| title | authors | authorLinks | affiliations | date | dataset | abstract |
|---|---|---|---|---|---|---|
Exploring the narrative functionality using the ongoing mumps epidemic in North America |
James Hadfield |
Fred Hutch, Seattle, USA |
August 2018 |
This content is here to test the potential of the nextstrain (auspice) narrative functionality. It uses the Publicly available North American mumps dataset [here](https://www.nextstrain.org/mumps/na) to explore what's possible using narratives. |
We can control which panels are displayed, for instance choosing to show only the map.
Since we control what's displayed, we can change visualisation features such as colour, subset the data using filters and time slices, and even turn on looping animation.
Here we've returned to the map and begun slicing time.
Different tree layouts are possible, this one shows the temporal divergence vs. inferred substitutions to see the presence of a constant clock signal.
By copying the text from twitter's "embed tweet" feature, we can render tweets in the narrative.
Harvard mumps outbreak, 2016: because vaccines aren't 100% effective. Efficacy of mumps vaccine for 1 dose is 78%, for 2 doses is 88%. Lots of people in close contact with less hygienic habits can lead to an outbreak of 40 students with mumps https://t.co/w3F5a27FLk
— Anke Jaanen (@AnkeJaanen) August 28, 2018
Here we have coloured the tree according to a single mutation (residue 22 in the SH gene) where there are two variants present in this dataset -- yellow tips have a Methionine (M) at this position, while aqua nodes indicate Isoleucine (I).
Here we have coloured the tree according to a single mutation (residue 22 in the SH gene) where there are two variants present in this dataset -- yellow tips have a Methionine (M) at this position, while aqua nodes indicate Isoleucine (I).
In addition, we've subsetted the data to isolates collected from British Columbia. You can see that all of the isolates with M come from BC!
We can pick multiple genotype positions to see them in combination. Here we combine all the nucleotide mutations in the SH gene into a single colouring. This is the result one would get by the "normal" method of Mumps typing -- you can see how much resolution is gained by examining whole genomes.
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