Filter cattle-outbreak using GenoFLU B3.13 #140
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The previous approach relied on broad filtering -- minimum date of 2024, region of North America -- a hardcoded exclude list and a clock filter. As the diversity of sequences increased the clock-filter became less effective and ultimately dropped all the desired strains. See <#133> for more. We now use GenoFLU constellations and can relax the date and region filters accordingly. This relaxation didn't result in any non-North-American samples included but did add one B3.13 genome from 2023: 'A/Goose/USA/23-038138-001-original/2023'. These changes to filtering will also apply to the D1.1 builds, but testing indicates no changes. The segment-level approach is not addressed here, but could be similarly adjusted to use the GenoFLU matching on the segment level. Specifically, <https://github.com/nextstrain/avian-flu/pull/138/files> adds the segment-level annotations and the expanded constellation is: B3.13 = PA:ea1, HA:ea1, PB1:am4, MP:ea1, NA:ea1, PB2:am2.2, NP:am8, NS:am1.1 Closes #133
This was referenced Feb 24, 2025
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Going to merge this now as the changes are relatively minor, the direction's been agreed in Slack, and it allows our automated builds to resume. |
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The previous approach relied on broad filtering -- minimum date of 2024, region of North America -- a hardcoded exclude list and a clock filter. As the diversity of sequences increased the clock-filter became less effective and ultimately dropped all the desired strains. See #133 for more.
We now use GenoFLU constellations and can relax the date and region filters accordingly. This relaxation didn't result in any non-North-American samples included but did add one B3.13 genome from 2023: 'A/Goose/USA/23-038138-001-original/2023'.
These changes to filtering will also apply to the D1.1 builds, but testing indicates no changes.
The segment-level approach is not addressed here, but could be similarly adjusted to use the GenoFLU matching on the segment level. Specifically, https://github.com/nextstrain/avian-flu/pull/138/files adds the segment-level annotations and the expanded constellation is: B3.13 = PA:ea1, HA:ea1, PB1:am4, MP:ea1, NA:ea1, PB2:am2.2, NP:am8, NS:am1.1
Closes #133