COVID-19 Coronavirus Containment Efforts

[Ygggdrasil]

High prevalence of infection is not necessarily protective in the long term. Researchers published a paper in Science, reporting that in the Brazilian city of Manaus, about 76% of the population had been exposed to COVID-19 by October (mostly during the surge of cases in April-May). Despite this, the city experience a huge resurgence beginning late December, and hospitalizations in Manaus have surpassed the levels seen during the April-May peak:

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)00183-5/fulltext

Resurgence of the virus could be related to to emergence of a new lineage of the virus in that region containing mutations in the spike protein receptor binding domain that could allow the virus to escape antibody-based immunity (see the Lancet article cited above for more discussion).

 

[nsaspook]

High prevalence of infection is not necessarily protective in the long term. Researchers published a paper in Science, reporting that in the Brazilian city of Manaus, about 76% of the population had been exposed to COVID-19 by October (mostly during the surge of cases in April-May). Despite this, the city experience a huge resurgence beginning late December, and hospitalizations in Manaus have surpassed the levels seen during the April-May peak:
View attachment 277004
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)00183-5/fulltext

Resurgence of the virus could be related to to emergence of a new lineage of the virus in that region containing mutations in the spike protein receptor binding domain that could allow the virus to escape antibody-based immunity (see the Lancet article cited above for more discussion).

Hopefully we can break this cycle with vaccines.

https://www.bbc.com/future/article/...iants-how-mutations-are-changing-the-pandemic

The Brazilian variant

The E484K mutation is proving to be important in another concerning variant that is now spreading around the world. The P1 variant contains 20 unique mutations, including the E484K change found in the South African variant. It seems to have first emerged in the city of Manaus, Amazonas state, in north Brazil, which has been particularly severely hit by the pandemic. The variant was also detected in four travellers who had flown from northern Brazil to Japan on 2 January this year.

This version of the virus also carries the N501Y mutation alongside the E484K change and one called K417T. Although the exact consequences of these mutations are still being investigated by scientists, the strain has been designated as a "Variant of Concern" by global health officials.

The emergence of the Brazilian P1 variant raises concerns that the virus may be developing anhttps://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html, according to the US's Centre for Disease Control and Prevention.

https://www.jpost.com/breaking-news/novavax-covid-19-vaccine-demonstrates-893-percent-efficacy-in-uk-phase-3-trial-657121

Novavax COVID-19 vaccine 89% effective in UK trial, less in South Africa
The study took place as the more highly transmissible UK variant was circulating, and the preliminary analysis suggests the vaccine was 85.6% effective against this mutation.

 

[Ygggdrasil]

Hopefully we can break this cycle with vaccines.

Moderna has also reported data suggesting that its vaccine could be less effective against the B.1.351 variant from South Africa:

In lab research that involved testing whether blood from people who had received the vaccine could still fend off different Coronavirus variants, scientists found that there was a sixfold reduction in the vaccine’s neutralizing power against the variant, called B.1.351, than against earlier forms of the coronavirus, Moderna reported.

There was no loss in neutralization levels against a different variant, called B.1.1.7, that was first identified in the United Kingdom.

https://www.statnews.com/2021/01/25/moderna-vaccine-less-effective-variant/

Unfortunately, we don't know enough about immunity to the virus to know how well the antibody reactivity tests done in the lab predict actual immunity, so it's hard to know how effective the Moderna vaccine would protect against the B.1.351 variant or other similar variants (such as the P.1 variant in Brazil). The Novavax data is worrying on that front, suggesting that these variants would at least partially escape immunity from either infection or vaccination.

 

[bhobba]

People might find the following from the WSJ interesting:
https://www.wsj.com/articles/new-pl...rges-after-year-of-study-missteps-11611680950

I listen to the WSJ everyday - it comes free with my membership to Audible. I found it useful - and a reminder of the 'falsehoods' I posted early in the pandemic - very humbling. It let my first few views through - but after that was behind a paywall so you may be able to view it. Can post a precis if people want.

Thanks
Bill

 

[morrobay]

Thanks, The compound interest formula, final=initial (1+%)^n is exactly how I am solving for the R0 from initial and final infections: 17(R0)^6 = 231. Then (R0)^6=13.58 and 6(logR0) = log 13.58. therefore log R0 =.1888 so R0 is 1.54 I just am asking if this is valid for solving R0. Note 6 infection periods from 24 days/4 day max.infectious period from initial infection.

Here is the correct way to confirm that the R0 1.54 , from compound interest formula above is valid: R0 = e^kt , y(24)= 17e^24k=231. So e^24k= 13.58. and 24k=ln13.58 then k= .1086 and tau=4days(as in post above) So R0 =e^.4347 = 1.54 in agreement with above independently. See estimation methods https://en.m.wikipedia.org/wiki/Basic_reproduction_number

 

[mfb]

I hope I'm not posting journalistic exaggeration, but according to the BBC, Germany is limiting the AstraZeneca vaccine to people under 65. What is going on here?

https://www.bbc.co.uk/news/world-europe-55839885

Germany is also using the Pfizer/BioNTech and the Moderna vaccine. People over 65 will get these two, the AstraZeneca vaccine will only be given to younger people for now.
Here is a German article.

Germany's vaccination rate reached 100,000 doses per day - about 2% of the population per month with two doses per person. That will cover the high risk groups, but a general vaccination campaign for the larger population will need far higher rates.

 

[Astronuc]

I heard a news report this evening that a case of B.1.351 variant from South Africa has been reported in the state of Maryland in someone who has no recent history of travel suggesting that the SA variant is spreading in the community.
https://governor.maryland.gov/2021/...ican-covid-19-variant-identified-in-maryland/
https://baltimore.cbslocal.com/2021/01/30/south-african-covid-19-variant-identified-in-maryland/

As of January 30, 2021, which means through yesterday, January 20, the US and top 10 states by COVID-19 cases:

       Cases     Deaths
US  25,697,888  430,120

CA   3,224,374   40,216
TX   2,349,262   36,320
FL   1,682,096    9,328
NY   1,399,863   35,036
IL   1,123,873   21,213
OH     892,781   11,121
PA     839,239   21,602
AZ     753,379   13,098
GA     746,867   14,196
NJ     692,543   21,455

The cases and deaths are confirmed and probable reported by the states and on CovidTracking.com

https://ncov2019.live/data/unitedstates - reports greater numbers, especially for NY state.
Johns Hopkins also reports slightly greater estimates: 26,052,135 cases with 439,347 deaths in the US.

The UK variant has been identified in 30 states with 434 cases, according to the CDC, with South Carolina reporting their first case today, and Delaware reporting three cases as of yesterday. As of Tuesday, January 26, Medscape reported the UK variant in 24 states in the US.
https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant.html (30 states with 434 cases of UK variant as of Jan. 30) - page will be updated so expect a different number by Monday.
https://www.medscape.com/viewarticle/944739

Unless more robust treatments are available, I expect the number of fatalities due to Covid-19 in the US to reach 500K by the end of February.December 30, 2020 - Missouri boy, 3, suffers a stroke after testing positive for COVID-19
https://www.kmbc.com/article/missou...after-testing-positive-for-covid-19/35101361#

January 29, 2021 - New Mexico Girl, 4, Left Paralyzed After Contracting COVID-19 and Developing a Rare Neurological Disorder (8 months in hospital)
https://www.msn.com/en-us/health/medical/new-mexico-girl-4-left-paralyzed-after-contracting-covid-19-and-developing-a-rare-neurological-disorder/ar-BB1ddR09

 

[morrobay]

While transverse myelitis is a tragedy for this girl, there are long lists of causes. https://www.mayoclinic.org/diseases... inflammation,nerves send throughout the body. Covid prevention : 2/3 of the U.S are overweight. 1/2 have hypertension. And 1/10 are diabetic.

 

[russ_watters]

"Delivered" doesn't even appear in the CDC page. I still don't know where you see a problem.

That's the problem. You've repeatedly cited "delivered" vaccines with few or no or corresponding statistics or even a clear definition. At best, you aren't being careful in your word usage.

I used "deliveries" to refer to the "distributed" number once. Distribution implies something is getting delivered somewhere. Is this really what you are arguing about the whole time? That would be quite a waste of time...

Yes, that's what I said the whole time [that the "missing doses" are between a warehouse and an arm]. Good that you came to the same conclusion now.

No "distributed" does not mean/imply "delivered" except perhaps in corporate spin. That may be the root of the problem. "Distributed" is the start and "delivered" is the end.

But if you think we are now in agreement (doubt it) I guess it would have been better for you to acknowledge you made a mess of things earlier, but if that's it, I'll take it. But I'm not sure it's clear, so I'll re-post where this started, for clarity:

If it's so easy [injecting a million a day], why isn't it done? The deliveries exceed the administered doses massively. [stats are] That's incompatible with deliveries being the bottleneck. Based on your graph there are 20 million doses somewhere that have been delivered but not being used yet. More than the total number of doses given to people. You expect some of these doses to be in the delivery chain, obviously, but not that many. At the current inoculation rate they have vaccines for over a month sitting somewhere in freezers. The Pfizer/BNT vaccine doesn't even last that long while it's deeper down the delivery chain: If these doses don't end up being thrown away then they are in deep freezers at a few central locations waiting for ... I don't know what.
...
Yes, that's what I said the whole time. Good that you came to the same conclusion now.

Every claimed reason for the disparity between "distributed" and "administered" in the CDC data is wrong. If we now agree on that, great. Here's a summary to re-cap:

• It's not easy to inject a million doses a day -- wrong
• Stats are incompatible with deliveries (to a usage site) being the bottleneck -- wrong
• 20 million doses "delivered but not being used yet" -- wrong
• "not that many ...doses...in the delivery chain" [re-organized] -- wrong
• The Pfizer/BMT vaccine doesn't even last that long while it's deeper down in the delivery chain -- that's a side issue, but it is also wrong.
• vaccines for over a month sitting somewhere in freezers -- wrong

I'll say again what my purpose is with this: I'm trying to project when I might be eligible to be vaccinated. In order to do that, I must project the vaccination rates for the next few months. The modeling I'm working on is based entirely on manufacturing capacity because the data suggests that manufacturing capacity is the only significant bottleneck, so my model is based entirely on the manufacturing capacity, as indicated by the "distributed" data and some announcements about what is promised in the future. For example, if over the next month the manufacturing ramps-up to 5 million doses a day (allocated to the US), then in a month + 16 days we'll be injecting 5 million doses a day into arms. Because injecting into arms is the easy part of this.

Note: there are anecdotes about unused/discarded doses, but they are thin and mostly lacking data. Actual data on wasteage suggests a fraction of a percent being lost and in some cases depending on how the data is framed it is sometimes a negative loss rate due to the potential for an extra dose in the Pfizer vials.

 

[mfb]

That's the problem. You've repeatedly cited "delivered" vaccines with few or no or corresponding statistics or even a clear definition.

I made clear that I mean the numbers CDC calls "distributed". I did so in every single post where wrote "distributed". "Based on your graph" which used CDC "distributed", again in reference to your graph, and direct reference to the distributed number.
Jan 22 I didn't know what exactly CDC meant by "distributed" (and based on your comments, I think neither did you), that has been clarified in the meantime. That made most of the following discussion outdated.

It's not easy to inject a million doses a day -- wrong

I never made that claim. My comment about "if it's so easy" referred to the idea of keeping up with distributed doses. But again, we learned more about what CDC tracks.

because the data suggests that manufacturing capacity is the only significant bottleneck

As I mentioned before, the CDC numbers are not sufficient to tell anything about manufacturing rate. They do not include the number of manufactured (and US-assigned) vaccines. A bottleneck from injecting the vaccines looks exactly the same if places only order what they will use in the near future (a wise decision given the limited shelf life). And your claim is incompatible with your own source, where only some places are limited by what they can get at the moment.

I'll say again what my purpose is with this: I'm trying to project when I might be eligible to be vaccinated. In order to do that, I must project the vaccination rates for the next few months.

And I fear this personal connection makes you start with a conclusion and then interpret everything to fit that conclusion.

We can set a lower limit, based on the assumption that the rate of administered doses won't decrease:
ourworldindata.org tracks 16.5 doses administered in the last 13 days. At that rate ~2/3 of the US population can get two doses within 2021. It's likely the rate will go up quite a bit over the year.

 

[russ_watters]

Current USA vaccination trends:

Observations:

• The 16 day distribution pipeline has remained remarkably consistent. I would have expected it to become more efficient over time, but it really hasn't. The slopes of the two graphs suggests it could start to narrow, but very slowly. Note: that's a poly vs linear trend, but I'll switch to both poly for next time. it doesn't have much impact on the observation.
• The "distributed" numbers have gotten more chaotic over time. I speculate that that's due to either improving efficiency in the distribution (time a batch takes to leave a warehouse decreasing) or batches becoming larger and wider-spaced. E.G., two days in a row of near zero "distributed" probably means they had almost no vaccine to distribute. Note: the numbers weren't exactly zero, so it wasn't a matter of not updating the website.
• I'm considering cutting-off the December "administered" data as the initial time to fill the pipeline skews the "administered" trend. If I feel like it -- the issue will decrease in impact over time.
• Obviously, the 100M doses administered in 100 days goal is not at significant risk, and wasn't, even before Jan 20. Even without the J&J vaccine we're looking at between 150M and 200M doses administered by April 30.

 

[atyy]

Likely case of COVID-19 re-infection in Singapore
https://www.channelnewsasia.com/new...ikely-reinfection-dormitory-resident-14127700
"In addition to his positive polymerase chain reaction (PCR) test results, there was a corresponding marked increase in antibody titres compared to the period prior to the likely re-infection, suggesting that he was exposed to a new infection which boosted his antibody levels."

 

[Ygggdrasil]

Likely case of COVID-19 re-infection in Singapore
https://www.channelnewsasia.com/new...ikely-reinfection-dormitory-resident-14127700
"In addition to his positive polymerase chain reaction (PCR) test results, there was a corresponding marked increase in antibody titres compared to the period prior to the likely re-infection, suggesting that he was exposed to a new infection which boosted his antibody levels."

We now have some statistics on the prevalence of re-infection by SARS-CoV-2. The SIREN study has been monitoring COVID-19 infections in hospital staff in the UK, identifying people who had previously been infected by the disease, then seeing how many would later become re-infected, and published some early results in a non-peer reviewed preprint on medRxiv:

Do antibody positive healthcare workers have lower SARS-CoV-2 infection rates than antibody negative healthcare workers? Large multi-centre prospective cohort study (the SIREN study), England: June to November 2020
https://www.medrxiv.org/content/10.1101/2021.01.13.21249642v1

Overall, they observed a 83% lower risk of infection among the previously infected group versus the control group who had not previously been infected, and the protection lasts at least five months.

Between 18 June and 09 November 2020, 44 reinfections (2 probable, 42 possible) were detected in the baseline positive cohort of 6,614 participants, collectively contributing 1,339,078 days of follow-up. This compares with 318 new PCR positive infections and 94 antibody seroconversions in the negative cohort of 14,173 participants, contributing 1,868,646 days of follow-up.

See also the press release from Public Health England: https://www.gov.uk/government/news/...but-people-may-still-carry-and-transmit-virus

 

[mfb]

You can hardly do this randomized. How did they make sure to account for different workplaces of the groups? People with a previous infection are more likely to work with COVID-19 patients (causal connection in both directions!).

There is a big difference in the results of an infection. In the negative group (first infection) only 12% were asymptomatic. In the positive group (reinfection) 66% were asymptomatic.

 

[atyy]

https://www.bbc.com/news/uk-55967767
Covid: Oxford jab protection against South Africa variant 'limited'

"First reported by the Financial Times, the study suggest the vaccine offers limited protection against mild and moderate disease caused by the variant.

The study is due to be published on Monday.

A spokesman for AstraZeneca said they had not yet been able to properly establish whether the jab would prevent severe disease and hospitalisation caused by the South Africa variant because those involved in the study had predominantly been young, healthy adults."

 

[atyy]

You can hardly do this randomized. How did they make sure to account for different workplaces of the groups? People with a previous infection are more likely to work with COVID-19 patients (causal connection in both directions!).

It depends on the PPE (personal protective equipment) situation. If there is enough PPE at work, then there may not be any increased risk from working with COVID-19 patients. For example, would it be possible for the health care workers were infected at mainly at home, outside of work - or if at work, from their interactions with colleagues in the cafeteria, where people eat unmasked? In Singapore, there have been health care workers infected, but IIRC they are all not infected from working with COVID-19 patients.

 

[mfb]

Even in other places you don't eliminate the bias. Different people will have different risks, and of course the people with the previous infection tend to have a higher risk on average.

 

[Ygggdrasil]

You can hardly do this randomized. How did they make sure to account for different workplaces of the groups? People with a previous infection are more likely to work with COVID-19 patients (causal connection in both directions!).

There is a big difference in the results of an infection. In the negative group (first infection) only 12% were asymptomatic. In the positive group (reinfection) 66% were asymptomatic.

Agreed, the study is an observational study, not a randomized controlled trial, so the numbers are subject to biases. As you note, people who were infected by COVID-19 during the first wave were probably more likely to participate in risky behaviors during the second wave that would put their exposure to the virus at a higher level than the people who avoided infection during the first COVID-19 wave.

However, the study is useful in that it documents a larger cohort of people re-infected with the Coronavirus (n=44) vs the anecdotal case reports of re-infection (e.g. the Hong Kong case, the Nevada case, and the Singapore case cited earlier in the thread). In particular, it confirms the expectation that re-infections generally result in more mild cases of COVID-19 (whereas the Nevada patient exhibited more severe during the reinfection).

 

[Ygggdrasil]

https://www.bbc.com/news/uk-55967767
Covid: Oxford jab protection against South Africa variant 'limited'

"First reported by the Financial Times, the study suggest the vaccine offers limited protection against mild and moderate disease caused by the variant.

The study is due to be published on Monday.

A spokesman for AstraZeneca said they had not yet been able to properly establish whether the jab would prevent severe disease and hospitalisation caused by the South Africa variant because those involved in the study had predominantly been young, healthy adults."

These results are consistent with similar studies looking at the ability of the B.1.351 strain from South Africa to escape natural immunity or immunity from other vaccines:

1) Laboratory experiments looking at how mutations to the spike (S) protein show that antibodies from convalescent sera are much less effective at recognizing S proteins with mutations at E484: https://www.biorxiv.org/content/10.1101/2020.12.31.425021v1

2) Sera from people immunized with the Moderna mRNA vaccine is less effective at neutralizing the B.1.351 variant than the original virus: https://www.biorxiv.org/content/10.1101/2021.01.25.427948v1
(note, however, that Pfizer reports that its vaccine is effective at neutralizing viruses containing the E484K mutation: https://www.biorxiv.org/content/10.1101/2021.01.27.427998v1)

3) Phase 3 clinical trials of new COVID-19 vaccines from Novavax and Johnson & Johnson showed lesser efficacy at preventing infection in South Africa and Brazil (where the newer variants are more common) versus in the UK (where the E484 mutant viruses are not as prevalent).

For more discussion see:
https://www.physicsforums.com/threads/covid-19-mutations-and-implications-for-the-vaccines.999297/
https://www.physicsforums.com/threads/sars-cov-2-mutations.998345/

 

[mfb]

https://www.jpost.com/israel-news/thousands-expected-at-funeral-of-senior-ultra-orthodox-rabbi-658131 ... who died of COVID-19. You would think people learned something in the last year.

This boy would have an excuse: He was in a coma for almost a year. Now his family is wondering how to explain the last year to him without sounding crazy.

 

[mfb]

White House staff made an AMA on Reddit:

With these additional doses, the U.S. will have enough vaccine to fully vaccinate 300 million Americans by the end of this summer.

Source

Edit: Biden's statement is more cautious:

The president said that he had already approached producers like Pfizer and Moderna to ask them to ramp up production, but said nonetheless achieving herd immunity before the end of summer would be "very difficult."

Biden says manufacturing is the limit to reach that.

CDC changed its "distributed" number to "delivered":
https://covid.cdc.gov/covid-data-tracker/#vaccinations

 

[mfb]

Reports of Anaphylaxis After Receipt of mRNA COVID-19 Vaccines in the US—December 14, 2020-January 18, 2021

~5 per million for Pfizer/BioNTech, ~2.5 per million for Moderna
61 of the 66 cases were known to be recovered at the time of the study, no death (in a total of 17 million vaccinations).

 

[Astronuc]

My wife just received her second shot of the Pfizer/BioNTech vaccine. So far, no adverse reaction. I'm not eligible yet, and even so, there is a long wait list to get vaccinated. Supply and distribution are still problematic.

Meanwhile -

New Zealand's Prime Minister Jacinda Ardern has ordered the country's biggest city Auckland to go into lockdown after the discovery of three new local cases of Covid-19. The three community cases were announced earlier on Sunday - a mother, father and daughter from South Auckland. All it takes is one person to bring it home. https://www.bbc.com/news/world-asia-56059960

Newsweek reported "the family of a Venezuelan woman who tested positive for Coronavirus died after she concealed her diagnosis from them." "Verónica García Fuentes, 36, from the state of Tachira in Venezuela, fell ill with a fever in mid-December." She had a positive PCR test, but told her family that she had the flu. Ms Fuentes subsequently develop pneumonia, but "her husband and three children, one aged 17 and twins aged 4, all tested negative in a rapid test." After her condition deteriorated, Ms Fuentes was admitted to hospital. Her husband and children subsequently tested positive. "Days later, her husband was admitted to hospital with severe symptoms and a week later, both died. The couple's three children had also passed away by the end of January." Such a senseless tragedy.

One can find the story in Newsweek, but I won't post a link since the opinion headlines at the side of the article are rather political. The article is entitled, "Woman's Entire Family Dies After She Hides Positive COVID Test"

 

[StevieTNZ]

New Zealand's Prime Minister Jacinda Ardern has ordered the country's biggest city Auckland to go into lockdown after the discovery of three new local cases of Covid-19. The three community cases were announced earlier on Sunday - a mother, father and daughter from South Auckland. All it takes is one person to bring it home. https://www.bbc.com/news/world-asia-56059960

Yup - Auckland is alert level three, while the rest of NZ is at alert level two until at least 11.59pm Wednesday. The strain is the UK one.

https://www.stuff.co.nz/national/he...linked-to-an-miq-case-are-uk-variant-of-virus

Of course the supermarkets got raided once more when the news was announced. I don't understand the stupidity of some people who know full well supermarkets remain open during these alert changes.

 

[morrobay]

Could Reichenbach's common cause principle (besides covid) apply to the entire Venezuelan family , parents and children who passed away ? This seems very extraordinary. https://www.csis.org/analysis/covid-19-venezuela-how-pandemic-deepened-humanitarian-crisis

 

[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

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[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"?