COVID COVID-19 Coronavirus Containment Efforts

[Astronuc]

The mother of a close friend passed away on Friday. She had been in an elder care facility and was receiving immunotherapy for cancer. However, she died from complications of COVID-19.

 

[fresh_42]

The mother of a close friend passed away on Friday. She had been in an elder care facility and was receiving immunotherapy for cancer. However, she died from complications of COVID-19.

I self-censored the rant against mask deniers I wrote as a reply. It makes me sad to hear such stories. I have a very good friend who also cannot afford to catch any virus, let alone SARS-covid-2, because of immune suppression. So I can imagine how this feels. It is frustrating that there are still people out there, and not only in the US, who actually dare to demand their freedom to - let's say it as it is - infect others.

 

[morrobay]

https://thethaiger.com/news/nationa...arbed-wire-security-increased-due-to-covid-19 I hope they have enough barbed wire for 2000 km

 

[atyy]

https://www.bbc.com/news/world-australia-55471235
Covid: Sydney beach party sparks backpacker deportation threat

 

[morrobay]

And Thailand is having outbreaks after months of no cases. The main outbreak last week is at the Central Shrimp Market in Samut Sakhon and the dormitory for the thousands of Burmese migrant workers. Now most ,90% , of the daily appx 100 transmissions are local .Such as 45 infections in a gambling den cluster a few days ago as well as a bikers crowd in Phuket, one member who had visited the Central Shrimp Market at North part of the gulf close to Bangkok.

 

[Astronuc]

A new variant of the novel Coronavirus that was first detected in the United Kingdom is most likely circulating across the United States, . . . .

The new variant of the SARS-CoV-2 virus—dubbed the B.1.1.7 lineage—appears to be more transmissible than the original, although a study from Public Health England found that it does not seem to cause more severe illness.

https://www.msn.com/en-us/health/medical/new-covid-19-strain-almost-certainly-in-multiple-states-biden-advisor-atul-gawande-says/ar-BB1clvvg?li=BBnb7Kz

The new variant has been reported in Colorado. On Tuesday, Colorado Gov. Jared Polis announced that a man in the state had been infected with the new variant—the first case detected in the United States. The individual in question is a male in his 20s and has no history of travel, Colorado health officials said. He is currently recovering in isolation in Elbert County. Prior to that confirmed case, the CDC indicated that the B.1.1.7 lineage has already been circulating in the United States undetected, but "genetic sequencing of the SARS-CoV-2 virus had only been carried out on a small fraction of the roughly 17 million COVID-19 cases in the US." So, did the variant travel from the UK to the US (meaning that it's spreading undetected, perhaps with asymptomatic persons), or the SARS-Cov-2 naturally mutates to this new variant regardless of location?

Meanwhile, in Louisiana, congressman-elect Luke Letlow died Tuesday evening from complications of Covid-19 days before he was set to be sworn into office, his spokesman announced. He was 41, and leaves behind a wife and two children.
https://www.msn.com/en-us/news/politics/congressman-elect-luke-letlow-dies-from-covid-complications-days-before-being-sworn-in/ar-BB1ckGjP

Apparently Letlow had received Remdesivir and steroids, but that was not enough. I don't know if he received the Regeneron monoclonal antibody, but I believe that he did not. It would seem that Remdesivir and steroids alone are insufficient in some (severe?) cases. I wonder if the Remdesivir was started too late.

 

[mfb]

So, did the variant travel from the UK to the US (meaning that it's spreading undetected, perhaps with asymptomatic persons), or the SARS-Cov-2 naturally mutates to this new variant regardless of location?

It's of course possible that the same set of mutations happens independently elsewhere at around the same time, but it doesn't sound particularly likely. As you wrote, most tests don't sequence the virus. This is in far more places than we know about.

 

[Astronuc]

Dec 30 (Reuters) - A 45-year-old nurse in California tested positive for COVID-19 more than a week after receiving Pfizer Inc's Coronavirus vaccine, an ABC News affiliate reported on Tuesday.

https://www.reuters.com/article/hea...ing-pfizer-covid-19-vaccine-abc-idUSL4N2JA181

Matthew W., a nurse at two different local hospitals, posted on social media on December 18 that he had received the Pfizer vaccine, and reporting his arm was sore for a day but that he had suffered no other side-effects. Six days later, on Christmas Eve, he became sick after working a shift in the COVID-19 unit, the report added. He got the chills and later came down with muscle aches and fatigue. He subsequently tested positive for COVID-19 the day after Christmas.

Apparently a single dose of Pfizer's vaccine takes time kickstart the immune system, and it may be insufficient to prevent onset of COVID-19. Time and a second dose are needed.

Meanwhile in NY State, infections and hospitalizations of younger folks are increasing, and the state is approaching 1 million confirmed cases and 30,000 deaths.

 

[fresh_42]

AFAIK it takes 2 doses with 3 weeks time in between. But even then, there is no guarantee that it works. IRC they claim around 90% efficiency, which is still above the quote of an ordinary flu vaccine.

 

[Rive]

...they claim around 90% efficiency, which is still above the quote of an ordinary flu vaccine.

As I recall the 'raw' efficiency of an ordinary flu vaccine is ~ in the same range (but without any seconds, usually).
I mean: against exactly matching strain, within a few months at most, and so on with the constraints...

I wish that that 90% would remain 90% after a year.

 

[Ygggdrasil]

https://www.reuters.com/article/hea...ing-pfizer-covid-19-vaccine-abc-idUSL4N2JA181

Matthew W., a nurse at two different local hospitals, posted on social media on December 18 that he had received the Pfizer vaccine, and reporting his arm was sore for a day but that he had suffered no other side-effects. Six days later, on Christmas Eve, he became sick after working a shift in the COVID-19 unit, the report added. He got the chills and later came down with muscle aches and fatigue. He subsequently tested positive for COVID-19 the day after Christmas.

Apparently a single dose of Pfizer's vaccine takes time kickstart the immune system, and it may be insufficient to prevent onset of COVID-19. Time and a second dose are needed.

Meanwhile in NY State, infections and hospitalizations of younger folks are increasing, and the state is approaching 1 million confirmed cases and 30,000 deaths.

This is not surprising. The phase 3 clinical trial for the Pfizer vaccine documented 39 people being infected up to three weeks after the first vaccination before getting the second dose (out of a total of 21,669 versus 82/21,686 infections in the placebo over the same time period). As others have mentioned, it takes time for the body's immune system to generate antibodies to the vaccine, and the 95% efficacy figure from the vaccine trial applies only when looking at data starting a week after receiving the second dose of the vaccine (four weeks after the initial dose). Furthermore, because the virus has an incubation period of up to 2 weeks, showing symptoms of the disease 6 days after getting the vaccine is not inconsistent with getting infected before receiving the vaccine.

According to the data from the Pfizer trial, it looks like you have to wait at least two weeks after the first dose before you begin to see signs of protection from the vaccine:

 

[mfb]

6 days (or 9 days if we take the test result) is well within the part where the two curves don't differ, so this is not surprising at all.
It's unclear how much the second dose helps, but expecting to be protected the day after the first one is unreasonable.

Based on this vaccination tracker Israel has already vaccinated 11% of its population. The worldwide average is 0.13%, or 10 million vaccinations.
The phase III vaccine trials used ~15,000 people over ~6 months each for each leading candidate. We get an equal product of people and time every 6 hours now, only rising as the number of vaccinated people goes up. About half of these vaccinations (4.5 million) are in China, however, where the disease is rare anyway. The US is second in absolute numbers, 2.8 million vaccinations. Almost all of them just got the first dose, but the number of people who got it at least 2 weeks ago (should have a good protection now) is rising quickly. Israel and the UK are at 1 million each.

 

[Astronuc]

From https://covidtracking.com/data/national/deaths (they mostly agree with the published data from the states and territories)
Oct 01, 2020 199,943 cumulative deaths due to COVID-19
Dec 31, 2020 336,779 cumulative deaths

Difference 136,836 deaths

Difference + Dec 31, 2020, projected by March 31, 2020 - 473,615 cumulative deaths, but it may be more like 480K to 500K, because the downward slope after a peak is not as steep as the ascension. Even though we have a vaccine, it's slowly rolling out, and we currently have a relatively high mortality rate.The mutation of SARS-Cov-2 from southern UK has apparently made it's way to Florida and California after being first identified in Colorado. Health officials believe it came from folks returning from the UK. The two persons in Colorado and Florida who have the new variant do not have a travel history to the UK.

https://www.wfla.com/community/health/coronavirus/new-covid-19-variant-found-in-florida/
https://www.usatoday.com/story/news/health/2021/01/02/new-covid-strain-b-117-explained/4112125001/
CDC (December 29, 2020) - https://www.cdc.gov/coronavirus/2019-ncov/more/scientific-brief-emerging-variant.html - seems to indicate it is not present in US, but other sources indicate otherwise.

 

[mfb]

because the downward slope after a peak is not as steep as the ascension.

I don't see a downward slope yet. New cases still hover at ~200,000/day, deaths at ~2500/day. Hospitalizations are at an all-time high (120,000).

Vaccines will help protecting the most vulnerable people, its early impact on deaths will probably be larger than its impact on cases, but it needs to be pretty strong to keep the deaths below 500,000 by the end of March.

 

[Astronuc]

I don't see a downward slope yet.

No, unfortunately, not yet. New York accumulated over 1 million positive cases on Jan 1. Illinois should exceed 1 million positive cases in about 4 or 5 days.

 

[PeroK]

The slope is far from downward in the UK.

 

[nsaspook]

National lockdown imposed across England

https://www.standard.co.uk/news/uk/new-lockdown-england-boris-johnson-announcement-b682744.html

People will be required to stay at home except in specific circumstances, including for food shopping, caregiving, medical care, exercise, and fleeing violence.

 

[Astronuc]

The governor of NY State announced that the UK strain B.1.1.7 of SARS-Cov-2 has been found in one individual in Saratoga County, NY. The individual has not history of travel to any area in the US or to the UK, but obviously he was exposed to someone who has, otherwise, the variant spontaneously developed independently from the population in the UK.

Gov. Andrew M. Cuomo on Monday afternoon announced the Wadsworth Lab in Albany had detected the U.K. strain of the virus, known as B.1.1.7, in the 67-year-old Saratoga County man.

The man, who Cuomo did not identify, as well as three other employees of N. Fox Jewelers, at 404 Broadway in Saratoga Springs, all tested positive for coronavirus. However, it is unknown whether the other employees contracted the more transmissible strain; Cuomo said they are waiting on the results of the other employees to answer that question.

Ref: https://www.timesunion.com/news/article/new-covid-strain-detected-saratoga-springs-15845420.php

At least three other persons from the same store have apparently tested positive for COVID-19, but the state is awaiting for a sequence analysis of the strain. The county and state are warning anyone who visited the store between December 18 and December 24 should be tested for COVID-19.

The state attributes the infection to community spread and believes others in the state have been infected with the B.1.1.7 variant, but others have not been analyzed.

The state will be setting up a rapid-testing site at the Saratoga State Park, 99 E. West Rd., Saratoga Springs, on Tuesday from 1 - 6 p.m. The state-run testing site will also be open from 10 a.m. - 6 p.m. on Wednesday, Thursday and Friday. The testing will be focused on individuals who went to the jewelry store between Dec. 18 and 24, state officials said.

 

[nsaspook]

https://www.statnews.com/2021/01/04...accines-upping-the-stakes-for-the-rest-of-us/

In an extraordinary time, British health authorities are taking extraordinary measures to beat back Covid-19. But some experts say that, in doing so, they are also taking a serious gamble.

In recent days, the British have said they will stretch out the interval between the administration of the two doses required for Covid-19 vaccines already in use — potentially to as long as three months, instead of the recommended three or four weeks. And they have said they will permit the first dose and second dose for anyone person to be from different vaccine manufacturers, if the matching vaccine is not available.

Paul Bieniasz of Rockefeller University is one of those who is watching the evolving situation in Britain with dread. A retrovirologist who turned from HIV research to work on SARS-2, Bieniasz is studying how the virus acquires mutations that allow it to evade the protective antibodies people develop when they have contracted Covid-19, or when they have been vaccinated against it.

Bieniasz believes Britain is replicating in people the experiments he’s been doing in his lab — and could be fostering vaccine-resistant forms of the virus.

 

[morrobay]

 

[PeroK]

https://www.statnews.com/2021/01/04...accines-upping-the-stakes-for-the-rest-of-us/

What's the opinion of the experts on here? Is this journalistic exaggeration, or are we risking everything by changing the double vaccination schedule?

 

[mfb]

We have seen that a single dose provides good protection - possibly as good as the two-dose protocol, at least for a while. The BioNTech/Pfizer graph is the most striking example of this. Even if it's not as good as two doses: Delaying the second dose means getting more people protected sooner. Two people with 60% protection are better than one with 80%.

Even rolling out the vaccine at all when there is so much transmission occurring is far from ideal, he said, suggesting it would have been safer to beat down the amount of virus in circulation before beginning the vaccine deployment.

That's a nice approach, but as we have seen that doesn't work well.

 

[atyy]

What's the opinion of the experts on here? Is this journalistic exaggeration, or are we risking everything by changing the double vaccination schedule?

The article has comments from a few other people, and there seem to be differing reasonable views, so I think it's not known for sure. There are other experts quoted in the article besides Paul Bieniasz.

BTW, when we go to Iwasaki's Twitter thread, we see she's concerned about the increased transmissibility of the UK variant. But although there is some evidence to support that, I think the increased transmissibility has not yet been solidly established, eg.Trevor Bedford comments "The @PHE_uk secondary attack rate analysis was not done on the matched cohort. There should be more stratification here. I'm sorry for the confusion. I'd take the 15% vs 10% secondary attack rate with a grain of salt for the moment.".

 

[Rive]

...are we risking everything by changing the double vaccination schedule?

The virus itself is known to cause only partial (? weak, maybe?) immunity: sometimes with very low antibody levels. Compared to - guess only! - 20% of the population having 'natural' unreliable immunity; 6% having artificial 60% immunity or 3% having 95% immunity... Well, the difference does not feels really dramatic.

I think the high number of copies (=> high number of mutations) racing to re-infest that 20% is a far more worse problem.

 

[PeroK]

The virus itself is known to cause only partial (? weak, maybe?) immunity: sometimes with very low antibody levels. Compared to - guess only! - 20% of the population having 'natural' unreliable immunity; 6% having artificial 60% immunity or 3% having 95% immunity... Well, the difference does not feels really dramatic.

I think the high number of copies (=> high number of mutations) racing to re-infest that 20% is a far more worse problem.

Sorry, I can't understand what you are saying here.

 

[mfb]

The virus itself is known to cause only partial (? weak, maybe?) immunity: sometimes with very low antibody levels.

It's good enough to protect almost everyone for at least ~9 months, because double infections are still incredibly rare. They do happen, but not at a level where they would be relevant for the pandemic. In particular, the protection from getting the disease itself is far better than 95% over the observable time range.

 

[Rive]

double infections ... do happen, but not at a level where they would be relevant for the pandemic.

Sorry, but you do not know that. There is no widespread random and regular PCR testing amongst the already infected.
The only thing actually known is that reinfections which are bad enough to be tested again are rare.

Sorry, I can't understand what you are saying here.

From the article:

if you wanted to make a vaccine-resistant strain, what you would do is to build a cohort of partially immunized individuals in the teeth of a highly prevalent viral infection

The virus itself known to be unreliable when it's about antibody levels after an infection. Compared to the virus (which is lacking any quality management standards, as it seems) the vaccine is actually far more reliable (again: it's about antibody levels).
So if somebody is worrying about new strains, then he should look for the growing number of already recovered patients first because at this point they are a far more 'beefy' population of interest for the virus (which were left to grew into a 'healthy' gene pool already, ready for some drifting to occur).

The situation is not good, but the vaccine and its usage is just a very minor part of it.

 

[Jarvis323]

Sorry, but you do not know that. There is no widespread random and regular PCR testing amongst the already infected.
The only thing actually known is that reinfections which are bad enough to be tested again are rare.From the article:

The virus itself known to be unreliable when it's about antibody levels after an infection. Compared to the virus (which is lacking any quality management standards, as it seems) the vaccine is actually far more reliable (again: it's about antibody levels).
So if somebody is worrying about new strains, then he should look for the growing number of already recovered patients first because at this point they are a far more 'beefy' population of interest for the virus (which were left to grew into a 'healthy' gene pool already, ready for some drifting to occur).

The situation is not good, but the vaccine and its usage is just a very minor part of it.

When I was studying the research on immunity months ago, it was thought that antibodies might not last long, but T-memory cell immunity was likely to be pretty reliable and long lasting. I haven't kept up on research since then, except that the vaccines were found to also trigger T-cell immunity. Does anyone know the current knowledge about this issue?

 

[atyy]

So if somebody is worrying about new strains, then he should look for the growing number of already recovered patients first because at this point they are a far more 'beefy' population of interest for the virus (which were left to grew into a 'healthy' gene pool already, ready for some drifting to occur).

It's probably on the time scale of a few years, if it's similar to other coronaviruses.

https://www.biorxiv.org/content/10.1101/2020.12.17.423313v1
A human Coronavirus evolves antigenically to escape antibody immunity
Rachel Eguia, Katharine H. D. Crawford, Terry Stevens-Ayers, Laurel Kelnhofer-Millevolte, Alexander L. Greninger, Janet A. Englund, Michael J. Boeckh, Jesse D. Bloom
Twitter summary by the authors

 

[Jarvis323]

I've been reading through this paper, which goes into depth about the issue.

What are the roles of antibodies versus a durable, high quality T-cell response in protective immunity against SARS-CoV-2?

These findings carry a potentially important message for SARS-CoV-2 vaccines. Most current vaccine candidates are focusing on spike protein as the immunizing antigen, but natural infection induces broad epitope coverage in T-cells. It will be essential to understand the relation between breadth, durability and quality of T-cell responses and resulting protective immunity with SARS-CoV-2 vaccines and natural infection.
...
It would be a public health and “trust-in-medicine” nightmare with potential repercussions for years - including a boost to anti-vaccine forces - if immune protection wears off or antibody-dependant enhancement develops and we face recurrent threats from COVID-19 among the immunized. Data correlating clinical outcomes with laboratory markers of cell-mediated immunity, not only with antibody responses, after vaccination or natural infection with SARS-CoV-2 or other betacoronviruses may prove critically valuable, particularly if protective immunity fades or new patterns of disease emerge.

https://www.sciencedirect.com/science/article/pii/S2590136220300231

Since T-cells give long lasting and cross-reactive protection, not dependent on the spike protein, I would guess that a good T-cell response would be important for minimizing risk of a mutation overcoming vaccine protection. We also already have spike protein mutations that occurred after the vaccines had been developed, so we don't know if the levels of antibody protection seen in trials will be the same against the new fast spreading variant. A population with waning antibody resistance primarily targeting the spike protein, but not good T-cell based protection, would probably be a bad recipe for adaptation. I'm not sure what is known about the effectiveness of vaccine induced T-cells immunity at this stage, except that it is triggered to some extent. The paper mentions some ways to measure T-cell effectiveness, and argues that antibody levels are a bad measure to look at. I also wonder how a second dose of the vaccine affects T-cell immunity.

Another issue I wish I understood more is antibody dependent enhancement.

Antibody-based drugs and vaccines against severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) are being expedited through preclinical and clinical development. Data from the study of SARS-CoV and other respiratory viruses suggest that anti-SARS-CoV-2 antibodies could exacerbate COVID-19 through antibody-dependent enhancement (ADE). Previous respiratory syncytial virus and dengue virus vaccine studies revealed human clinical safety risks related to ADE, resulting in failed vaccine trials. Here, we describe key ADE mechanisms and discuss mitigation strategies for SARS-CoV-2 vaccines and therapies in development. We also outline recently published data to evaluate the risks and opportunities for antibody-based protection against SARS-CoV-2.

https://www.nature.com/articles/s41564-020-00789-5

Is this something we've avoided, having successful trials, or something we need to keep worrying about down the line?