Evolution of Covid Strains.

[mistermack]

2 hours ago, swansont said:

Unvaccinated got infected at 4.6 times the rate as fully vaccinated, data from Jan 17 2021 through Nov 20.

Except that you changed the vital words when quoting. You said "got infected", they said "developed Covid". Which conveniently completely changes the meaning. Nice one !

 

[swansont]

10 hours ago, mistermack said:

Except that you changed the vital words when quoting. You said "got infected", they said "developed Covid". Which conveniently completely changes the meaning. Nice one !

 

Seriously? How do you develop COVID other than by infection? The COVID fairy?

You also might note that just above that passage, where they present the numbers, they say "rate of infection per 100,000" so clearly the two descriptions mean the same thing, and I didn't misrepresent anything.

What straws are you clutching at here?

Here's the whole shebang

[studiot]

It should be noted that data from all countries/regions contains considerable hidden unknowns.

Also the methods used for recording the data are different in different countries, making comparison a bit tricky.

The UK defines death from covid as "Death within 28 days of a positive covid test"

It defines infection rates as "recorded by a positive covid test", not as presenting with covid symptoms

But only a minor % of the population undergoes routine testing. Most only test if the have symptoms.

Also what is meant by 'fully vaccinated' has never been clear.

 

[Sensei]

It is difficult to be infected by a microbe known to the immune system, but it is still possible especially if the immune system began to lose its "memory" of the microbe's structure.. Or its structure changed significantly due to a random mutation.. The more people are infected (due to i.e. anti-vaxxers), the more chance of development of vaccine resistant mutation..

@CharonYany work on the decline of immunity over time (e.g. the amount of antibodies/antigens in a blood sample?) , after being vaccinated, on a graphs (picture to attach on the forum, i.e. a picture is worth a thousand words), with data records per week or month, per vaccine brand, per virus strain (if they are reinfected), on a carefully selected group of people, tested frequently.. ?

Maybe it might be worth creating tests available in pharmacy "how much can I trust my vaccination", e.g. a person takes a blood sample and test calculates the amount of antibodies/antigens, compares it to a previous reading (per month) and knows how much it has dropped over time..

Instead of giving straight answer, person can enter result from the readings into website to learn it, and at the same time, database is updated to gather information from patients to learn vaccination efficiency in "real-time" by scientists..

..or a group of 10k volunteers receiving $100/€100 each time, donating blood samples to collect the above data.. per week/month.. Small cost, but would show the decline in immunity over time, per brand of vaccine, etc. useful data....

..or pay $100/€100 per person going for a vaccination for the 1st/2nd/3rd time, and take a blood sample to check the amount of antibodies/antigens in it to find out the above data and put it in the db for further analysis..

Edited November 29, 2021 by Sensei

[swansont]

3 minutes ago, studiot said:

Also what is meant by 'fully vaccinated' has never been clear.

In the form I recently had to fill out, it was quite clearly defined as two weeks after the second shot if it's a two-shot vaccine, and two weeks after the shot of it's a one-shot vaccine.

Quote

 

The UK defines death from covid as "Death within 28 days of a positive covid test"

It defines infection rates as "recorded by a positive covid test", not as presenting with covid symptoms

 

Which is a reason to pay attention to results from clinical trials and controlled tests, which do this rigorously, and show that the vaccines are effective in reducing infection.

[studiot]

1 minute ago, swansont said:

In the form I recently had to fill out, it was quite clearly defined as two weeks after the second shot if it's a two-shot vaccine, and two weeks after the shot of it's a one-shot vaccine.

Thank you it is useful to be able to compare data standards.

One thing immediately stands out from that.

When do you become 'unvaccinated' after the one or two shots ?

The UK is managing boosters for about six months and two weeks.

But many mean fully vaccinated  =  after the booster.

Edited November 29, 2021 by studiot

[swansont]

1 minute ago, studiot said:

Thank you it is useful to be able to compare data standards.

We have a vaccine mandate, so the letter of the law needs to be spelled out.

The annoying thing is I got my first two shots at Walter Reed, so these records are already somewhere in the system, and yet my colleagues and I still have to fill out paperwork to confirm the information the system already has. 

[studiot]

1 minute ago, swansont said:

so these records are already somewhere in the system, and yet my colleagues and I still have to fill out paperwork to confirm the information the system already has. 

I have that beef about the UK Inland Revenue and tax forms.

[mistermack]

55 minutes ago, swansont said:

Seriously? How do you develop COVID other than by infection? The COVID fairy?

The question under dispute was how many were infected without developing covid so your change of wording was conveniently deceptive. Nice try.

In fact, the charts that I put up will have underestimated the numbers of infections, because they only publish the numbers of postive tests, and that obviously does not cover all infections, as some people would rather not be tested, and others are not sure when they have got it. The fact that you are supposed to self-isolate is enough to put many people off having a test. 

[swansont]

1 hour ago, mistermack said:

The question under dispute was how many were infected without developing covid so your change of wording was conveniently deceptive. Nice try.

Developing COVID and developing symptoms are different things. The website is quite clear that the numbers are infections, and that infection and "developing COVID" are the same thing.

You keep insinuating that this is deceptive, and yet have provided no evidence to the contrary.

1 hour ago, mistermack said:

In fact, the charts that I put up will have underestimated the numbers of infections, because they only publish the numbers of postive tests, and that obviously does not cover all infections, as some people would rather not be tested, and others are not sure when they have got it. The fact that you are supposed to self-isolate is enough to put many people off having a test. 

Your graph doesn't distinguish between vaccinated and unvaccinated people, so for this discussion it's irrelevant, and I've already linked to a rigorous study where everybody was tested. This is also true of the original clinical trials (such as https://www.nejm.org/doi/full/10.1056/nejmoa2034577).

Do you have anything pertinent to offer?

[mistermack]

2 hours ago, swansont said:

and that infection and "developing COVID" are the same thing.

Really? Since "COVID-19 is the name of the disease, not the virus, you seem to be claiming that they don't know the difference. Perhaps you should get in touch. You could point them to the first line of the wikipedia article on Covid-19 :  Coronavirus disease 2019 (COVID-19) is a contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 

Anyway, if you really thought that, I don't know why you bothered to change the quote.           

[TheVat]

4 hours ago, swansont said:

Seriously? How do you develop COVID other than by infection? The COVID fairy?

 

Do gain of function research at a lab in Wuhan?  

JK

Anyway, thanks for a chuckle this morning.  

 

 

[CharonY]

2 hours ago, swansont said:

Developing COVID and developing symptoms are different things. The website is quite clear that the numbers are infections, and that infection and "developing COVID" are the same thing.

You keep insinuating that this is deceptive, and yet have provided no evidence to the contrary

I don't think that this is even actually relevant. The original hypothesis was that vaccines are only (or mostly) effective protecting against developing symptoms.

  

On 11/28/2021 at 7:01 AM, mistermack said:

Citation needed. Not that I can prove otherwise, but whenever I read reports of effectiveness, they have been carefully qualified by saying "symptomatic" infection, and there is no dispute about that, the vaccines are very effective at prevention and reduction of that.

But symptomatic infection doesn't tell the whole story, with this virus and it's variants. 

The poster did not spell it out and went on a tangent with an anecdote, but I took it as assuming that it is ineffective at preventing spread. That is also the only way the overinterpretation of the supplied graph in a later post makes sense. The focus is on transmission, so that is the element that needs to be traced in vaccinated and unvaccinated folks. The critical point that needs to be answered with regard to efficacy of the vaccine to curb spread is the difference in infection rate between these groups, which the poster continues to ignore (and which already has been posted).

 

3 hours ago, Sensei said:

ny work on the decline of immunity over time (e.g. the amount of antibodies/antigens in a blood sample?) , after being vaccinated, on a graphs (picture to attach on the forum, i.e. a picture is worth a thousand words), with data records per week or month, per vaccine brand, per virus strain (if they are reinfected), on a carefully selected group of people, tested frequently.. ?

With regard to graphs I remember a few, but most are not neat comparative analyses, mostly individual patients with either condition (e.g. infection with SARS-CoV-2, one of the vaccinations etc.). I could pick out some if you'd like. However, it is important to note that antibodies are not telling the whole story when it comes to immunization. 

In all cases of infection and immunization the various antibody titres decline (but with vastly varying kinetics). However, an important of the adaptive immune system is the eventual formation of memory cells. Long-term protection is mediated by these T and B cells, as opposed to circulating antibodies. In the case of a new infection, these cells are necessary to produce new neutralizing antibodies to combat that disease. This is why even vaccinated folks with low circulating antibodies can mount effective responses, when exposed to the virus. Even in cases of successful infections (which practically means that the virus is able to replicate until they go over the sensitivity limit of established tests), the virus can be cleared out without resulting in associated damages and symptoms.

Thus, declining antibody titres alone are insufficient to fully establish protective levels of a vaccine over time.

That being said, a faster decline could indicate overall reduced responses, which see for example in the elderly. Recent infection data does indeed suggest that in these groups antibody titers decline faster and unfortunately also become more vulnerable to infections and sever outcomes (or to put it differently, the differential outcome between vaccinated and unvaccinated started to shrink in this group).

[studiot]

4 hours ago, swansont said:

We have a vaccine mandate, so the letter of the law needs to be spelled out.

Yes, but what is the letter of the law ?

The UK advisory body has just advised that fully vaccinated for folks in the age range 12 - 15 should be increased from one shot to two. But it is not yet law.

I think age grouping of data is another effect not properly spelled out in these summary charts.

[swansont]

1 hour ago, mistermack said:

Anyway, if you really thought that, I don't know why you bothered to change the quote. 

I didn't quote (couldn't copy/paste). I relayed the information; 4997/1098  (the number presented as infection rates per 100k) is 4.6

 

8 minutes ago, studiot said:

Yes, but what is the letter of the law ?

For me, it's having to have been fully vaccinated by Nov 22, per directives stemming from an executive order for US federal employees  

[mistermack]

21 minutes ago, CharonY said:

but I took it as assuming that it is ineffective at preventing spread.

I certainly didn't claim that. I simply responded to Swanson's claim that "reports of their effectiveness that show this very thing." Meaning preventing infection. I just asked for citation, because the reports that I read are talking about prevention of the disease, not infection. 

The uk graphs that I posted show that before mass vaccination, the infection and deaths graphs tracked each other rise for rise, drop for drop with deaths lagging a couple of weeks behind. Since substantial numbers got vaccinated, there is virtually no link between the two. I concluded that vaccination is far more effective against serious illness and death, than it is against transmission.

The facts bear it out. The uk government calculate that the risk of death is 32 times higher, for unvaccinated people. If the same applied to transimission, then we would be on top of it now. About 50 million have had 2 jabs, and ten million have had covid. That only leaves about 17 million people available to spread it if vaccination is so effective against transmission. But lately, the people I'm hearing about who have got covid are vaccinated people. Not a scientific figure I know, but the actual figure for vaccinated people testing positive seems very hard to find. Maybe they think it would put people off having the jab.

Not me though. Being 32 times more likely to die is more than enough to convince me. 

[swansont]

7 minutes ago, mistermack said:

I certainly didn't claim that. I simply responded to Swanson's claim that "reports of their effectiveness that show this very thing." Meaning preventing infection. I just asked for citation, because the reports that I read are talking about prevention of the disease, not infection. 

And I've provided two sources that specifically say the rate of infection is lower in vaccinated people in the groups in question.

Meanwhile, the original claim goes unsupported.

[studiot]

7 minutes ago, mistermack said:

The uk graphs that I posted show that before mass vaccination, the infection and deaths graphs tracked each other rise for rise, drop for drop with deaths lagging a couple of weeks behind. Since substantial numbers got vaccinated, there is virtually no link between the two. I concluded that vaccination is far more effective against serious illness and death, than it is against transmission.

The facts bear it out. The uk government calculate that the risk of death is 32 times higher, for unvaccinated people. If the same applied to transimission, then we would be on top of it now. About 50 million have had 2 jabs, and ten million have had covid. That only leaves about 17 million people available to spread it if vaccination is so effective against transmission.

 

1 minute ago, swansont said:

And I've provided two sources that specifically say the rate of infection is lower in vaccinated people.

I think both these graphs are perfectly compatible, but they show different things.

Swansont's graphs are specifically the relationship between infection and vaccination.
That is one effect only, with other effects not included

Mistermack's graphs are a composite of different effects.
Yes the trend in the 7 day average new cases within 24 hours and deaths tracked each other pretty closely.
And they still do.

But they also show a dramatic of deaths suppression following significant mass vaccination of the population.

Nothing wrong with either of them

[CharonY]

50 minutes ago, mistermack said:

I certainly didn't claim that. I simply responded to Swanson's claim that "reports of their effectiveness that show this very thing." Meaning preventing infection. I just asked for citation, because the reports that I read are talking about prevention of the disease, not infection. 

The data provided by Swansont as well as the REACT-1 data from the UK both indicate lower infection rates in vaccinated folks. 

37 minutes ago, studiot said:

Mistermack's graphs are a composite of different effects.
Yes the trend in the 7 day average new cases within 24 hours and deaths tracked each other pretty closely.
And they still do

Indeed, but if you are wondering about the impact of vaccinations, you need to know the proportion of vaccinated folks in that graph. If for example the vaccine was 100% effective in preventing infections, the data could only contain unvaccinated folks and then the differential death rate would necessarily be caused by something else (e.g. age differences). 

 

[swansont]

48 minutes ago, studiot said:

Nothing wrong with either of them

They show what they show, so there's nothing "wrong" with that, but the question is whether they support the claim that the vaccine does nothing to prevent infection, while reducing mortality. It's clear that the latter happens. The question was about the former.

If a graph doesn't indicate vaccination status, it's hard to tease such information out of it.

edit: especially in light of the delta variant being more contagious 

[CharonY]

@Sensei From this study: Levin et al. DOI: 10.1056/NEJMoa2114583

I have attached two graphs showing the 50% neutralization titer after Pfizer-BioNTech vaccination as well as an age-separated graph. It shows the decline within 6 months which can correlate to some degree with lower resistance to infections, especially with fast developing infections (such as delta), though as mentioned before, it is only one piece of the puzzle. The dots are the actually measured values, showing quite a range of individual responses.

[swansont]

1 hour ago, mistermack said:

The facts bear it out. The uk government calculate that the risk of death is 32 times higher, for unvaccinated people. If the same applied to transimission, then we would be on top of it now.

But nobody is saying this

1 hour ago, mistermack said:

About 50 million have had 2 jabs, and ten million have had covid. That only leaves about 17 million people available to spread it if vaccination is so effective against transmission.

No, this is suggesting the vaccine is 100% effective and nobody is claiming that.

1 hour ago, mistermack said:

But lately, the people I'm hearing about who have got covid are vaccinated people.

That's a misconception that many have pointed out.

Let's say you have 1000 people and 900 of them are vaccinated. The chance of getting infected is 5% in unvaccinated and 1% in vaccinated. You will have 100*5% = 5 unvaccinated people getting infected, and 900 * 1% = 9 vaccinated people getting infected

So it should be unsurprising that you have more vaccinated people getting infected when vaccination rates are high.

[mistermack]

Even with the highest vaccine efficiency claimed in the study, (90%) that would indicate a non-vaccinated person being nine times more likely to catch covid. According to the second link, the claim was five times more likely. But currently after the Delta surge, that dropped to 66% effective, which I'm guessing means 2 to 1. 

If you compare that to the figure of 32 times more likely for death, then there appears to be a very big gap between infection efficiency, and death efficiency. 

"In a second MMWR report today, results from the ongoing HEROES-RECOVER study of COVID-19 among frontline workers showed unvaccinated workers were much more likely to become infected during the current Delta surge, but vaccine effectiveness (VE) dropped from roughly 90% to 66%."      

   https://www.cidrap.umn.edu/news-perspective/2021/08/cdc-unvaccinated-5-times-more-likely-get-covid-19           

Two to one is better than nothing, but it's not in the same league as 32 times.

[CharonY]

34 minutes ago, mistermack said:

If you compare that to the figure of 32 times more likely for death, then there appears to be a very big gap between infection efficiency, and death efficiency. 

That is very much expected. Preventing infection also prevents death from illness. Your original question was asking for evidence of efficacy of preventing infections, which you have received (repeatedly).

And just to prevent a few rounds of arguing semantics I would like to point out some common usages in epi-data:

"Infection" commonly refers to all positive tests, regarding of symptom status. Technically it refers specifically to the virus, but for communication with the broader population (e.g. via dashboards) it is sometimes conflated with COVID-19 infection (or similar). While this is technically inaccurate, it is simply a messaging strategy as the population was found to be more familiar with the name for the disease than for the virus.

"Asymptomatic" is used if a positive test is found, but the patient does not present symptoms at time of testing. The issue is that folks are typically not tracked over time, so in some cases folks are actually pre-symptomatic (i.e. develop symptoms later in the infection process).

Often the status of the patient at testing is not documented at all, so the frequency of asymptomatic cases is usually not well established. Moreover, in several areas testing strategies have switched to testing symptomatic cases only. As such in literature you will find a large range of estimates of symptomatic vs asymptomatic cases. 

Vaccine efficacy is the ability of the vaccine itself to improve disease outcome. This is generally done in controlled trials and historically this is based on disease presentation (i.e. showing symptoms of the disease). One of the reason is that in many diseases individuals do not spread the disease if they do not present symptoms (often indicating a low viral load).  Due to the ability of pre-and asymptomatic spread of SARS-CoV-2 transmission is also monitored, but it is not as easy as tracking of symptoms.

Vaccine effectiveness is basically a measure to look how efficacy translates into reality. This is done by capturing data during vaccine rollouts in an observational study. Here, it is important to segment the cohort according to the specific question. I.e. for example look at infected vs non-infected groups and check the vaccination status. Or conversely, segment for vaccination status and check for the variable of interest (e.g. infection rate or hospitalization).

[CharonY]

Going back to omicron, retrospective analyses indicate that omicron has been around in Europe as early as Nov 18 (i.e. before their identification):

https://www.bbc.com/news/world-europe-59473131

While its potential to cause severe illness compared to delta is not known yet, the fact that it seems to be spreading (even in the background of delta) is of concern and worldwide efforts have increased to monitor their presence, both in retrospective (as the one linked above) or prospective surveillance.

While the data could be biased due to ongoing efforts, preliminary data suggest that in SA omicron might be outcompeting delta. I have attached a figure showing the frequency of mutations in alpha, delta, and omicron in three of the genes (darker colour indicates higher frequency of a given mutation). Considering seemingly high transmissibility already indicates that the additional mutations in alpha do not hamper its effectiveness in infection. The important bit to figure out now are the health risks and then how well vaccinations are holding up.