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Full Version: New variant: omicron
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I think the latest variant is referred to by "omicron" although yesterday morning one article called it "nu".   Potentially more transmissible and with 50 mutations some concern about evading established immunity--although one article this morning implied that the vast majority of hospitalized cases in South Africa are unvaccinated persons.   To me it will be interesting to see if it fizzles or if it truly takes hold and challenges delta's current dominance.   I am also interested if it gives rise to boosters tweaked to this variant.

https://www.cnbc.com/2021/11/26/pfizer-b...st-it.html
WHO's listing of Variants of Concern.  WHO on Omicron.
Omicron is the first VOC since Delta 6 months ago.

Concerns are that it has a number of genetic changes, some of which may increase infectivity, and some of the triggers for immunity are missing.   Apparently there are some COVID tests which detected some of the now-missing markers.  So negatives on those test(s) and positives on other tests can be used to preliminarily diagnose this variant.  (A full genome check is necessary to confirm.)
Read in Newsweek this morning about a South African doctor anecdotally stating that symptoms seem both different and milder than other strains.   Still more to learn . . .
I have been getting very current information on Twitter. Yes, this is weird and dangerous. However, following some well respected people gets you a long way. You can google the names and determine whether they are crackpots or not. 

For instance, the last tweet from Sandra Ciesek was very interesting. Three common (at least common in Germany) PCR tests can detect Omicron. Apparently PCR is used to detect multiple proteins and the different manufacturers may detect different proteins. (What if the mutation evaded detection by the testing infrastructure?) It seems as though the scientists have been using the slow and difficult genetic sequencing and comparing to PCR results so that they can be sure that PCR does indeed detect Omicron well. Note that the wording is difficult, these PCR tests detect Omicron as Covid, it does not differentiate between Delta and Omicron.

Link: https://twitter.com/CiesekSandra/status/...8506034182

I have been following the following (pun intended)
  • Sandra Ciesek (@CiesekSandra)
  • Tom Peakcock (@PeakockFlu)
  • Christian Drosten (@c_drosten)
  • Eric Feigl-Ding (@DrEric-Ding)
  • John Burn-Murdoch (@jburnmurdoch)
John Burn-Murdoch is a data scientist and tries to interpret data. Not being an epidemiologist or virologist, one has to be more careful with conclusions from him. However he posted a simple to explain chart about why the majority of people that get covid are vaccinated in highly vaccinated populations. (We all know why, but this is a useful tool in talking to people that say there is no reason to take the vaccine because it doesn't stop the disease.)

Only Ciesek and Drosten post in German, the rest post in English.

Eric Ding is the most prolific and he referred to the mutation as Nu until the Who named it. He looked up the reports that Omicron is milder and shows that it was cherry picking from something someone wrote. There is no conclusion regarding severity of the disease.


I really hate twitter, but some of the above are following events obsessively so I don't have to.
Here is a link to known Omicron cases. 

https://bnonews.com/index.php/2021/11/omicron-tracker/

I never heard of BNO News before, but they list sources for their cases. Remember this is not comprehensive because lots of places don't have adequate surveillance due the expense of sequencing. So there's not much to conclude except that the variant is not isolated.

Do you suppose anyone in the US is validating our PCR tests to make sure that they can detect Omicron?
If you want to track Omicron, I suggest GISAID
Besides tracking they phylogeny of the variant, you also get to see a 3-d structure of the spike, with the amino acid changes.
More on detection/monitoring from the WHO:
Quote: Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation.

By the way, the Alpha variant (B.1.1.7) that came out of England had the S-gene dropout as well.

Here's a ThermoFisher page on a test that detects S gene dropout. Lots of info at their site - follow their links.

Per this FDA letter (early 2021), it appears that the Linea COVID-19 Assay Kit may also detect the S gene dropout.
If we can assume that the S-Gene dropout means Omnicron, then we are fine. We already know that Beta is not common, so this could be a super efficient way of tracking the new variant.
(11-28-2021, 09:18 AM)Hurlburt88 Wrote: [ -> ]Read in Newsweek this morning about a South African doctor anecdotally stating that symptoms seem both different and milder than other strains.   Still more to learn . . .

The report I heard, from a not very reliable source (i.e. TV doctor), was that the South African doctor's account involved several patients that had been vaccinated with Pfizer a few months ago. If true, the milder symptoms may be result of vaccination, not because virus inherently causes milder symptoms. Also, anecdotal reports are interesting but may not paint accurate picture.
I don't know if it is the man-bites-dog issue of calling attention to unexpected situations, but it seems that most of what I've heard so far of Omicron infections in the news are with vaccinated people. Maybe the vaccinated are more out and about and traveling. So the vaccinated subset of the population is being more exposed.

Israel #1 and #2 were vaccinated (AZ for one; 3x Pfizer for the other). Both had traveled recently. Severity of infection not described.
Israel #3 is a Cardiologist, with 3 Pfizer vaccinations, that got COVID either at a professional meeting in London, or as he traveled back to Israel.
US #1 was vaccinated and recently returned to San Francisco from South Africa.
US #2 was vaccinated and recently returned to Minnesota from NYC.

That is obviously a small set. But it is enough to make me concerned that the reports are true that the vaccination may be less effective against catching this variant. However, all of the cases described were mild for the vaccinated patient, so maybe that's the silver lining.

BUT, it looks like one (unreviewed) study suggests Omicron gets past natural immunity more easily, causing higher reinfection rates:
Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa
Quote:Population-level evidence suggests that the Omicron variant is associated with substantial ability to evade immunity from prior infection. In contrast, there is no population-wide epidemiological evidence of immune escape associated with the Beta or Delta variants. This finding has important implications for public health planning, particularly in countries like South Africa with high rates of immunity from prior infection. Urgent questions remain regarding whether Omicron is also able to evade vaccine-induced immunity and the potential implications of reduced immunity to infection on protection against severe disease and death.

By the way, I thought this was interesting from the article on US #1:
Quote:The suspect sample was confirmed overnight, with stunning speed. Chiu received the sample at 8 p.m. on Tuesday, then ran a very fast molecular test that looks for one of the variant’s mutations for the spike protein, called a spike “gene dropout.” The result, obtained in only two hours, signaled the possible detection of omicron — but it wasn’t conclusive.

Proof was obtained after sequencing of the viral genome with a pocket-sized tool made by Oxford Nanopore Technologies.

The lab was able to confirm the sample was omicron within five hours, and the entire genome was assembled within eight hours, Chiu said.

“So at 4 a.m. last night, we actually had assembled most of the genome, and we were able to conclusively demonstrate that this was, indeed, infection from the omicron variant,” Chiu said.
I think the fact that we are detecting Omicron in almost only vaccinated people in Europe and the US is the result of extreme selection bias. Some countries require full vaccination for entry. If not, being vaccinated makes things easier (by avoiding potential isolation requirements). Furthermore, I suspect that international travelers are far more likely to be vaccinated because they know that travel poses exposure risk.

It still underscores that some of the mutations may constitute "immune escape."
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