ArticleMolecular biology and evolution2021
Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuhan SARS-CoV-2 Epidemic.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers, 1 of them a synthesis that pooled it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Tracing the origin of Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): A systematic review and narrative synthesis.Journal of medical virology · 2022Pooled it
- The Data are Insufficient to Confidently Root the SARS-CoV-2 Phylogenetic Tree.Molecular biology and evolution · 2025Article
- A Critical Reexamination of Recovered SARS-CoV-2 Sequencing Data.Molecular biology and evolution · 2025Article
- Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.Cell · 2024Article
- What we can and cannot learn from SARS-CoV-2 and animals in metagenomic samples from the Huanan market.Virus evolution · 2024Article
- The Question of the Origins of COVID-19 and the Ends of Science.Journal of bioethical inquiry · 2023Article
- Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.bioRxiv : the preprint server for biology · 2023Article
- Article
- Genomic Analysis of the Suspicious SARS-CoV-2 Sequences in the Public Sequencing Database.Microbiology spectrum · 2023Article
- Article
- Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market.Virus evolution · 2023Article
- Evolutionary Challenges to Humanity Caused by Uncontrolled Carbon Emissions: The Stockholm Paradigm.International journal of environmental research and public health · 2022Review
- Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy.Environmental research · 2022Article
- The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2.Science (New York, N.Y.) · 2022Article
- A call for an independent inquiry into the origin of the SARS-CoV-2 virus.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity.Bioinformatics (Oxford, England) · 2022Article
- Waiting for the truth: is reluctance in accepting an early origin hypothesis for SARS-CoV-2 delaying our understanding of viral emergence?BMJ global health · 2022Review
- Preprint servers and patent prior art: Preprints can jeopardize the patentability of an invention: Preprints can jeopardize the patentability of an invention.EMBO reports · 2022Article
- Both simulation and sequencing data reveal coinfections with multiple SARS-CoV-2 variants in the COVID-19 pandemic.Computational and structural biotechnology journal · 2022Article
- Continuous mutation of SARS-CoV-2 during migration via three routes at the beginning of the pandemic.PeerJ · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
1 author.
Funding
Abstract
The origin and early spread of SARS-CoV-2 remains shrouded in mystery. Here, I identify a data set containing SARS-CoV-2 sequences from early in the Wuhan epidemic that has been deleted from the NIH's Sequence Read Archive. I recover the deleted files from the Google Cloud and reconstruct partial sequences of 13 early epidemic viruses. Phylogenetic analysis of these sequences in the context of carefully annotated existing data further supports the idea that the Huanan Seafood Market sequences are not fully representative of the viruses in Wuhan early in the epidemic. Instead, the progenitor of currently known SARS-CoV-2 sequences likely contained three mutations relative to the market viruses that made it more similar to SARS-CoV-2's bat coronavirus relatives.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.