Anyone who has visited the Galapagos will remember seeing the Flightless Cormorants. These big sea birds have evolved to have very small, non-functioning wings. This type of mutation in most other parts of the world would have resulted in birds with a decreased ability to forage because of their lack of ability to fly, and so, they would never have survived. But in the Galapagos, this mutation allows these birds to dive into and swim in the ocean far better than the large-winged cormorants and therefore they have a much better ability to feed and thrive. They have become the dominant species of this type of bird specifically on these islands.
It may seem counterintuitive, but the emergence of 7-8 new COVID-19 variants in the US combined with the variants identified in the UK, South Africa and Brazil has resulted in what could actually be called “good news”.
Why would I say that? These variants all seem to more infective, more transmissible, and possibly (not well documented) may cause more severe disease.
The reason that I am encouraged is because these variants ALL seem to have mutations in the very same spot in the protein chain of the Spike protein.
So, a little refresh. The spike protein is a chain of about 1,200 amino acids. This long chain of “beads” results in a protein of a particular shape with one part of it buried in the lipid envelope of the virus, the bulk of it extending into the surrounding medium and a binding site at the very tip of the protein that allows the virus to attach to target cells.
As we have talked about quite a bit before, mutations in the virus constantly occur. Most of the mutations result in a virus that is no longer able to replicate, or release from cells or infect other cells, or have less ability to bind to receptors on cell surface. These variants, like the Flightless Cormorant simply die out; we never see them.
Some of the mutations result in changes that have little or no effect on the virus replication or infection and are carried along during replication and can accumulate over time.
However, once in a while a mutation allows the virus to have an evolutionary advantage over other strains and begins to show up and take over in the population. This is more often than not a change that allows the virus to bind better to human cells.
These virus mutations that allow the virus to bind better to other target cells allows those viruses to “jump to the front of the line” when multiple viruses are attempting to infect other people, and they become dominant.
Now, what is particularly interesting is that all of these new variants which are showing a greater ability to be transmitted from one human to another have a similar mutation. Looking at the 1,200 amino acids in the chain of the Spike protein, the amino acid at position 677, normally a GLUTAMINE has been changed to a different amino acid, sometimes HISTIDINE, sometimes PROLINE.
If you remember, the RNA “codon” is a string of 3 RNA bases which act as an instruction to the cell on which amino acid to add at each point in the synthesis of a protein. Interestingly, each of the changes in each of these emerging variants is a single base change in the RNA codon for those amino acids. So, GLUTAMINE has a codon of “CAG”. Change the “G” to a “C” (“GAC”) and you get the instruction to put a HISTIDINE in location #677 rather than a GLUTAMINE.
Likewise Take the GLUTAMINE “CAG” and change the “A” to a “C” (“CCG”) and you tell the cell to replace the GLUTAMINE with a PROLINE.
If what we are now seeing is that a change at position #677 is one that allows a virus to bind better to human cells, that makes the job of developing new vaccines much, much easier.
It seems that mutations at other positions simply don’t emerge as significant new strains.
Now we might predict that most if not all newly emerging virus variants with a better binding site at the end of their Spike proteins do so by switching the amino acid in position #677, we can simply alter the mRNA or the other “vectors” that are used for immunization and include that in new vaccines.
The good news is that it may appear that variants of COVID-19 that have an evolutionary advantage are restricted to a small easily identifiable change in the Spike protein.