Question

Probably this is very trivial but I am self-learning bioinformatics and I don't know who to ask for this kind of stuff. Also, apparently it is really hard to find information on general topics like this.

I am learning how to use BLAST. I tried to use the sequence of the COVID-19 delta variant spike protein. I used BLASTP and I obtain as results a lot of proteins (all classified as surface glycoprotein [Severe acute respiratory syndrome coronavirus 2]) that vary just for a single aminoacid. The majority of these changes is I to V or viceversa.

What does it mean? Are these all variants of the protein? Are these all sequences with mistakes? And why does it entail only the interchange between I and V?

Answer 1

The variations in the COVID-19 delta variant spike protein sequence obtained using BLAST are genetic variations or mutations. The interchange between I and V is common due to similar properties of these amino acids. Monitoring these variations helps understand the virus and develop treatments and vaccines.

Step-by-step explanation:

When using BLAST to compare the sequence of the COVID-19 delta variant spike protein, you obtained multiple proteins classified as surface glycoprotein [Severe acute respiratory syndrome coronavirus 2] that vary by a single amino acid, often interchanging I and V. These changes indicate genetic variations or mutations in the spike protein sequence. It is not necessarily an indication of mistakes, but rather natural variations in the virus.

The interchange between I and V is common because these amino acids have similar properties. They are both non-polar, hydrophobic amino acids. Therefore, a mutation that changes one to the other may not significantly affect the structure or function of the protein.

These variations in the spike protein can lead to different attributes of the virus, such as its speed and severity. It is important to monitor these variations to understand their impact on the virus and develop appropriate treatments and vaccines.

The interchange between isoleucine and valine is a common mutation because they are chemically similar, both being nonpolar amino acids with similar sizes. These kinds of mutations can potentially affect how the virus is recognized by the immune system and might influence vaccine effectiveness, which is why RNA vaccines like Pfizer and Moderna are updated to combat new variants.