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

[Mariner]

The biggest question at the moment is going to be the prevalence of MIS-C and long covid from infections with Omicron. The number of expected cases with previous variants is understood to some degree. If Omicron is anything similar, we're going to be seeing a relatively large number of very poorly kids being admitted for treatment with MIS-C over the next couple of months. Too early to say for sure yet because it still isn't even 2 months since Omicron emerged! Given that MIS-C doesn't seem to require more than mild covid infection to potentially occur and Omicron isn't any milder than prior variants in unvaccinated children, there's a distinct possibility this will be an issue. Same goes for long covid which seems to have been disregarded as being of any relevance.

Has to be said, I've been fully aware that new variants were likely to arise following Omicron, but it seems that the next one may already be here!

https://twitter.com/x/status/1485375883066101763

The BA.2 variant of Omicron (most places are currently experiencing Omicron BA.1 waves) has a lot of different mutations, is already dominant in countries such as Denmark and India and is heading that way in many others. It doesn't seem to cause any more serious illness than BA.1, but is it different enough that even people recently infected with BA.1 might be susceptible to infection with BA.2? Could lead to a long and drawn out 'Omicron' wave with a number of peaks and troughs. Let's hope that isn't the case!

 

[orangpelupa]

Indonesa, a video of people being fake injected with covid vaccine went viral. Basically they jab people with empty syring. So they just jab and pull.

The person doing the fake injection is being ridiculed and the media says gonna be held accountable in the face of the law.

But none of the mass media investigating or at least hinting that this is a bigger problem. That there must be a mastermind.

The people also didn't suspect any mastermind.

Despite its quite common in Indonesia for there to be a mastermind, and the mastermind walks free with all the benefits, while few "grunts" became black sheep.

My suspicion: the vaccine supply was not enough but they were pressured to have high vaccination rate. Thus they do the jab with empty syringe. Why the vaccine supply was not enough? Probably bad storage/handling. Or even being "sold/funneled" to private back channels. As money/nepotism/connection can get you anything in Indonesia. I'm also one of the people that use these hidden back channel to get my 2nd covid vaccine because I missed my 2nd shot schedule because I got Covid.

 

[Shifty Geezer]

Indonesa, a video of people being fake injected with covid vaccine went viral. Basically they jab people with empty syring. So they just jab and pull.

That would be pretty dangerous. You'd be injecting air into the bloodstream and risking a severe embolism with a bubble potentially screwing up blood flow. A 'fake' injection needs a fluid, typically saline.

 

[orangpelupa]

That would be pretty dangerous. You'd be injecting air into the bloodstream and risking a severe embolism with a bubble potentially screwing up blood flow. A 'fake' injection needs a fluid, typically saline.

The syringe is already empty. No air. The only air is on the needle probably. And it was not injected as the syringe already empty (so it cannot be pushed further).

 

[Shifty Geezer]

From 31st January, English Case numbers will report reinfections:

https://coronavirus.data.gov.uk/details/whats-new/record/af008739-ffa3-47b8-8efc-ef109f2cfbdd

From 31 January 2022, UKHSA will move all COVID-19 case reporting in England to this a new episode-based definition which includes possible reinfections.

On the dashboard, this means:

• cases in England by report date will change to the new definition of an episode of infection
• historical numbers by report date will not be revised, so there will be a step increase in the cumulative numbers of cases on that date
• specimen date metrics will be revised back to the beginning of the pandemic.
• the same metric names will still be used
• new metrics will show first episodes of infection (equivalent to the current case definition) and episodes of reinfection, shown by specimen date only.

UKHSA is working with the devolved administrations to align definitions across the UK.

 

[Mariner]

It will be interesting to see what happens to the reported numbers from around the peak of the Omicron wave. You'd expect that the infection numbers will rise a significant amount to perhaps more closely reflect what the ONS survey has been telling us about prevalence. It will also be interesting to see what happens to the positivity rates.

My son tested positive this morning, so I'm assuming he caught it from his sister who tested positive about 36 hours before my wife. Poor lad has a very sore throat at the moment and has been up a few times already so it is set to be a very long night, possibly a tough week. I certainly might have the start of a sore throat coming (feels a little off) so we'll have to see what tomorrow brings for me.

I found this slightly amusing:

https://twitter.com/x/status/1486087643632971779

What's the odds of the major variants (sub-variants at present with BA.2) switching between SGTF and back again with this pattern?

 

[WhiningKhan]

What's the odds of the major variants (sub-variants at present with BA.2) switching between SGTF and back again with this pattern?

I would guess there is combination going on, perhaps with common cold coronaviruses which are in good supply this time of year as well.

As for odds - apparently the changes do not make significant difference in terms of becoming prevalent variant or not. In such case the odds would not differ from coin toss - getting different result 4 times in a row isn't that spectacular in that sense.

 

[wco81]

In this Omicron wave, hospitalization rate differential between the unvaccinated and vaccinated has been as high as 50X greater for the unvaccinated.

But the unvaccinated aren't immunologically-naive. An estimated 60-70% of the have been previously infected with earlier covid variants.

That means so-called "natural immunity" is not holding up, not preventing hospitalization, nearly as well as vaccination. Or not at all, in many cases.

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We see large gaps in hospitalizations between vaccinated and unvaccinated

But unvaccinated are not immunologically naïve

At this point, probably 2/3 have been previously infected

And yet, we still see 50X differences in hospitalizations between vaccinated and unvaccinated

Denmark was one of the first countries to enter the Omicron wave. Now it's seeing that wave extended by the BA.2 or Omicron Plus variant. Worldmeters shows a 19% increase in new cases over last week.

Yet they are dropping all covid restrictions, only recommending masking for certain situations such as visiting nursing homes.

Why? Because they're seeing low hospitalizations and deaths, lower than with previous variants.

According to the NY Times vaccination tracker, Denmark is over 81% fully vaccinated vs. just under 65% for the US. But Denmark is at 61% for additional dose or booster while the US is at 26% boosted.

https://www.nytimes.com/interactive/2021/world/covid-vaccinations-tracker.html

Someone will probably overlay Omicron hospitalization rates against vaccination and booster rates and show the clear causation.

But we'll probably still hear about "natural immunity!" a year from now.

 

[Shifty Geezer]

Finally have some insight on reinfections in the UK:

https://www.gov.uk/government/news/covid-19-daily-dashboard-amended-to-include-reinfections

As of 31 January, updated figures for England show 14,845,382 episodes of infection since the start of the pandemic with 588,114 (4.0%) reinfections added to the total case number for England, covering the whole pandemic.

The new data shows that reinfection rates averaged around 1.4 percent of cases until 16 November 2021, when a spike in infections took place following the emergence of the Omicron variant. Following that increase in the number of people infected, reinfections rose – with reinfections now representing around 10% of episodes per day.​

 

[Mariner]

Here at the homestead, daughter returned to nursery yesterday. No side effects after infection, although she is still sleeping an hour later than she usually would, so still obviously recovering. My son has appeared as right as rain during the day for several days now but is waking up at night upset and dripping wet with sweat. Still faintly positive 8th day after his first positive on lateral flow tests. He'll probably have to wait the whole 10 day period before going back to school. More tests to come during the next couple of days. We'll be on the look out for signs of PIMS-TS in the children for the next month or two, though the risks are obviously slim. My wife has been the most unwell of the three, spending much of the first week in bed and is still coughing and with a sore throat. She had her first negative LFT result yesterday - day 10.

As for me, I had continued to test negative, which was a surprise. Until this morning. Very faintly positive on the LFT this morning (about 16 hours ago) and I'm still symptom free now. A mild headache for a few days but that could be as much due to lack of sleep/interrupted sleep as anything. It will be interesting to see if/when symptoms kick in. I've been off work looking after the whole family and the only minor mitigation against risk of infection we could manage is that I've slept in the spare room so I thought it strange that I had appeared to fight it off this time around, but it seems to have got me in the end.

I'm assuming it is Omicron (BA.1) my family have all had. I was rather hoping to hold off catching Covid until BA.2 was dominant as it would seem that it has greater immune escape than BA.1 from the latest study out of Denmark!

https://en.ssi.dk/news/news/2022/ba...ted-less-likely-to-infected-pass-on-infection

On the other hand, I might well have caught BA.1 and then BA.2 in any case. As with everything Omicron-y, it's happening so fast that we still don't know where we really stand. Here's another study indicating that Omicron breakthrough infections don't seem to lead to great Omicron-specific immunity:

https://twitter.com/x/status/1488321416755761154

As one of the comments to the above thread points out, it might just be that Omicron infections tend to be much milder than those of previous variants, so the immune response isn't likely to be as strong which, of course, means less future protection.

For the UK data, good to see reinfections are now being counted, but the 90 day limit for 'episodes' initially selected could be troublesome as I've read many reports of people infected in October/November/December catching Covid again recently due to Omicron. These wouldn't be counted in the numbers as reinfections as it stands. I suspect that they'll probably drop the time limit for the reporting of a reinfection to perhaps 60 days or less in time.

 

[Shifty Geezer]

As one of the comments to the above thread points out, it might just be that Omicron infections tend to be much milder than those of previous variants, so the immune response isn't likely to be as strong which, of course, means less future protection.

What do you mean by future protection? A weaker response could mean infection by another agent in the shorter term with fewer antibodies producing a barrier, but in lifelong terms, every exposure trains the body's response to make it better at dealing with future exposures. Personally I want an Omicron infection at this point. I've had three exposures to the virus in vaccinations, but they are fake virus and don't train the body as well as the real thing. Knowing those vaccines provide pretty much complete protection against serious disease, I could do with exposure to a weak flavour of the virus for training purposes so if a tougher version appears years down the line, I'm better equipped to deal with it naturally.

For the UK data, good to see reinfections are now being counted, but the 90 day limit for 'episodes' initially selected could be troublesome as I've read many reports of people infected in October/November/December catching Covid again recently due to Omicron. These wouldn't be counted in the numbers as reinfections as it stands. I suspect that they'll probably drop the time limit for the reporting of a reinfection to perhaps 60 days or less in time.

Realistically people should be protected for about 90 days after infection from the antibodies. If you test positive within that time, it's more likely you weren't recovered. It's only an issue if Omicron manages an infection on a recovered patient.

For me, the bigger concern is the drop in testing. Cases are levelling off but testing is going down, so in real terms there's potential for the disease to be growing. However, it's really only hospitalisations that matter at this point. So long as severe disease is kept at bay, it's 'just another cold'. Thankfully those graphs continue their downward trend.

 

[wco81]

Early studies from 2020 showed that people who had infections had wildly varying levels of antibodies. So asymptomatic or mild infections may not give you much protection against future infections.

What's harder to track is T cell levels. There are vaccines in development which try to stimulate T cell production.

 

[Shifty Geezer]

Again, what do you mean by 'future infection'? Just contracting the disease, or developing notable symptoms? There's protection against getting infected, but that's minimal, short term resistance. The primary protection of the immune system is against serious disease the body cannot recover from, not from getting infected*. Infections happen, but the body mounts an effective defence that stops the pathogen spreading uncontrolled. Every infection results in a cellular response to remove it, which results in memory T-cells developing that are geared for rapid response in subsequent exposures to the same antigen(s).

If you have been exposed to SARS-Cov-2 antigens and fought off an infection with no to mild symptoms, you will have 1) natural ability to fight of the disease without getting seriously ill and 2) a body better equipped to react faster next infection. The vaccines also train the immune system, first motivating the generation of antigen specific antibodies, and then recording a memory T-cell library of the antigen(s) for rapid response. If you are generating antibodies to a vaccine, you are also training T cells for faster, more effective response next infection.

I believe most infections we get in life are actually are asymptomatic (or with very mild symptoms not necessarily attributed to a disease infection) without us ever knowing because they are repeats of previous infections**. Sure, the virus, whether coronavirus or rhinovirus or adenovirus, successfully infects the host and potentially reproduces enough to infect another host, but it is swiftly eradicated with minimal impact on the host. That's what'll happen with SARS-Cov-2. People will still get infected, but they won't get particularly ill.

* That's a simplification - there are measures in place to help resist infection in the first place such as immunoglobulins in saliva.

** https://journals.asm.org/doi/10.1128/mSphere.00249-18

We actively recruited participants from among visitors to a New York City tourist attraction. Nasopharyngeal swabs, demographics, and survey information on symptoms, medical history, and recent travel were obtained from 2,685 adults over two seasonal arms. We used multiplex PCR to test swab specimens for a selection of common respiratory viruses. A total of 6.2% of samples (168 individuals) tested positive for at least one virus, with 5.6% testing positive in the summer arm and 7.0% testing positive in the winter arm. Of these, 85 (50.6%) were positive for human rhinovirus (HRV), 65 (38.7%) for coronavirus (CoV), and 18 (10.2%) for other viruses (including adenovirus, human metapneumovirus, influenza virus, and parainfluenza virus). Depending on the definition of symptomatic infection, 65% to 97% of infections were classified as asymptomatic.

 

[Mariner]

Realistically people should be protected for about 90 days after infection from the antibodies. If you test positive within that time, it's more likely you weren't recovered. It's only an issue if Omicron manages an infection on a recovered patient.

For me, the bigger concern is the drop in testing. Cases are levelling off but testing is going down, so in real terms there's potential for the disease to be growing. However, it's really only hospitalisations that matter at this point. So long as severe disease is kept at bay, it's 'just another cold'. Thankfully those graphs continue their downward trend.

We already know that the current vaccines and infection with prior variants don't offer a huge amount of protection against Omicron when there is repeated exposure due to the immune evasion properties. Therefore, those infected in October and November in the UK aren't going to have a huge amount of immunity to Omicron (regardless of type). Same goes for many of those infected in December when Delta was still the variant in play for a significant chunk of the cases. A lot of anecdotal data about kids catching Covid twice over the past 3 months which shouldn't be a surprise, especially as so many (and virtually none under 12) have been vaccinated and Delta was the predominant variant in schools well into December.

It remains to be seen how long the immunity from an Omicron infection might last - BA.1 and BA.2 have many different mutations, so it is quite feasible that BA.1 might not provide a great amount of protection against quick reinfection with BA.2 and vice versa. I'll not even mention BA.1.1 which should be passing BA.1 infections in the UK any time now, though still falling behind BA.2! This is the first report which seems to indicate that BA.2 probably won't reinfect those who have have BA.1 previously, though it's not exactly packed full of data:

https://www.timesofisrael.com/nearl...-health-official-denies-omicron-reinfections/

 

[wco81]

Well there are a lot of infections occurring from December to June or so.

someone will do studies and categorize which percentages of these reinfections are asymptomatic, mild, moderate or severe.

Is it clear that most reinfections are relatively benign? We will see.

 

[Mariner]

I believe most infections we get in life are actually are asymptomatic (or with very mild symptoms not necessarily attributed to a disease infection) without us ever knowing because they are repeats of previous infections**. Sure, the virus, whether coronavirus or rhinovirus or adenovirus, successfully infects the host and potentially reproduces enough to infect another host, but it is swiftly eradicated with minimal impact on the host. That's what'll happen with SARS-Cov-2. People will still get infected, but they won't get particularly ill.

A bold prediction, given what we've seen over the past 2 years. The endemic infections which have been in the human population for some time, many centuries in some cases, may have taken years to become endemic and would have had serious impacts in mortality and morbidity. Providing it doesn't have any longer-term health impacts about which we aren't yet aware, Omicron would seem to be a step in the right direction, but it is by no means certain that this is the last trick that Covid will play on us. Three months ago, we were watching AY4.2 slowly becoming the dominant subvariant of Delta in most places and everyone was talking about how a Delta-specific vaccine/booster would solve most of our problems. Today, Delta of any sort is just a tiny fraction of cases quickly being supplanted by Omicron (BA.1) which is even more quickly being supplanted by BA.2 and we'll have to see where BA.1.1 takes us as well. Pfizer and Moderna are testing vaccines targetting Omicron, but which subvariant? Will they even be relevant when available given the speed things are moving with mutations? A variant of the virus which has similar immune evasion to BA.2 but is more closely related to Delta (or Alpha, or Beta, or Gamma, or Mu or just something completely new) could quite easily put us back into a bad place. Most likely not as bad as before the vaccines/mass infection, but still bad.

The ability of this virus to mutate so quickly and so comprehensively has been pretty remarkable. Omicron is greatly different to anything we've seen before. An interesting rundown of the differences in the following thread, with an important point highlighted:

https://twitter.com/x/status/1489263774133473286

It would be nice if Omicron did mark the start of a move towards relatively benign endemicity, but I'm not holding my breath...

 

[Davros]

Just learned today that the U.S Military are working on a vaccine
https://www.webmd.com/vaccines/covi.../u-s-army-developing-its-own-covid-19-vaccine

 

[Shifty Geezer]

A bold prediction, given what we've seen over the past 2 years.

How does anything in the past two years suggest things will play out differently with this disease? It's mortality in the young and healthy is far below other diseases when exposed to an immune naive population.

The ability of this virus to mutate so quickly and so comprehensively has been pretty remarkable. Omicron is greatly different to anything we've seen before

Not necessarily. The conditions for SARS-Cov-2 are unprecedented and so basic comparisons of limited value. Given a combination of a massive, immune-naive population coupled with dense populations and wider travel and more old/weak hosts, SARS-Cov-2 has far more evolutionary opportunities versus diseases that appeared thousands of years ago. This 'fast' iteration of varieties might well be the norm for a new virus until biological equilibrium is reached, only we're seeing the process accelerated over years instead of decades as the virus passes through all populations instead of piecemeal. Once everyone has some resistance, opportunity to mutate will be significantly suppressed. Furthermore, we have real-time genetic sequencing mapping mutations at a level never had before, so what we're seeing now is just a first look at something that's possibly always been there, akin to Galileo looking out at the stars and seeing there were astral bodies. And from that info it seems SARS-Cov-2 isn't showing anything special:

The SARS-CoV-2 global population has accumulated only moderate genetic diversity at this stage of the COVID-19 pandemic with an average pairwise difference of 9.6 SNPs between any two genomes, providing further support for a relatively recent common ancestor. We estimated a mutation rate underlying the global diversity of SARS-Cov-2 of ~6 × 10−4 nucleotides/genome/year (CI: 4 × 10−4–7 × 10−4) obtained following time calibration of the maximum likelihood phylogeny. This rate is largely unremarkable for an RNA virus (Domingo-Calap et al., 2018; Holmes et al., 2016),...

https://www.sciencedirect.com/science/article/pii/S1567134820301829?via=ihub

 

[Mariner]

Did you seriously just quote a study published in September 2020 which would have been based on work in the summer of 2020?!? The fact that Francois Balloux is one of the contributors to the paper is telling as he's been pretty much wrong about everything since the pandemic began! Actually, that's probably a bit harsh, as they were only working with the limited data they had at the time. There have been hundreds of millions of infections around the world since then, so not too surprising there have been a lot of deleterious mutations.

Before the Alpha, Beta, Delta, Gamma and Omicron (BA.1) variants emerged and caused serious waves of infections, some globally, some regionally.

What a odd link to quote given this context.

I'll requote the tweet by Ravi Gupta in my last post:

Important to re-iterate that the next VOC will likely have been evolving from a previous virus over many months and will likely not share these tropism differences. Hence pathogenicity of next VOC likely to be higher, and in context of declining vaccine responses. Time to prepare.

There's a lot of potential for more virulent variants to emerge and this could be an issue given that most countries seem to have decided to give up following the Omicron wave.

 

[Shifty Geezer]

Once again you just dismiss a source as if it's common knowledge something should be known about it. Such poor discussion form! If a source is no good, provide a better one. Please provide improved data on estimates of SARS-Cov-2 mutation rates - you provided no data whatsoever, only an assertion that SARS-Cov-2 has extraordinary mutation powers, leaving me to spend considerable time researching and only coming upon that research that actually linked to meaningful numbers.

There's a lot of potential for more virulent variants to emerge and this could be an issue given that most countries seem to have decided to give up following the Omicron wave.

I'm not sure what your point is. Everyone should be bunkered down against Omicron to prevent nastier mutants appearing? Everyone should be reducing exposure of their immune system to a largely benign flavour of SARS-Cov-2 in the expectation there'll be another, nastier variant? Exposure to Omicron will be bad for our immune systems?