Two features carry the inference. First, host specificity: each recovered viral genome sits within the clade of viruses reported from a single host species, so its presence indexes that particular animal, not generic contamination. Second, viability signal: recovering a mostly-complete viral genome at appreciable abundance from a stall where the host’s mtDNA is concentrated is best explained by an actively-shedding, live-infected animal, because a dead frozen carcass or trace environmental DNA would not typically yield abundant replicating-virus reads co-localised with host tissue. The phylogenetic placement of the bamboo-rat betacoronavirus next to a 2019 Guangxi-farm virus, and the civet kobuvirus next to Sichuan/Guangxi market-animal sequences, further shows a live wildlife-trade conduit from southern China into Wuhan. This establishes that the market contained infected live wildlife of exactly the candidate intermediate-host species, raising the prior that SARS-CoV-2 could have entered humans by the same route (though these are not SARS-CoV-2 itself).
Step 6 verdict — corrected (checked)
Reconstructed step, two components. (a) Host-specificity → the recovered genome indexes that particular species’ body being present, not generic environmental contamination: valid and holds, since a genome nested within a single host’s viral clade, at appreciable abundance, and co-located with that host’s mtDNA cannot be explained by drift-in contamination. (b) The abundance/viability signal → the animal was live and productively infected in the market: this over-reaches. The undercutting defeater the argument itself raises (“dead frozen carcass”) is dismissed too quickly — an animal infected before slaughter (e.g. amdoparvovirus persistently infects raccoon dogs; a coronavirus-viremic bamboo rat) carries a high viral load in its tissues, and freezing preserves that RNA, so a freshly-killed or frozen infected carcass/meat would also yield abundant host-co-located viral reads. Viral abundance therefore cannot distinguish a live shedding animal from a slaughtered-but-infected one. The defeater survives against “live,” but the weaker conclusion — infected animals of these species (live or as carcasses/tissue) were physically present and trace/generic contamination is excluded — is immune to it, and still supports the wildlife-trade conduit (the farm-traceable phylogenetics stand regardless). Hence corrected to that weaker form. Traced directly, so checked.
Original
Reconstructing near-complete genomes of viruses with narrow, known host ranges (raccoon-dog amdoparvovirus, bamboo-rat betacoronavirus, civet kobuvirus), each found where its host’s mtDNA was and nested phylogenetically among that single host’s viruses, implies live productively-infected animals of those species were physically in the market — not merely frozen carcasses or residual DNA.