13  Did SARS-CoV-2 Change During the COVID-19 Pandemic?

As the pandemic raged around the world (Figure 13.1), increasing numbers of people became infected.

Figure 13.1: Early COVID-19 global spread

More infections meant more virus, which implies more viral replication and individual virus particles. This in turn implies more opportunities for mistakes during reproduction: more opportunities for mutation to occur. There was both a larger population of virus, and a larger effective population of the virus.

Any of the resulting sequence variants might have an important effect, maybe changing the clinical profile of the virus - its virulence, its residence time, ease of shedding, or some other characteristic. The variants might also provide a way to track transmission geographically, and over time.

Important

We need you to identify and interpret SARS-CoV-2 sequence variants, and identify and interpret any changes that have occurred!

13.1 Your challenge

We need you to:

1. Use the Oxford Nanopore (ONT) reads from the Sutch SARS-CoV-2 isolate ERR4164769
2. Carry out quality control on the reads
3. Call sequence variants between the Dutch isolate and your Wuhan 1 assembly
4. Report on the SNPs you find
5. Map the ONT reads to your Wuhan 1 assembly and visualise them

CautionHints

• Be sure to visualise read quality with FastQC and note any differences from the Wuhan 1 isolate reads
• Remember - ONT reads are single-ended
• When considering SNPs
  • How many are there?
  • Do any lie within feature boundaries?
  • What are the biological implications of changes to that feature’s product?
• You will need to increase the maximum size of bam chunks setting in JBrowse to visualise ONT reads
• How do the ONT reads look different, visually, from Illumina data?

ImportantWhen you have finished…

Please complete the formative quiz on MyPlace to earn your bioinformatics wings!

• BM425 link
• BM932 link