Introduction and community transmission of SARS-CoV-2 lineage A.2.5 in Florida with novel spike INDELS

  1. Sarah E. Schmedes
  2. Taj Azarian
  3. Eleonora Cella
  4. Jessy Motes
  5. Omer Tekin
  6. James Weiss
  7. Nancimae Miller
  8. Jason Blanton

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Abstract

SARS-CoV-2 (SC2) variants of concern (VOC) continue to emerge and spread globally, threatening the use of monoclonal antibody therapies and vaccine effectiveness. Several mutations in the SC2 spike glycoprotein have been associated with reduction in antibody neutralization. Genomic surveillance of SC2 variants has been imperative to inform the public health response regarding the use of clinical therapies in specific jurisdictions based on the proportion of particular variants (e.g., Gamma (P.1)) in a region. Florida Department of Health Bureau of Public Health Laboratories (BPHL) performs tiled-amplicon whole genome sequencing for baseline and targeted surveillance of SC2 isolates in Florida from clinical specimens collected from county health departments and hospitals throughout the state. Here, we describe the introduction of SC2 lineage A.2.5 in Florida, which contains S:L452R (a substitution of therapeutic concern) and two novel Spike INDELS, the deletion of 141-143 and ins215AGY, with unknown implications on immune response. The A.2.5 lineage was first detected in Florida among an outbreak at a healthcare facility in January 2021, and subsequent A.2.5 isolates were detected across all geographical regions throughout the state. A time-scaled maximum clade credibility phylogeny determined there were at least eight separate introductions of A.2.5 in the state. The time of introduction of a monophyletic Florida clade was established to be December 2020. The Spike INDELS were determined to reside in the N-terminal domain, a region associated with antibody neutralization. As community transmission of SARS-CoV-2 in Florida continues, genomic surveillance of circulating variants in Florida and the detection of emerging variants are critical for informing public health response to COVID-19.

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  1. ScreenIT

    SciScore for 10.1101/2021.12.03.21266538: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Ethics Statement: This work has been reviewed by the Florida Department of Health Ethics and Human Research Protection Program and the Institutional Review Board determined that the ‘activity is public health practice and not research involving human subjects.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    RNA was purified by multiple methods, including: Kingfisher combined with the Thermo Fisher MagMAX Viral/Pathogen II (MVP II) Nucleic Acid Isolation kit (Applied Biosystems by Thermo Fisher Scientific, Waltham,
    Thermo Fisher MagMAX
    suggested: None
    MA); Abbott m2000 System combined with the Abbott RealTime SARS-CoV-2 assay (Abbott, Lake County, IL;
    Abbott
    suggested: (Abbott, RRID:SCR_010477)
    Quality metrics were generated for raw sequence reads using fastqc v0.11.9 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and raw fastqs were quality filtered and trimmed (SLIDINGWINDOW:4:30 MINLEN:75 TRAILING:20) using trimmomatic v0.39 (17)
    http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
    suggested: (FastQC, RRID:SCR_014583)
    trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    Sequence adapter and Phix contamination were removed using bbduk (BBMap v38.79) (
    BBMap
    suggested: (BBmap, RRID:SCR_016965)
    Read mapping metrics were generated using samtools coverage v1.10 (19).
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Phylogenetic and coalescent analysis: Full genome sequences were aligned with MAFFT v7.475 (23), and a maximum likelihood phylogeny was inferred using IQtree (24) with the following settings: iqtree -T AUTO -s aligned.fasta -m MFP -nt AUTO - B 1000.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    A coalescent analysis was carried out using BEAST v1.10.4 (26) with a strict molecular clock model, HKY nucleotide substitution model, and exponential growth coalescent model.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    The structure was then visualized and annotated with PyMOL v2.4.2 (29).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    Ethics Statement: This work has been reviewed by the Florida Department of Health Ethics and Human Research Protection Program and the Institutional Review Board determined that the ‘activity is public health practice and not research involving human subjects.
    Human Research Protection Program
    suggested: None

    Results from OddPub: Thank you for sharing your code and data.

    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.

    About SciScore

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  2. Version published to 10.1101/2021.12.03.21266538v1 on medRxiv