A year and six months later, or the Covid-19 pandemic in the second year: Mutations or Variants?
The choice of words is interesting. Using the word variant we think of another version of the same thing, like a red rose that suddenly blooms a pink rose! Aha, a variant! We might even find that the cause of this change in color is the consequence of a viral infection with the rose bush. In some respects, the use of the word, variant, is correct in noting it is different from the “standard”. This viewpoint also clouds our understanding of the virus being a dynamic global entity that has never been a “standard” one type but always included variations and diversities of characteristics. This is one of the reasons why it is so difficult to test for its positivity, and how negative results can mask the presence of the virus which has already changed into new forms.
If we use the word mutation or mutant there is an understanding that nucleic acids are being deleted, inserted, or rearranged in a dynamic genetic process according to the vertical lineage of Mendelian genetics. However, the virus (mass noun) is not one “variant” but are configurations of many mutating viral components of virus and sub-viral particles. They are a quasispecies. Domingo and Perales writing in the journal Virology 11 May 2009 noted that “virologists now understand that virus populations are not a single member with a defined nucleic acid sequence. Rather they are dynamic distributions of non-identical but related members called a quasispecies…The consequence is that most viral infections are initiated not by a single viron but by populations of particles”.
Because of this complexity we tend to simplify our expression to a more comfortable level of using the word, variant. Metaphorically, virus is like a bag of m&m candies of different colors. When the pandemic was first detected, or its genome was first described, it was like, okay, the virus are all the green m&ms. And when we tested for the presence (or prevalence) of the green ones, we got a positive result. If an individual had only a few green ones, we might have gotten a negative result. But the person’s bag of m&ms had a lot of other colors not detected at that time because we were only testing for the green ones!
As of this writing (June 24, 2021) there are reports about the mutation of the delta variant into a more contagious and lethal form, named “delta plus”. Scientific and medical institutions are limited in their ability to monitor the rapid rate of mutation on a global scale (see, covid.cdc.gov). Even the early genetic history of the SARS-CoV-2 now has become political and further obfuscates our understanding of viral dynamics (see, “Covid sequences erased from Int’l database shed light on initial spread” by Tzvi Joffre in The Jerusalem Post 24 June 2021). Looking for a genetic “lineage” does not fit the gestalt of the virus which are: collections of closely related viral genomes subjected to a continuous process of genetic variation, competition among the variants generated, and selection of the most fit distributions in a given environment.” (Domingo et al. 2012). Thus the viral properties of the whole cannot be directly inferred from the properties of the “individuals” and the most distinctive feature is the emphasis placed on the occurrence of mutations during replications (R. Andino, Virology, May 2015). These mutations are not limited to genetic codes in the cell’s nucleus (vertical transmission of DNA from parent to child). An important process, especially from an ecosystems approach, is horizontal gene transfer which is the movement of genetic material between unicellular and multicellular organisms. This is a continual process. It is not static, fixed or a standard individual. As is all life forms, the entire set of mobile genetic elements in a genome (a mobilome requires a systems approach that emphasizes networks and cybernetic activity. We need to accept and understand how humans are part of the ecological relationship with microbial life, and how all life is part of all life.
John Marcucci, Ph.D.