Evolution of SARS-CoV-2, Course of Pandemic and Precautions

Omicron is the variant with the best S1-S2 cleavage ability by the human protease furin.

The spike protein of the Omicron variant is in the open conformation. The spike protein of the original virus had almost completely closed and loose conformation. In the original virus, the S1-S2 regions on the spike are mixed and loosely connected to each other.

Due to mutations, S1 subunits and neighboring S2 regions are more tightly packed together in Omicron.

This is why Omicron's spike protein is stronger, more stable and capable of better ACE II affinity than previous variants.

 In the evolutionary history of SARS-CoV-2, we have seen more infectious variants arise.

Mutations such as D614G, N501Y have made the spike protein more open. This may result in more RBD regions being exposed and this may mean that the virus has better receptor binding and tends to be more contagious.

More than 1 million variants of SARS-CoV-2 have emerged. However, since most of these contain mutations in regions different from the spike protein, they did not make a difference in terms of contagion and immune avoidance.

However, some mutations occurred on the spike protein and caused the character of the virus to change. The character of the virus may change as a result of mutations on the spike. More contagious, more immune-escaping, or more virulent variants may emerge.

Before Omicron, the number of different variants identified as having Spike mutations exceeded 3000.

In the pre-Omicron era, the number of RBD variants was doubling on average every 89 days.

In some periods of the pandemic, the rate of emergence of new variants slowed down, and increased in some periods. In particular, many new variants have emerged, descended from infectious variants such as Alpha, Gamma, Delta.

According to researches; 6 new variants appear for every 1 million cases.

Variant spawn speed increased after Omicron. In January-February 2022, countries were detecting more than 1 million cases per day.

Especially after BA.2, the rate of emergence of spike RBD variants increased a lot. The number of variants detected in April 2022 is more than 15.

If the spread continues, the number of RBD variants could double every 89 days compared to the previous one.

BA.2, BA.4 and BA.5 are spreading very fast in the world. Considering that 6 new variants emerge in every 1 million cases; SARS-CoV-2 is spinning a spider web around the world.

And if we don't stop the spread, the risk of a more virulent and more contagious variant is too great.

 

The world must focus on stopping the spread of SARS-CoV-2. We have stopped all measures due to vaccines, but vaccines do not stop the spread of the virus. 

To stop the virus, we must review our methods of fighting the virus. 

Our SARS-CoV-2 measures should include strict quarantines and the use of FFP2 masks.

 

Abdulkadir YILMAZ

Ankara University Faculty of Veterinary Medicine

Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain | Nature Communications

Evolution of the SARS-CoV-2 spike protein in the human host | Nature Communications

Rapid evolution of SARS-CoV-2 challenges human defenses | Scientific Reports (nature.com)