Variants, Lineages, and Strains of Coronavirus

All viruses mutate. How fast depends on several factors. Viruses with an RNA genome tend to mutate faster than viruses with a DNA genome. This is because RNA viruses have less ability to fix errors when their genetic material is copied to make virus particles inside infected cells.

All viruses mutate. How fast depends on several factors. Viruses with an RNA genome tend to mutate faster than viruses with a DNA genome. This is because RNA viruses have less ability to fix errors when their genetic material is copied to make virus particles inside infected cells. So every time a virus replicates, there is the chance of a mutation occurring.

Most mutations do not change the encoded viral protein. These are considered “silent” mutations. Others do change the amino acid sequence of the encoded viral protein. However, most mutations have no functional consequence for the virus. The amino acid change does not make the virus pathogenic or not pathogenic (able to cause disease), more or less transmissible (contagious), or more or less disease causing (virulent). So, these mutations are functionally inert. Some mutations may be functionally inert to the virus but alter the ability of the infected host to recognize and eliminate the virus. These do not alter the function of the viral protein, but they do change the immunogenicity of the viral protein, which can impact virulence and transmissibility.

Mutations can result in a new “lineage” of the virus. This is not the same as a new strain. Tracking these lineages can be very useful for determining how a virus spread through communities or populations (Figure 1). For a cool interactive that shows how the various lineages of SARS-CoV-2, which causes COVID-19, spread throughout the globe visit nextstrain.org/ncov.

Figure 1. Tracking the spread of the coronavirus SARS-CoV-2 throughout the world using viral genomic data. From https://nextstrain.org/ncov . Read more

Mutations that alter any of the following can lead to a new strain:

• pathogenicity
• virulence
• immunogenicity.

Not all changes that affect immunogenicity of the viral protein affect the function of the viral protein, and not all changes that alter viral protein function affect immunogenicity (Figure 2).

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