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phiweger / zoo

A portable datastructure for rapid prototyping in (viral) bioinformatics (under development).
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use case SBT: identify reassortment (context: Swine flu) #33

Open phiweger opened 7 years ago

phiweger commented 7 years ago

From a previous report:

I took some human IAV isolates from this publication [^1] on triple reassorted subtypes from the swine flu outbreak of 2009:

- Influenza A virus (A/Iowa/01/2006 (H1N1), FJ986618
- Influenza A virus (A/Wisconsin/87/2005 (H1N1)), FJ986619
- Influenza A virus (A/Ohio/01/2007 (H1N1)), FJ986620
- Influenza A virus (A/Ohio/02/2007 (H1N1)), FJ986621
- Influenza A virus (A/Michigan/09/2007 (H1N2)), FJ986622
- Positive control: Simulated reassortants.
- Negative control: Avian strains with probably no reassortment (other than from Avian).

Then I queried the "HA" protein against zoo and recorded the similarity (y-axis) of its documents coloured by host. The x-axis simply sorts the matches by similarity. Remember, the isolated are from humans, but the plot neatly shows that they are most similar to swine.

[^1]: Shinde, V. et al. Triple-Reassortant Swine Influenza A (H1) in Humans in the United States, 2005–2009. New England Journal of Medicine 360, 2616–2625 (2009).