Why did a single Idaho H5N1 lineage survive the 2025 bottleneck to drive the 2026 dairy cattle outbreak while California’s 3,216-genome clade went extinct? We ran a temporal dN/dS scan across all 4,467 codons (10 proteins) of the Nextstrain H5N1 cattle tree using HyphAeon Temporal Instead of adapting gradually, H5N1 evolved in 4 synchronized selection waves (79 sweeps). Three waves built the surviving Idaho trunk step-by-step: 🟦 Pulse 1 (Mid-2024 — Idaho Trunk Base) 6 mutations across 5 segments swept in lockstep: • HA: D104G, S336N (receptor base & cleavage loop) • PB2: K670R (627-domain) • NS1: R67G • M1: S82N • NP: I119V 🟧 Pulse 2 (Early 2025 — Surviving Idaho Founder) • NA: K111R (#2 strongest site in proteome; tetramer assembly) & I19V • NS2: D27G (#7 in proteome; nuclear export) • NS1: A60T (#3 in proteome; dsRNA-binding helix) ⬜ Mid-2025 Dead-End Burst (Extinct Clades) Isolated HA antigenic bursts (E201K, K250R, R343K) without whole-genome coordination → died out by late 2025. 🟥 Pulse 3 (Late 2025 / 2026 — Bottleneck Sweep) Simultaneous 8-protein overhaul before the 2026 expansion: • NS1: M124T (#1 site in proteome; PKR/CPSF30 motif), Q25R, I54L • HA: S233P (RBS rim) + M2: V51I (amphipathic helix) • NA: N434S & K432E (430-loop 2nd sialic acid site) • Polymerase/NP: PA I219T, V44I, L425F • PB1 T543S • NP A27T 💡 What temporal dN/dS teaches us: When an adaptive mutation fixes once on a surviving trunk branch, static dN/dS misses it because there are no repeated parallel hits—catching only 8 of the 79 sweeps. Meanwhile, recurrent dead-end mutations (like HA:V147M, LRT=12.1) inflate static scores. Regressing branch selection over time with date-shuffling permutations rescues 71 single-branch trunk sweeps and filters out recurrent noise (HA:V147M p_perm=0.35). 🤖 100% Agentic Workflow: This entire analysis was executed end-to-end by an AI coding agent from a single prompt: extracting the 10-protein codon alignments from Nextstrain JSONs, running GPU-accelerated HyphAeon neural inference + 500-permutation temporal wave decomposition across 4,467 codons, decoding the 79 sweeps, and rendering the figure.

I spent some time tonight looking at the Nextstrain H5N1 dairy cattle tree that @SolidEvidence shared. What jumps out at me is not an uncontained national wave, but a dramatic evolutionary bottleneck. Every major 2024 and 2025 lineage went extinct. The massive California wave vanished last fall. So did the Colorado and Midwest lineages, along with the original Texas and Michigan clades. Every single 2026 sequence on that tree traces back to one late-2025 ancestor in Idaho. Bulk milk testing worked. Mandatory bulk-tank screening and farm quarantines in Colorado and California, followed by the USDA National Milk Testing Strategy, cleared the virus from most dairy states. That state-by-state clearance is why the January 2026 USDA guidance added an exemption for certified unaffected states. Rather than circulating across the country, roughly 96% of the 2026 sequences come from two neighboring states, Idaho and Utah, plus one small secondary jump to Texas. Why does the 2026 cluster sit on such a long branch? Sampling cadence explains a lot of the visual gap. Sequencing in Idaho went quiet for five months in late 2025 and then ramped back up this spring with much faster GenBank turnaround. Even with uneven sampling, the fact that every 2026 sequence across cattle, birds, and mink coalesces to a single late-2025 Idaho ancestor points to a real contraction. We ran our selection, clock, and reassortment tools across all eight segments to see what carried that lone Idaho lineage through the bottleneck. Reassortment played no role. All eight segments tracked together clonally, and PB2 did not pick up a single nucleotide change along the entire bottleneck stem. The other seven segments went through a sharp clock acceleration and fixed a tight cluster of co-evolving changes in NS1, HA, and NA. When that lineage spilled into a Utah mink farm, it picked up a set of polymerase changes and immediately reverted an NS1 mutation (A60T) that the virus had acquired in Idaho cattle back in 2024. Inside the surviving Idaho and Utah pocket, peridomestic birds and small mammals sit interleaved with dairy cattle on the tree. Curious what @SolidEvidence and others think: is this last lineage holding on in the Intermountain basin through local farm-to-wildlife cycling, or did those NS1 and surface changes alter within-herd persistence? xitter.cf/SolidEvidence/status/2…