Genome Testing of SARS-CoV-2

An important tool in tracking the sources of outbreaks

Identifying the source of new COVID-19 infections is an important part of controlling the spread of the disease.  In addition to identifying close contacts of new patients, authorities are using the genome of the virus itself to identify where the infection came from.

All organisms carry their genetic information in the form of a string of nucleotides we can sequence or read. We abbreviate the sequence to the initial letters of each nucleotide; A, G, C, T or U.  The SARS-CoV-2 virus has about 30,000 letters.

Every time the sequence is copied to make new virus copies, there is a chance of a change in one of these letters, which we call a mutation.  Most mutations don’t change how the virus works but they occur at a steady rate which helps us to track the movement of the virus through the population. 

You may know how DNA can be used to identify the father of a child. Just like your genome is most similar to your parents and siblings, molecular geneticists can use the virus genome sequence to construct family trees for the virus. Working back to find common ancestors and linking the virus found in different parts off the world to each other builds a picture of transmission. 

For example, this type of testing has allowed authorities to trace the source of 90% of the Victorian July outbreak to one family who returned from overseas and were placed in hotel quarantine.  This is important information since multiple different common ancestors could indicate multiple breaches of quarantine or infection coming from other sources.

In time, viral genome sequencing may also reveal if some mutations are changing the behaviour of the virus such as how easily it is spread or how severely it affects those who catch it. For now though it is all about ancestry.

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