SARS-CoV-2 Breakthrough Infections in Fully Vaccinated Individuals
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Abstract
Importance
While COVID-19 vaccines are highly effective against disease, breakthrough infections may occur in the context of rising variants of concern.
Objective
We paired random and passive surveillance nucleic acid testing with analysis of viral whole genomic sequences to detect and describe breakthrough infections, focusing in a university community.
Design
Anterior nasal swabs were collected from individuals for a nucleic acid amplification test (NAAT) for detection of SARS-CoV-2. A subset of NAAT positive samples was sequenced to determine variants associated with infections. Included in the testing and sequencing protocol were individuals that were fully vaccinated.
Setting
This study was performed as part of a surveillance program for SARS-CoV-2 on a university campus with 49,700 students and employees.
Participants
Surveillance testing was random and included approximately 10% of the population each week. Additionally, individuals self-identified with COVID-19 related symptoms or those that had close contact with SARS-CoV-2 positive individuals were also tested.
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SciScore for 10.1101/2021.06.21.21258990: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Approval from the One-to-One Health review board was obtained. Sex as a biological variable not detected. Randomization Samples that were sequenced were randomly selected based on Ct values (Cts ≤30 could be included). Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources The Institutional Review Board from the Purdue University Human Research Protection Program determined that viral genome sequencing of deidentified remnant RNA samples included in this study is not research involving human subjects (IRB-2021-438). Human Research Protection Programsuggested: NoneViral whole genome sequencing was performed on at least 15% (34% on average) … SciScore for 10.1101/2021.06.21.21258990: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Approval from the One-to-One Health review board was obtained. Sex as a biological variable not detected. Randomization Samples that were sequenced were randomly selected based on Ct values (Cts ≤30 could be included). Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources The Institutional Review Board from the Purdue University Human Research Protection Program determined that viral genome sequencing of deidentified remnant RNA samples included in this study is not research involving human subjects (IRB-2021-438). Human Research Protection Programsuggested: NoneViral whole genome sequencing was performed on at least 15% (34% on average) of positive samples per week in the Carpi Lab using MinION Mk1B or GridION Mk1 Nanopore devices (Oxford Nanopore Technologies, ONT, UK). MinIONsuggested: (MinION, RRID:SCR_017985)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.
Results from scite Reference Check: We found no unreliable references.
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