Direct rebuttal of Tang et al. 2020 (S-5). Shows that the two mutations Tang et al. use to define “L” and “S” types are two of thousands of nonsynonymous substitutions already segregating in the earliest SARS-CoV-2 sample, none of which had (or has since, at time of writing) any demonstrated functional/fitness effect; that the observed frequency shift over time is well within what founder effects and stochastic transmission-chain dynamics predict without invoking differential “aggressiveness”; and that calling either variant a distinct “type” is not statistically or biologically supported by the data presented. Establishes the general methodological standard — that a lineage split needs more than 1-2 linked SNPs and a temporal frequency change to justify functional/ancestral claims — that later two-introduction critiques (S-7, S-12, and Weissman’s re-analysis) apply to the A/B lineage-count argument.
relevance_note: the field’s standing methodological rebuttal to over-reading small numbers of early-lineage-defining mutations, a template directly reused by critics of the later A/B two-introduction claim.