Covid Variant Omicron (B.1.1.529)

[Astronuc]

Minnesota health authorities confirmed the 2nd U.S. case of the Omicron variant, in a resident who recently returned from New York City. The man, who was fully vaccinated and has since recovered. The individual had traveled to NY City for a convention Nov. 19-21.

He developed symptoms shortly after returning and tested positive on Nov. 22.

The question would be 'was the individual infected in Minnesota, traveled to NYCity, returned, and then tested positive'? Or was this person exposed upon arrival in NY City and then incubated for three days, or less? Who else has been exposed in the following 10 days?

 

[valenumr]

Follow up: https://www.hawaiinewsnow.com/2021/...t-holds-news-conference-discuss-covid-hawaii/

Individual previously had covid, no travel history. It's been here for a while.

 

[kyphysics]

 

[Astronuc]

Follow up: https://www.hawaiinewsnow.com/2021/...t-holds-news-conference-discuss-covid-hawaii/

Individual previously had covid, no travel history. It's been here for a while.

Axios reported "Hawaii became on Thursday the fifth state to confirm the newly discovered Omicron variant after New York announced five new cases earlier in the day.

In Hawaii, the variant was found in an unvaccinated O'ahu resident with moderate symptoms who had previously been infected with COVID-19, per a state health department statement."

And NY State has confirmed 5 cases of Omicron variant: Two cases were in Queens, one in Brooklyn and a fourth, from a test on Nov. 30, in Suffolk County. The location of the fifth individual was unidentified.

https://www.axios.com/omicron-cases-confirmed-3-us-states-4040d14b-1669-4168-b95a-4c639a5662b6.html

 

[artis]

I personally am not worried about the spread of it as that is already inevitable rather I care to see whether it is a milder form or a worse one. So far it seems everyone who has had it is doing fine. Including the original news from South Africa.

 

[Rive]

twitter

I can't actually guess the actual level of immunized (by any means) people in the population, but I think that at this point it's significant enough that the real deciding factor between the speed of spreading already would be about the success of bypassing that previously built immunities, and not just the raw R0 value.

I wonder if there is any study about 'repeaters' having consistent 'easy' or 'hard' cases (with or without different variants/variants noted)?

 

[kyphysics]

I personally am not worried about the spread of it as that is already inevitable rather I care to see whether it is a milder form or a worse one. So far it seems everyone who has had it is doing fine. Including the original news from South Africa.

The highly infectious Delta wreaked tremendous havoc, so if Omicron is even more transmissible (seems like it from early data and worries about the large number of spike protein mutations), this could make for yet another potentially stressful winter.

While Delta wasn't more virulent/deadly in generating worse health complications than other strains, the sheer impact of higher transmissibility on absolute numbers of people ending up hospitalized and taxing our ICUs across the U.S. was a concern.

Even if Omicron is not more deadly than other strains, if it's more infectious than the already super infectious Delta, and people are getting COVID reinfections with Omicron (from early reports), we could have a similar situation. Just from the sheer number of people getting it - even if it's not more deadly - lots of people could end up hospitalized and straining our systems again. Let's hope not! But, better to over-prepare than under-prepare just in case.

 

[nsaspook]

It will be interesting to see if spreading Omicron infections breaks the current US North vs South case barrier. Delta seems to be in a steady low ebb below a moving north wave. SA was in much the same low case condition before Omicron.

https://www.nytimes.com/interactive/2021/us/covid-cases.html
https://covidestim.org/

 

[artis]

I find this explanation by Dr. Mobeen Syed rather well, what I found interesting in the study is that it seems these Omicron mutations have happened multiple times before and at varying times in the infection.
I do wonder one thing, do we have any estimates or is it possible to estimate how many different working mutations can the S protein for example evolve in total? The reason I ask this is because I would suspect that a protein much like a cell or any other mechanism cannot have infinite amount of possible states in which it can exist and still function.
Do we have any such simulations or are they possible which could tell us for example the possible changes/mutations that a certain protein or other biological entity can undergo and still be functional and how they affect the functionality of it? To rephrase I'm asking is it possible to simulate a virus knowing it's RNA and details without actually waiting for it to undergo the changes it makes with time in real biological organisms as it spreads?

https://www.medrxiv.org/content/10.1101/2021.06.03.21258228v1.full

 

[kyphysics]

Age Group of 0-4 years old in a SA metro seeing huge rise in hospitalizations.
3rd Wave: ~15 hospitalizations vs.
4th Wave: ~110 hospitalizations

Age Group of 5-9 years old
3rd Wave: ~7 hospitalizations vs.
4th Wave ~20 hospitalizations

Age Group of 10-19 years old
3rd Wave: ~10 hospitalizations vs.
4th Wave: ~45 hospitalizations

Age Group of 20-29 years old
3rd Wave: ~20 hospitalizations
4th Wave: ~120 hospitalizations

Look at a reversal as you get higher in age? Is it due to the elderly having a higher vaccination rate maybe? Other factors going on? It's interesting.

 

[jim mcnamara]

Preprint of case studies, plus review of recent new infections.

"Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa"
https://www.medrxiv.org/content/10.1101/2021.11.11.21266068v2.full.pdf

I am not sure about methods and some claims of multi-reinfections. Before I come to a solid position we need a peer reviewed study. More data and reports are going to start appearing soon, so we can get corroboration that way as well.

Bottom line per report:
Omicron is more transmissible and has a higher reinfection rate than previously seem in other variants.

 

[Astronuc]

Omicron is more transmissible and has a higher reinfection rate than previously seem in other variants.

Nevertheless, the surge around the US at the moment seems to be predominantly Delta variant.

New York State has had a second day over 11,000 new positive cases, and nearly 50 fatalities per day for the last three days.

California reported 7,612 new cases and 127 new fatalities today.

Texas reports 2005 new confirmed cases (and another 1006 probable cases), and 74 new fatalities, however, Texas had some days without reporting.

Similarly, in Florida, some days are missing, and they report on a weekly basis. For the week ending Dec 2, Florida reported 10,892 new positive cases (an increase of ~1250 from the previous week), 35 new deaths.

 

[jim mcnamara]

@Astronuc
My quote was from the paper - your examples show a surge, so do theirs. Let's wait until we get better research results. Or at least a peer review. The reason I posted was to head off chicken little posts. - the sky is not falling. I guess I was not clear

 

[nsaspook]

https://www.msn.com/en-us/health/me...common-cold-coronavirus-study-says/ar-AARscA9

The omicron variant is likely to have picked up genetic material from another virus that causes the common cold in humans, according to a new preliminary study, prompting one of its authors to suggest omicron could have greater transmissibility but lower virulence than other variants of the coronavirus.

pre-print
https://osf.io/f7txy/

 

[Evo]

Wow.

• In Norway, a Christmas party turned into an Omicron "super spreader event," with up to 60 possible infections.
• The party on November 26 was organized by renewable energy company Scatec, which also has operations in South Africa.
  
  At least one person who attended the party had recently returned from South Africa, according to multiple reports.
  
  All attendees were fully vaccinated and had tested negative before the event, Reuters said.
  
  Fifty people who attended the party had positive PCR tests for coronavirus, while another ten have tested positive on lateral flow tests, according to the Norwegian state broadcaster NRK.
  
  After sequencing, health authorities have confirmed that 13 of the cases were the Omicron variant, and more are expected to be confirmed, Reuters reported.

https://www.yahoo.com/news/corporate-christmas-party-turned-biggest-132307836.html

 

[Astronuc]

Speaking of spreader events, the gentlemen from Minnesota (fully vaccinated + booster) met up with 30 or so friends at the convention in NY City. The friends came from other locations/states. Now, it appears 15 have tested positive for SARS-Cov-2, but variants are not yet known, so could be Delta or Omicron.

https://www.nytimes.com/2021/12/04/world/omicron-anime-convention-nyc.html
Also reported by WP - https://www.washingtonpost.com/health/2021/12/03/nyc-anime-covid-omicron/

Questions remain as to who was the initial infection in the group, and did they bring it to NY City, or contract in NY City. Folks traveled on 18 or 19 Nov, convention started 19 Nov and ended 21 Nov, and the Minnesota man presented symptoms and tested positive on 22 Nov, which could mean as little as 3 days or less for incubation. An related attendee has tested positive for SARS-Cov-2, but doesn't know if his sample was tested for variant type.

From NY Times article:

Dr. Ted Long, who oversees the city’s contact tracing program, said that he was aware of five positive cases so far among New York City residents who attended the anime convention. But he said it was not yet known if those people had been infected by Omicron or Delta, nor was the convention known to be the site where they had gotten sick.

Meanwhile, on 2 Dec, the governor and NY City mayor have indicated 5 Omicron cases: 1 in NY City (Manhattan?), 1 in Brookly, 2 in Queens, and 1 in Suffolk County. The last was a 67-year old woman who had recently returned from southern Africa, and she had mild symptoms.

Prof. Anne von Gottberg from S. Africa has indicated a previous infection of SARS-Cov-2 does not provide much protection from infection by the Omicron variant.

A now a twist - The new COVID-19 variant had cases in Europe prior to the South African announcement, and is said to have at least 50 mutations.
https://www.insideedition.com/omicr...ns-and-started-in-europe-before-south-african

The new variant of the coronavirus, called Omicron, was first identified in Europe, according to Dutch health authorities.

The dates on the cases discovered by the RIVM health institute — from November 19 and November 23 — showed that the variant was already spreading by the time the first cases were found from passengers that flew in from South Africa.

 

[valenumr]

Speaking of spreader events, the gentlemen from Minnesota (fully vaccinated + booster) met up with 30 or so friends at the convention in NY City. The friends came from other locations/states. Now, it appears 15 have tested positive for SARS-Cov-2, but variants are not yet known, so could be Delta or Omicron.

https://www.nytimes.com/2021/12/04/world/omicron-anime-convention-nyc.html
Also reported by WP - https://www.washingtonpost.com/health/2021/12/03/nyc-anime-covid-omicron/

Questions remain as to who was the initial infection in the group, and did they bring it to NY City, or contract in NY City. Folks traveled on 18 or 19 Nov, convention started 19 Nov and ended 21 Nov, and the Minnesota man presented symptoms and tested positive on 22 Nov, which could mean as little as 3 days or less for incubation. An related attendee has tested positive for SARS-Cov-2, but doesn't know if his sample was tested for variant type.

From NY Times article:Meanwhile, on 2 Dec, the governor and NY City mayor have indicated 5 Omicron cases: 1 in NY City (Manhattan?), 1 in Brookly, 2 in Queens, and 1 in Suffolk County. The last was a 67-year old woman who had recently returned from southern Africa, and she had mild symptoms.

Prof. Anne von Gottberg from S. Africa has indicated a previous infection of SARS-Cov-2 does not provide much protection from infection by the Omicron variant.

A now a twist - The new COVID-19 variant had cases in Europe prior to the South African announcement, and is said to have at least 50 mutations.
https://www.insideedition.com/omicr...ns-and-started-in-europe-before-south-african

My impression at this point is that it has been going around for a while, but we only now now what to look for. I'm not at all aware how the variant monitoring works from country to country though. It's just that the current data seems to indicate that current detections abroad don't fit the timeline that the SA case in question is the index case.

 

[kyphysics]

re: spread

At this point, there are too many stories of new cases popping up here and there for me to keep track of. Lots more cases just recently reported within the U.S.

I pretty much assume it's everywhere now (or soon to be). Once it was found on both coasts (NY and CA) and then in the Mid-West, I figured it's just a matter of time before it's in every state.

 

[Twigg]

Age Group of 0-4 years old in a SA metro seeing huge rise in hospitalizations.
3rd Wave: ~15 hospitalizations vs.
4th Wave: ~110 hospitalizations

Age Group of 5-9 years old
3rd Wave: ~7 hospitalizations vs.
4th Wave ~20 hospitalizations

Age Group of 10-19 years old
3rd Wave: ~10 hospitalizations vs.
4th Wave: ~45 hospitalizations

Age Group of 20-29 years old
3rd Wave: ~20 hospitalizations
4th Wave: ~120 hospitalizations

Look at a reversal as you get higher in age? Is it due to the elderly having a higher vaccination rate maybe? Other factors going on? It's interesting.

Just want to point out that these numbers aren't normalized in any way and are just raw numbers of patients admitted. Can't infer anything yet. To make any claim about the effect on different age groups, we'd need these numbers normalized by how many people were exposed per age group. The numbers we see being admitted could just reflect a university outbreak. As you say, it also doesn't indicate anything about vaccination rates in different age groups. This sucks though :/ Stay safe everyone!

 

[jim mcnamara]

One of the problems with similar US data like the above in @Twigg 's post is that the US with similar datasets on average does genomic analysis on less than ~1% of positive tested samples. So we can say little accurately about Omicron variant spread until we do some serious testing.

I do not know why this is true. Data Source: Daniel Webster MD PhD, Optum NYC

 

[kyphysics]

 

[pinball1970]

https://www.msn.com/en-us/health/me...common-cold-coronavirus-study-says/ar-AARscA9

pre-print
https://osf.io/f7txy/

That's good news? Spreads very quickly out runs more dangerous variants and is less likely to put you in hospital?

 

[nsaspook]

That's good news? Spreads very quickly out runs more dangerous variants and is less likely to put you in hospital?

Good is relative. This early data could have been a lot worse.
https://www.samrc.ac.za/news/tshwane-district-omicron-variant-patient-profile-early-features

It is essential to recognize that the patient information presented here only represents the first two weeks of the Omicron wave in Tshwane. The clinical profile of admitted patients could change significantly over the next two weeks, by which time we can draw conclusions about the severity of disease with greater precision.

A snapshot of 42 patients in the ward on 2 December 2021 reveals that 29 (70%) are not oxygen dependent. These patients are saturating well on room air and do not present with any respiratory symptoms. These are the patients that we would call ‘incidental COVID admissions’, having had another medical or surgical reason for admission. Thirteen (13) patients are dependent on supplemental oxygen of which nine (21%) have a diagnosis of COVID-19 pneumonia based on a combination of symptoms, clinical signs, CXR and inflammatory markers. All are being prescribed steroids as the mainstay of therapy. The remaining 4 patients are on oxygen for other medical reasons (2 previously on home oxygen, 1 in heart failure and 1 with a confirmed diagnosis of Pneumocystis Pneumonia).
This is a picture that has not been seen in previous waves. In the beginning of all three previous waves and throughout the course of these waves, there has always only been a sprinkling of patients on room air in the COVID ward and these patients have usually been in the recovery phase waiting for the resolution of a co-morbidity prior to discharge. The COVID ward was recognizable by the majority of patients being on some form of oxygen supplementation with the incessant sound of high flow nasal oxygen machines, or beeping ventilator alarms.

There are only 4 patients in high care and one in the ICU. The numbers of patients in high care on double oxygen, High Flow Nasal Oxygen or non-invasive ventilation (NIV) were noticeably higher in previous waves. This is anecdotal but confirmed by numerous clinicians who have previously worked in the COVID wards in the hospital complex.

Of 38 adults in the COVID wards on 2 December 2021, 6 were vaccinated, 24 were unvaccinated and 8 had unknown vaccination status. Of 9 patients with COVID pneumonia 8 are unvaccinated, 1 is a child. Only a single patient on oxygen was fully vaccinated but the reason for the oxygen was Chronic Obstructive Pulmonary Disease.

 

[atyy]

The early South Africa cases suggest the Omicron cases are milder than those in previous waves, but that does not mean Omicron is milder for the unvaccinated. Some estimates are that about 80% of South Africa's population has been previously infected, and about 24% of the population vaccinated. So although previous infection or vaccination will protect much less against infection, they are expected to still largely protect against severe illness, which is consistent with the early data out of South Africa.

Even if previous infection or double vaccination largely protect against severe illness, rapid transmission amongst can lead to a surge in hospitalizations among those who have not been infected or vaccinated, and those who remain vulnerable despite vaccination.

So it is important to get eligible people vaccinated and boosted.

 

[pinball1970]

https://assets.publishing.service.g...t_data/file/1038404/Technical_Briefing_30.pdf

The link above reports 32 Omicron cases on Friday 3rd, 4th Dec Guardian reported 160 cases and Sky 5th Dec yesterday reported 246 so it is living up to its reputation for high transmission.

Summary from Nature below 2nd of Dec on a few of the topics covered.

https://www.nature.com/articles/d41586-021-03614-z

One thing I was not aware of was waste water sampling in England, page 35-36 in the technical briefing.

 

[artis]

One thing I was not aware of was waste water sampling in England, page 35-36 in the technical briefing.

I thought this was common knowledge , it's been going on where I live too and for quite some time, in fact pretty much all this year and started in 2020,

One thing you can do is determine the approximate hospital admission count about 2 weeks ahead of time given how much "Covid piss" is sloshed down the pipes and then divide that concentration by the number of people/age groups in the city from which it was collected
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8421077/

Recently we had a third wave of delta and the labs predicted it would end in about 2 weeks based on the decreasing wastewater levels and "lo and behold" it did just that, now the numbers are back to pre wave levels for winter conditions

There are even studies coming out of how this excreted Covid virus and it's parts affect marine life
https://pubmed.ncbi.nlm.nih.gov/34216962/

 

[Sagittarius A-Star]

Latest data, looking good:

 

[Astronuc]

Forbes reports, "California was the first state to report a case of omicron Wednesday, and others have subsequently been found in Colorado, Connecticut, Hawaii, Louisiana, Maryland, Massachusetts, Minnesota, Missouri, Nebraska, New Jersey, New York, Pennsylvania, Utah, Washington and Wisconsin." The state of Georgia confirmed its first omicron case in an Atlanta resident who had recently traveled from South Africa, according to the newspaper Atlanta Journal-Constitution. The Washington Post, NY Times and other news sources also published the same information.
https://www.forbes.com/sites/teakvetenadze/2021/12/05/omicron-detected-in-these-16-states/

The Washington Post reports that the Minnesota man contracted the Omicron variant after returning from NY City convention on 22 Nov. had received the Johnson and Johnson (JNJ) vaccine and Moderna booster. The booster was in early November. He was feeling tired/fatigue and otherwise mild symptoms, but he got a rapid test when a friend (one of the 15 friends?) tested positive.

New York state saw a drop in cases as of yesterday, but new cases are still fairly high compared to a month ago. As 5 Dec, New York state reports Total COVID-19 Patients 3,285 Hospitalized with 621 in ICU.
https://coronavirus.health.ny.gov/daily-hospitalization-summary

In our area we see hospitalizations actually falling during the last 4 days after a recent peak, even though positive tests have increased. We expect the Delta variant to be dominant still, but there is no indication of the number of cases of break-through infections. Omicron has not yet been detected, but perhaps not every specimen is tested for type.

 

[kyphysics]

Give it one more week, Astronuc, and we may see the curve rise dramatically for Omicron in the U.S.

If memory serves me correct, we tend to lag Europe by about two weeks (eta: or, was it two months) for each wave (maybe with a few exceptions). As Europe goes, the U.S. often goes ...two weeks later.

Jim Bianco has some interesting charts/data on vax/booster rates:

 

[Astronuc]

USA Today reported, "Studies have shown that people in treatment for cancer, immunosuppressed after an organ transplant or weakened by HIV can remain infected with COVID-19 for months, while the Coronavirus accumulates changes that make it harder to wipe out.

No "patient zero" has been found for omicron or any other variant, but scientists think they likely evolved within a single immunocompromised person."

The headline stated "Where did the Coronavirus omicron variant come from? Scientists suggest it evolved in one person." However, it's clear that the person is unidentified.

Did Omicron incubate and evolve from the original Wuhan strain, or perhaps an alpha variant? Independent of SARS-CoV-2 501Y.V2 (B.1.351)?
https://www.nature.com/articles/s41591-021-01285-x

I was trying to understand its evolution based on the first figure here -
https://en.wikipedia.org/wiki/SARS-CoV-2_Omicron_variant

 

[Sagittarius A-Star]

Sandra Ciesek reports via twitter:

Sandra Ciesek
@CiesekSandra
our first dates for Neutralization of Omicron versus Delta is done: 2x Biontech, 2x Moderna, 1xAZ / 1x Biontech after 6 months 0% neutralization with Omicron, also 3x Biontech 3 months after booster only 25% NT versus 95% with Delta. Up to 37 times the reduction in Delta vs. Omicron

Source:


via Google translate:
https://translate.google.com/?hl=de...ache Reduktion Delta vs. Omicron&op=translate

 

[Astronuc]

Here's another twist. The Omicron variant of SARS-Cov-2 apparently shares genetic code with a common cold coronavirus!

Nference, a biomedical company, released data revealing that omicron shares similar genetic material to HCoV-229E, a human Coronavirus that causes common cold symptoms. Researchers posit that omicron evolved from an individual who was "co-infected" with Sars-CoV-2 and HCoV-229E.

https://thehill.com/homenews/corona...-be-more-transmissible-due-to-sharing-genetic

https://www.cdc.gov/coronavirus/general-information.html
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7204879/

 

[artis]

It will be interesting to see whether these "genetic adventures" of Covid as it changes more and more away from it's original form make it less severe. From current news I get that although it's different spike mutations make it more effective at evading vaccine and pre infection antibodies the actual infection outcomes seem somewhat promising, and by promising I mean not worse than delta perhaps lighter

 

[Sagittarius A-Star]

BionTech held a press conference about vaccine against Omicron:

 

[Rive]

The Omicron variant of SARS-Cov-2 apparently shares genetic code with a common cold coronavirus!

First shift after the slow drift?

We may have lucked out this time, as apparently the key parts are still close enough to the original to leave cross-immunity in play.