Covid Variants

[Sam the Centipede]

Yeah, that's what I'm hearing in Yurrp, so the same will be true in Amuricky. Doubling of infections every 2ish days. That is serious exponential growth!

Measles is a very infectious virus (hence the need for high vaccination rates to control it, big R₀, about 12 iirc) and it's said that if a carrier comes into a room and spends some time there, pretty much everybody will catch it, unless immune. SARS-CoV-2 wasn't that bad, but Omicron heads in that direction. I have just looked: the original SARS-CoV had R₀≈2.5 but Omicron has R₀≈7, possibly higher, according to an article in The Lancet: Omicron variant and booster COVID-19 vaccines. Aaaaggghhhh!

So, if R₀≈10 (which Professor Martin Hibberd, professor of emerging infectious diseases at London School of Hygiene & Tropical Medicine, suggests it could be), any infected person could easily become a super-spreader. Even if 9 out of 10 people behave perfectly, not transmitting within the home, workplace or public areas due to their extreme diligence, if 1 out of 10 carries on as normal, the infection level could increase.

I'll be working in a hospital on Monday, and I certainly plan on being very diligent with masks, sanitizer, distancing when possible, etc. It shouldn't be too bad, as I don't go into "red zones" and all patients are tested on admission … but test results aren't available immediately so there could be unidentified carriers inconveniently close. Ho hum, one does one's best.

[Azastan]

Yeah, that's what I'm hearing in Yurrp, so the same will be true in Amuricky. Doubling of infections every 2ish days. That is serious exponential growth!

Measles is a very infectious virus (hence the need for high vaccination rates to control it, big R₀, about 12 iirc) and it's said that if a carrier comes into a room and spends some time there, pretty much everybody will catch it, unless immune. SARS-CoV-2 wasn't that bad, but Omicron heads in that direction. I have just looked: the original SARS-CoV had R₀≈2.5 but Omicron has R₀≈7, possibly higher, according to an article in The Lancet: Omicron variant and booster COVID-19 vaccines. Aaaaggghhhh!

So, if R₀≈10 (which Professor Martin Hibberd, professor of emerging infectious diseases at London School of Hygiene & Tropical Medicine, suggests it could be), any infected person could easily become a super-spreader. Even if 9 out of 10 people behave perfectly, not transmitting within the home, workplace or public areas due to their extreme diligence, if 1 out of 10 carries on as normal, the infection level could increase.

I'll be working in a hospital on Monday, and I certainly plan on being very diligent with masks, sanitizer, distancing when possible, etc. It shouldn't be too bad, as I don't go into "red zones" and all patients are tested on admission … but test results aren't available immediately so there could be unidentified carriers inconveniently close. Ho hum, one does one's best.

Was just reading that King County, WA State, expects that by Dec 22, there will be 2100 cases of Omicron DAILY.

[Volkonski]

[Lani]

How bad is Omicron? Here’s what to watch for
https://www.latimes.com/science/story/2 ... -watch-for

The situation with the Omicron variant is changing so rapidly, it’s hard to know where things stand.

Sometimes the news seems ominous, as when the Centers for Disease Control and Prevention said the strain went from 0.7% to 73% of new infections in the U.S. in just two weeks.

Other times the news seems encouraging, as when South African officials observed that Omicron cases appeared to recede almost as dramatically as they had spiked.

How can we tell what’s really going on? Which indicators will reveal the variant’s true powers?

It's an informative article about what is known and what is unknown. Basically, there are a lot of unknowns.

[notorial dissent]

It is going to be interesting to see what happens in the UK and Europe between now and NY's as their numbers have been all over the place.

[Sam the Centipede]

It is going to be interesting to see what happens in the UK and Europe between now and NY's as their numbers have been all over the place.

One of the concerns is that Omicron often presents with only the symptoms of an ordinary cold: runny nose, sore throat, etc. People have learnt that loss of senses of taste and smell indicate probable Covid, but the absence of those symptoms is now a much less reliable guide in the "Covid or cold?" question now.

I wonder if we are seeing the virus evolve towards becoming another common cold virus … but that won't become clear for a long time. (Common colds are caused by a variety of viruses from several different groups, including about four coronaviruses, iirc, and some are thought to be descended from from ancestral viruses that were more lethal.)

[Lani]

It is going to be interesting to see what happens in the UK and Europe between now and NY's as their numbers have been all over the place.

I wonder if we are seeing the virus evolve towards becoming another common cold virus … but that won't become clear for a long time. (Common colds are caused by a variety of viruses from several different groups, including about four coronaviruses, iirc, and some are thought to be descended from from ancestral viruses that were more lethal.)

We're months away from knowing whether omicron damages the body as much as the other variants.

But it’s been abundantly clear for more than a year that even asymptomatic infection brings a significant risk of long Covid – a wide spectrum of more than 200 symptoms and conditions that can appear months after initial infection or apparent recovery, and leave children, adults and elders disabled, chronically ill and desperate for medical care, income, housing or even recognition that their suffering is from real physical conditions.

On 15 December, South Africa’s Dr Salim Abdool Karim, who co-authored Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic in the Lancet, told a global Zoom audience:

“I have no idea what’s in store for us as far as long Covid is concerned … It’s a really important question, and it’s particularly so because Omicron is spreading so fast and so widely so quickly – the number of people getting infected is so big that … if it’s a common consequence of even mild infection, you can imagine, even if in 10% of people, there’s going to be a lot of people with long Covid. It’s certainly something we want to keep a beady eye out on.”

https://www.theguardian.com/commentisfr ... ong-hauler

[Sam the Centipede]

From the UK, in The Guardian:
Omicron is ‘not the same disease’ as earlier Covid waves, says UK scientist. One paragraph:

Sir John Bell, regius professor of medicine at Oxford University and the government’s life sciences adviser, said that although hospitalisations had increased in recent weeks as Omicron spreads through the population, the disease “appears to be less severe and many people spend a relatively short time in hospital”. Fewer patients were needing high-flow oxygen and the average length of stay was down to three days, he said.

The article quotes several infectious disease people, with mixed messages of optimism, realism and caution, reflecting and respecting the fact that Omicron hasn't been bouncing around for many weeks yet. One message is that the increased transmissibility puts strain on health services even if most infected people have only mild symptoms, so being milder isn't a get out of jail free card.

Off Topic

It still surprises me how rapidly and completely waves of some novel variants of SARS-CoV-2 displace the resident variant. My intuition expects a slower, less absolute displacement, but it's a reminder that intuition is not always a reliable guide in science or medicine.

[Volkonski]

[Volkonski]

Josh Gerstein
@joshgerstein
·
1h
US District Court in DC suspends jury trials for 3 weeks, closes public counters at clerk's office due to Omicron spread. Doc: https://dcd.uscourts.gov/sites/dcd/file ... 211230.pdf

[Lani]

From my morning NYT email (which doesn't require subscribing btw):

Several studies have offered a possible explanation for Omicron’s milder effects: It often concentrates in the nose, throat and windpipe rather than damaging the lungs, as previous variants did.

That explains why people have a sore throat and sniffling initially.

I wonder if that means omicron doesn't infect the brain. On the other hand, the nose is a pathway to the brain. I guess we'll know in a few months. If the virus causes loss of smell & taste, then it's likely. I haven't seen anything yet about that.

[Sam the Centipede]

I wonder if that means omicron doesn't infect the brain. On the other hand, the nose is a pathway to the brain. I guess we'll know in a few months. If the virus causes loss of smell & taste, then it's likely. I haven't seen anything yet about that.

There are many reports in Europe that anosmia and ageusia (loss of senses of smell and taste) are rarer with Omicron, leading to concerns that Omicron presents so like a common cold so people might think "huh, I've had colds before, I tested then and was negative, the symptoms are the same, no need to test or isolate". After struggling to get smell/taste symptoms recognized as strong indicators of Covid, the public now must learn that those previously common symptoms might be absent!

I had a cold two days ago so tested (negative!) whereas last year I might have counted back and wondered whether it was worth testing if I didn't plan to meet anybody that day.

There are questions about how accurate the lateral flow (antigen) tests are for Omicron, whether they might be giving false negatives, especially for poorly taken swabs. I don't know how much the different LFTs vary in the antibodies they use or what the targets are, and whether it's only typically one target antigen/epitope or several. I imagine there's some information and research somewhere, but I haven't looked. So it's good to be cautious and certainly to assume (as the instructions say) that even a very weak positive line on the test probably indicates the presence of virus.

[Lani]

There are questions about how accurate the lateral flow (antigen) tests are for Omicron, whether they might be giving false negatives, especially for poorly taken swabs. I don't know how much the different LFTs vary in the antibodies they use or what the targets are, and whether it's only typically one target antigen/epitope or several. I imagine there's some information and research somewhere, but I haven't looked. So it's good to be cautious and certainly to assume (as the instructions say) that even a very weak positive line on the test probably indicates the presence of virus.

We're still learning about the variant. We got a lot of things initially wrong about covid, and I suspect we'll have the same situation with Omicron as more research continues.

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[jcolvin2]

Was just reading that King County, WA State, expects that by Dec 22, there will be 2100 cases of Omicron DAILY.

I think we are are at that level (or slightly above). There were more than 2,300 cases reported through December 29,
2021 (the most recent day for which info is available on the King County DOH Covid Dashboard). My understanding is that test positivity rates are about 25%, as compared to a pandemic average of 5%. Given that many sites are limiting testing to the symptomatic because of testing capacity issues, our true rate may be substantially higher.

[Azastan]

Was just reading that King County, WA State, expects that by Dec 22, there will be 2100 cases of Omicron DAILY.

I think we are are at that level (or slightly above). There were more than 2,300 cases reported through December 29,
2021 (the most recent day for which info is available on the King County DOH Covid Dashboard). My understanding is that test positivity rates are about 25%, as compared to a pandemic average of 5%. Given that many sites are limiting testing to the symptomatic because of testing capacity issues, our true rate may be substantially higher.

Also considering that many testing sites were not open due to the weather and the two holidays, I would expect that the true rate IS substantially higher.

Parents in my local school district (Tahoma SD) are worried about kids going back to school this Monday, as the free testing site for students has not been open, appointments have been hard to get and then cancelled due to weather, and at-home tests have been nearly impossible to find.

[AndyinPA]

From my morning NYT email (which doesn't require subscribing btw):

Several studies have offered a possible explanation for Omicron’s milder effects: It often concentrates in the nose, throat and windpipe rather than damaging the lungs, as previous variants did.

That explains why people have a sore throat and sniffling initially.

I wonder if that means omicron doesn't infect the brain. On the other hand, the nose is a pathway to the brain. I guess we'll know in a few months. If the virus causes loss of smell & taste, then it's likely. I haven't seen anything yet about that.

I can't remember where I saw it, but I think I've heard that omicron doesn't affect the senses of taste or smell. People are sort of conditioned to look for that, but I think with omicron they shouldn't expect that.

[Sam the Centipede]

I can't remember where I saw it […]

About 4 posts up-page?

[AndyinPA]

I can't remember where I saw it […]

About 4 posts up-page?

[raison de arizona]

Lots of chatter about a new French variant on teh Twitters. Here's a brief MSN story:

Covid warning as new variant with '46 mutations' infects 12 in southern France

Scientists have rung the alarm bells over "the emergence of a new variant" in southern France.

It comes after 12 patients tested positive in the same region, but their tests showed "an atypical combination".

The index case had returned from travelling to Cameroon, suggesting to experts that it may have originated in the African country.

https://www.msn.com/en-gb/news/world/co ... hn?ocid=st

[W. Kevin Vicklund]

Lots of chatter about a new French variant on teh Twitters. Here's a brief MSN story:

Covid warning as new variant with '46 mutations' infects 12 in southern France

Scientists have rung the alarm bells over "the emergence of a new variant" in southern France.

It comes after 12 patients tested positive in the same region, but their tests showed "an atypical combination".

The index case had returned from travelling to Cameroon, suggesting to experts that it may have originated in the African country.

https://www.msn.com/en-gb/news/world/co ... hn?ocid=st

Pi for Epiphany?

[Volkonski]

Laurie Garrett
@Laurie_Garrett
·
51m
Both #Israel & #Brazil report "flurona" -- cases of simultaneous infection w/#flu & #COVID19 #Omicron especially in pregnant women. It means 3 lung targets are under viral attack at once: ACE2, neuraminidase & haemagglutinin.
https://independent.co.uk/news/world/mi ... 86357.html

[AndyinPA]

https://www.cnbc.com/amp/2022/01/08/cyp ... delta.html

A researcher in Cyprus has discovered a strain of the coronavirus that combines the delta and omicron variant, Bloomberg News reported on Saturday.

Leondios Kostrikis, professor of biological sciences at the University of Cyprus, called the strain "deltacron," because of its omicron-like genetic signatures within the delta genomes, Bloomberg said.

So far, Kostrikis and his team have found 25 cases of the virus, according to the report. It's still too early to tell whether there are more cases of the strain or what impacts it could have.

"We will see in the future if this strain is more pathological or more contagious or if it will prevail" against the two dominant strains, delta and omicron, Kostrikis said in an interview with Sigma TV Friday. He believes omicron will also overtake deltacron, he added.

[Volkonski]

The New York Times
@nytimes
·
53m
Replying to
@nytimes
In cities hit early by Omicron, Covid deaths have begun to spike, although at a slightly reduced scale compared to previous peaks. But with the extraordinarily high case count, even a proportionally lower death toll could be devastating. http://nyti.ms/34p2eUq

[Volkonski]

The New York Times
@nytimes
·
53m
Hospitals in early-hit cities such as Chicago are seeing more patients with Covid than at any time last year. Some doctors say patients are faring better than in previous waves. But the number needing intensive care or ventilation is approaching levels not seen since last winter.


The New York Times
@nytimes
·
51m
Since vaccines became available, the unvaccinated have been far more likely to be hospitalized with severe Covid-19 than people who have been vaccinated.

Early data from New York City shows that the gap became even wider during the first weeks of the city’s Omicron surge.

[Kriselda Gray]

From ABC News :

Scientists are seeing signals that COVID-19′s alarming omicron wave may have peaked in Britain and is about to do the same in the U.S., at which point cases may start dropping off dramatically.

The reason: The variant has proved so wildly contagious that it may already be running out of people to infect, just a month and a half after it was first detected in South Africa.

...

At the same time, experts warn that much is still uncertain about how the next phase of the pandemic might unfold. The plateauing or ebbing in the two countries is not happening everywhere at the same time or at the same pace. And weeks or months of misery still lie ahead for patients and overwhelmed hospitals even if the drop-off comes to pass.

“There are still a lot of people who will get infected as we descend the slope on the backside,” said Lauren Ancel Meyers, director of the University of Texas COVID-19 Modeling Consortium, which predicts that reported cases will peak within the week.