Section 3: Nextstrain

You’ve decided to look at what is happening globally using the NextStrain website. You can find a tree based on this stage of the early pandemic here.

Spend some time exploring the tree, and the options available on Nextstrain. You can:

Dive into the tree
Colour by different options
Experiment with different layout types
Use clock mode to see how the date of genomes corresponds to the number of mutations they have from the original virus as it spilled over into humans and estimate the clock rate
In fact this tree has been pre-processed with a molecular clock approach, to estimate dates of the internal nodes so you can switch to “Time mode”. However for these exercises we recommend primarily using the “divergence” mode, as “time” in Nextstrain makes guesses to resolve polytomies, which can be misleading.

Use the filtering function to find the sequence Australia/VIC295/2020 and zoom in on its context. You may want to toggle the filter on and off with the eye icon to see the context of the sequence.

Question: What is the closest relative on the tree of this sequence?

Question: Give an example of a mutation we can be confident happened in Australia. Is it synonymous or non-synonymous?

Question: What mutations occurred on the branch leading to these two sequences?

Question: From where do you think this clade of the virus was introduced into Australia? Can we be certain?

Question: Do you think this person acquired the virus from the person who was infected with the closest relative? Why/ why not?

One reason you’ve come to Nextstrain is because you want to understand whether the mutation you’ve seen in your patient, S:D614G has occurred in other patients. To look into this, colour the tree by genotype at the S:614 position.

Question: According to the time tree, at what sort of date did this mutation first occur?

Question:

According to the tree, is S:D614G homoplasic?