Wednesday, March 24, 2021

The Evolution of the SARS-CoV-2 Virus

Updated July 29, 2021

While public health officials and governments around the world are hard-selling us the COVID-19 variant fear porn in an effort to keep us under control, in fact, as you will see in this posting, the original SARS-CoV-2 virus has been evolving over the past year.

From the CDC website, here is a description of the first three SARS-CoV-2 variants that have been detected in the United States and other nations around the world along with the date and location of first detection in the United States:


1.) The B.1.1.7 variant was first detected in the United Kingdom in December 2020 and likely first emerged there in September 2020. Colorado reported the first U.S. case of the B.1.1.7 variant in late December 2020. Since then, B.1.1.7 has been detected in at least 42 jurisdictions. Preliminary data from the United Kingdom suggest that the B.1.1.7 variant spreads more easily and may cause more severe disease than previous variants of SARS-CoV-2.4 


2.) The B.1.351 variant was first detected in the Republic of South Africa in December 2020, and likely first emerged there in October 2020. At least 35 countries, including the United States, have detected COVID-19 cases of infection with the B.1.351 variant. The first detected U.S. cases of infection with the B.1.351 variant occurred in South Carolina and Maryland in late January 2021 and have now been documented in at least 10 jurisdictions. Some data suggest that people previously infected with SARS-CoV-2 may have less immune protection if they are re-infected with the B.1.351 variant.


3.) The P.1 variant was first detected in Japan in travelers from Brazil in January 2021. Minnesota reported the first U.S. case of infection with the P.1 variant in January 2021 and P.1 has now been identified in Oklahoma, Maryland, and Florida.


Here is a graphic showing the variants circulating in the United States and the percentage of cases associated with each:

Now, let's look at additional information about the evolution of the SARS-CoV-2 virus. Let's start by looking at the concept of phylogeny.  According to an article on ThoughtCo, phylogeny attempts to trace the evolutionary history of all life on earth.  More specifically, phylogeny looks at the relationship among organisms as indicated by the use of genetic comparisons.  A phylogeny is represented in a diagram known as a phylogenetic tree with the branches of the tree representing ancestral or descendent lineages, much like a human family tree.  Relatedness in a phylogenic tree is determined by descent from a common ancestor.  Here is a link to a very basic description of phylogeny and how it is used to classify organisms.


With that background, let's look at the phylogeny of the SARS-CoV-2 virus as reported on the Nextstrain website.  Here is a graphic showing the very complex phylogeny of the SARS-CoV-2 virus:

The horizontal lines on this graphic show the genetic relationships between each of the variants and depict how closely related the viruses are to each other with the longer horizontal lines meaning that there are more differences between them.  As you can see, since SARS-CoV-2 first appeared in December 2019, the virus has undergone significant evolution.


Here is a map showing the geographical spread of the evolution of the SARS-CoV-2 virus:

Let's look at a quote from the Nextstrain website regarding these graphics:


"This phylogeny shows evolutionary relationships of SARS-CoV-2 viruses from the ongoing COVID-19 pandemic. Although the genetic relationships among sampled viruses are quite clear, there is considerable uncertainty surrounding estimates of specific transmission dates and in reconstruction of geographic spread. Please be aware that specific inferred geographic transmission patterns and temporal estimates are only a hypothesis.


There are hundreds of thousands of complete SARS-CoV-2 genomes available and this number increases every day. This visualization can only handle ~3000 genomes in a single view for performance and legibility reasons. Because of this we subsample available genome data for these analysis views. Our primary global analysis subsamples to ~600 genomes per continental region with ~400 from the previous 4 months and ~200 from before this. This results in a more equitable global sequence distribution, but hides samples available from regions that are doing lots of sequencing. To mitigate against this, we've set up separate analyses to focus on particular regions. They are available on the "Dataset" dropdown on the left or by clicking on the following links: Africa, Asia, Europe, North America, Oceania and South America.


Site numbering and genome structure uses Wuhan-Hu-1/2019 as reference. The phylogeny is rooted relative to early samples from Wuhan."


Let's close with a quote from an article by Erin Garcia de Jesus from


"Viruses are always changing. When a virus infects a cell, it begins making copies of its genetic instructions. Most viruses don’t have the necessary tools to proofread each string of RNA for mistakes, so the process is error-prone and differences build up over time. 


Coronaviruses like SARS-CoV-2, on the other hand, do have a proofreading enzyme — a rarity for RNA viruses. But that doesn’t mean their genomes don’t have errors. Changes still accumulate, just more slowly than in other RNA viruses such as influenza. “Strains,” “variants” or “lineages” are all terms researchers might use to describe viruses that have identical or closely related strings of RNA. 


But for the general public, a word like “strain” is often interpreted to mean a whole new scourge. “I think the use of the term ‘strain’ does little more than cause panic,” says Jeremy Luban, a virologist at the University of Massachusetts Medical School in Worcester. “It doesn’t really get at what the important issues are.”


A mutation can affect a virus in a number of ways, but only certain kinds of mutations might make the virus more dangerous to people. Perhaps the change shields the virus from the immune system, or makes it resistant to treatments. Mutations could also alter how easily the virus spreads among people or cause shifts in disease severity. 


Luckily, such mutations are rare. Unfortunately, they can be hard to identify."

There have been preliminary studies on the new variants:

1.) P.1 variant - research here which states that "The recent emergence of variants with multiple shared mutations in spike raises concern about convergent evolution to a new phenotype, potentially associated with an increase in transmissibility or propensity for re-infection of individuals."

2.) Notes from a January 21, 2021 meeting of the U.K.'s influential Committee New and Emerging Respiratory Virus Threats Advisory Groups (NERVTAG) quoted modelling papers that have not yet been published.  Minutes of the meeting show this:

Studying viral mutations is a long and complicated process and is well beyond the intellectual capabilities of most of our elected leaders. In order to understand whether a viral mutation is dangerous to humans, animal or human studies are necessary and these studies take time.  Given the hasty response to the current variants suggests that governments are using the appearance of new strains of the SARS-CoV-2 virus to bolster their fear porn-based agendas when, in fact, viruses have mutated for millennia.

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