There is minimal cross over for T-Cell Epitopes and the Omicron SARS-CoV-2 Virus.

[NNadir]

This the general tenor of this preprint, which is subject to review:

Minimal cross-over between mutations associated with Omicron variant of SARS-CoV-2 and CD8+ T cell epitopes identified in COVID-19 convalescent individuals

An epitope is a short peptide present in T-Cells, which acts to bind to infectious agents. T-cells are the active cellular component of the immune response.

From the text giving the significance, which is what non-scientists actually care about:

The newly identified Omicron variant of concern contains more mutations than any of the previous variants described to date. In addition, many of the mutations associated with the Omicron variant are found in areas that are likely bound by neutralizing antibodies, suggesting that the first line of immunological defense against COVID-19 may be compromised. However, both natural infection and vaccination develop T-cell based responses, in addition to antibodies. This study examined if the parts of the virus, or epitopes, targeted by the CD8+ T-cell response in thirty individuals who recovered from COVID-19 in 2020 were mutated in the Omicron variant. Only one of 52 epitopes identified in this population contained an amino acid that was mutated in Omicron. These data suggest that the T-cell immune response in previously infected, and most likely vaccinated individuals, should still be effective against Omicron.

Generally in the popular media, and indeed much of the scientific media, the big concern is about the neutralizing antibodies, which are known to be weaker for omicron.

This result however suggests that the immune response in vaccinated people is not totally disabled by the mutations in the omicron variant, and it may account for why vaccinated people, while testing positive, may have relatively mild disease.

My wife and I both experienced illness over the holidays, more severe for my wife than for me, and we believe we may have found a place that can test us if we get up real early in the morning: It has been very difficult to find testing availability in New Jersey over the last few days.

None of us have experienced symptoms that would compel us even to go to a doctor, we just don't feel all that good, are tired, headache prone, and have digestive symptoms. I'm pretty much fully recovered.

There are a few reports at variance with this one, but a search on Google scholar using the search terms (t-cell epitopes omicron covid) suggest that the consensus, from the titles and abstracts I've scanned, that this paper's general conclusion holds.

Both Pfizer and Moderna are rapidly developing RNA vaccines to address the omicron S-sequences, and since the infrastructure for the production of lipid particles is already in place, I would expect them to be widely available in the Spring.

Hang in there; don't get depressed.

Happy New Year!!!! Be well, be safe, and have a rewarding New Year!

[MLAA]

1. Thank you for the article and your commentary. I appreciate your posts.

[NNadir]

4. You're very welcome. n/t.

[stopdiggin]

6. +1. very informative.

and bringing us stuff that nobody else (currently) is. So - big thanks!

[Haggard Celine]

2. I think I've had it over the holidays as well.

It never was all that bad except for some breathing problems I had several days ago. I got some OTC drugs to deal with the symptoms and most of the breathing problems went away. I haven't gotten tested yet either. I tried to schedule an appointment to be tested today, but I couldn't find an appointment that was less than 40 miles away. I'll see if I can find an appointment close by on Monday. I'm pretty sure it would've been bad without the vaccine.

[Busterscruggs]

3. It looks like

Our presidents strong leadership and determination have overcome this horrific plague. We would still be struggling under trump

[stopdiggin]

5. well, they've certainly been more proactive

and taken the pandemic much more seriously. But (while appreciating the plug for Biden and the administration) - were still quite some ways away from having 'overcome' this virus/pandemic.

[Busterscruggs]

7. Oh I know

But in the balance of life on earth, our president has vastly outdone anything that Trump was willing to do about it

[stopdiggin]

8. no argument -(nt)-

[ismnotwasm]

9. Had an exposure on the 24th of December

Family dinner. Four adults, two kids. My SIL felt like crap the next day, fever, chills and body aches, stuffy nose and loss of taste, mostly—went and got a cheap rapid Covid test from his work. Positive. He checked two more times, both negative. Went to the ED at the hospital I work at—definitely positive. My daughter became sick one day after he did, with headaches, body aches and nausea with vomiting. She has MS and is immunocompromised, so her neurologist ordered monoclonal antibodies.

My SIL is pretty sure he got it from his work.

I have no symptoms, so I go to work for a couple of days My husband informs me, on my third 12 hour shift, while driving me to work, during lots of snow, that he is getting a cold. Told my work, of course— I’m a nurse— they sent me home.

Well, we are both positive for Covid, finally got the results on New Year’s Eve. Getting tested with a bit of a trial. Anyway my husband, who also has MS, is mildly sick, although that term is relative, I have some body aches and tiredness. I’ll find out Monday when I can go back to work.

Thank God for vaccination. Omicron is fantastically contagious. We are all vaccinated and boosted. My daughter and SIL are already much better.

So if I had to have it, I’m glad it turned out this way.

[orleans]

12. glad to hear your daughter and son in law are much better

i'm sorry you and your husband tested positive. hopefully you'll both feel better very soon

[ismnotwasm]

22. Thank you!

[EarnestPutz]

10. Thanks for the pep talk and bit of good news. I'm glad you and your wife were.....

....not too ill and have recovered well. Hanging in there.

[SergeStorms]

11. Is it possible...

that Omicron, because it's so virulent, will have burned itself out by the time the vaccine companies have perfected a new vaccine, tested it, had it approved, and it was distributed throughout the U.S.?

I just wonder if they're going through all of this for nothing. We could be well into another variant by the time they catch up to Omicron.

[live love laugh]

15. Wonder the same thing. nt

[Hugin]

19. Valid point.

I have to wonder, though. Since the Omicron variant has become the dominant strain at an incredible rate, if it's peculiarities won't become a permanent fixture of the majority of future high-profile 'ronas. So, targeting those idiosyncrasies might be useful in the long term.

I say this, of course. As a complete layman.

[herding cats]

13. I wish you fast healing and good health.

Our immune systems are complex and amazing.

My 3 year old grand daughter who I just kept this past week tested positive. She showed symptomatic while I had her, it scared me to death for her, but she's doing great now just 3 days later.

I'm up. Triple vaxxed. Wish me luck.

[littlemissmartypants]

14. Thank you. ❤

[Raftergirl]

16. Study out of South Africa has similar findings.

“The study from the University of Cape Town’s Institute of Infectious Disease and Molecular Medicine looked at patients who had recovered from COVID or been vaccinated with shots from Pfizer Inc. and partner BioNTech SE or Johnson & Johnson. They found that 70% to 80% of the T cell responses they assessed held up against Omicron.”


“Another study found booster shots increased the production of T cells in the face of an Omicron infection. Giving J&J’s vaccine to people who had previously received a messenger RNA shot yielded better results, though a third dose of Pfizer and BioNTech’s immunization also led to higher levels of cellular immunity and neutralizing antibodies after one month, according to findings from Beth Israel Deaconess Medical Center.”


https://fortune.com/2021/12/30/t-cells-omicron-covid-dutch-south-african-study/

[Sgent]

17. Wouldn't this mean

that you would be more likely to get it and symptoms initially since T cells take 3-5 days to activate?

[Raftergirl]

18. Yes.

It’s why vaccinated and previously infected can get Omicron and have symptoms for a few days, before B and T cells are activated and case resolves.

The same thing happens with cold virus we get. We get sick for a few days and then it resolves as our B and T cells recognize the antigen and activate our immune system. We have cross immunity from previous cold viruses.

[NNadir]

20. You would not be more likely to get it; you'd have the same probability as everyone else.

But yes, you could get it, test positive and would be more likely to recover quickly with minimal symptoms.

[Raftergirl]

21. True, but with the previous

variants the antibodies are much more effective, so if you were exposed the antibodies would protect one from getting the virus. This is why there are many more breakthrough cases with Omicron than Delta.