A critical reexamination of recovered SARS-CoV-2 sequencing data DOI Creative Commons
Florence Débarre, Zach Hensel

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 16, 2024

Abstract SARS-CoV-2 genomes collected at the onset of Covid-19 pandemic are valuable because they could help understand how virus entered human population. In 2021, Jesse Bloom reported on recovery a dataset raw sequencing reads that had been removed from NCBI SRA database request data generators, scientific team Wuhan University (Wang et al ., 2020b). concluded deletion obfuscated origin and suggested may have requested to comply with government order; further, he questioned sample collection dates after January 30, 2020. Here, we show were published in 2020 by Wang . together reads, match given authors 2021. Collection manually during his analysis data. We examine mutations these sequences confirm entirely consistent previously known genetic diversity late Finally, explain an apparent phylogenetic rooting paradox described was resolved subsequent analysis. Our reanalysis demonstrates there no basis question .. Note for bioRxiv readers The automatically generated Full Text version our manuscript is missing footnotes; available PDF version.

Language: Английский

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic DOI

Alexander Crits‐Christoph,

Joshua I. Levy, Jonathan E. Pekar

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(19), P. 5468 - 5482.e11

Published: Sept. 1, 2024

Language: Английский

Citations

26
Transformative Approaches in SARS-CoV-2 Management: Vaccines, Therapeutics and Future Direction DOI
Ankita Saha,

Shweta Choudhary,

Priyanshu Walia

et al.

Virology, Journal Year: 2025, Volume and Issue: 604, P. 110394 - 110394

Published: Jan. 11, 2025

Language: Английский

Citations

1
Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived DOI Creative Commons
Jonathan E. Pekar, Niema Moshiri, Philippe Lemey

et al.

Virus Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 22, 2025

Understanding the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at outset disease 2019 pandemic can provide insight into circumstances leading to its emergence. Early SARS-CoV-2 has been classified two distinct viral lineages, denoted "A" and "B," which we hypothesized were separately introduced humans. Recently published data contain genomes with a haplotype suggested be an evolutionary intermediate these known as "T/T." We used phylodynamic approach analyze from early 2020 determine whether T/T represent evolutionarily between lineages A B, or if they are later descendent either lineages. find that recently do not were, instead, derived lineage B. However, cannot conclusively derived. After including additional start pandemic, genomes, again discrepancy in molecular clock when inferring ancestral SARS-CoV-2, corroborating existing evidence for separate introductions B human population late 2019.

Language: Английский

Citations

0
Structural Virology: The Key Determinants in Development of Antiviral Therapeutics DOI Creative Commons
Tanuj Handa, Ankita Saha, Aarthi Narayanan

et al.

Viruses, Journal Year: 2025, Volume and Issue: 17(3), P. 417 - 417

Published: March 14, 2025

Structural virology has emerged as the foundation for development of effective antiviral therapeutics. It is pivotal in providing crucial insights into three-dimensional frame viruses and viral proteins at atomic-level or near-atomic-level resolution. Structure-based assessment components, including capsids, envelope proteins, replication machinery, host interaction interfaces, instrumental unraveling multiplex mechanisms infection, replication, pathogenesis. The structural elucidation enzymes, proteases, polymerases, integrases, been essential combating like HIV-1 HIV-2, SARS-CoV-2, influenza. Techniques X-ray crystallography, Nuclear Magnetic Resonance spectroscopy, Cryo-electron Microscopy, Tomography have revolutionized field significantly aided discovery ubiquity chronic infections, along with emergence reemergence new threats necessitate novel strategies agents, while extensive diversity their high mutation rates further underscore critical need analysis to aid development. This review highlights significance structure-based investigations bridging gap between structure function, thus facilitating therapeutics, vaccines, antibodies tackling emerging threats.

Language: Английский

Citations

0
A critical reexamination of recovered SARS-CoV-2 sequencing data DOI Creative Commons
Florence Débarre, Zach Hensel

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 16, 2024

Abstract SARS-CoV-2 genomes collected at the onset of Covid-19 pandemic are valuable because they could help understand how virus entered human population. In 2021, Jesse Bloom reported on recovery a dataset raw sequencing reads that had been removed from NCBI SRA database request data generators, scientific team Wuhan University (Wang et al ., 2020b). concluded deletion obfuscated origin and suggested may have requested to comply with government order; further, he questioned sample collection dates after January 30, 2020. Here, we show were published in 2020 by Wang . together reads, match given authors 2021. Collection manually during his analysis data. We examine mutations these sequences confirm entirely consistent previously known genetic diversity late Finally, explain an apparent phylogenetic rooting paradox described was resolved subsequent analysis. Our reanalysis demonstrates there no basis question .. Note for bioRxiv readers The automatically generated Full Text version our manuscript is missing footnotes; available PDF version.

Language: Английский

Citations

1