Are there really six strains of SARS-CoV-2, the virus that causes COVID-19?

Today headlines declared that there are six different strains of SARS-CoV-2 circulating the globe. This seemed to imply that the virus causing COVID-19 had significantly mutated into multiple different forms. But the data presented in the article these press releases were based upon gives a very different story.

First, a strain is defined as a genetic variant or subtype of a microorganism (e.g., virus or bacterium or fungus). As an example, a “flu strain” is a unique biological form of the influenza or “flu” virus. These flu strains are characterized by different activities, such as the ability to infect different types of cells in different animals. Often this is associated with the ability to escape immunity, so that the new flu strain can infect a person immune to a prior strain. This is called antigenic drift and is the result of significant alterations in surface proteins of the virus.

While it is now known that different strains come from changes in viral genetic material, strains were initially defined solely on the functional and immunological differences. Thus, there is general agreement that the definition of a strain requires some unique difference in the virus function or immune characteristics. Small numbers of genetic changes in a virus without defined, functional significance doesn’t define a new strain.

The article in question, published in Frontiers in Microbiology, performed an analysis of 48,635 coronavirus genomes and identified six “strains” based solely on genetic sequence of the SARS-CoV-2 virus. It calls these changes “mutations” even though there is no evidence of mutated function for these changes. Most people would call these variations “polymorphism” unless a specific function was associated with the change, so the terminology they use is wrong on both strain and mutation.

Most remarkably, they show very few changes (7.23) in the SARS-CoV-2 viral genomes, with most being the substitution of a single nucleotide (one letter of the genetic code). In fact, only four total changes in the genetic code define the three most common “strains” the investigators identify. One of these changes is the now infamous D614G substitution (aspartic acid for glycine at position 614 in the spike protein) for which functional activities have been ascribed but not definitively documented. 

Data showing an average of only 7 genetic changes in SARS-CoV-2, with little variation across the world.

In fact, the investigators find the lack of genetic variability “encouraging” since influenza has a variability rate that is more than double the 7.23 for SARS-CoV-2. Federico Giorgi, a researcher and coordinator of the study, indicated “this means that the treatments we are developing, including a vaccine, might be effective against all the virus “strains“. Despite this, he suggested that these few genetic changes lead to “characteristics that probably facilitate the spread of the virus” without any supporting data.

The major difference between the “strains” defined by these authors is that they predominate in different parts of the world. This is likely due to a founder effect, which means they got to a particular continent first and populated it. The fact that viruses with various differing genetic substitutions predominate in different parts of the world supports this, since a virus with better infectivity should have taken over all parts of the globe.

Data showing distribution of SARS-CoV-2 around the world. Note that no virus with a particular set of genetic changes is dominant everywhere in the world.

Bottom line, there is only one type of COVID-19 virus, and drugs or vaccines developed against it should work anywhere in the world.

Published by jbakerjrblog

Immunologist, former Army MD, former head of allergy and clinical immunology at University of Michigan, vaccine developer and opinionated guy.

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