Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study
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Abstract
A number of highly effective vaccines have been developed and deployed to combat the COVID-19 pandemic. The emergence and epidemiological dominance of SARS-CoV-2 mutants with high transmission potential and immune evasion properties, the so-called variants of concern (VOC), continue to be a major concern.
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SciScore for 10.1101/2021.06.30.21259761: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The study was approved by Hackensack Meridian Health Institutional Review Board (IRB). Sex as a biological variable not detected. Randomization Population sampling and screening of SARS-CoV-2: SARS-CoV-2 positive swabs collected from seven HMH network hospitals were shipped to CDI on a weekly basis and stored at −80°C. 1,404 swabs collected during the same time frame as the vaccinated samples were randomly selected and subjected to a molecular beacon-based real-time asymmetric PCR and melting curve analysis to identify the SARS-CoV-2 E484K/Q and N501Y mutations, as previously described (10). Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Re… SciScore for 10.1101/2021.06.30.21259761: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The study was approved by Hackensack Meridian Health Institutional Review Board (IRB). Sex as a biological variable not detected. Randomization Population sampling and screening of SARS-CoV-2: SARS-CoV-2 positive swabs collected from seven HMH network hospitals were shipped to CDI on a weekly basis and stored at −80°C. 1,404 swabs collected during the same time frame as the vaccinated samples were randomly selected and subjected to a molecular beacon-based real-time asymmetric PCR and melting curve analysis to identify the SARS-CoV-2 E484K/Q and N501Y mutations, as previously described (10). Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Final libraries were quantified using fluorescent-based assays including PicoGreen (Life Technologies), Qubit Fluorometer (Invitrogen), and Fragment Analyzer (Advanced Analytics). PicoGreensuggested: NoneProcessed read pairs were then aligned to the SARS-CoV-2 reference genome, using BWA-MEM v0.7.17 (35) and only read pairs with at least one alignment spanning a minimum of 50 bp in the reference were kept. BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)Next, read pairs that did not contain a single 19bp seed k-mer in common with the SARS-CoV-2 genome reference (NC_045512.2) were discarded and adapter sequences and low-quality bases (Q < 20) were trimmed from the 3’ end of the remaining reads, using Cutadapt v2.10 (34). Cutadaptsuggested: (cutadapt, RRID:SCR_011841)Processed reads pairs were then merged using NGmerge v0.2 (36), allowing for dovetailed alignments. NGmergesuggested: NoneA maximum likelihood phylogenetic tree was constructed using IQ-TREE v2.1.2 (39) with automatic model selection and 1000-bootstrap replicates. IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)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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