Today’s news is filled with reports about the Omicron variant of SARS-CoV-2 virus and how contagious it is.  It follows a number of other recent mutations.  Omicron was detected in Africa, where successive waves of SARS-CoV-2  have resulted in prevalence of past infection higher than 80% in some regions despite greatly increased vaccine supplies.  

The first four variants of concern were discovered in settings with high infection pressure before vaccines were available. The Alpha variant of concern was detected in the U.K., Beta in South Africa, Gamma in Brazil and Delta in India during the second half of 2020, but Delta was not designated as a variant of concern until May 2021.

Delta has infectivity around three-fold greater than the other variants, which were more infectious than the Wuhan strain and by July 2021 had attained global dominance. By contrast, the Omicron variant was first brought to the attention by an outbreak among adults (those younger than 30 years), in the South African province of Gauteng, a setting of high infection-acquired immunity following a third Delta wave but low vaccine coverage in this age group. Omicron was declared a variant of concern on the basis of an unprecedented number of mutations, almost three-fold greater than Delta.  

As for previous variants of concern, disease severity can be anticipated to be greatest in infection-naïve (never having or been exposed to the disease), unvaccinated people, with substantial preservation of protection against severe disease in the vaccinated. Much remains to be learned about the evolution of SARS-CoV-2; if it follows the pattern seen with the 2009 H1N1 influenza virus, capacity for immune escape from vaccine immunity will become more important as population immunity increases.

Viruses

Viruses may be the most bizarre of all life forms,  although they are not truly living. They are however a form of life and consist of mere short pieces of infectious deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) wrapped in a simple protective coat.  

The famous immunologist Sir Peter Medawar termed the virus "as a piece of bad news wrapped up in protein."   Of course, there is more than just the structure  (a virion) to consider, there is an outer coat called the capsid.  

Capsids come in various sizes and shapes, each characteristic of the virus family to which it belongs. They are built up of protein subunits called capsomeres and it is the arrangement of these around the central genetic material that determines the shape of the virion.  

Most viruses are too small to be seen under a light microscope as they are about 100 to 500 times smaller than bacteria, varying in size from 20 to 300 nanometers in diameter (one nanometer is a thousand millionth of a meter).  Inside the virus capsid is its genetic material, or genome, which is either DNA or RNA depending on the type of virus. The genome contains the virus's genes, which carry the code for making new viruses, and transmits these inherited characteristics to the next generation.  Viruses usually have between four and 200 genes.

Omicron

When Omicron took off in southern Africa in November, scientists were taken by surprise by its genetic makeup.  Whereas earlier variants had differed from the original Wuhan version of the coronavirus by a dozen or two mutations, Omicron had 53 — a shockingly large jump in viral evolution.  Thirty mutations occur in the gene for the spike protein. (The spike protein that studs Omicron’s surface allows it to latch on to cells.)  

In a study posted recently, an international team of scientists further deepened the mystery. They found that 13 of those mutations were rarely, if ever, found in other coronaviruses, suggesting they should have been harmful to Omicron. Instead, acting in concert, these mutations appear to be key to some of Omicron’s most essential functions.

Mutations

Mutations are a regular part of the coronavirus’s existence. Every time a virus replicates inside a cell, there is a small chance that the cell will create a flawed copy of its genes. Many of these mutations would make new viruses defective and unable to complete with other viruses.  

But a mutation can also improve a virus. It could make the virus stick more tightly to cells, for example, or make it replicate faster.  

According to a recent article in the New York Times, viruses that inherit a beneficial mutation may outcompete others. Over most of 2020, scientists found that different lineages of the coronavirus around the world gradually picked up a handful of mutations. The evolutionary process was slow and steady, until the end of the year.  

In December 2020, British researchers were jolted to discover the new variant Alpha mentioned above, that carried 23 mutations not found in the original coronavirus isolated in Wuhan a year before. The Delta variant had 20 distinctive mutations, and it became dominant over the past summer.

Final Thoughts

According to the Centers for Disease Control, Omicron now accounts for more than 99.5% of new infections in the United States.  The nation reported as many as 800,000 new cases a day in mid January, more than three times as many as at any previous point in pandemic.  Omicron has a short incubation of roughly three days. Other variants are sure to follow.

Max Sherman is a medical writer and pharmacist retired from the medical device industry.  His new book “Science Snippets” is available from Amazon and other book sellers. It contains a number of previously published columns.  He can be reached by email at  maxsherman339@gmail.com.