Origins & Phylogenetics
Delta Variant
Since COVID-19 first emerged in 2020, several variants have evolved. Most of these variants were common for a relatively short period of time and have since become extinct due to being outcompeted by other variants.
The Delta variant was first reported in late 2020 and became widespread by 2021. This variant differed from previous variants in its ability to spread quickly, infecting people who had been previously infected by other strains or had been fully vaccinated. It was also associated with some of the most serious symptoms. Mutations on the gene coding for the spike protein allowed this variant to go undetected by host antibody defense mechanisms. The rise of this variant is an example of a host-pathogen arms race, where the pathogen evolved and emerged as a result of defense mechanisms of the host.
Host Pathogen Arms Race
As hosts in human populations are exposed to a particular pathogen, the adaptive immune system begins to produce antibodies that provide long-term immunity to that particular virus. As a result, viruses that harbor mutations that give them a slight edge against the host’s adaptive immunity replicate in greater numbers compared to viruses that don’t have these mutations, ultimately leading to the emergence of new variants (i.e. natural selection!). As these new variants emerge, hosts in the population gain immunity to these new variants, and the process repeats itself – sometimes indefinitely (hence, the name “arms race”).
In the case of the Delta variant, there were 10 mutations on the spike gene that differentiate it from prior variant strains. These mutations were on the spike protein gene and many increased the virus’s capacity for evading antibodies and other defense mechanisms acquired from prior viral exposure (or vaccine response). One specific such mutation was the L452R mutation. “L452R” is a specific notation that is sometimes used to describe mutations. The 452 means that the 452nd amino acid in the spike protein was changed. The L indicates that the original amino acid at that position was a leucine (standard 1-letter abbreviation = L). The R indicates that the amino acid at that position in variant strains was now an arginine (standard 1-letter abbreviation = R). This switch, from a leucine to an arginine, is a relatively simple genetic mutation that involves a single nucleotide substitution. However, this single change resulted in a modified shape for the viral spike protein. This allowed it to be more effective at binding to the host cell’s ACE2 receptor, thus improving its ability to infect host cells.
Omicron Variant
The Omicron variant was first reported in November 2021, near the peak of Delta variant infections. Omicron contained 37 novel mutations in the gene coding for the spike protein. These mutations resulted in increased transmissibility and have allowed the virus to evade previously established immune responses. As a result, people who had been previously infected with another variant or had been fully vaccinated could still contract Omicron.
Evolutionary Trade-Offs
Airborne respiratory viruses with fast reproduction rates, like SARS-CoV-2, sometimes evolve traits that simultaneously increase their transmissibility, but decrease their virulence (i.e. a trade-off). However, these trade-offs can be maintained when the reproductive benefit of being more transmissible outweighs the cost of being less virulent. In the case of Omicron, the tendency to infect upper airway tissues instead of the lungs is a clear example of a transmissibility-violence trade-off. The virulence of this variant is lower because it is no longer infecting vital organ tissues in the same way, but its transmissibility is higher because more replication occurs in the upper airways where it can readily spread. There are a couple of mechanisms that underlie this trade-off, such as the way the virus enters the cell and the way it interacts with the immune system.
Zoonotic spillover
A zoonotic spillover is when a pathogen that typically infects a specific animal species “jumps” to a different host species. Before the new virus can spread throughout the new host species, there are typically many generations of selection for traits that allow the virus to effectively infect this new host.
Phylogenetics
SARS-CoV-2 viruses are classified into different variants based on their genetic features. Differences between these variants can also help paint a picture regarding how the virus has evolved over time. In order to analyze and depict this, a phylogenetic tree can be used. Variants that are more genetically similar will share a recent common ancestor on the tree, whereas less genetically similar will share a more distant common ancestor. These trees allow us to visually depict the evolutionary journey of a species, over time
The evolutionary history of SARS-CoV-2 is well characterized. The Alpha and Gamma variants were widespread in 2020. The most recent ancestor between these variants is referred to as 20B. Since Alpha and Gamma are genetically very similar, this supports the notion that the last common ancestor between these two straits occurred rather recently.
The Delta variant was dominant for much of 2021 before being overtaken by Omicron in late 2021 into early 2022. The common ancestor of Delta and Omicron is referred to as 20A. Since Omicron and Delta are more dissimilar, we can hypothesize that these strains share a more distant common ancestor.