Here comes COVID-19 version BA.2, BA.4, BA.5,...

[kyphysics]

^^^I realized I'm dumber than a doorknob:

https://www.cnbc.com/2022/09/27/pfi...ew-omicron-specific-covid-booster-to-get.html

Pfizer’s booster is cleared for anyone 12 and older, while Moderna’s booster is for people 18 and older. To get either one, you’ll need to be at least two months removed from completing a primary vaccine series or receiving any other Covid shot.

Beyond those eligibility guidelines, the new boosters aren’t that different from each other. Both shots are bivalent, meaning they target omicron’s BA.4 and BA.5 subvariants alongside the original Covid strain.

Federal health officials say both shots will serve as a desperately needed layer of protection for the coming months, as the weather turns colder and immunity from previous vaccines wanes. In other words, you can’t go wrong with either.

But if you’re still trying to decide which one to get, here’s what you need to know — from mixing-and-matching and side effects to the makeup of the two new shots. . .

 

[Godot_]

BA.4, .5 = Omicron.

[Edit:] Self awareness was faster... :D

...but, eventually, Omicron might probably mutate "around" this vaccine, too. And probably get some fresh Greek letter, then.

 

[pinball1970]

I got both my flu shot and COVID Pfizer booster today (the one with targeted Omicron protection).

I previously got Moderna only, so this was a switch up (only b/c Sam's Club didn't offer Moderna yet).

Will there be a BA.xxxxxx booster coming out anytime. Does the Omicron version help with the BA.xxxxxxx one at all?

And if more and more variants come out, how many targeted boosters do you think we'll ultimately get. Would this go the way of flu shots, where they target 3 or 4 expected strains each year?

Thanks, that reminded me I need to book mine in! Flu and Covid!

 

[Laroxe]

Yes, apparently we are now seeing a small rise in the number of cases so this might be the start of a new season for Covid. There still seems to be some debate about how useful these variant specific vaccines might be. It seems with the Omicron variants the transmissibility makes protection from infection very unlikely, the marked increase in antibodies following vaccination seems to be rather short lived. However the illness does seem milder and all the vaccines continue to offer significant protection against serious disease for a much longer period. This is based on the T cell response's which target conserved parts of the virus so all the variants are targeted and all the vaccine's reinforce these responses.
While logic seems to suggest that a more specific vaccine would be better, its not at all that simple. Its true that the vaccines specific to variants increase the variant specific antibodies, though there isn't a great difference and researchers have largely lost interest in antibodies. The levels achieved simply don't seem to have much on an impact on B5 transmission. Unfortunately there is also the possibility that giving a half dose of the original vaccine and half dose of the new omicron specific vaccine may actually reduce protection because of interference, due to the "original antigenic sin". Basically these are all things we simply don't know yet but it does seem that this year flu will be a more significant problem.

 

[kyphysics]

Thanks, that reminded me I need to book mine in! Flu and Covid!

FWIW, experts recommend getting the flu shot LATER (late October/early November), b/c that would allow our peak defenses to be in place during peak flu season. See article below:

‘When should I get my flu vaccine?’

The timing of when you get your flu shot should be aligned with the time frame that would allow you to have the best antibody response during the beginning of flu season, Hatziioannou tells CNBC Make It.

It’s important to look at data from recent years, prior to the pandemic, in your local area to determine when cases historically start to increase in your community, Hatziioannou says.

The standard rule of thumb is get your vaccination four weeks before the beginning of flu season in order to have the most protection because that’s when you’ll have the best antibody response, she notes.

“In New York and several other areas with the same geographical latitude, flu season usually starts in December and lasts until March,” she says. “So, if you have it [the flu shot] now, at the end of September or [early] October, your peak antibody responses will be in November. It’s a little bit too early.”

At this time, Hatziioannou recommends getting your flu shot at the end of October or early November to have the highest protection throughout December.

https://www.cnbc.com/2022/09/20/should-you-get-your-covid-booster-and-flu-shot-at-the-same-time.html

I got mine at the same time, b/c it was offered and I hadn't read this article yet.

 

[kyphysics]

How to perfectly time your new omicron-specific Covid booster

Published Sat, Oct 1 20229:00 AM EDT

https://www.cnbc.com/2022/10/01/how-to-perfectly-time-your-new-omicron-specific-covid-booster.html

For those interested, I saw this today.

 

[Astronuc]

New BA.2.75 sub-variant has some folks wondering if it will lead to another COVID-19 wave in the world.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9420005/

https://newsnetwork.mayoclinic.org/...s-dominant-strain-ba-2-75-is-being-monitored/

https://www.deseret.com/coronavirus/2022/9/27/23375242/ba-2-75-2-variant-omicron-symptoms

According to the report, Dr. Anthony Fauci said that the emerging mutation was “suspicious” and could become a variant of concern in the fall.

It's evolving similarly to BA.5, which is the dominant strain behind 83% of reported infections in the U.S., as per Centers for Disease Control and Prevention estimates.

BA.2.75.2, for now, is expanding its reach in India and accounts for about 0.5% of cases worldwide. The World Health Organization hasn’t separated this mutation from BA.2.75, but it is singled out under “Omicron subvariant under monitoring.”

One preprint study, published in mid-September, found that the mutation exhibited a tendency to extensively escape neutralizing antibody treatments authorized by the Food and Drug Administration, except for one — bebtelovimab.

But the findings of another study published in the New England Journal of Medicine were more encouraging. Bebtelovimab was also reported to work against the variant as well as other antiviral treatments like remdesivir, molnupiravir and Paxlovid.

Omicron has over 200 sublineages being monitored. Here are the subvariants driving cases in the U.S.:

• BA.5 — 83.1% of cases.
• BA.4.6 — 11.9% of cases.
• BF.7 — 2.3% of cases.
• BA.4 — 1.4% of cases.
• BA.2.75 — 1.4% of cases.

BF.7?! On rise in CDC Region 2 (NY, NJ, VI and Puerto Rico (see below)).

https://khn.org/morning-breakout/alarm-bells-ring-over-new-omicron-variants-ba-2-75-and-ba-5-2-1/
BA5.2.1

https://www.reuters.com/world/china/chinas-shanghai-says-new-omicron-subvariant-found-2022-07-10/

https://covid.cdc.gov/covid-data-tracker/#variant-proportions

The Omicron variant was first confirmed in New York State on December 2, 2021. During the winter Omicron wave that followed, the lineages BA.1 and BA.1.1 were most prevalent, and in February, a rapid growth of BA.2 began.

On April 13, 2022, the Department announced the emergence of two recently-identified Omicron subvariants in New York State, BA.2.12 and BA.2.12.1. Both subvariants are sub-lineages of BA.2, and at that time, were estimated to have a 23% – 27% growth advantage above the original BA.2 variant. BA.2.12.1 has been noted to be of higher concern, given additional mutations.For samples of SARS-CoV-2 collected between September 11 -- September 24, 2022 from New York that are sequenced and uploaded into GISAID, 99.5% were the Omicron variant. During this time period 3.1% of sequences were lineage BA.2, 0.2% were BA.2.12.1, 1.5% were BA.4, 16.7% were BA.4.6 and 78.1% were BA.5 .

Between September 18 and September 24, 2022 CDC’s program for HHS Region 2 (New York, New Jersey, Virgin Islands, Puerto Rico) estimated 100% of samples were the Omicron variant. During this time period 2.3% of sequences were BA.2.75, 1.1% were BA.4, 14.1% were BA.4.6, 79.8% were BA.5, and 2.8% were BF.7.

Ref: https://coronavirus.health.ny.gov/covid-19-variant-data (subject to change weekly/biweekly with new data)

 

[kyphysics]

Most Americans don’t plan to get a flu shot this season — lots of them say they’ll mask to avoid germs instead

Published Tue, Oct 4 20222:24 PM EDT
https://www.cnbc.com/2022/10/04/fewer-americans-plan-to-get-a-flu-shot-this-season-2022.html

Hmmm...some interesting rationale in this piece. . .I used to never get flu shots either until COVID hit. Then, I became more virus-aware.

I would think MORE people would want to get vaccines post-COVID (for all sorts of viruses - not just COVID). . .. .*shrug*

 

[Tom.G]

Natural selection in action?

 

[Laroxe]

New BA.2.75 sub-variant has some folks wondering if it will lead to another COVID-19 wave in the world.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9420005/

https://newsnetwork.mayoclinic.org/...s-dominant-strain-ba-2-75-is-being-monitored/

https://www.deseret.com/coronavirus/2022/9/27/23375242/ba-2-75-2-variant-omicron-symptoms
BF.7?! On rise in CDC Region 2 (NY, NJ, VI and Puerto Rico (see below)).

https://khn.org/morning-breakout/alarm-bells-ring-over-new-omicron-variants-ba-2-75-and-ba-5-2-1/
BA5.2.1

https://www.reuters.com/world/china/chinas-shanghai-says-new-omicron-subvariant-found-2022-07-10/

https://covid.cdc.gov/covid-data-tracker/#variant-proportions
Ref: https://coronavirus.health.ny.gov/covid-19-variant-data (subject to change weekly/biweekly with new data)

Its difficult to know what role any new variants will have in future outbreaks, there will always be new variants but it looks as if there are conserved areas on the virus that maintain the vaccine effectiveness against serious illness across the various strains. Really the ground rules have changed with populations with very high levels of immunity and variants that appear to have been selected for short incubation periods and reduced sensitivity to antibodies. The Omicron variant for example appears to have an incubation period of < 3.5 days so doesn't allow much of an antibody increase, this effectively means that the vaccine provides very little protection against infection but the response over time still protects against serious disease. This means the case fatality rate has fallen below that of flu and the risks very clearly focussed on specific populations, though co-infection of Covid 19 with flu significantly increases risk and it is still the unvaccinated that are over represented in the hospitalised.

Its become increasingly clear that this virus is very "promiscuous" it appears able to cause infection in a wide range of species, many of which live close to human populations. This does suggest we are likely to be stuck with this virus and we can expect regular waves of infection. We still don't really know how these waves of infection will propagate around the globe, there are still large areas with low vaccination rates and the belief that they will remain relatively untouched represents a triumph of hope over experience. Early in the pandemic India experienced low rates of infection leading to the belief that something about their lifestyle protected them, we now know how that turned out. Despite the huge research effort and the exponential growth in our understanding of viral diseases, this virus still manages to come up with some surprises, hopefully this will also reduce over time.

 

[Astronuc]

The Omicron variant for example appears to have an incubation period of < 3.5 days so doesn't allow much of an antibody increase,

That appears to be the case, based on my son's exposure, and more recently, my brother-in-law and sister (both are vaccinated and double-boosted, but not Omicron vaccine), who recently participated in a family gathering, but did not wear masks; brother-in-law and my sister developed symptoms on Monday and Wednesday, respectively. They had traveled by air on Thursday, and they presented symptoms as early as ~3.5 days later. Both a quite ill (fever, chills, cough and fatigue).

My kids, my wife and I still wear masks in public, but most don't. Those not wearing masks in public are at risk of contracting the Omicron variant, even if they have had Covid previously.

Meanwhile, ABC reports "86% of kids under 17 have antibodies from a past COVID infection, CDC data shows"
https://abcnews.go.com/Health/86-kids-17-antibodies-past-covid-infection-cdc/story?id=91106508

More than eight in 10 kids under the age of 17 have antibodies from a past COVID-19 infection, according to new data from the Centers for Disease Control and Prevention.
The analysis shows that as of August, 86% of children between 6 months and 17-years-old have had at least one COVID infection since the pandemic began.

That number is an increase from data in April, when the public health agency found 75% of people under the age of 17 had been infected with the virus.

"What we have to recognize is this is more of an indication that there's been broad spread of this virus in the pediatric community," said Dr. John Brownstein, an ABC News contributor and chief innovation officer at Boston Children's Hospital. "And that, you know, the kids are not sheltered from this virus. And we know that in a small number of cases, there's severe impacts."

What the findings don't mean is that 86% of children and adolescents are now protected against COVID reinfection because they've had COVID before. Experts have noted that they don't know exactly how long protection from infection lasts after contracting the virus.

 

[OmCheeto]

...This means the case fatality rate has fallen below that of flu...

I'm not qualified to dispute this claim, but I would like to point out that in the USA, Covid is currently killing 3 times as many people as the flu, statistically speaking:

Per the CDC, 300,000 people died of the flu for the years 2010 thru 2017, yielding a death rate of 100 people per day. Current CDC Covid claims are about 300 deaths per day.

Again, I'm not disputing your claim. I'm just reminding people that this is still a complicated and dynamic situation.

 

[Astronuc]

This means the case fatality rate has fallen below that of flu

I thought the case fatality rate for influenza is something like 0.1%. I've been collecting statistics on two states that indicate a mortality rate of about 1% based on confirmed positive infections and deaths attributed to COVID-19. Of course, the number of infected could be a factor of 2 or 3. In New State, there have been 6067755 positive cases of COVID-19, or about 0.305 based on an estimated population of 19,835,913. A factor of 2 would make that 61% and a factor 3 would yield 91.5%, with a case fatality rate decreasing to between 0.5 to 0.33%, which is still about 5 to 3 times greater than the case mortality rate of influenza (which may also include influenza with pneumonia).
Ref: https://www.census.gov/quickfacts/NY
https://coronavirus.health.ny.gov/covid-19-testing-tracker

BTW, NY State reports that another child (age 0-9) has died from COVID within the last two days, bring the total to 37 of 58,234 deaths reported in hospital or care facilities, or 74,363 reported to the CDC, which includes those dying outside of medical/care facilities, since March 2020. The number of children succumbing is of course low, but it the child of ~37 sets of parents.

Edit/update: New York State has about 20 fatalities per day from SARS-Cov-2.

Edit/update(2): Symptoms of COVID-19
· Fever or chills
· Cough
· Shortness of breath or difficulty breathing
· Fatigue
· Muscle or body aches
· Headache
· New loss of taste or smell
· Sore throat
· Congestion or runny nose
· Nausea or vomiting
· Diarrhea

My sister and brother-in-law have the first 8 symptoms excluding Shortness of breath or difficulty breathing. My sister was too tired to text, so she called me. She described something like 'brain fog'.

 

[Tom.G]

Seems that BA.4 and BA.5 aren't quite as different as feared.

from: https://www.nejm.org/doi/full/10.1056/NEJMc2209306

The effectiveness of pre-omicron infection against symptomatic BA.4 or BA.5 reinfection was 35.5% (95% confidence interval [CI], 12.1 to 52.7);

the effectiveness against any BA.4 or BA.5 reinfection regardless of the presence of symptoms was 27.7% (95% CI, 19.3 to 35.2) (Table 1).

The effectiveness of post-omicron infection against symptomatic BA.4 or BA.5 reinfection was 76.2% (95% CI, 66.4 to 83.1);

the effectiveness against any BA.4 or BA.5 reinfection was 78.0% (95% CI, 75.0 to 80.7).

(reformatted for readability)

Cheers,
Tom

 

[Astronuc]

My sister and her husband are slowly recovering. They are still congested, but lungs are functioning. Fever is down.

My sister mention BA6, but I believe she was referring to BA4.6, which seems to be on the rise.

 

[Astronuc]

Move over BA.5, here comes BQ.1.1!

Could omicron subvariant BQ.1.1 render COVID drugs useless?​

https://www.msn.com/en-us/health/me...bq-1-1-render-covid-drugs-useless/ar-AA12JLtT

The omicron variant of COVID-19 is still evolving, and new omicron subvariants have a better ability to evade Coronavirus drugs or immunity acquired through past infection or vaccination.

The list of variants that may be a cause for concern is only growing. Subvariant BQ.1.1, an offspring of the BA.5, may be able to evade all defense tools we have against COVID-19, leading to more hospitalizations and more cases of long COVID and death.

From BQ.1.1 to XBB and beyond: How the splintering of Omicron variants could shape Covid’s next phase​

https://www.statnews.com/2022/10/06/bq11-omicron-variants-splintering-covid-next-phase/

The strains virologists are tracking — from BA.2.75.2 to BQ.1.1 to XBB and beyond (“The names are getting ridiculous,” Peacock said) — are themselves descendants of earlier forms of Omicron, such as BA.2 and BA.5. It’s an example of how, since Omicron emerged nearly a year ago, the coronavirus’s evolution has been more akin to the “drift” seen with influenza, rather than the earlier succession of very different variants, from Alpha to Delta to the original Omicron.

 

[Laroxe]

I'm not qualified to dispute this claim, but I would like to point out that in the USA, Covid is currently killing 3 times as many people as the flu, statistically speaking:

Per the CDC, 300,000 people died of the flu for the years 2010 thru 2017, yielding a death rate of 100 people per day. Current CDC Covid claims are about 300 deaths per day.

Again, I'm not disputing your claim. I'm just reminding people that this is still a complicated and dynamic situation.

Well yes, dynamic is a good word to describe it and don't worry about disputing my claims, I'll try not to get upset. :)

There is no doubt that Covid 19 has had a significantly higher case mortality rate than flu and this will still be true if we used the cumulative case fatality rate, but remember how estimates have progressively changed over the length of the pandemic. At the start of the pandemic in some areas the case fatality rate was reported as high as 15% but as our understanding of the disease increased the reported rate dropped very quickly, we then had the introduction of vaccine's, antibody treatments,
anti-viral's and better care protocols alongside increasing numbers of deaths in the high risk populations and more recovered individuals. The latest variable was the spread of the Omicron variants, which appear to be much more transmissible but less virulent, causing a milder disease. So, as you say this is a dynamic response to the situation and the metrics change.

Forgive me if I us the numbers from the UK's office of statistics, I'm in the UK but I expect there will not be huge differences. So, in the UK, at the end of December 2021, the rolling seven-day Case Fatality Rate (CFR) for Coronavirus was about 0.3 per cent or one death in 333 cases. As a comparison the commonly used estimate of the death rate for flu sits somewhere between 0.1 and 0.2 per cent - or between one death in 1,000 and one death in 500. So Covid 19 was still killing more people, however since then the numbers have continued to change, in England, the case fatality rate, in the seven days up to January 26 was then just 0.14 per cent - one death in 714 positive cases. The large change seen in such a short period was at least partly due to the correction of a distortion, when hundreds of thousands of reinfections were added to the case data.

The infection fatality rate, a different metric that looks at all cases not just the confirmed cases offers a similar picture. The Covid symptom tracker app, suggested an estimated 9.2 million Covid infections since the start of December in the UK, and 10,670 reported deaths, an IFR of 0.11 per cent over that data collection period.
Getting a reasonably representative estimate of deaths from flu is equally problematic and we really need to go back to the years pre Covid 19. Again as an example, the figures from the US Centers of Disease Control from 2017 to 2018 estimate the IFR of flu to be around 0.12 per cent and the case fatality rate to be 0.27 per cent. The main issue is in avoiding Covid 19 estimates using cumulative deaths, there has never been a single representative fatality rate for either Covid 19 or Flu, we need to use the current figures for Covid with more accepted estimates for flu, because the current figures are not representative.

Sorry this is so long.!

 

[Astronuc]

BA.5 waning, BF.7 and BQ.1 variants gaining
https://www.cnbc.com/2022/10/14/omi...ging-variants-gain-ground-cdc-data-shows.html

Although the omicron BA.5 variant remains dominant in the U.S., it is starting to lose some ground to other versions of the virus, according to CDC data. The omicron subvariants BQ.1, BQ.1.1 and BF.7 have gained ground and are causing about 17% of new infections, according to the data. Scientists and health officials are closely monitoring these emerging variants because they appear to have a growth advantage over BA.5.

Omicron BA.5 has splintered into several new but related variants that include BQ.1, BQ.1.1 and BF.7. The U.K. Health Security Agency, in a report earlier this month</a>, said these three variants are demonstrating a growth advantage over BA.5, which was the most contagious version to date.

In the U.S., omicron BA.5 makes up about 68% of all new infections, down from about 80% at the beginning of October. BQ.1, BQ.1.1 and BF.7 are now causing about 17% of new infections combined, according to the CDC data. About 3% of new infections are attributable to BA.2.75. and BA.2.75.2, which are related to the omicron BA.2 variant that caused a bump in cases during the spring but was pushed out. Scientists at Peking University in China found that omicron BA.2.75.2 and BQ.1.1 were the most adept at evading immunity from prior BA.5 infection and several antibody drugs. The study, published earlier in October, has not been peer reviewed.

https://www.usnews.com/news/health-news/articles/2022-10-14/new-omicron-subvariants-bq-1-bq-1-1-spread-amid-concerns-of-next-coronavirus-wave

 

[Astronuc]

Subvariant XBB?!
https://news.yahoo.com/nightmare-covid-variant-beats-immunity-025733218.html

A new subvariant of the novel-coronavirus called XBB dramatically announced itself earlier this week, in Singapore. New COVID-19 cases more than doubled in a day, from 4,700 on Monday to 11,700 on Tuesday—and XBB is almost certainly why. The same subvariant just appeared in Hong Kong, too.

A highly mutated descendant of the Omicron variant of the SARS-CoV-2 virus that drove a record wave of infections starting around a year ago, XBB is in many ways the worst form of the virus so far. It’s more contagious than any previous variant or subvariant. It also evades the antibodies from monoclonal therapies, potentially rendering a whole category of drugs ineffective as COVID treatments.

“It is likely the most immune-evasive and poses problems for current monoclonal antibody-based treatments and prevention strategy,” Amesh Adalja, a public-health expert at the Johns Hopkins Center for Health Security, told The Daily Beast.

Meanwhile,

In the United Kingdom, infections from a highly mutated subvariant called BQ.1.1 are doubling every week—a rate of growth that far exceeds other leading subvariants. In the U.S., BQ.1.1 is spreading twice as fast as its cousin subvariant BA.2.75.2.

That means BQ.1.1 is very contagious. But that’s not the subvariant’s most alarming quality. What’s most worrying is that it also evades certain antibodies. In fact, BQ.1.1 seems to be the first form of COVID against which antibody therapies—evusheld and bebtelovimab, for instance—don’t work at all.

https://www.thedailybeast.com/deadly-twist-in-covid-variant-takes-the-world-by-surprise

BQ.1.1 wasn’t the inevitable winner of the viral competition that raged, mostly unseen, in the months following the peak of the BA.5 wave. There were other highly contagious and somewhat evasive subvariants, including BA.2.75.2 and BA.4.6.1.

But BQ.1.1 had an advantage, thanks in part to an eyebrow-raising three major mutations on its spike protein, the part of the SARS-CoV-2 virus that helps it grab onto and infect our cells. These mutations—N460K, K444T, and R346T—make BQ.1.1 more contagious than its cousins.

 

[Astronuc]

In New York - October 17, 2022

For samples of SARS-CoV-2 collected between September 25 -- October 8, 2022 from New York that are sequenced and uploaded into GISAID, 99.0% were the Omicron variant. During this time period 3.0% of sequences were lineage BA.2, 0.9% were BA.4, 15.6% were BA.4.6, 67.0% were BA.5, 4.7% were BF.7, 5.0% were BQ.1, and 2.8% were BQ.1.1 .

Between October 9 and October 15, 2022 CDC’s program for HHS Region 2 (New York, New Jersey, Virgin Islands, Puerto Rico) estimated 100% of samples were the Omicron variant. During this time period 1.9% of sequences were BA.2.75, 2.3% were BA.2.75.2, 0.4% were BA.4, 12.5% were BA.4.6, 57.4% were BA.5, 5.9% were BF.7, 11.6% were BQ.1, and 8.0% were BQ.1.1.

Omicron subvariants dominate in NY and CDC Region 2.

BA.4 reached a peak of 16% of sequenced variants last couple of weeks in June before decreasing. BA4.6 showed up, and is now about 15.6% of SARS-Cov-2 infections. On the other hand, BA.5 was about 5% of sequenced variants the two weeks ending 4 June, but in the two weeks ending Aug 27, it accounted for 84% of SARS-Cov-2 sequenced variants, and now represents about 67% of sequenced variants. Now BF.7, BQ.1, BQ1.1 and something considered 'other' are being sequenced.

 

[Laroxe]

I think when we consider the evolving pandemic, its useful to consider how evolution actually works. We know there are a huge number of variants out there and some of these variants are able to evade some of the effects of the antibodies we produce following vaccination or natural infection. The emphasis here is on the word "some", we produce a wide range of antibodies to all parts of the virus and these antibodies vary in their effects on the virus. Its clear that some variants that have changed the structure of the spike protein may be able to reduce the effects of some of the antibodies. However none of the variants have so far shown the ability to escape all of the antibodies, they can avoid some, but not all.
We now know that most of the variants seen have actually been around since the very early days of the pandemic and generally natural selection occurs when a particular variant gains a selective advantage over the others because of the way it interacts with its environment. Remember that since the pandemic got started, we have been taking actions that can significantly effect the way the virus spreads, while at the same time, the vaccination campaigns have rapidly changed the population level immunity. In fact with each of the vaccines there are some differences in the antibodies produced. We need to stop thinking that the emergence of new variants occurs because of recent mutations, the fact is we have introduced huge changes in the environment and so the selective pressures on the virus change.
While we tend to focus on issues like transmissibility and disease severity, its often the case that the changes we see, occur because of, other, often minor changes. A virus capable of faster reproduction, even quite small changes can shorten the incubation period and if virus reproduction precedes the onset of symptoms the onset of symptoms so much the better. A virus that rapidly leads to symptomatic disease is likely to avoid the rapid rise in antibody levels because of the short period of time, so we would see increased rates of reinfections and perhaps more sever disease. It can in-fact be very difficult to make sense of all the changes that might exert a selective pressure, we don't even know what we should be looking at until a new variant starts to take over.
All of these issues mean that the studies on serum antibodies can be misleading, we know they have a very limited role in preventing infections and their effectiveness varies. Its now considered the the role of various T cells, particularly those in local tissues my be far more important in slowing the progression of disease and preventing death. It also appears to be the case that the various T cells and other memory cells are activated by highly conserved parts of the virus so there can be little resistance developed.

 

[kyphysics]

I have a love-hate relationship with Eric Feigl Ding's tweets. He's obviously uber qualified (Harvard Professor of Epidemiology), but I honestly feel he can be "overly dramatic" with his "tone." Some have called him sensationalist. I don't think he is in intent, but his "interpretation" of data and what it means is sometimes "worse" than how I perceive things.

Anyhow, this is an interesting thread on latest variants and what they could mean for the winter.


Part way down the thread, he posts this, which I agree is the million dollar question. It's still worth tracking to see if this holds in new data.

I got my bivalent booster a few weeks ago, thankfully.

^^^Long thread, but worth checking out his opinion on timing of winter surge, etc.

 

[Laroxe]

Throughout much of history, claiming to be able to predict the future, particularly a future filled with death and disaster has been an effective way of becoming well known. Its perhaps worth considering some of the issues around Covid 19 to give this claim some context.

Among the 5 main variants there are a large number of sub variants and currently in the currently dominant Omicrom variant, more than 300 subvariants have been identified. Many of these have genetic changes that could alter the criteria that label them as “of concern”. The majority of these changes lead to alterations in the spike protein of the virus, particularly in the receptor binding domain. It seems that the number of changes in the spike protein correlates with the degree of antibody evasion seen in the virus. However, vaccination and prior infections do mean that all of the variants have to overcome the same antibody defences, this has lead to convergent evolution in which different strains share similar mutations in order to overcome these defences. It has been suggested that the greater the number of these changes, the faster the virus seems to take over from the previous dominant strains.

Really, predicting how the virus and the disease it causes will evolve, is really a triumph of hope over experience, we simply have to little information about the selective forces at work and what evidence we do have is inconsistent and confusing.
The initial indicators were that cases involving the variants BQ1 and BQ11 were increasingly being identified and they appeared to be set to become the dominant strains, however, the rates of these increases was highly variable depending on where the sampling was carried out. In some areas in which a rapid rise was detected, it suddenly seemed to stop, in the UK for example which appeared to be heading rapidly into a new wave of infections, the rate of increase has stalled with some suggestion that the numbers are actually dropping again. There are also, several other variants that appear to have greater immune evasion abilities and that have cause rapid increases then simply fizzled out. It is thought that the most immune evasive variant is in fact BA4.6, currently the second-most-prevalent strain in the U.S. And for many of the previous weeks, while its share of cases has increased over that time, (@ 11%), its growth nationally has been rather slow. Another new variant BF7 is also circulating in the US and is increasing, currently causing around 7% of cases. Its interesting that despite the evidence of antibody resistance, none of these variants stand out as particularly more dangerous, which is rather curious. So despite calls to increase surveillance, the reduced risks, seems to have reduced its importance, and the level of surveillance has actually fallen as concern shifts to other respiratory diseases and new information about older diseases. This means the data we have has become increasingly less reliable. We also need to consider that most of the variants identified for increased surveillance in the past and found in significant numbers of people, have simply disappeared from sight.Of course if a variant can resist the effects of circulating antibodies its hardly surprising that humoral antibodies will become increasingly less less effective in preventing initial infection and symptomatic disease. This will depend on the number of antibodies that are effected and their relative importance in resistance. Unfortunately most of the information we have only looks at overall antibody levels and we simply don't know the levels of antibodies needed to have a significant effect. Its certainly true that there are a significant number of cases arising in the vaccinated population and even in people during the periods they should have the highest levels. Measures of antibodies without some baseline level of known effectiveness really tells us nothing, a vaccine might be very good at creating an antibody response but that doesn't really tell us it effects on infection.Many virologists have suggested we should not consider a vaccine as offering significant protection from symptomatic infection, its function is in protecting people from serious disease and death, something which it appears to do quite well.Unfortunately for most viral diseases antibody levels provided a reliable measure of resistance, this actually meant that other parts of the immune system attracted far less attention and have been relatively poorly understood. Covid appears to have changed that, it seems that cell based immunity and tissue resident T cells play a very significant role in immunity and have their own persistent memory systems. Luckily all of the vaccines also stimulate significant T cell and tissue immunity, even though that was never really considered in their design. Currently there is no evidence that the effects of these systems can be effectively avoided by any of the variants

As most of these variants reduce the effectiveness of particular antibodies, it isn't surprising that they can impact on the effectiveness of antibody treatments used in prophylaxis for vulnerable people. This has caused significant concern.

 

[Sagittarius A-Star]

Spread of the SARS-CoV-2 Omicron variant sub-lineage BQ.1 in the EU/EEA​

...
European Union/European Economic Area (EU/EEA) countries have detected the circulation of SARS-CoV-2 variant sub-lineages BQ.1 in levels ranging from 0−19% during week 40. This variant originates from the BA.5 Omicron Variant of Concern (VOC).
...

• BQ.1, including its sub-lineages, has been designated as Variant of Interest (VOI) by ECDC as of 20 October 2022. Based on modelling estimates, it is expected that by mid-November to beginning of December 2022, more than 50% of SARS-CoV-2 infections will be due to BQ.1/BQ.1.1. By the beginning of 2023, more than 80% of SARS-CoV-2 cases are expected to be due to BQ.1/BQ.1.1.
• The observed increase in the growth rate of BQ.1 is probably driven mainly by immune escape. This variant and its sub-lineages will probably contribute to a further increase in cases of COVID-19 in the EU/EEA in the coming weeks and months. The extent of the increase in COVID-19 cases will depend on various factors, including immune protection against infection influenced by the timing and coverage of COVID-19 vaccination regimes, and the extent, timing and variant landscape of previous SARS-CoV-2 pandemic waves. Based on limited available data, there is no evidence of BQ.1 being associated with a greater infection severity than the circulating variants BA.4/BA.5.

Source:
https://www.ecdc.europa.eu/en/publi...s-cov-2-omicron-variant-sub-lineage-bq1-eueea

 

[Astronuc]

Locally, we've had 8 deaths due to Covid-19 during the month of October, which is about the same for September, and down slightly from 12 in August, 13 in July. During last summer, we dropped below 100 active cases per day, but then increased after July 4 holiday. With each holiday, we seem to see a slight increase in positive cases and hospitalizations. I believe most, if not all, hospitalizations and fatalities involve unvaccinated people, and most are elderly, 60+. I suspect by next weekend, 5 days after Halloween, we will see an increase in positive cases.

Looking at NY State, which I have been following since March 2020, as of October 28, the state has performed 121,492,632 tests (~6x entire state population) for SARS-Cov-2 and reported 6,157,918 cumulative positive results, including reinfections. The positive cases could be under-reported by a factor of 2. I've heard estimates of something like 75 to 80% of children have contracted the virus, but I can't remember if that is NY state, or nationwide, or perhaps both.

 

[Sagittarius A-Star]

Clinical severity of, and effectiveness of mRNA vaccines against, Covid-19 from omicron, delta, and alpha SARS-CoV-2 variants in the United States: prospective observational study
...
Results: Effectiveness of the mRNA vaccines to prevent Covid-19 associated hospital admissions was 85% (95% confidence interval 82% to 88%) for two vaccine doses against the alpha variant, 85% (83% to 87%) for two doses against the delta variant, 94% (92% to 95%) for three doses against the delta variant, 65% (51% to 75%) for two doses against the omicron variant; and 86% (77% to 91%) for three doses against the omicron variant. In-hospital mortality was 7.6% (81/1060) for alpha, 12.2% (461/3788) for delta, and 7.1% (40/565) for omicron. Among unvaccinated patients with Covid-19 admitted to hospital, severity on the WHO clinical progression scale was higher for the delta versus alpha variant (adjusted proportional odds ratio 1.28, 95% confidence interval 1.11 to 1.46), and lower for the omicron versus delta variant (0.61, 0.49 to 0.77). Compared with unvaccinated patients, severity was lower for vaccinated patients for each variant, including alpha (adjusted proportional odds ratio 0.33, 0.23 to 0.49), delta (0.44, 0.37 to 0.51), and omicron (0.61, 0.44 to 0.85).

Conclusions: mRNA vaccines were found to be highly effective in preventing Covid-19 associated hospital admissions related to the alpha, delta, and omicron variants, but three vaccine doses were required to achieve protection against omicron similar to the protection that two doses provided against the delta and alpha variants. Among adults admitted to hospital with covid-19, the omicron variant was associated with less severe disease than the delta variant but still resulted in substantial morbidity and mortality. Vaccinated patients admitted to hospital with Covid-19 had significantly lower disease severity than unvaccinated patients for all the variants.

Source:
https://pubmed.ncbi.nlm.nih.gov/35264324/

 

[kyphysics]

With each holiday, we seem to see a slight increase in positive cases and hospitalizations.

I remember reading this pattern in the news in 2021 (national cases that is). It makes sense, as people often get together in tighter spaces for longer periods of time during holidays.

Although, is Halloween considered as "dangerous," given it happens mostly outside (kids trick or treating)? I'm more worried about Thanksgiving and Christmas. Although, I wouldn't be surprised to see a significant pop up in cases post-Oct 31st.

 

[Astronuc]

Although, is Halloween considered as "dangerous," given it happens mostly outside (kids trick or treating)?

Apparently people congregate at parties. It is the congregation indoors where someone is infected and contagious that the virus is transmitted to others. Locally, in 2020 and 2021, the county where I live experienced a rise in infections within 10 days of Halloween, then the trend of new cases slowed, then picked up after Thanksgiving holiday, then slowed, then picked up with Christmas and New Year's Day, with a peak of positive cases in January the following year, 2021 and 2022, respectively. Let's see if the pattern repeats this year into next.

 

[kyphysics]

COVID booster may lower protection against omicron reinfection, study finds. Here’s why​

Julia Marnin
Thu, November 3, 2022 at 12:18 PM·4 min read

A COVID-19 booster, specifically a third vaccine dose, may lower protection against getting infected with the omicron variant again for some people — and there’s a reason why, new findings suggest.

In contrast, two vaccine doses, followed by an initial omicron infection, may protect more against a second omicron infection than an extra jab, according to a preprint study published Nov. 1 to medRxiv, a server run by Yale, BMJ and Cold Spring Harbor Laboratory. This is due to a specific reaction within the immune system, researchers concluded.

Here’s what the findings mean. . . [see full article]

Kind of a whacky finding.

 

[Astronuc]

While the situation is certainly different from last winter when Omicron dominated all other variants, a new “variant soup” of Omicron sublineages like XBB, BQ.1, and BQ.1.1 are gaining ground across the country, wiping out key tools used to protect immune-compromised people.

https://fortune.com/2022/11/04/fauc...ew-omicron-variants-bloom-winter-coming-soon/

COVID booster may lower protection against omicron reinfection, study finds. Here’s why

Pfizer/BioNTech say updated Covid-19 booster generates ‘substantially higher’ protection against Omicron subvariants than original vaccine
https://www.cnn.com/2022/11/04/health/pfizer-covid-bivalent-booster-omicron-data/index.html

NBC and ABC are broadcasting much the same story.

 

[Laroxe]

https://fortune.com/2022/11/04/fauc...ew-omicron-variants-bloom-winter-coming-soon/Pfizer/BioNTech say updated Covid-19 booster generates ‘substantially higher’ protection against Omicron subvariants than original vaccine
https://www.cnn.com/2022/11/04/health/pfizer-covid-bivalent-booster-omicron-data/index.html

NBC and ABC are broadcasting much the same story.

I remember them talking about this on TWiV and they were a bit less impressed. While it true that the bivalent vaccines do generate greater antibody responses, no one is quite sure what the antibody levels would need to be to offer any sort of protection The new variants clearly evade at least some of the antibody defences, so while there are claims of a four fold increase in the antibody levels, that really doesn't mean that it offers greater protection. We simply don't know the levels that might be needed, and the higher levels are likely to fall quickly. Some earlier studies have suggested that in terms of disease outcomes there is no difference, the vaccines are already very effective, and at that level, it will be hard to show much of a difference.

 

[Astronuc]

Some earlier studies have suggested that in terms of disease outcomes there is no difference, the vaccines are already very effective, and at that level, it will be hard to show much of a difference.

Yes, I heard the same this afternoon. While cases of BQ.1 and BQ.1.1 seem to be on the rise, the severity of illness does not appear to be greater, although I don't know if that applies to unvaccinated or immunocompromised. I do know of friends and family who contracted the virus, in the past month or two, and they all indicated it was the worst they've felt in a long time. For some, they slept a lot, and didn't eat much. Sounds like a response to the flu. Hospitalization was not required.

Locally hospitalizations have subsided, but there is a persistent low level, and in the past week, we seem to be on an upward trend. We did see a slight rise in fatalities, but that too seems to have subsided for now.

On the other hand, we are seeing an increase in influenza and RSV cases, in addition to COVID. I don't know if there are data form combined infections.

 

[Sagittarius A-Star]

mRNA bivalent booster enhances neutralization against BA.2.75.2 and BQ.1.1
...
In the one monovalent booster cohort, relative to WA1/2020, we observed a reduction in neutralization titers of 9-15-fold against BA.1 and BA.5 and 28-39-fold against BA.2.75.2 and BQ.1.1. In the BA.5-containing bivalent booster cohort, the neutralizing activity improved against all the Omicron subvariants. Relative to WA1/2020, we observed a reduction in neutralization titers of 3.7- and 4-fold against BA.1 and BA.5, respectively, and 11.5- and 21-fold against BA.2.75.2 and BQ.1.1, respectively.

Source:
https://www.biorxiv.org/content/10.1101/2022.10.31.514636v1

 

[Laroxe]

Source:
https://www.biorxiv.org/content/10.1101/2022.10.31.514636v1

The problem with a lot of studies like this is the assumption that the increases seen in antibody levels are clinically significant. Covid 19 has proven to be confusing in this respect with the risk of infection proving to be highly variable in a population, variations in the response to vaccines and considerable variations in the nature of the antibodies generated, when they are. It's increasingly thought that while antibody levels are the standard way to assess vaccines and for many disease seem to provide a good match to effectiveness, this doesn't appear to be true of Covid 19.

We are however aware of the fact that the high antibody levels seen following any of the Covid 19 vaccines is very short lived and may only provide enhanced protection for a matter of weeks. Remember that even as these bivalent vaccines are being rolled out, in populations already highly immune, its difficult to see any obvious impact on the rates of infection, its the rates of serious disease that are better, but this is true of both types of vaccine This explains why the focus of attention in both understanding immunity and future vaccine development has shifted beyond humoral immunity.

Its also now considered that what is called "original antigenic sin" which was thought to have a role in relatively few diseases may represent a core process in immunity, one which we are still trying to understand. Its still not clear how important this is in Covid 19 but it appears that introducing a new strain of a virus to someone immune to the original strain can significantly effect the overall immunity to both strains. This has the potential to alter the antibody mix so effecting the effectiveness and a broader antibody range has the potential to increase the risk of adverse events. However, studies that attempt to identify the various antibodies and there targets are very difficult.

The huge amounts of money for Covid 19 research has certainly lead to a great deal of new information and has significantly enhanced our understanding, but as a result of some variant of "Sods Law", each new piece of understanding generates several new questions, there is still a great deal of work that needs to be done.

 

[Astronuc]

In late October, the UK Health Security Agency assigned variant designations to two new omicron “grandchildren”: BQ.1 and XBB. This means they will be monitored by health authorities, but are not at this stage regarded as variants of concern.

https://theconversation.com/xbb-and-bq-1-what-we-know-about-these-two-omicron-cousins-193591

n the UK, Europe and North America, the prevalence of BQ.1 is rising quickly. Recent data from the UK’s Office for National Statistics (ONS) estimated BQ.1 sub-lineages (including BQ.1 and the similar BQ.1.1) made up 16.7% of infections. In the US, BQ.1 and BQ.1.1 together make up around 35% of infections.

XBB seems to be more prevalent in Asia. While the ONS data suggests it makes up only 0.7% of infections in the UK, in Singapore some 58% of recently sequenced cases are XBB. But whereas sequences of XBB are increasing globally, XBB cases in Singapore now appear to be starting to fall.

https://www.cidrap.umn.edu/news-per...dvisers-weigh-omicron-xbb-and-bq1-subvariants

As of November 14, in NY State and CDC Region 2
https://coronavirus.health.ny.gov/covid-19-variant-data (updated weekly or biweekly)

For samples of SARS-CoV-2 collected between October 23 -- November 5, 2022 from New York that are sequenced and uploaded into GISAID, 94.8% were the Omicron variant. During this time period 5.0% of sequences were lineage BA.2, 0.1% were BA.2.12.1, 0.4% were BA.4, 4.5% were BA.4.6, 30.4% were BA.5, 3.7% were BF.7, 26.4% were BQ.1, and 24.2% were BQ.1.1 .Between November 6 and November 13, 2022 CDC’s program for HHS Region 2 (New York, New Jersey, Virgin Islands, Puerto Rico) estimated 100% of samples were the Omicron variant. During this time period 0.7% of sequences were BA.2, 1.3% were BA.2.75, 1.2% were BA.2.75.2, 0.1% were BA.4, 4.5% were BA.4.6, 19.5% were BA.5, 2.9% were BA.5.2.6, 5.7% were BF.7, 2.1% were BN.1, 31.4% were BQ.1, and 28.5% were BQ.1.1 .

EU side seems relatively up-to-date
https://www.ecdc.europa.eu/en/covid-19/variants-concern

https://www.cbsnews.com/news/cdc-now-tracking-bn-1-the-latest-new-covid-variant-on-the-rise/

The Centers for Disease Control and Prevention is now tracking the rise of another COVID-19 variant known as BN.1, according to figures published by the agency this month, marking the latest new Omicron descendant now spreading around the country this fall.

Some 4.3% of new COVID-19 cases nationwide are now linked to the BN.1 variant, according to "Nowcast" estimates released on Friday by the CDC.

Prevalence of the new strain is largest in the West, in the region that spans Arizona, California, Hawaii, and Nevada. 6.2% of new cases in that area, HHS Region 9, are from BN.1.

New variants just keep coming, and there appears to be some conflict in reports of new ones like BQ.1 and subvariants and XBB being able to bypass the immune system. BN.1 is a new one to me.