The correct rooting of the early SARS-CoV-2 phylogenetic tree is uncertain
2 events · 1 assessment
Assessed Contested
verdict confidence 0.70
Whether the early SARS-CoV-2 phylogenetic tree can be confidently rooted is itself an open question, actively disputed by qualified researchers in the peer-reviewed literature. All sides agree the task is intrinsically hard: only a handful of genomes predate January 2020, the virus had accumulated very few distinguishing mutations, and early sampling was geographically and temporally skewed. The disagreement is over whether that difficulty has been overcome. One line of work (Bloom 2025) argues the available data cannot discriminate among several candidate roots, so that confidence in any single root — including the widely cited lineage B — is unwarranted. The opposing line (Débarre & Hensel 2025; Crits-Christoph et al. 2024, alongside the phylodynamic analyses of Pekar, Worobey and colleagues) holds that the sequences underpinning alternative roots are contamination or bioinformatic artifacts, and that once these are set aside the data point to a lineage B root. The crux is empirical and, in principle, resolvable: it turns on whether the reported intermediate/non-lineage-B early genomes are genuine. Because that authenticity question is unresolved, the rooting cannot presently be treated as settled — though whether the remaining uncertainty is genuine or merely an artifact of discredited data is exactly what the two camps dispute.
Claim entered the graph