Question

1. If this insertion is within the coding region of a viral protein, will this insertion result in a frameshift for the rest of the protein? How do you know?

2. The insertion mutation is in a gene that codes for a protein on the surface of the virus, probably a glycoprotein. Assume that this protein is involved in attachment to a host cell. How might a change in a protein involved in attachment change the potential hosts for the virus?

3. How long does it typically take a person's adaptive immune system to make antibodies in a primary response to an antigen? Is it likely that a person would have memory B cells that recognize a new surface protein on the virus? Why or why not?

4. Why is a population unlikely to have herd immunity to a virus that has a new protein on its surface?

Answer 1

1. If this insertion is within the coding region of a viral protein, will this insertion result in a frameshift for the rest of the protein? How do you know?

• Insertion is of single nucleotide: Then definitly this will cause the change in the coding region reading frame and protein.

Example: 5' ATT TGC CGA GGC AAT TTA 3' is the coding sequence, and it is followed by insersion of a A in the codon TGC, then the sequence will be:

5' ATT TGA CCG AGG CAA TTT A 3'

Comparing the reading frame of both the sequnces, we can see only first codon will code for the same amino acid, while rest of the codon sequence has been changed, leading to the complete change in amino acid sequence.as comapre to 5' ATT TGC CGA GGC AAT TTA 3'

• Insertion is of two nucleotide: This also will cause the change in the reading frame of codons and amino acid. Taking the same example,now where AG is inserted in the codon TGC.

Now the sequence will be :

5' ATT TAG  GCC GAG GCA ATT TA 3'

As we can see here reading frame is changed again as compare to original sequence.

So the amino acid are encoded by this seqnece will be different from amino acid encoded by 5' ATT TGC CGA GGC AAT TTA 3' , there is complete change in amino acid sequence.

• Insertion is of three nucleotide: their could be change in the sequnece but not whole frame will shif, there is only one or two codon change rest of the codons in coding region will remain the same.

5' ATT TCA AGC CGA GGC AAT TTA 3'

• The new sequence have TCA and AGC, that are coding only two different amino acid from rest of coding region as compare to 5' ATT TGC CGA GGC AAT TTA 3'

2. The insertion mutation is in a gene that codes for a protein on the surface of the virus, probably a glycoprotein. Assume that this protein is involved in attachment to a host cell. How might a change in a protein involved in attachment change the potential hosts for the virus?

Now assuming that the insertion mutation is of only one or two nucleotide, then this will lead to the change in the whole amino acid sequence of the gycoprotein. There would be no attachment of the virus to the host cell surface, as it will not be able to recognise the host receptor protein.

If the insertional mutation is of three nucleotide then whole sequence of the viral gycoprotein will be same bu there will only one to two amino acid difference, so this change might be bearable by the virus and still it will be able to recognise the receptor.

3. How long does it typically take a person's adaptive immune system to make antibodies in a primary response to an antigen? Is it likely that a person would have memory B cells that recognize a new surface protein on the virus? Why or why not?

Primary immune response generally takes 5-7 days to make antibodies. But once antibodies are made against an antigen, the memory for that antigen is created. Antibodies have a half life, and it will remain in blood after 15 days immune response. Whereas memory B cells for the same antigen will remain in body for 10-15 years and kill same foreign antigens robustly and quickly if infection occurs for second time. But same memory cell will not be able to recognise the new antigen. For the new antigen the body will go through the same process where it would take 5-7 days to make plasma and memory B cell for new antigen. As memory cell act against only the previusly encounter antigen only.

4. Why is a population unlikely to have herd immunity to a virus that has a new protein on its surface?

Herd immunity is achieved when whole population is resistant to any bacteria or virus. For example now we all are resistant to Polio. As polio virus has been eradicated from earth in 1994. But initially we do not acquire herd immunity for a bacteria or virus because they evolve much faster than humans this is the reason that we don't have a vaccine against malaria.

Talking about Covid 19 which is a new virus on earth, it's surface antigens are also new and as for now no vaccine has been designed for it but some previously worked vaccines can act on it and save us from this disease but these vaccines do not provide us herd immunity.