COVID COVID-19 Coronavirus Containment Efforts

[mfb]

Israeli study finds 94% drop in symptomatic COVID-19 cases with Pfizer vaccine
No surprise here, but it's nice to see that the ~95% holds even when people know they got the Pfizer/BioNTech vaccine. The Israeli study compared 600,000 vaccinated people to 600,000 unvaccinated people: Far more people but with a shorter time span than the phase III trials. Severe illnesses dropped by 92%.

 

[russ_watters]

Updated vaccination stats below. I've added weekly stats.

Thoughts/notes:

• Due to some gaps in the reporting the first three weekly points are estimated from the daily trends. The last three are exact counts. They are Monday to Sunday in the published counts, but that probably means the day reported is the day before's count.
• Weekly administrations are now exceeding distributions, so the 16 day pipeline is starting to shrink. But I don't think it's enough points yet to reduce the shift in the graphs.
• There was no update of the totals today due to the federal holiday.

 

[Astronuc]

Homegrown Coronavirus variants are on the rise in the US
https://www.yahoo.com/now/homegrown...ow-worried-should-americans-be-100018010.html

researchers at the Cedars-Sinai Center for Bioinformatics and Functional Genomics in Los Angeles last month identified a new variant, named CAL.20C, that had become detectable over the summer but now accounts for nearly half of all cases in Southern California — and may benefit from a spike-protein mutation (L452R) that hasbeen shown to resist some neutralizing antibodies. A new study shows that CAL.20C has spread to 19 U.S. states plus Washington, D.C., and six foreign countries.

I assume it's in the neighboring western states.

https://www.cidrap.umn.edu/news-per...vid-variant-5-mutations-identified-california

The new JAMA study reported that as of Jan. 22, CAL.20C had been detected in the states of Alaska, Arizona, California, Connecticut, Georgia, Hawaii, Maryland, Michigan, New Mexico, Nevada, New York, Oregon, Rhode Island, South Carolina, Texas, Utah, Washington, Wisconsin, Wyoming and in Washington, D.C.. Abroad, it was found in Australia, Denmark, Israel, New Zealand, Singapore and the United Kingdom.

https://www.cedars-sinai.org/newsro...covid-19-strain-rapidly-expands-global-reach/

"CAL.20C is moving, and we think it is Californians who are moving it," Plummer said.

Los Angeles International Airport (LAX) has long been among the busiest in the U.S., ranking #2 in total passengers boarded in 2019, according to the U.S. Department of Transportation. While air traffic across the U.S. has plummeted in the last year during the pandemic, about 2 million domestic and international passengers still traveled through LAX each month in November and December 2020.

LAX is a key U.S. gateway for a number of the foreign destinations, including Australia, and New Zealand, where CAL.20C now is found. Several Western states that have the strain, including Arizona, Nevada and New Mexico, are popular vacation destinations for Southern Californians.

https://jamanetwork.com/journals/jama/fullarticle/2776543See PF thread on SARS-COV-2 variants/mutations
https://www.physicsforums.com/threads/sars-cov-2-mutations.998345/

 

[PeroK]

Homegrown Coronavirus variants are on the rise in the US

It must be the case that there is an expectation of a significant variant every N cases, where N is some number in the millions. Given that the USA has had about 30 million cases, then it must be statistically inevitable that there be dangerous US variants.

We didn't hear a lot about variants until the UK (Kent) variant, but it must have been well known to epidemiologists that this was an inevitable consequence of not controlling the virus better in the first place. That must have been another piece of scientific advice ignored, rather than followed, by most western governments.

 

[Ygggdrasil]

An interesting theory surrounding the emergence of new variants is that they might arise during long term infection of immunocompromised individuals:

So far, SARS-CoV-2 typically acquires only one to two mutations per month. And B.1.1.7 is back to this pace now, suggesting it doesn’t mutate faster normally than other lineages. That’s why scientists believe it may have gone through a lengthy bout of evolution in a chronically infected patient who then transmitted the virus late in their infection. “We know this is rare but it can happen,” says World Health Organization epidemiologist Maria Van Kerkhove. Stephen Goldstein, a virologist at the University of Utah, agrees. “It’s simply too many mutations to have accumulated under normal evolutionary circumstances. It suggests an extended period of within-host evolution,” he says.

People with a weakened immune system may give the virus this opportunity, as Gupta’s data show. More evidence comes from a paper published in The New England Journal of Medicine on 3 December that described an immunocompromised patient in Boston infected with SARS-CoV-2 for 154 days before he died. Again, the researchers found several mutations, including N501Y. “It suggests that you can get relatively large numbers of mutations happening over a relatively short period of time within an individual patient,” says William Hanage of the Harvard T.H. Chan School of Public Health, one of the authors. (In patients who are infected for a few days and then clear the virus, there simply is not enough time for this, he says.) When such patients are given antibody treatments for COVID-19 late in their disease course, there may already be so many variants present that one of them is resistant, Goldstein says.

https://www.sciencemag.org/news/202...nocompromised-patients-role-covid-19-pandemic

Long term replication of the virus in a person with a weakened immune system would provide the virus with the opportunity to evolve new mutations to better adapt to and combat the human immune system and transmit within human hosts. Two recent studies have documented seeing large numbers of mutations arise in immunocompromised patients with long term infections (and seeing various mutations that seem to increase the transmissibility of the virus or its ability to evade the immune system):

Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation
https://www.medrxiv.org/content/10.1101/2020.12.05.20241927v3

Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host
https://www.nejm.org/doi/full/10.1056/NEJMc2031364

Popular press coverage:
Science
NPR

 

[russ_watters]

Could someone see if they can figure out a data discrepancy for me please. Below is a screenshot from the PA COVD tracking website:

https://www.health.pa.gov/topics/disease/coronavirus/Pages/Cases.aspx

I've been tracking the data since the beginning of the pandemic and doing my own analysis. I realized recently my calcs of the positivity % was no longer tracking with what is on the Johns Hopkins Testing Trends website:
https://coronavirus.jhu.edu/testing/individual-states/pennsylvania

Looking back, the positivity % never tracked, but the discrepancy only became large recently. The daily case numbers exactly match. The discrepancy has to do with the number of tests. I've been adding total cases (899,237) to negatives (3,783,099) to get the number of tests (4,682,336). But clearly, the actual number of tests is more than twice that (9,910,886). Can anyone explain this?

 

[BillTre]

For one thing, patients in a hospital (both those who recover and those that don't) could be tested more than once.

 

[russ_watters]

For one thing, patients in a hospital (both those who recover and those that don't) could be tested more than once.

That would cause the count and percent of positives to go up instead of down. Here's the daily numbers for 2/12, extracted from the totals:

• New Positive tests/cases: 3,987 (JH lists this number; "new positive tests" = "new cases")
• Cases + Negative tests: 12,537
• My positivity rate: 29.2% cases/(cases + negatives)
• Total tests: 41,801 (JH lists this number)
• JH positivity rate: 9.5% (they actually use a moving average in their graph and over two weeks it was 8.3%)

So, what I'm apparently missing here is 30,000 negative tests. Now that I'm aware of the discrepancy I'll start using the correct number, but I'm just confused as to why positives + negatives /= total.

 

[BillTre]

That would cause the count and percent of positives to go up instead of down. Here's the daily numbers for 2/12, extracted from the totals:

Are you sure that positives test results equal patient cases?

I have seen records of dead people who were tested 2 or three times in the hospital.
They are one positive patient but might have had multiple either positive or negative test results.
Same could happen with survivors (whose records I don't see).
The positivity of a test could come and go during their stay in a hospital:

1. early; not enough of whatever to detect (or possibly uninfected)
2. middle; ill and detected virus
3. late, recovered; virus not detected, tested on the way out.

All one case; one positive case , two negatives.
Of course there could be additional tests at any stage.

 

[russ_watters]

Are you sure that positives test results equal patient cases?

The JH graph is of "new positive tests" and it exactly matches PA's "cases" (today's total minus yesterday's total). So I'm as sure as I can be -- the discrepancy is in the negative tests, not the positive tests.

I have seen records of dead people who were tested 2 or three times in the hospital.
They are one positive patient but might have had multiple either positive or negative test results.
Same could happen with survivors (whose records I don't see).
The positivity of a test could come and go during their stay in a hospital:

1. early; not enough of whatever to detect (or possibly uninfected)
2. middle; ill and detected virus
3. late, recovered; virus not detected, tested on the way out.

All one case; one positive case , two negatives.
Of course there could be additional tests at any stage.

Perhaps. Here's what the PA website says for a definition of "Negatives":
Negative case data only includes negative PCR tests. Negative case data does not include negative antibody tests.

This definition is apparently intended to say that post-case antibody testing isn't included. Fine, whatever -- but what is the definition of "negatives"? Maybe the first sentence is the key due to how they sloppily switched terminology? Maybe a "negative case" ("negatives") isn't a "negative test"? Maybe it means that (per your example), someone who is tested three times and comes up positive once is counted as one "positive case", zero "negative cases" and three "tests"?

 

[BillTre]

I need a confused reaction emoji for this stuff.

 

[russ_watters]

I need a confused reaction emoji for this stuff.

Does the "skeptical" emoji work?

Its not clear what they mean (in at least some cases) and interpretation is therefore suspect.
[reverse quote edit]

I think you led me to the answer, so thanks. This is why I'm harping on precision of descriptions for the statistics. It's critical to understand what the stats mean. I've been manually typing that number into a spreadsheet every day for 10 months, thinking it meant something else!

 

[BillTre]

I consider the numbers in all this stuff confusing.
Its not clear what they mean (in at least some cases) and interpretation is therefore suspect.

 

[BillTre]

Does the "skeptical" emoji work?

I try to reserve the skeptical emoji for when I am skeptical of the poster's reasoning, which is not in this case.

 

[Ygggdrasil]

The COVID Tracking project probably has the most experience tracking these data from various states and has some interesting notes regarding data from PA that might be relevant:

On February 1, 2021, we backfilled the full time series of Total Test Encounters (PCR), from data now available on Open Data Pennsylvania, and cleared our Total Tests (PCR) column. Going forward, we will enter PA's "Total PCR Tests" into Our Total Test Encounters (PCR) column rather than Total Tests (PCR), as the state's site describes the data as encounters.

On December 28, 2020, Pennsylvania's Total PCR tests (specimens) value increased by ~690,000 from 7,202,533 tests to 7,892,184 tests. On December 29, 2020, this Total PCR tests value decreased by ~580,000 to 7,312,858 tests. We were unable to find an explanation for this fluctuation.

On December 14, 2020, Pennsylvania’s Total PCR tests (specimens) decreased by roughly 297k without explanation.

On September 3, 2020, Pennsylvania clarified that the test numbers they have been reporting previously are in units of unique people and began publishing new test data in units of specimens. On September 4, 2020, we therefore moved the appropriate historical data to the Total tests (people) field and began capturing Total PCR tests (specimens).

https://covidtracking.com/data/state/pennsylvania/notes

They also note that the state "does not have a clear full definition of cases." (https://covidtracking.com/data/state/pennsylvania/assessment#state-metrics), so they may be experiencing similar confusion over the data as @russ_watters

 

[Astronuc]

Could someone see if they can figure out a data discrepancy for me please. Below is a screenshot from the PA COVD tracking website:
View attachment 278143

https://www.health.pa.gov/topics/disease/coronavirus/Pages/Cases.aspx

I've been tracking the data since the beginning of the pandemic and doing my own analysis. I realized recently my calcs of the positivity % was no longer tracking with what is on the Johns Hopkins Testing Trends website:
https://coronavirus.jhu.edu/testing/individual-states/pennsylvania

Looking back, the positivity % never tracked, but the discrepancy only became large recently. The daily case numbers exactly match. The discrepancy has to do with the number of tests. I've been adding total cases (899,237) to negatives (3,783,099) to get the number of tests (4,682,336). But clearly, the actual number of tests is more than twice that (9,910,886). Can anyone explain this?

https://covidtracking.com/data/state/pennsylvania/tests-viral (about 24 hours behind the PA site)

Total PCR tests (people) 4,550,692
Total PCR tests (test encounters) 9,799,882

https://covidtracking.com/data/#state-pa
If I wonder about a states statistics, I go to the official state site.

 

[Astronuc]

They also note that the state "does not have a clear full definition of cases." (https://covidtracking.com/data/state/pennsylvania/assessment#state-metrics), so they may be experiencing similar confusion over the data as @russ_watters

Each state reports cases differently, i.e., there is no uniform reporting template. I follow Washington and New York, with the latter being more consistent. Washington state was an early leader in cases, then NY overtook Washington and became the leader until CA and TX overtook NY.

Washington state has changed there format several times, and stopped reporting on weekends and holidays. Sometimes the number of cumulative positive cases and deaths have decreased because they reconciled some data.

https://covidtracking.com/data/#state-wa
https://covidtracking.com/data/#state-ny

 

[Ygggdrasil]

The vaccines seem to be having an effect on reducing deaths in nursing homes:

In another promising sign Illinois is beating back the COVID-19 pandemic, cases and deaths at Illinois long-term care facilities have dropped to levels not seen since late summer, according to state data released Friday.

Following weeks of focused vaccination of long-term care residents and workers, the state reported 33 residents died from the virus over the past week. That’s the lowest reported tally since mid-August and exponentially lower than the 650 weekly deaths reported in early December.

Long-term care residents not only have seen a sizable drop in the number of deaths, they also now make up a far smaller share of those who are dying of COVID-19 each week — going from roughly half or more of these deaths in Illinois to near 10% now.

https://www.chicagotribune.com/coro...220-ehid36jz6vgpjhuyqshdxh2cbi-htmlstory.html

While part of the decline could be due to the overall decline in cases in Illinois since late December, the fact that nursing home death have declined as a percentage of total deaths suggests that the vaccines (which have been administered to healthcare workers, people in nursing homes, and is in the process of being rolled out to those over 65 over the next month or so, but is not yet available to the general public) is having some success in preventing deaths at nursing homes.

 

[nsaspook]

and now the good news.

https://www.theatlantic.com/ideas/archive/2021/02/why-covid-19-cases-are-falling-so-fast/618041/

One month ago, the CDC published the results of more than 20 pandemic forecasting models. Most projected that COVID-19 cases would continue to grow through February, or at least plateau. Instead, COVID-19 is in retreat in America. New daily cases have plunged, and hospitalizations are down almost 50 percent in the past month. This is not an artifact of infrequent testing, since the share of regional daily tests that are coming back positive has declined even more than the number of cases. Some pandemic statistics are foggy, but the current decline of COVID-19 is crystal clear.

https://www.theatlantic.com/health/archive/2021/02/major-covid-19-metrics-are-falling/618068/

All major indicators of COVID-19 transmission in the United States continue to fall rapidly. Weekly new cases have fallen from 1.7 million at the national peak in early January to fewer than 600,000 this week, and cases have declined in every state. As we’ve seen at many points in the pandemic, case numbers are changing most quickly, with hospitalizations and deaths declining after a delay: Cases have been falling sharply for five weeks, hospitalizations for four, and deaths for two. In this week’s numbers from nursing homes and other long-term-care facilities, we are now seeing solid declines in deaths correlated with COVID-19 vaccinations in this most vulnerable population.

https://www.who.int/docs/default-so...update_27.pdf?sfvrsn=94da8979_9&download=true

Global overview
The number of global new cases reported has continued to fall, with 2.7 million new cases last week, a 16%
decline over 500 000 fewer new cases compared to the previous week (Figure 1). The number of new deaths
reported also fell, with 81 000 new deaths reported last week, a 10% decline as compared to the previous
week. A total of five out of six WHO regions reported a double-digit percentage decline in new cases (Table 1),
with only the Eastern Mediterranean Region showing a 7% rise. Europe and the Americas continue to see the
greatest drops in absolute numbers of cases. Meanwhile, the number of new deaths declined in all regions.

 

[mfb]

New cases in Germany are down to ~30% of the peak in late December. ICU beds used for COVID-19 are down to 50% of the peak around new year, and will drop below the peak in April in the next days. Only 6% have been vaccinated so far, so this decline is largely not the result of vaccinations.

Israel exceeded 80 vaccinations per 100 people. Israel's cases are going down quickly, but we see that trend in places with fewer vaccinations as well.

 

[mfb]

Update from Israel
Two weeks after the second dose, the Pfizer/BioNTech vaccine reduces the risk to die by ~98.9% and the risk of serious illness by ~99.2%. That's not exactly 100%, but pretty close. Israel had 2000 pandemic deaths this year with only a smaller fraction of the population being in the "two weeks after the second dose" group, so this ~1.1% risk is probably just a handful of deaths.
Here I don't know if they mean symptomatic infections or all infections. The latter would be revolutionary:

According to the data, after one week, the vaccine is 91.9 percent effective in preventing the illness altogether. After two weeks, it jumps to 95.8 percent.

 

[nsaspook]

Lets see what the pandemic forecasting models say now.

https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/forecasts-cases.html

 

[Astronuc]

February 22, 2021 - Covidtracking - https://covidtracking.com/data
In the US
Covid-positive cases (confirmed+probable): cumulative 27,932,810, new today 52,530
Currently/now Hospitalized 55,403, in ICU 11,536, on Ventilator 3,804
Covid-19, deaths (confirmed+probable): cumulative 490,382, new today 1,235

Positive cases should exceed 28 million by Wednesday, February 24.
Deaths will probably exceed 500 K by February 28.

CA 3,446,611 Cases, 49,338 deaths
TX 2,594,466 Cases, 41,407 deaths
FL 1,838,745 Cases, 30,595 deaths
NY 1,584,931 Cases, 37,941 deaths
IL 1,175,655 Cases, 22,506 deaths

The COVID Tracking Project will stop collecting data on March 7, 2021

ncov2019.live/data/unitedstates has US at 512,526 deaths, new +1,309, already exceeding 500K, >28.8 million cases

 

[mfb]

https://www3.nhk.or.jp/nhkworld/en/news/20210217_39/
Australia has started vaccinations.
New Zealand has started vaccinations.
https://www.msn.com/en-au/lifestyle/wellbeing/south-korea-to-begin-using-pfizer-coronavirus-vaccines-on-feb-27-pm-says/ar-BB1dS7k5
It's complicated in Taiwan
Unless I missed something all highly developed countries have now started vaccinations or (see above) plan to do so as soon as possible.

210 million doses have been administered worldwide, or 2.7 per 100. The current rate is ~5 million/day: https://ourworldindata.org/covid-vaccinations

 

[WWGD]

Is it fair to assume that " Internationalism" has taken a hit given its biological implications and its correlation with the number of cases/deaths( meaning the number ( and rate) of cases/deaths is higher in countries with dense connections to other countries)? Is it fair to say this is a lesson most have taken out of this pandemic? If so, will we be seeing a downturn in travel, commuting ( issue at a li al level), conferences?

 

[WWGD]

My data, from Worldometer:

 

[russ_watters]

Is it fair to assume that " Internationalism" has taken a hit given its biological implications and its correlation with the number of cases/deaths( meaning the number ( and rate) of cases/deaths is higher in countries with dense connections to other countries)? Is it fair to say this is a lesson most have taken out of this pandemic? If so, will we be seeing a downturn in travel, commuting ( issue at a li al level), conferences?

I agree the premise is correct, but I don't see that the conclusion necessarily follows. Business travel had already been decreasing due to the prevalence and quality of videoconferencing and COVID likely accelerated that some. But otherwise, I don't see a reason for a connection. For me, personally, I can hardly wait for a return to leisure travel.

[Edit]
To put a finer point on it; this was almost exactly a once in a hundred year event. There should be no need for it to substantially affect long term behavior beyond basic preparedness (which will surely fade over the next 100 years).

 

[WWGD]

I agree the premise is correct, but I don't see that the conclusion necessarily follows. Business travel had already been decreasing due to the prevalence and quality of videoconferencing and COVID likely accelerated that some. But otherwise, I don't see a reason for a connection. For me, personally, I can hardly wait for a return to leisure travel.

[Edit]
To put a finer point on it; this was almost exactly a once in a hundred year event. There should be no need for it to substantially affect long term behavior beyond basic preparedness (which will surely fade over the next 100 years).

I agree with you, but The Economist has written an article ( An editorial, IIRC) to this effect. I am in agreement with you and I believe they have overstated their case.

 

[russ_watters]

I agree with you, but The Economist has written an article ( An editorial, IIRC) to this effect. I am in agreement with you and I believe they have overstated their case.

Do you have a link? Google finds me one from September...

 

[Astronuc]

Why the vaccine rollout in the U.S. has been slower than expected
https://www.pbs.org/newshour/show/why-the-vaccine-rollout-in-the-u-s-has-been-slower-than-expected

Supply shortages and delays leave Europe’s vaccination campaign in crisis
https://www.pbs.org/newshour/show/s...-leave-europes-vaccination-campaign-in-crisis

Twenty-six million vaccine doses were delivered to the European Union by mid-February, with around two-thirds of them used. That's just a fraction of the E.U.'s population of 450 million.

All three of the vaccines authorized for use, Moderna, BioNTech/Pfizer and Oxford-AstraZeneca, have cut deliveries in the first quarter. Pfizer has not yet delivered around 10 million doses that were due in December, leaving the bloc a third short.

Rates of production at European sites across the board have been unable to meet demand. Ursula von der Leyen, European Commission president, and German herself, has admitted mistakes were made.

I heard somewhere a comment about the supply of nano-lipids to the effect that the demand was underestimated. It was one of several challenges in the supply chains for the vaccine producers.

See also - https://www.physicsforums.com/threads/coronovirus-vaccine-progress.992484/