12.4 Tracking SARS-CoV-2 with phylogenetics

Go to the Nextstrain browser to explore the phylogeny of SARS-CoV-2 sequences.

• Note that you can use the PLAY button on the left sidebar to watch its progression over time.
• Hovering over a specific node tells you the ID of the virus that was sequenced.
• It also tells you the divergence, which is the number of mutations it carries with respect to the root of the tree.

Fig. 3. SARS-CoV-2 phylogeny from Nextstrain (source).

One example of the public health value of this phylogenetic analysis was the observation that the second reported case of novel coronavirus in Washington state (WA2) was genetically similar to the first reported case (WA1) six weeks earlier, suggesting ongoing community transmission. Click the tweet expand the full thread.

(kevin_purcell?) Please feel free to try (click the menu Embed Tweet here) and let me know if it does not work.

— Yihui Xie ((xieyihui?)) July 28, 2016

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