Coronavirus Pandemic (COVID-19) (SARS-CoV-2) [2020]

[Shifty Geezer]

Effectiveness of public health measures in reducing the incidence of covid-19, SARS-CoV-2 transmission, and covid-19 mortality: systematic review and meta-analysis

https://www.bmj.com/content/375/bmj-2021-068302

An overview of the current research into mitigation measures. For me, the standout is how few useful investigations there are and how scientific quality is severely lacking.

 

[Xmas]

In the UK a lot of testing is often symptomless and precautionary; there are about 1 million C19 tests conducted every day. The beginning of my graph shows selective testing of people suspected of having C19. Once lateral flow test rolled out in the summer, tests became more of a general sampling and not focussed on being potentially infected. eg. All secondary (high) school age children are testing every week. I test every week a lateral flow test - these are free from the government. However, breakdown of tests by age groups isn't provided.

Do the test numbers you used for the graph include lateral flow tests? These days, does everyone with a positive LFT take a confirmatory PCR test? There are a few problems with simply summing up the different test types, and numbers are probably not comparable over time as policies and availability of tests change:
- These days many more tests will be precautionary rather than symptomatic (high availability of LFT home tests for going to school and work, legal requirement of testing for travel)
- at-home LFT probably have underreported negative results. Many people won't bother registering the test if it's negative.
- At the same time, LFT have higher false-positive rate than PCR/LAMP. If these are taken as-is, there will literally be thousands of people daily counted as positive who don't have Covid.

 

[Shifty Geezer]

Do the test numbers you used for the graph include lateral flow tests?

For the last half, post March, yes. The testing conditions for the numbers are different so the beginning of the graph isn't comparable to the latter. LFT came in March.



From March onwards, we should have a reasonable approximation of normalised test incidence rates. With far more tests in March, the number of captured positives would be higher than September, Only by comparing positive count to samples taken can we actually filter out the impact of sample count.

- at-home LFT probably have underreported negative results. Many people won't bother registering the test if it's negative.

That's an unquantified assumption. We've a million tests reported every day - not sure unreported negatives will be that significant. But even if that's happening in large numbers, that'll mean the incidence rate will just be slightly higher. Trends will be unaffected so long as people's behaviour is consistent. If people start to lose interest in reporting negatives, positivity rate will increase. I don't see evidence of that in the numbers myself.

At the same time, LFT have higher false-positive rate than PCR/LAMP. If these are taken as-is, there will literally be thousands of people daily counted as positive who don't have Covid.

False positives are reportedly very low, 1 in a thousand (3 in 10,000 even).

https://www.gov.uk/government/news/...-flow-tests-shows-specificity-of-at-least-999

LFT's have more false negatives but very few false positives.

So one thousand false positives from a million tests is 0.1% additional case rates. And again, so long as the results are consistent, trends will be accurately presented even if the actual numbers are a little low or high. The focus here is moving away from measuring growth from case counts to normalised case counts as the latter provides a better indicator of disease spread. If the disease growth was static, R0 = 1, if testing increases 50% over three months, you'll get a 50% increase in case rates looking like higher growth, and vice versa; if testing dropped to 10% over, case rates would drop, and perhaps some politicians would use that to pretend there was no disease!

 

[Arnold Beckenbauer]

Germany, the land of Biontech. Germany, the land, which fucked its vax campaign.

 

[Mariner]

Ah, the situation in South Africa looks, erm, not good:

https://twitter.com/x/status/1463975708770897923

What makes it even worse is that this Covid-nasty B.1.1.529 is likely to be designated the 'Nu' variant. Discussion of it is going to confuse all sorts of people (including me) a lot of the time.

Let's hope for some decent news about the efficacy of the vaccines, against serious illness, if nothing else.

 

[Davros]

The u.k has just banned travellers from 6 African countries

 

[Mariner]

Nu Metal was bad enough, but Nu Covid could be even more painful!

 

[Deleted member 2197]

Could mRNA make us superhuman? - BBC Future
November 22, 2021

The genius of mRNA vaccines is there's no need to inject the antigen itself. Instead, these vaccines use the genetic sequence or "code" of the antigen translated into mRNA. It's a ghost of the real thing, fooling the body into creating very real antibodies. The artificial mRNA itself then disappears, degraded by the body's natural defences including enzymes that break it down, leaving us with only the antibodies.
...
If we are currently witnessing mRNA vaccine 1.0 for Covid-19, then 2.0 will address two further categories of disease, says Fu: "one is pathogens, like Sars, but you can apply this technology to other foreign invaders such as HIV. Already before Covid, companies were in development making mRNA vaccines against HIV." He also cites Zika, herpes and malarial parasites in the pathogens camp.

"The other category is autoimmune diseases," he says. "That is intriguing because it's verging beyond the very strict definition of a vaccine." Fu says the future could involve mRNA "treatments", for example to reduce inflammation. "In theory, that opens up so many possibilities," he says.
...
Several pharmaceutical companies are also pursuing mRNA vaccines and treatments for cancer. "Cancer cells will often have certain surface markers that the rest of the cells in your body don't have," says Blakney. “You can train your immune system to recognise and kill those cells, just like you can train your immune system to recognise and kill a virus: it's the same idea, you just figure out what proteins are on the surface of your tumour cells and use that as a vaccine".

The idea of patient-specific, individualised medicine has been a tantalising prospect for years – this could be another door pushed wide open by mRNA, according to Blakney. In theory, "they take out your tumour, they sequence it, see what's on the surface of it, and then they make a vaccine specifically for you".
...
There's also the potential to mix various mRNA vaccines together into a single health booster vaccine, which could ward off cancers and viruses at the same time. While it's just speculation at present, Fu says, "you could take a whole bunch of different flavours… a cocktail of mRNAs that make different proteins selective for your particular need." Both Moderna and Novavax already have combined Covid-19 and flu vaccines in development.

 

[Mariner]

Derek Lowe's In the Pipeline blog has some good discussion about what may be possible with mRNA. Don't expect anything to happen immediately, however, especially in the field of autoimmune treatments. There's a heck of a lot we just don't know yet about most of this stuff and it's likely to take many years to develop further treatments using mRNA. Should be good for some types of vaccines in the shorter term though HIV/Malaria and others will reportedly be very tough to develop.

 

[Mariner]

So, Omicron it is then. Sounds like a character from a console game.

Less confusing than Nu, however.

Let's hope it all turns out to be a fuss over nothing.

 

[zed]

Yes Omicron sounds like a name from pharmaceutical/chemical company in a film

https://www.bbc.com/news/world-59442129

The dumbest sentiment I have read recently from anyone not connected with trump
Sure perhaps SA should get a bonus, eg 100 million free covid vaccines & $100 million to aid combat etc so to encourage other countries to come forward with new variants (instead of sweeping it under the rug to avoid the financial fallout)

WRT the 1918 epidemic, Had a quick look but couldnt find anything, why did it die out so quickly? Was it cause nearly everyone got infected with it thus either died or became immune, nowadays with our better knowledge, communication, policies (some countries ) etc it doesnt run through a population so much, maybe just 1-10% infected in a wave, so herd immunity is never reached, but because of this it just keeps coming back over and over again for decades to come.

 

[BRiT]

Less travel back then so less spread, at least across continents?

 

[milk]

Regarding variants, isn't it more advantageous, evolutionarily speaking, for the virus to become more contagious, yet ever less deadly? Doesn't natural selection push it in that direction? A variant that hits a person hard, will have that person in bed all day, and eventually maybe even in a hospital, with very reduced chances of spreading much. While a tamer variant, that sees more infected feeling mostly ok, will have much higher chances of spreading to other, no? Isn't that the case with the variants we've seen so far? Aren't they less lethal? And if not, why so?

 

[Jay]

Yes Omicron sounds like a name from pharmaceutical/chemical company in a film

Omicron is the covid Decepticon.

While a tamer variant, that sees more infected feeling mostly ok, will have much higher chances of spreading to other, no? Isn't that the case with the variants we've seen so far? Aren't they less lethal? And if not, why so?

May be less deadly but being more infectious means the total number of people who could die will be much higher simply due to the higher number of infections possible.

That's not including the higher demand it puts on health services.

 

[Mariner]

Regarding variants, isn't it more advantageous, evolutionarily speaking, for the virus to become more contagious, yet ever less deadly? Doesn't natural selection push it in that direction? A variant that hits a person hard, will have that person in bed all day, and eventually maybe even in a hospital, with very reduced chances of spreading much. While a tamer variant, that sees more infected feeling mostly ok, will have much higher chances of spreading to other, no? Isn't that the case with the variants we've seen so far? Aren't they less lethal? And if not, why so?

What actually happens, evolutionarily speaking, is that the people who are most susceptible become seriously ill and may die and those less so survive. The virus doesn't do anything but replicate. We know that it takes a few weeks from infection before people start dying so the virus can be passed on a few times before the first person infected succumbs (if they are susceptible). If you're talking about something which has a much higher mortality rate such as Ebola then it is more likely to die out because it is killing people quickly in such high numbers but Covid-19 is an entirely different beast. This is where the Herd Immunity crowd have got it especially wrong. The evolutionary pressure is on people infected to survive the virus, not for the virus to become less dangerous to those unlucky enough to be particularly susceptible.

 

[Mariner]

WRT the 1918 epidemic, Had a quick look but couldnt find anything, why did it die out so quickly? Was it cause nearly everyone got infected with it thus either died or became immune, nowadays with our better knowledge, communication, policies (some countries ) etc it doesnt run through a population so much, maybe just 1-10% infected in a wave, so herd immunity is never reached, but because of this it just keeps coming back over and over again for decades to come.

The 1918 pandemic had multiple waves over a few years, I seem to recall. Seems to be the case with most pandemics where the IFR isn't ridiculously high.

 

[Mariner]

One other thing to mention - the relatively low vax rate in South Africa isn't mainly an artefact of lack of supply, it's a lack of willingness for people to be vaccinated. Social Media Bullshit wins once again!

 

[Arnold Beckenbauer]

So, they called it Omicron.

Futurama - Lrrr - Ruler of the Planet Omicron Persei 8 - YouTube

 

[Shifty Geezer]

This is where the Herd Immunity crowd have got it especially wrong.

I'm not sure what you mean by that. There are two options possible for a new disease - 1) Suppression until it dies out (MERS, SARS, etc) which was the intention that was messed up all round, or 2) Herd Immunity and intrinsic species-wide resistance (to serious illness). By the time we discovered SARS-Cov-2, it was too late for suppression on a global scale because of the silent transmission and international travel; there was no keeping a lid on this disease. Even if at a national level you are capable of suppressing outbreaks completely, you can't operate in isolation (unless you're North Korea) and will have to interact with the rest of the infected world sooner or later.

If 'herd immunity' is wrong, what's the third choice?

One other thing to mention - the relatively low vax rate in South Africa isn't mainly an artefact of lack of supply, it's a lack of willingness for people to be vaccinated. Social Media Bullshit wins once again!

I was speaking with Polish friends this week. C19 is on the up there. Vaccination rates aren't great, and they were saying a lot of people don't believe in the risk of C19. Even people who are ill don't think it's anything. Anecdotally, the guy's sister had all the symptoms of C19 but didn't test for it and didn't think it anything p- one wonder's if actual case rates are notably higher than reported as a result? I asked what the reason was for lack of vaccination, was it a mistrust of the government? He said is was mostly young folk and social media.

In real, universal terms, this is evolution in action. If social media causes people to not get vaccinated and die, the gene pool is filtered of those sorts of people. Although this disease doesn't work that way, sadly, and the consequences aren't directly linked on such a personal level.

 

[Mariner]

The Herd Immunity by infection guys - the GBDers. That's what I'm talking about. They are still there pulling the strings in the background and claiming that 'natural immunity' is the most effective protection. Their preferred route in the UK (through the 'UsForThem' group purporting to represent parents) is to try and ensure that kids don't receive vaccines now that the vast majority of adults have been vaccinated. Expect them to get noisy again with the emergence of Omicron.

No doubt that the way that social media works is going to make those mildly sceptical at the start ever more so as one click brings another which brings another and so forth. As I've said in the past, the way this virus works is that the deaths and serious illness tend to be out of sight and out of mind. Right now in the UK, with cases rising but the death rate falling (almost certainly due to the boosters), you wouldn't know much about it unless you'd visited hospitals and seen the queues of ambulances or if you knew somebody who actually worked there. Only a very small proportion of people face serious illness, but a small proportion of pretty much everyone makes a very large number. Your Polish friends who are shrugging at the risk aren't generally seeing the hospitalisations and deaths in the elderly and vulnerable that community tranmission of the virus (which they help by their actions) causes.