A Critical Reexamination of Recovered SARS-CoV-2 Sequencing Data

2025/05/15 by Florence Débarre, Zach Hensel · 1 voice · 1 citation
Medicine · Agricultural and Biological Sciences · #SARS-CoV-2 and COVID-19 Research #Animal Virus Infections Studies #Viral Infections and Outbreaks Research

paper · doi:10.1093/molbev/msaf109

openalex publication_date 2025/05/15 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/02

Abstract

In 2021, Jesse Bloom published a study addressing why the earliest SARS-CoV-2 sequences in Wuhan from late December 2019 were not those most similar to viruses sampled in bats. The study concluded that recovered partial sequences from Wuhan and annotation of Wuhan links for other sequences increased support for one genotype as the progenitor of the SARS-CoV-2 pandemic. However, we show that the collection date for the recovered sequences was January 30, 2020, later than that of hundreds of other SARS-CoV-2 sequences. Mutations in these sequences also exhibit diversity consistent with SARS-CoV-2 sequences collected in late January 2020. Furthermore, we found that Wuhan exposure history was common for early samples, so Bloom's annotation for a single familial cluster does not support that an early genotype was undersampled in Wuhan. Both the recovered partial sequences and additional annotation align with contemporaneous data rather than increase support for a progenitor. Our findings clarify the significance of the recovered sequences and are supported by additional data and analysis published since mid-2021.

Citations

• A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster
• First Case of 2019 Novel Coronavirus in the United States
• A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
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Cited by

• The Data are Insufficient to Confidently Root the SARS-CoV-2 Phylogenetic Tree

Discussions

• @flodebarre.bsky.social and @zachhensel.bsky.social offer a new perspective on available SARS-CoV-2 sequencing data, in particular regarding the earliest reported sequences. 🔗 doi.org/10.1093/molbev [bsky, 0 points, 2 comments]