The newly introduced SARS-CoV-2 variant A222V is rapidly spreading in Lazio region, Italy

  1. Barbara Bartolini
  2. Martina Rueca
  3. Cesare Ernesto Maria Gruber
  4. Francesco Messina
  5. Emanuela Giombini
  6. Giuseppe Ippolito
  7. Maria Rosaria Capobianchi
  8. Antonino Di Caro

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Abstract

A new SARS-CoV-2 clade (GV) characterized by S substitution A222V, first reported from Spain in March, is rapidly spreading across Europe. To establish the A222V variant involvement in the infection rise in Italy, all GISAID sequences from Italy and those from our Laboratory (Lazio) in the period June-October were analysed. A222V, first recognized in August, represents 11.2% of sequences in this period, reaching 100% of autochthonous sequences in October, supporting increased GV circulation in Italy.

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  1. ScreenIT

    SciScore for 10.1101/2020.11.28.20237016: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Whole genome sequencing (WGS) was performed on residual respiratory samples by using Ion AmpliSeq™ SARS-CoV-2 research panel on GeneStudio™ S5 Prime System (Thermofisher).
    WGS
    suggested: None
    Raw reads with mean quality Phred score >20 were selected and trimmed using Trimmomatic software v.0.36 [4].
    Phred
    suggested: (Phred, RRID:SCR_001017)
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    SARS-CoV-2 genomes were assembled using reference-based assembly method, with BWA v.
    BWA
    suggested: (BWA, RRID:SCR_010910)
    0.7.12 [5] and Samtools v.
    Samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Assembled contigs were then verified using Geneious 2019.2.3.
    Geneious
    suggested: (Geneious, RRID:SCR_010519)
    Maximum likelyhood phylogenetic analysis was performed with IQ-TREE v.
    IQ-TREE
    suggested: (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.

    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.

  2. Version published to 10.1101/2020.11.28.20237016v1 on medRxiv