In the viral genomes, nucleotide changes occur much more frequently than in the genomes of living organisms. In the case of SARS-CoV-2, the most commonly reported infections are currently caused by four variants: Alpha, Beta, Gamma, and Delta. These variants, due to mutations in their genome, can spread faster, make the disease more severe or bypass the antibodies produced after vaccination.
How is SARS-CoV-2 built?
SARS-CoV-2 is a circular-shaped virion. Its genome is up to 30,000 nucleotides long. The structure of SARS-CoV-2 is characterized by the presence of distinct protrusions, so-called spikes, which are responsible for attaching to the host cells. The most significant mutations which facilitate the infection process, occur in the spike protein.
This variant was detected in September 2020 in Great Britain. The most common mutation in this strain is the N501Y mutation.
It is characterized by a doubled transmission and a potentially increased risk of more serious symptoms of infection, also in younger age groups.
Visualization of the genome of the alpha variant with marked mutations in the genome:
Discovered in December 2020 in southern Africa. The most common mutations of this strain are the N501Y, K417N and E484K mutations.
It is characterized by doubled transmission and effectiveness of infection, also in younger age groups.
Discovered in Japan by tourists from Brazil in January this year. The most common mutations of this strain are the N501Y, K417T and E484K mutations.
Discovered in India in December 2020. The most common mutation in this strain is the L452R mutation. It is characterized by increased transmission.
How to interpret the names of the coronavirus mutation?
During the constant replication of viruses, errors known as mutations often develop. The most significant and popular changes in the SARS-CoV-2 genome are listed below:
- Spike N501Y – it is a replacement of asparagine (N) with tyrosine (Y) in the 501st amino acid position of the spike, which leads to a change in the structure of this protein and thus a more efficient way for the virus to enter the cell.
- Spike E484K- it is a change of glutamic acid (E) to lysine (K) at the 484th amino acid position in the spike protein.
- Spike L452R – this is a change of leucine (L) to arginine (R) at the 452nd amino acid position in the spike protein.
- Spike K417T – this is a change of lysine (K) to threonine (T) at the 417th amino acid position in the spike protein.
- Spike K417N- it is a change of lysine (K) to asparagine (N) at the 417th amino acid position in the spike protein.
If the mutation occurs within the PCR primer binding site, we can get a false negative result. Therefore, PCR tests must include the detection of several genes, and PCR primers are constantly updated based on the sequencing results.
The most frequently used PCR tests in Poland are 3-gene tests. At genXone SA, PCR reactions are carried out in the direction of the presence of 4 SARS-CoV-2 genes. Additionally, 8 mutations are detected for the initial identification of the virus variant.