Immunology simplified

A map of our immune response to viral infection shared by @papaphone2002

I have added (in red) the role of the much-discussed neutralising antibody, thread👇

Our immunity team has so many more players, who cannot be fooled by the virus.

Here’s why

1/5
Please note the diagram only presents an outline, not the whole thing.

Neutralising antibodies form only a tiny fraction of our TOTAL antibody response. Most antibodies are produced AFTER the attack occurs, helping eliminate virus.

(Labs measure Ab’s ALREADY in circulation)

2/
In other words, neutralising antibodies aren’t everything.

And, importantly, a “loss of neutralisation” (‼️🔴alarmist language that lab researchers love to use while describing their work to a clueless public) doesn’t mean “we have lost against the virus”.

3/
The virus has so many other parts that our system recognises.

In fact even after delta arrived, upto 97% of the T cell epitopes haven’t been altered (the mutations affect only about 3%)

Epitopes are parts of the virus that the body picks up as specific “identifying marks”

4/
Specifically, epitopes are ultra short sequences of 4-17 amino acids (basic building blocks of protein).

❗️If antigen is a mango tree, epitopes are the mangoes.

T cells and other parts of our immune system learn to recognise specific epitopes of specific viruses.

5/
Our immune system learns about these epitopes after vaccination (when we introduce harmless components of the virus) or through natural infection or both.

Note: There are 100’s of epitopes that get recognised for each infective agent. (A few are on the RBD of spike protein)

6/
❗️The virus will NEVER be able to change ALL of these epitopes (or even 20% of ‘em) because it will “lose fitness”. In other words, some parts are ESSENTIAL for the virus to work.

(For example, a plane cannot take off if its propeller blades are cut in half by some mutation)

5/
The spike protein itself has 1273 amino acids, and many immovable or unchangable epitopes on it.

Antibodies target these areas too, and help eliminate infection in many ways (not just by neutralisation).

Eg. they flag our infected cells to be killed by immune cells (ADCC)

6/
Ab’s can also tag infected cells to be eliminated by a series of destroyer proteins called “C”or “Compliment system” (C is gun powder)

Ab’s can directly flag the virus by attaching to parts of it, hanging on tight and then inviting our immune cells to come and swallow them.

7/
There are other ways by which antibodies work.

And then there are our CD8 T-cells which come & destroy infected cells, preventing the virus from getting any further.

It is like bombing the building where some real bad thugs are huddled together, so that they don’t get out.

8/
Our CD4 T cells work like choirmasters, coordinating the immune response in a seamless manner, they also boost other players into action.

After the action settles, some of these B and T cells retire and live peacefully forever as memory cells in remote parts of our body.

9/
These normally peace-loving memory cells get activated at the slightest hint of a future infection, losing absolutely no time in recreating the original task force (only 10 times bigger and meaner), thus taking out the offender without breaking a sweat.

10/
And the best part is that our immune system is continuously learning and upgrading its skills, even after the infection or vaccination period is over, so that the next time around, the antibodies stick better and work faster.

This process is called affinity maturation.

11/
Immunology is fascinating and complicated. I have given the highlights above.

Just to show that our systems are well-equipped to handle the virus regardless of alarmist messaging based on lab studies.

12/12
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More from @RajeevJayadevan

11 Dec
Long lived T memory cells one year after COVID-19.

Authors studied CD8 memory cells that persisted after the initial effector response, followed by contraction.

They noted phenotypical differences between memory cells in mild & severe COVID-19.

1/12

nature.com/articles/s4158…
Authors believe that factors such as antigen availability, type of antigen-presenting cells, and cytokine milieu – might influence the type of memory formed.

Note: T cell memory cells are of multiple categories, not all of which are detected in peripheral blood.

2/
Some memory cells live in tissue and others in lymph nodes.

This study looked only at peripheral blood, and hence is not a description of T rm or T cm memory cells.

T rm’s live in tissues and do not move out. They defend tissues (e.g. lungs & mucosa) when an attack occurs.

3/
Read 16 tweets
10 Dec
“Immortal Time Bias” produces exaggerated positive results in observational studies. Thanks @DrToddLee for pointing it out

e.g. Booster studies give reliable results when subjects are randomised to booster or placebo. RCT ensures ~equal comparison.

1/9

academic.oup.com/aje/article/16…
What is immortal time bias?

When a group under observation has a fixed advantage at the outset.

In heart transplantation VS non heart transplantation studies, this bias was first described (those who got the transplant had the opportunity to survive till they got operated)

2/
That is, the transplanted group were the healthier of the lot, they survived longer than those who died while waiting for surgery.

This was projected as an apparent outcome of transplant in some studies.

3/
Read 9 tweets
9 Dec
Large study on boosters in Israel

Summary

>60 age

Risk of death among those who got infected: No difference between 2 or 3 dose groups

Risk of picking up an infection was 12 times lower after booster

Note: this was not a randomised trial

1/10

nejm.org/doi/full/10.10… Image
The study compared the outcomes among 7,58,118 people who got booster with 85,090 who did not.

We do not know if there was a baseline difference in COVID- appropriate behaviour between the 2 groups.

Assuming no such difference, infection risk is reduced 12 fold by booster.

2/
A few calculations based on the table:

Age > 60, non boosted (2 dose)

Infection rate 62 per 100,000 person days
Death rate 2.3
Ratio = 1 : 27

Age >60 (boosted)
Infection rate 5.1 per 100,000 person days
Death rate 0.2
Ratio = 1 : 26

(Ratio = chance of death if infected)

3/ Image
Read 10 tweets
9 Dec
No waning of immunity against severe disease: New York data NEJM

Note the effectiveness is calculated by comparing with unvaccinated group, which is gradually acquiring immunity from natural infection. Hence, there will be a decrease in the difference as time moves forward.

1/n ImageImage
There is a marked difference in hospitalisation rates among vaccinated people compared to unvaccinated.

I have calculated some numbers for three age groups👇

🔹For >65

Unvax Risk of Hospitalisation 1:87 (1:1000 for vax)
Difference is 12 times

See below 👇
🔹For 50-64

Unvax Risk of Hospitalisation 1:186 (1:3636 for vax)
Difference is 20 times

🔹For 18-49

Unvax Risk of Hospitalisation 1:453 (1:9899 for vax)
Difference is 22 times

All calculations based on Pfizer (see table below for others) Image
Read 4 tweets
8 Dec
Tuesday COVID meeting updates this week (been holding these ever since the onset of the pandemic)

#1

In a series of 70 consecutive COVID deaths reported at a large Kerala hospital, 69 were unvaccinated, one had received 1 dose vaccine.

That was 98.6% unvaccinated, May-Sept

1/
This data is powerful evidence that vaccination has made a significant reduction in the severe outcomes of delta.

Remember, these are vaccines based on the old Wuhan strain of the SARS-CoV-2 virus.

Yet they are protective against delta variant.

This is hard evidence.

2/
This is real-world evidence that vaccine protection (against severe disease, mainly cell mediated immunity) kicks in with the first dose itself.

In fact we know from lab studies that T cells arrive by day 10 after the first dose.

Let me explain the immunology.

3/
Read 9 tweets
8 Dec
Discussed a few aspects of vaccination among children in India with @snehamordani @IndiaToday
Link to 24 minute video of the panel discussion 👇

Read 4 tweets

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