1. SciScore for 10.1101/2021.11.29.21266109: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: This study was approved by the Ethics Committee of the Amazonas State University (CAAE: 25430719.6.0000.5016) and by the Ethics Committee of the FIOCRUZ (CAAE: 68118417.6.0000.5248).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Serological analyses: A total of 14 serum samples collected from 12 to 70 days after the second episode of COVID-19 were tested for SARS-CoV-2-specific neutralizing antibodies (NAb) by plaque reduction neutralization test (PRNT90).
    SARS-CoV-2-specific neutralizing antibodies
    suggested: None
    suggested: None
    Software and Algorithms
    The FASTQ reads were obtained following the Illumina pipeline on BaseSpace, imported into Geneious v10.2.6, trimmed (BBDuk 37.25) or into CLC Genomic Workbench (Qiagen), and mapped (BBMap 37.25) against the reference sequence EPI_ISL_402124 available in EpiCoV database from GISAID
    suggested: (Illumina, RRID:SCR_010233)
    suggested: (Geneious, RRID:SCR_010519)
    suggested: (BBmap, RRID:SCR_016965)
    The final dataset of each variant to which primoinfection and reinfection sequences were previously assigned were obtained by clusterization of their GISAID complete datasets using CD-HIT v.4.8.131.
    suggested: (CD-HIT, RRID:SCR_007105)
    The resulting dataset was aligned by MAFFT v7.46732 and subjected to a maximum likelihood (ML) phylogenetic analysis with IQ-TREE v2.1.233 under the best nucleotide substitution model selected by the ModelFinder application34.
    suggested: (MAFFT, RRID:SCR_011811)
    suggested: (IQ-TREE, RRID:SCR_017254)
    suggested: None
    Graphics and statistical analyses were performed using GraphPad v9.02
    suggested: (GraphPad Prism, RRID:SCR_002798)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Our study has several limitations. First, although Ct values could be used as a surrogate of infectivity, we have no contact-tracing information to demonstrate that reinfected subjects were able to transmit the virus to susceptible individuals. Second, our study was limited by the absence of longitudinal data of anti-SARS-CoV-2 NAb, particularly between the first and the second COVID-19 episodes. Thus, we could not confirm if primo-infections effectively induce a transient neutralization response, we could not measure the level of NAb immediately before reinfections and no definitive conclusions could be drawn about the precise impact of reinfections on NAb titers. In summary, these findings confirm that natural infection by SARS-CoV-2 do not necessarily prevent subsequent infections and further demonstrate that reinfection with the VOC Gamma in people who had a first symptomatic infection between 3 to 12 months earlier was not a rare phenomenon in Brazil. Although, reinfections cases were observed in individuals without comorbidities and with mild disease, no significant decrease in viral load, represented by Ct values, during reinfection was observed when compared with primo-infection. Further studies are necessary to determine whether reinfection with Gamma and other VOCs is a widespread phenomenon and to understand to what extent reinfection will contribute to the onward endemic transmission of SARS-CoV-2. Further work is also needed to understand how primary infections i...

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

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