gtrichard/pigie-2012-2022

Nextstrain Instance for the PIGIE European Swine Influenza A Virus Surveillance Compilation from 2012 to 2022

Nextstrain Instance for the PIGIE European Swine Influenza A Virus Surveillance Compilation from 2012 to 2022

Potentially interesting plots:

H1C

• H1C clades geographic distribution between 2012 and 2022: https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1C?c=HA_clade&d=map&dmin=2012-01-01&p=full
• H1C scatter plot over time, clades and countries with associated frequencies: https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1C?c=Country&d=tree,frequencies&l=scatter&p=full&scatterY=HA_clade
• H1avN2 1C.2.4 frequencies and phylogenetic tree: https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1C?c=Country&dmin=2012-01-01&f_HA_clade=1C.2.4&f_Subtype=H1N2
• H1avN1 1C.2.1 frequencies and phylogenetic tree: https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1C?c=Country&dmin=2012-01-01&f_HA_clade=1C.2.1
• H1avNx 1C.2.2 frequencies and phylogenetic tree: https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1C?c=Country&d=tree,frequencies&f_HA_clade=1C.2.2&p=full
• The peculiar case of H1C.2.2-N2 in Spain: https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1C?c=Country&d=tree,frequencies&f_HA_clade=1C.2.2&f_Subtype=H1N2&p=full
• The peculiar case of 1C.2.5 viruses (H1N1 and H1N2 separation, found mostly in Italy): https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1C?c=Country&d=tree,frequencies&f_HA_clade=1C.2.5&f_Subtype=H1N1,H1N2&p=full
• H1N1 1C from UK? https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1C?c=Country&d=tree,frequencies&f_HA_clade=1C.1&p=full
• 1C.2 viruses? https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1C?c=Country&d=tree,frequencies&f_HA_clade=1C.2&p=full

H1B

• H1B clades geographic distribution between 2012 and 2022: https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1B?c=HA_clade&d=map,frequencies&dmin=2012-01-01&p=full > each country has a different dominant 1C clade.
• H1B HA tree: https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1B?c=Country&d=tree&p=full
• H1B scatter plot over time, clades and countries with associated frequencies: https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1B?c=Country&d=tree,frequencies&l=scatter&p=full&scatterY=HA_clade

H1A

• H1A clade = 1A.3.3.2 only : https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1A?c=HA_clade&d=map,frequencies&dmin=2012-01-01&p=ful
• H1A subtype map: https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1A?c=Subtype&d=map,frequencies&dmin=2012-01-01&p=full > H1pdmN1 prevalent in France, Italy and Danemark. H1pdmN2 more prevalent in Germany, Belgium and The Netherlands.
• H1A tree: https://nextstrain.org/community/gtrichard/pigie-2012-2022/H1A?c=Country&p=full&transmissions=hide

To do:

• Remove non-PIGIE countries sequences potentially (very sparsely sampled countries like Austria, Sweden, Finland, Portugal, Serbia, Poland, Czech Republic, Switzerland, etc)?
• Remove A/swine/London/Scholtissek_lab strain (unknow origin, old clade).
• Remove A/swine/England/405741/1994 (too old).
• Finalize H3 instance (latest NCBI strains from Denmark + check the Human sequences that were considered too divergent).