Amino acid changes in SARS-CoV-2. A snapshot from More details

Variants, Lineages, and Strains of Coronavirus

What defines a new strain of a virus?

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

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).

How do strains contribute to the response to vaccines?

If a mutation affects the part of a virus that is used in a vaccine or that the immune system uses to neutralize the virus, then this new variant becomes a strain that can infect people who have previously been vaccinated or previously infected. This is why a new vaccine is needed for the seasonal flu each year. The virus mutates so that the previous vaccine no longer provides an effective immune response to the new strain of the same influenza virus.

It is unknown if SARS-CoV-2 will mutate such that long-lasting immunity will not be achievable. Assuming that one or more vaccines can be developed to the current variants, future mutations could result in the necessity of new vaccines to maintain immunity.

Another way that the term strain is used is when a particular variant of the virus (the virus with a specific set of mutations) becomes the dominant variant in a population. This can relate to functional mutations or mutations that alter immunogenicity, or it can relate to how that variant was spread. For example, if there was a particular “super-spreading” individual that infected many people in a population, the variant in that individual can become the main form in a population even if the variations do not affect function or immunogenicity. In this case, an existing vaccine would work against this dominant variant because the proteins that trigger the immune response would be unaffected.

This dual use of the term strain can be confusing. It can mean the most common variant of a virus in a population, or it can mean a functionally or immunogenetically different version of the virus. Reports in the popular press, and even the scientific literature, will occasionally use the words “strain” and “lineage” as if they mean the same thing. Some press outlets have claimed that there are >1000 “strains” of the SARS-CoV-2 virus, but this is incorrect. There are >1000 lineages, but far fewer strains (likely between 1 and 10, so far in the world). Researchers are working to determine how many medically relevant strains are circulating and what the consequences are for treatment and vaccine development.

Until there is clear evidence supporting functional or immunogenic differences among the variants, it is appropriate to consider all of these lineages of the same virus.

Also of Interest

The Startup

Get smarter at building your thing. Join The Startup’s +792K followers.

Sign up for Top 10 Stories

By The Startup

Get smarter at building your thing. Subscribe to receive The Startup's top 10 most read stories — delivered straight into your inbox, once a week. Take a look.

By signing up, you will create a Medium account if you don’t already have one. Review our Privacy Policy for more information about our privacy practices.

Check your inbox
Medium sent you an email at to complete your subscription.

Nancy R. Gough, PhD

Written by

Ph.D. scientist with a passion for scientific communication and > 20 years editorial experience

The Startup

Get smarter at building your thing. Follow to join The Startup’s +8 million monthly readers & +792K followers.

Nancy R. Gough, PhD

Written by

Ph.D. scientist with a passion for scientific communication and > 20 years editorial experience

The Startup

Get smarter at building your thing. Follow to join The Startup’s +8 million monthly readers & +792K followers.

Medium is an open platform where 170 million readers come to find insightful and dynamic thinking. Here, expert and undiscovered voices alike dive into the heart of any topic and bring new ideas to the surface. Learn more

Follow the writers, publications, and topics that matter to you, and you’ll see them on your homepage and in your inbox. Explore

If you have a story to tell, knowledge to share, or a perspective to offer — welcome home. It’s easy and free to post your thinking on any topic. Write on Medium

Get the Medium app

A button that says 'Download on the App Store', and if clicked it will lead you to the iOS App store
A button that says 'Get it on, Google Play', and if clicked it will lead you to the Google Play store