O-39 - Market-associated SARS-CoV-2 genomes' tMRCA matches the global pandemic tMRCA and both lineages A and B are present in market environmental samples
Recovered environmental viral genomes (A20 = lineage A; F54, F13, B5 = lineage B) place the market’s viral diversity at the root of the pandemic tree rather than downstream of it. Presence of both lineages at the market argues against the market outbreak being merely a lineage-B superspreading amplification of prior community transmission. Rests on the early-genome collection (D-3) plus the market metagenomic reads.
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Why this is evidence
A downstream amplifier of prior community transmission (H-15) or an incidental venue (H-19) would carry viral diversity younger than the pandemic root; market genomes’ tMRCA matching the pandemic tMRCA, with both lineages present, favors emergence at the market (H-14).
Likelihood
# E-19 (HC-3) — lone edge, one observation O-39: the market-associated genomes' tMRCA overlaps the global
# pandemic root AND both basal lineages A and B are present in market environmental samples (lineage A in
# A20). Members in HC-3.hypotheses order: [H-14 primary wildlife-spillover origin, H-15 externally-seeded
# amplifier, H-19 detection/ascertainment artifact, H-45 residual]. Anchored on H-14 = 1 (best fit); others
# priced as ratios to it (rule 7). Direction from `## Why this is evidence` + A-51 (approved, checked):
# a root-matching tMRCA with BOTH basal lineages present is the "market is at the origin" signature that a
# downstream amplifier or an incidental venue does not predict.
lik_tmrca_H14 = 1.0 # anchor: market = emergence locus is exactly what predicts market genomes at the ROOT
# of the tree with both basal lineages present — the modal expectation under this member
lik_tmrca_H15 = 0.35 # 0.35x: an amplifier seeded from outside would tend to coalesce AFTER the root (younger
# tMRCA) and carry the amplified lineage only; reproducing root-tMRCA + BOTH lineages
# needs an early, already-diverse external seeding — a specific coincidence. Not tiny:
# A-51's verdict grants that a diverse community outbreak feeding the market stays
# logically possible
lik_tmrca_H19 = 0.3 # 0.3x: a causally-incidental venue (positives = contamination from tested cases) has
# even less reason than an active amplifier to hold both basal lineages at the root —
# its environmental genomes would reflect later community diversity. Slightly below
# H-15, which at least channels virus through the market
lik_tmrca_H45 = 0.5 # residual, unconstrained (rule 3): some unlisted roles (a genuine co-spillover site,
# cold-chain-as-origin AT the market) fit root-tMRCA + both-lineages well, others don't
# — middling. Above H-15/H-19 because it includes origin-flavoured variants
t_tmrca = 0.7 # cap = trust_score(S-35) = 0.75; docked modestly for the raw-data->observation step:
# the tMRCA overlap rests on a molecular clock with wide (only "overlapping") 95% HPD
# intervals, and the lineage-A-at-market claim rests on a SINGLE environmental read (A20)
# whose metagenomic lineage assignment is contestable
evidence("HC-3", ["O-39"], [lik_tmrca_H14, lik_tmrca_H15, lik_tmrca_H19, lik_tmrca_H45], t=t_tmrca)