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O-5 - The 20 apparent A-B intermediate genomes are low-coverage and lab-clustered

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type
observation
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O-5
statement
The 20 early genomes carrying an intermediate haplotype (C/C or T/T, i.e. only one of the two lineage-defining mutations) had low sequencing coverage (about 10x or less) at the diagnostic positions and frequently shared rare mutations with, and were sequenced in the same laboratory as, lineage A or B genomes.
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S-1 - Pekar et al. 2022 — molecular epidemiology of multiple zoonotic origins of SARS-CoV-2
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Results, intermediate-haplotype analysis
quote
numerous instances of C/C and T/T genomes sharing rare mutations with lineage A or lineage B viruses, often sequenced in the same laboratory

Twenty genomes contained either T28144C or C8782T but not both (C/C or T/T). Examination showed depth of coverage at or below ~10x at the key positions and lab-specific shared rare mutations — the empirical pattern the authors use to argue these are not genuine circulating intermediates.

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