Unwarranted exclusion of intermediate lineage A-B SARS-CoV-2 genomes is inconsistent with the two spillover hypothesis of the origin of COVID-19

Pekar et al. (2022) propose that SARS-CoV-2 was a zoonotic spillover that first infected humans in the Huanan Seafood Market in Wuhan, China. They propose that there were two separate spillovers of the closely related lineages A and lineage B in a short period of time. The two lineages are differentiated by two SNVs, hence a single-SNV A-B intermediate must have occurred in an unsampled animal host if the two spillover hypothesis is correct. Consequently, confirmation of the existence of an intermediate A-B genome from humans would falsify their hypothesis of two spillovers. Pekar et al. identified and excluded 20 A-B intermediate genomes from their analysis. A variety of exclusion criteria were applied, including low read depth, and the assertion of repeated erroneous base calls  at lineage defining positions 8782 and 28144.  However, data from GISAID shows that most of the genomes were sequenced to high average sequencing depth, appearing inconsistent with these criteria. The decision to exclude the majority of genomes was based on personal communications, with raw data unavailable for inspection. Multiple errors, biases and inconsistencies were observed in the exclusion process. For example, 12 intermediate genomes from one study were excluded, however 54 other genomes from the same study were included, indicating selection bias. Puzzlingly, two intermediate genomes from Beijing were discarded despite an average sequencing depth of 2175X, however 4 genomes from the same sequencing study were included in their analysis. Lastly, we discuss 14 additional possible intermediate genomes not discussed by Pekar et al. and note that genome sequence filtration is inappropriate when considering the presence or absence of a specific SNV pair in an outbreak. Consequently, we find that exclusion of many of the intermediate genomes is unfounded, leaving the conclusion of two natural zoonoses unsupported.