Thread by @RajeevJayadevan

The rise of variants in India, 2021. Monthly genomic analysis of multiple districts in Kerala.

Over 5 months, the B.1.617 has had a steep growth, now standing tall at ~60% of genomes.

B.1.1.7 rose quickly in February, but is slowly being replaced by B.1.617.

Thread 👇
1/15

I have manually modified the graphs to accommodate the latest numbers to put them all in one picture. The bar on the right end shows a high prevalence of variants (approx %).

The bars on the left (each representing one month of 2021) are smaller.

2/15

In the beginning of 2021, there were very few variants; the bars are almost flat. Then came the rise of B.1.1.7 (UK), and the B.1.617(India) in April.

But now the “India variant” B.1.617 is fast-replacing all other viruses in circulation, accounting for ~60% of genomes.

3/15

The B.1.617.2 (which has lost the E484Q mutation from the so-called “double mutant”), is now fast-growing in many countries, also in UK.

See my tweet from 2 days ago about the latest findings on B.1.617.2. Will attach it at the end of this thread.

4/15

While the rise can seem scary, one must remember that B.1.617 has no extra powers to damage our health. Its hospitalisation rate is the same as the “old virus”. (so far) It has also been effectively stopped by existing vaccines.

The chief problem is, it is faster spreading.
3/15

When a virus spreads faster it does two things:

1. Affects more people in the same timeframe

2. When more people fall sick at the same time, healthcare systems get overwhelmed

When healthcare systems are under strain, mortality rates go up. We have seen that elsewhere.

4/n

One concern about B.1.617.2 is whether it will evade vaccination protection. There is no clear evidence that it will happen. Theoretically in lab neutralisation studies we can see, as in the case of other variants, there’s slight reduction in “power of the serum” against it.
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The “reduction in neutralising power” itself is relatively small for the B.1.617 at this time. Besides, vaccine protection is multipronged and our T cells (the heavyweights of our immune system) are expected to take care of most variants.

Will explain what this means: 👇

6/15

Vaccines are expected to protect on two levels.

First, they stop the virus from entering our body, and then they stop our organs from being damaged as a result of the dysregulated excessive immune response that occurs in some people.

Both are different entities. 👇

7/15

The first process is like closing our gates so that a thief cannot enter our premises. However a smart thief (variant) might still jump over the gate and get into the premises.

The second part is stopping the thief from breaking into our house and inflicting harm on us.

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All vaccines are considered equally good at the 2nd part. i.e. Even if the thief gets past the gate, our house is still secure, and the thief can’t break in. In other words, even if the virus enters our body, our vital organs are safe. For this, T cells are the main players.
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T cells have an extraordinary ability (more than antibodies) to remember and attack more and multiple parts of the virus, called epitopes.

Even the most advanced variant is unable to change ALL its epitopes, therefore they cannot fully escape detection from our T cells.

10/15

Can the virus add more mutations endlessly so that it can escape our T cells?

Unlikely. Why?

Remember that every mutation puts the virus at risk for its own survival because it may damage its own mechanisms in doing so.

11/15

Many experts in this field believe that the repertoire of mutations for this virus is this limited.

In other words, this virus might not really have an endless number of tricks (super-clever mutations like E484K) up its sleeve - that can help it escape more from T cells.

12/15

It is worth remembering that the predecessor of this virus, that is the SARS virus of 2003, disappeared from earth after about two years, most likely because of such deleterious mutations that threatened its own survival.

13/15

To conclude, as of now there is NO direct evidence that these variants can:

1) cause more damage to our body than the past virus or 2) have become smart enough to evade our T cells.

The fact that vaccines prevent hospitalisation is proof of protection by T cells.

14/15

These graphs were provided to me by @vinodscaria our brilliant genomic scientist and I appreciate the work of all his colleagues and the whole team at genescov2.genomes.in

15/15

Vaccine efficacy data against B.1.617.2 is just coming in. Two doses are good. Note that some vaccines take longer to build full adaptive immunity. These are early data thanks to @PHE_uk

https://twitter.com/RajeevJayadevan/status/1396298515358253058

On variants and vaccines

https://twitter.com/rajeevjayadevan/status/1396763017321189378

C. Maya of The Hindu reports on variants in Kerala
thehindu.com/news/national/…

How saturation of healthcare systems can complicate things. Thanks @vinodscaria

nature.com/articles/s4146…