BA.2.75.2 and BQ.1.1

[Woodchopper]

Seems to be one to look out for.

Immune escape in Swedish blood donors: https://twitter.com/benjmurrell/status/ ... Pl5J93VdpQ

Background and links to other threads: https://twitter.com/mike_honey_/status/ ... KZ_YDzEYAg

Looks like it’s the fastest growing UK variant: https://twitter.com/peacockflu/status/1 ... j2pDicSGFg

[Woodchopper]

Update here: https://twitter.com/yunlong_cao/status/ ... zf796Nc9fA

I adjusted the thread title as BQ.1.1 is also worrying.

Good summary by the excellent Emma Hodcroft: https://twitter.com/firefoxx66/status/1 ... jxRv7HYB1Q

Some discussion:
https://twitter.com/twenseleers/status/ ... jxRv7HYB1Q

And some commentary: https://www.theguardian.com/world/2022/ ... cases-rise

[Woodchopper]

looking like Omicron has a remarkable capacity for more evolution. One of the newest subvariants, called BA.2.75.2, can evade immune responses better than all earlier forms of Omicron.

For now, BA.2.75.2 is extremely rare, making up just .05 percent of the coronaviruses that have been sequenced worldwide in the past three months. But that was once true of other Omicron subvariants that later came to dominate the world. If BA.2.75.2 becomes widespread this winter, it may blunt the effectiveness of the newly authorized boosters from Moderna and Pfizer.

[…]

But it soon became clear that the name “Omicron” hid a complex reality. After the original Omicron virus evolved in the fall of 2021, its descendants split into at least five branches, known as BA.1 through BA.5.

[…]

The U.S. Food and Drug Administration responded by inviting vaccine makers to produce booster shots that included a BA.5 protein along with one from the original version of the virus. Those boosters are now rolling out to the public, at a time when BA.5 is causing 85 percent of all Covid cases in the United States.

But BA.5 could be fading in the rearview mirror by winter, scientists said. Omicron has continued to evolve — likely by sometimes jumping among hosts, and sometimes hiding for months in one of them.

Since these new lineages belong to Omicron, they haven’t gotten a Greek letter of their own. But that doesn’t mean they’re just a slight twist on the original. Antibodies that could latch onto earlier forms of Omicron fare poorly against the newer ones.

“They could arguably have been given different Greek letters,” Dr. Robertson said.

BA.2.75.2 is among the newest of Omicron’s grandchildren, identified just last month. It’s also the most evasive Omicron yet, according to Dr. Murrell. In lab experiments, he and his colleagues tested BA.2.75.2 against 13 monoclonal antibodies that are either in clinical use or in development. It evaded all but one of them, bebtelovimab, made by Eli Lilly.

They also tested the antibodies from recent blood donors in Sweden. BA.2.75.2 did substantially better at escaping those defenses than other Omicron subvariants did.

The researchers posted their study online on Friday. Researchers at Peking University reached similar conclusions in a study posted the same day. Both have yet to be published in a scientific journal.

Dr. Murrell cautioned that scientists have yet to run experiments that will show the effectiveness of BA.5 booster shots against BA.2.75.2. He suspected that getting a big supply of BA.5 antibodies would provide some protection, especially against severe disease.

“It’s still important, but we’ll have to wait for the data to come out to see exactly what the magnitude of the boosting effect is,” Dr. Murrell said.

There’s no reason to expect that BA.2.75.2 will be the end of the evolutionary line. As immunity builds to previous versions of Omicron, new versions will be able to evolve that can evade it.

“I don’t think it’s going to hit a wall in the mutational space,” said Daniel Sheward, a postdoctoral researcher at the Karolinska Institute and co-author on the new study.

Lorenzo Subissi, an infectious disease expert with the W.H.O., said that the organization was not giving Greek letters to lineages like BA.2.75.2 because they are much like the original Omicron viruses. For example, it appears that all Omicron lineages use a distinctive route to get into cells. As a result, it is less likely to lead to severe infections but possibly better able to spread than previous variants.

“W.H.O. only names a variant when it is concerned that additional risks are being created that require new public health action,” Dr. Subissi said. But he did not rule out a Pi in our future.

“This virus still remains largely unpredictable,” he said.

https://www.nytimes.com/2022/09/22/scie ... riant.html

[Woodchopper]

Growth in Denmark, Belgium and England: https://twitter.com/JosetteSchoenma/sta ... n8qUagGPmQ

[Woodchopper]

Big COVID-19 waves may be coming, new Omicron strains suggest

https://www.science.org/content/article ... ns-suggest

Summary of what is known so far.

[Woodchopper]

Ouch: https://twitter.com/bristoliver/status/ ... Bx4D4dyQSw

[Woodchopper]

Prevalence appears to be growing: https://twitter.com/corneliusroemer/sta ... pMP2CRcV6Q

[Woodchopper]

For the UK, BQ.1.1 is showing a growth advantage of 12% per day against all other BA.5.* lineages, which predicts a crossover in mid-October.

For France, BQ.1.1 is showing a growth advantage of 8% per day against all other BA.5.* lineages, which predicts a crossover in late October.

Start of the thread: https://twitter.com/mike_honey_/status/ ... pMP2CRcV6Q

[Woodchopper]

Will there be a COVID winter wave? What scientists say
Emerging variants and waning immunity are likely to push infections higher in the northern hemisphere as influenza also makes a comeback.

https://www.nature.com/articles/d41586-022-03157-x

[Woodchopper]

Projections for ‘The Pentagon’ a collection of five variants which have similar spike protein mutations:
https://twitter.com/jpweiland/status/15 ... 9zjZ1G_EmQ

[Woodchopper]

Updates preprint on the five variants which have evolved similar immune escape mutations: https://www.biorxiv.org/content/10.1101 ... 5.507787v3

Thread by one of the authors:

Updating results regarding convergent variants BU.1, BR.2, BM.1.1.1, CA.1, and XBB.
XBB is currently the most antibody-evasive strain tested, and BR.2, BM.1.1.1, CA.1 are more immune evasive than BA.2.75.2 and BQ.1.1.

Details at the link: https://twitter.com/yunlong_cao/status/ ... 338D7KBK2g

[Woodchopper]

More on the collection of variants: https://twitter.com/CorneliusRoemer/sta ... 6OS3STH8PQ

[Woodchopper]

thread in Germany: https://twitter.com/MoritzGerstung/stat ... 075uZ_x5IQ

tl;dr increase in cases isn't due to the new variants, more likely due to waning immunity and changes in behaviour.

IMHO there will be a longer autumn/winter wave than we have become used to. It'll start with waning immunity and people spending more time in crowded places. later the variants will be more significant. However, as there are five of them we'll probably be hit be one after the other rather than all at once.

[Brightonian]

A couple of weeks ago my father (in Ireland) and I (in France) had separately noticed that there seemed to be a slight increase in the numbers of people wearing masks. And today I myself masked up for a metro journey, first time in ages, with news of variants multiplying and dividing or something, especially the B&Q.SPQR.3.1415926 sub-sub-variant or whatever it is now. I think I noticed a few more people today who were also masked up, maybe 1 in 10 or 15, compared with 1 in 15 or 20 a couple of weeks ago, but maybe that's one of these psychological biases.

[Woodchopper]

Back to this:

U.S. health regulators on Friday estimated that BQ.1 and closely related BQ.1.1 accounted for 16.6% of coronavirus variants in the country, nearly doubling from last week, while Europe expects them to become the dominant variants in a month.

https://www.reuters.com/business/health ... 022-10-21/

[Woodchopper]

Update on BQ.1.1 and XBB
https://twitter.com/yunlong_cao/status/ ... Vx7Zm9y8Fg

[Woodchopper]

Possibly some good news from Germany:

There are some positive signs in Germany's most recent SARS-CoV-2 genomic data.

* The share of BQ.1.1 doubles every 10d, but ...
* Overall cases have solidly declined (-5% per day)
* Absolute BQ.1.1's numbers increased only slowly (0-5% per day)

https://twitter.com/moritzgerstung/stat ... sMP4CFjdLw

[Woodchopper]

COVID ‘variant soup’ is making winter surges hard to predict

https://www.nature.com/articles/d41586-022-03445-6

[Woodchopper]

Latest update on some new convergent variants

https://twitter.com/yunlong_cao/status/ ... 7405348865

[Woodchopper]

Map of the variant tree: https://twitter.com/rquiroga777/status/ ... QsklYJaGOQ

[Woodchopper]

Map of the variant tree: https://twitter.com/rquiroga777/status/ ... QsklYJaGOQ

Part of a summary of what that means by Eric Topol

[…]

We’ve been worried about BQ.1.1 but now there’s BQ.1.1.10 which shows more evasion (than BQ.1.1) after 3 CoronaVac shots plus a BA.5 breakthrough infection (below). There’s also XBB.1, XBB.3 add ons (beyond XBB), along with BA.4.6.3, CH.1.1, that similarly take immune evasion to a higher level than what we’ve previously seen.

The growth advantage compared with BA.5 is substantial, such that for each of the convergent mutations that the swarm of variants are accruing, the growth advantage increases, as nicely shown in this graph by Rodrigo Quiroga. In the early watch of these converging mutations seen in the new variants it was 4 or 5, but now we’re getting up to even 8 or 9 mutations with almost doubling of the growth advantage vs BA.5.

Has this induced clinical impact yet? The only place that has seen a wave due to one of these new variants is Singapore (graph below), which is now in descent, and did not have a major corresponding spike in hospitalizations or deaths. XBB is dominant in other countries like Bangladesh and India, which have not shown any spike in cases or deaths to date. Keep in mind that the vaccination and booster rate in Singapore is extremely high (boosters were the original, not bivalent), whereas the prior Covid infection rate in the other countries that have had high XBB exposure is also high.

We haven’t yet seen countries with BQ.1.1 reach dominance. France is the closest but has yet to exhibit an increase in cases or hospitalizations (in contrast, see below), which is also reassuring. But we will need to see how this particular variant fully plays out in many countries before saying that the immune evasion properties are not correlating with a surge of infections and adverse outcomes.

More at the link: https://erictopol.substack.com/p/pandem ... tober-2022

[Woodchopper]

Good news

mRNA bivalent booster enhances neutralization against BA.2.75.2 and BQ.1.1

https://www.biorxiv.org/content/10.1101 ... 1.514636v1