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Got the cut & paste

The single COVID RNA contains all the virus’ genomic information, similar to human DNA, and also acts as its own messenger, similar to human mRNA. It is then evident that the viral capsid—the spherical part surrounding the RNA in fig. 1—can be correspondingly smaller, and easier to construct when it only has to contain this RNA. COVID RNA also contains the information for an enzyme that will make more COVID RNA (step 3) to accelerate the ability to make viral proteins (step 2) needed to make many more viral capsids. A majority of viruses have an RNA genome because it can be very small, and this feature makes it easier for them to spread.

The virus needs only a few proteins to form the viral capsid, or shell, and it also has the blueprint in its own RNA that enables the invaded human cell to make the viral enzyme reverse transcriptase. This enzyme then makes a DNA version of the viral mRNA (step 4). From this viral DNA the cell’s RNA polymerase (step 1) can make many new copies of the viral mRNA, each of which will be inside a new viral capsid (fig. 2).

A more devious feature is that the virus also contains an integrase, an enzyme that can insert a piece of the new viral DNA somewhere into human DNA (step 5). With HIV (human immunodeficiency virus), this insertion of the viral DNA happens in almost all infected humans. A similar insertion of COVID DNA into human DNA has recently been observed by three science laboratories studying SARS CoV-2. With HIV patients there is no cure after this happens, and they are on antiviral medication for the rest of their life. How frequently COVID DNA becomes inserted into human DNA has not yet been determined.

Survival of the Fittest—By Being Much Less Efficient?

Since Charles Darwin developed the theory of evolution we have had thousands of examples of “survival by the fittest,” which we normally understand to mean the best. Polymerases are enzymes that form polymers of nucleotides to make either DNA or RNA. “Polymer” simply means a molecule with many components. They do this by sliding along a template, the DNA to be copied, and choosing the correct matching nucleotide at that same position in the new DNA or RNA being made. These enzymes are so good that they let the incorrect nucleotide slip in only once in every 20 million steps. Imagine a typist being that good. By comparison the reverse transcriptase for the HIV virus makes one error in every 2,000–4,000 steps, or about 3 million times worse!

Every time an HIV virus’ RNA is duplicated to DNA, an average of 2 mutations occur. When the human RNA polymerase then makes RNA from that new viral DNA (fig.4, step 1), the mutations are passed along, and one or two of the proteins now made from that viral RNA will have a mutation. All of this has been verified many times with HIV, but as yet we do not have such detailed results with the COVID system. But since COVID viral RNA codes for the enzymes reverse transcriptase and integrase (fig. 4) it may well have comparable inefficiency, consistent with the emergence of so many new variants in only one year.

For the virus the clear benefit is that many copies are always being made, and if some have a bad mutation, they will not survive, but most viruses will continue. But in a world with vaccines, if a mutation allows the virus to escape detection by antibodies against an earlier version of the virus, then the new variant virus and its descendant will become the dominant strain and continue. The sloppy virus lives forever!