Section 1: the first sequence

It is early in the SARS-CoV-2 pandemic. You are working at a hospital in London. The hospital has just received its first patient, a swab has been taken and amplicon sequencing performed to generate a genome. You have been sent a FASTA file containing the genome sequence.

Click here to download the FASTA file

Question: What is the ID number of the patient?

Nextclade

You can use Nextclade to align the sequence to the reference genome and identify differences from the reference.

Use Nextclade to have a look at this genome. Change the panel at the right hand side to show the Nucleotide sequence.

Question: What mutations does this genome have compared to the reference?

Question: Which nucleic acid mutation do you think is most likely to affect the phenotype of the virus?

Question: In words, describe the amino acid change that has occurred here (gene, position, and two amino acids - in full words)

You might find Wikipedia’s table of amino acids helpful.