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SARS-CoV-2: Viral Evolution

Information and resources on SARS-CoV-2 (the virus that causes COVID-19)

SARS-CoV-2 Evolution Explained

Divergence vs Convergence
 
Divergent Evolution

Divergent (homologous) evolution occurs when similar traits (ex. fur in mammals) are shared between different species because they inherited that trait from a shared common ancestor ("homology").

 
Convergent Evolution

Convergent (analogous) evolution occurs when similar traits (ex. bird wings and bat wings) in different species did not arise through a common ancestor, but rather they evolved independently under similar environmental conditions or pressures ("homoplasty").


Intra-Host vs Inter-Host
 
Intra-host Evolution

Intra-host evolution is within individual hosts. These are [often] immunocompromised individuals that become infected with a virus. If they are unable to clear the virus, a prolonged infection can lead to mutations occurring within that individual.

 

Inter-host Evolution

Inter-host evolution is within a host population. Inter-host evolution occurs when multiple variants are circulating within a population at the same time and none are able to dominant and replace the others, but rather there are multiple variants all co-circulating at the same time, overlapping and simultaneously and independently mutating for similar environmental fitness.


Early SARS-CoV-2 Evolution

In the early days of Covid-19, evolution occurred divergently and within hosts.

An immunocompromised person infected with SARS-CoV-2. If they are unable to clear the virus, a prolonged infection can lead to mutations occurring within that individual. These mutated strains of Covid-19 could be shed from this individual person and transmitted to others leading to the development of new variants.

This is how early variants such as Alpha, Beta, and Delta occurred and spread across the globe. It is also believed that the original Omicron variant (BA.1) evolved in a single immunocompromised individual. With past variants, there were clear waves of dominance, where one variant would peak and fall and then be overtaken by a new variant.


Omicron Evolution

Since Omicron, most new variants appear to be resulting from inter-host evolution, where there are multiple variants jockeying for dominance while no single variant takes over, instead there is a swarm, or "soup" of variants.

What is essentially happening is that all of these variants are simultaneously evolving and overlapping, but never replacing each other. Since most of the population has varying levels of immunity (either from vaccination, previous infection, or both), the goal of these new variants is to do two things: 1) increase transmission, and 2) evade immunity.

What we are seeing with the current "soup" of Omicron variants is that each of these variants are finding the same specific mutations independently (convergence), specifically to increase transmission and evade immunity.

SARS-CoV-2 "Family Tree"

SARS-CoV-2 Phylogenetic Tree

As genetic changes to the virus happen over time, the SARS-CoV-2 virus begins to form genetic lineages. Just as a family has a family tree, the SARS-CoV-2 virus can be similarly mapped out. Sometimes branches of that tree have different attributes that change how fast the virus spreads, or the severity of illness it causes, or the effectiveness of treatments against it. Scientists call the viruses with these changes “variants”. They are still SARS-CoV-2, but may act differently.

Source: Raj Rajnarayanan @RajlabN

Omicron Evolution Map

Convergent Evolution in XBB*

Updated: June 17, 2023

Image: Daniele Focosi, MD PhD MSc @dfocosi

SARS-CoV-2 Scaled Radial Evolution

Image: Daniele Focosi, MD PhD MSc @dfocosi