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A Critical Reexamination of Recovered SARS-CoV-2 Sequencing Data
Florence Débarre1, Zach Hensel2
1Institute of Ecology and Environmental Sciences, CNRS UMR 7618, Sorbonne Université, UPEC, IRD, INRAE, Paris, France.
Molecular Biology and Evolution
|June 9, 2025
Summary
Early SARS-CoV-2 sequences in Wuhan were not from January 2020 as suggested. Analysis shows these samples are consistent with later collection dates and do not support a specific progenitor genotype.
Area of Science:
- Virology
- Genomics
- Epidemiology
Background:
- Jesse Bloom's 2021 study proposed a specific genotype as the SARS-CoV-2 progenitor based on early Wuhan sequences.
- The study suggested that certain recovered partial sequences and annotations supported this progenitor hypothesis.
Purpose of the Study:
- To re-evaluate the collection dates and significance of early SARS-CoV-2 sequences from Wuhan.
- To assess whether the recovered sequences and annotations support a specific progenitor genotype for the pandemic.
Main Methods:
- Analysis of SARS-CoV-2 sequence collection dates.
- Examination of sequence mutation diversity.
- Review of Wuhan exposure history for early samples.
Main Results:
- The recovered partial sequences were collected on January 30, 2020, later than hundreds of other SARS-CoV-2 sequences.
- Sequence mutations indicate diversity consistent with late January 2020 sampling.
- Wuhan exposure history was common in early samples, not limited to a single familial cluster.
Conclusions:
- The recovered partial sequences and annotations align with contemporaneous data, not supporting an undersampled progenitor genotype.
- The findings clarify the significance of early Wuhan sequences in understanding SARS-CoV-2 origins.
- Subsequent data published since mid-2021 supports these revised interpretations.
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