12.11 Conclusion

In this module, we visualized evolutionary relationships between coronavirus strains using Nextstrain and by constructing our own phylogenies in R.

• We first explored Nextstrain, a browser that summarizes historical sequencing data from SARS-CoV-2 strains around the world.
  
  
• We observed independent recurrent mutations in pathogenically relevant regions of the SARS-CoV-2 genome, suggesting that such mutations confer a fitness benefit and are under positive selection.
  
  
• Using the sequences of other coronavirus strains from GenBank, we placed SARS-CoV-2 onto a neighbor joining phylogeny of closely related viruses.
  • We used bootstrapping to provide confidence estimates for branches on our neighbor joining tree.

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