Molecular evidence of SARS-CoV-2 in New York before the first pandemic wave
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Abstract
Numerous reports document the spread of SARS-CoV-2, but there is limited information on its introduction before the identification of a local case. This may lead to incorrect assumptions when modeling viral origins and transmission. Here, we utilize a sample pooling strategy to screen for previously undetected SARS-CoV-2 in de-identified, respiratory pathogen-negative nasopharyngeal specimens from 3,040 patients across the Mount Sinai Health System in New York. The patients had been previously evaluated for respiratory symptoms or influenza-like illness during the first 10 weeks of 2020. We identify SARS-CoV-2 RNA from specimens collected as early as 25 January 2020, and complete SARS-CoV-2 genome sequences from multiple pools of samples collected between late February and early March, documenting an increase prior to the later surge. Our results provide evidence of sporadic SARS-CoV-2 infections a full month before both the first officially documented case and emergence of New York as a COVID-19 epicenter in March 2020.
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SciScore for 10.1101/2021.02.08.21251303: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Ethics statement: This study was reviewed and approved by the Institutional Review Board of the Icahn School of Medicine at Mount Sinai (protocol: HS# 20-00141). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources For each pool that did not yield a complete genome in the initial sequencing attempt, 4 additional sequencing libraries were prepared from re-extracted RNA. 1) Nextera XT Illumina amplicon sequencing as described above, 2) Nextera XT sequencing of 1.5 to 2kb amplicons targeting only regions containing clade-defining SNVs … SciScore for 10.1101/2021.02.08.21251303: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Ethics statement: This study was reviewed and approved by the Institutional Review Board of the Icahn School of Medicine at Mount Sinai (protocol: HS# 20-00141). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources For each pool that did not yield a complete genome in the initial sequencing attempt, 4 additional sequencing libraries were prepared from re-extracted RNA. 1) Nextera XT Illumina amplicon sequencing as described above, 2) Nextera XT sequencing of 1.5 to 2kb amplicons targeting only regions containing clade-defining SNVs (positions 1059, 8782, 14408, 23403, 25563, 28144, 28881 and 28882, https://nextstrain.org/blog/2020-06-02-SARSCoV2-clade-naming), and the Swift Normalase® Amplicon Panel (SNAP) SARS-CoV-2 SNAPsuggested: (SNAP, RRID:SCR_007936)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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