health-food/2995232001/
Wa state - https://www.tri-cityherald.com/news/coronavirus/article242117246.html

Washington Post reports on differences between Rhode Island and Kentucky with respect to impact of Coronavirus and testing.
https://www.msn.com/en-us/news/us/in-two-states-a-vast-testing-gap-shows-what-it-means-to-have-no-national-strategy/ar-BB130p7D
https://www.washingtonpost.com/health/2020/04/21/kentucky-rhode-island-coronavirus-testing (subscription required)

 

[atyy]

LVRR

Lehigh Valley Railroad or Lehigh Road Runners?

 

[Astronuc]

Lehigh Valley Railroad or Lehigh Road Runners?

LV Railroad, and Erie+DLW = Erie Lackawanna, RDG, CNJ, LHR and LNE, and New Haven, and others like the CRIP, MKT, MILW, NKP, WAB, MON (CIL), Frisco (SLSF), ICG (IC + GMO). Basically I have affection for the underdogs and fallen flags. At university, I watched the MP and SP pass through town on a joint line, and I'd visit the ATSF, BN and MKT, which were some distance away.

Historical background - https://www.american-rails.com/fallen-flags.html

That's topic for another thread. I seriously considered becoming a locomotive engineer, but physics and nuclear engineering won out.

 

[OmCheeto]

...

Washington Post reports on differences between Rhode Island and Kentucky with respect to impact of Coronavirus and testing.
https://www.msn.com/en-us/news/us/in-two-states-a-vast-testing-gap-shows-what-it-means-to-have-no-national-strategy/ar-BB130p7D
https://www.washingtonpost.com/health/2020/04/21/kentucky-rhode-island-coronavirus-testing (subscription required)

Were those articles supposed to be putting Rhode Island in a good light?
Because that's what it sounded like to me.
Running the numbers, it looks like Rhode Island is doing about as bad as you can.

OR = Oregon
TN = Tennessee
KY = Kentucky
RI = Rhode Island

Although New York currently has a VERY bad mortality rate of 1800 deaths per million, it's currently doubling deaths every 12 days, which is twice as long as Rhode Island.

The article strikes me as saying; "Rhode Island has the best bean counters. Therefore, things are going much better in Rhode Island."

 

[Astronuc]

The article strikes me as saying; "Rhode Island has the best bean counters. Therefore, things are going much better in Rhode Island."

The articles states that Rhode Island has the highest per capita testing rate of the 50 states. I have not independently verified. Rhode Island apparently also benefits from being the headquarters of the CVS pharmacy chain. And, Rhode Island is tied with Hawaii for having the second-fewest (5) counties of any U.S. state (only Delaware has fewer, with 3 counties). As far as I can tell, it is the county health departments, which collect the data, at least in the states with which I am familiar.

On March 29, Time magazine reported that Data compiled by John Hopkins University shows that 1,297 counties have no confirmed cases of COVID-19 out of 3,142 counties nationwide.
https://time.com/5812186/counties-coronavirus-rural-poor/

NY Times is mapping the pandemic in the US - https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html - along with others. Certainly, major metropolitan areas have high incidence of COVID-19 cases (especially those with airports serving as international gateways), while smaller metropolitan areas see some moderate incidence, and there appears to be some correlation for incidence between metropolitan areas along interstates. See Where cases are rising fastest.

https://coronavirus.jhu.edu/us-map

 

[mfb]

You guys are aware that Google and Apple already track your every move as an integral part of the phone OS, right?

In iOS you can disable it. One of the reasons I use iOS. The service provider still knows which cell phone masts the phone connects to, of course, that's unavoidable if you want a connection.

All they have to do is provide that data to the government

That's part of "measures that would be very, very unpopular in western countries" I mentioned.

Even if you let your OS send all its data to Google or Apple: At least they have good security standards. That's not necessarily true for a third party app.

----

Germany keeps its (sort of) weekly pattern of new cases but the numbers keep going down despite a roughly constant rate of 50,000-60,000 tests per day. Active cases went down to 2/3 its peak, new cases are ~1/3 the peak rate after three weeks. If this trend continues the restrictions will be loosened at a time of 1000 new cases per day, or 1 in 80,000. That means 50+ tests for each new case - in principle enough to test all the closer contacts and then some more.

New confirmed cases in the US stabilized at ~25,000. They will reach a million in about 8 days and will have ~1/3 of the global reported cases by then.

 

[chemisttree]

I’ve heard that we are still limited by a shortage of ‘reagents’ for our testing. Any idea what exactly the hard to source ‘reagents’ are?

 

[TeethWhitener]

Germany keeps its (sort of) weekly pattern of new cases

Any reason for the periodicity? It shows up in US data as well. It seems to peak in the Thursday-Friday range.

 

[chemisttree]

I wonder if the periodicity would remain apparent if positives were reported on sampling days rather than test result days. Obviously a retrospective analysis...

 

[TeethWhitener]

I wonder if the periodicity would remain apparent if positives were reported on sampling days rather than test result days. Obviously a retrospective analysis...

Good point, hadn’t thought about that. A friend tested positive very early in the outbreak—it took her 12 days to get the results. She looked at the daily data for her city, and reasons it’s far more likely that her result was counted when it was reported, not when the test was administered.
(She recovered, btw)

 

[mfb]

Any reason for the periodicity? It shows up in US data as well. It seems to peak in the Thursday-Friday range.

Analysis date as far as I understand, and fewer tests analyzed at the weekend. Plus some reporting lag, so tests from one day can appear in the statistics of the next day. More discussion here and details in its German source.