Coronavirus Activity

What virus is responsible for the COVID-19 pandemic?

The COVID-19 disease is caused by a virus called SARS-CoV-2. It belongs to a family of viruses known as coronaviruses.
This virus is a tiny sphere about 100 nm in diameter with protrusions on its surface called spike proteins.

Figure 1: 3D medical animation showing the structure of a coronavirus (

Inside the SARS-CoV-2 virus is a long strand of RNA. The RNA genome contains about 30,000 bases.
A team of researchers at the University of Dundee have developed a software called Jalview that helps scientists view and analyse this genomic data.

The genome of the COVID-19 virus

CLICK this link to open Jalview and view the SARS-CoV-2 genome in an adjacent web browser tab

The genome is made up of 4 different bases with letters A, C, G or T.
In the Jalview viewer that has opened in an adjacent tab, place the mouse cursor on a letter and look at the status bar (lower left-hand corner of the alignment window), it will tell you the name of the nucleotide bases and its number.
Scroll to the end of the genome using the mouse wheel or the scroll bar (on the right-hand side of the alignment window).
Q. What is the last letter?
Click on the last letter C in the sequence, look at the status bar (in the lower left-hand corner of the alignment window).
Q. How many bases are in the SARS-CoV-2 virus genome?

Figure 2: The SARS-CoV-2 Coronavirus genome


The genome of the COVID-19 virus

There are about 80 spike proteins on the surface of the virus and they are about 20 nm long. The virus uses these spike proteins to enter the human cell as shown in the model below.

Scientists are very interested in these spike proteins as changes in the spike protein molecules can affect how easily human's are infected by the virus, whether a person will catch COVID-19 a second time, as well as the long term effectiveness of vaccines.
In December 2020 a new variant of SARS-CoV-2 virus called B.1.1.7 was detected in the UK, it appears to be linked with an increase in transmission (1).

The Spike Protein Sequence

CLICK this link to launch Jalview and compare the original SARS-CoV-2 spike protein sequence with that of the B.1.1.7 variant

In the Jalview viewer, the SARS-CoV-2 spike protein sequence is above the B.1.1.7 variant protein sequence.
Compare the amino acid letters in each sequence.
Q. Can you spot the differences between the sequences?
The 'Conservation' row below the sequences may help.

Figure 3: The original SARS-Cov-2 spike protein sequence (above) aligned with the B.1.1.7 variant (below)


The Spike Protein 3D Structure

The 3D structure of the spike protein can be viewed below, the position of the B.1.1.7 variant mutations are coloured red and the location of the amino acid deletions are coloured green. These small changes affect the shape of the spike protein, which in turn change their properties.