Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 variant transition in the Swedish population reveals higher viral quantity in BA.2 cases

  1. Antonio Lentini
  2. Antonio Pereira
  3. Ola Winqvist
  4. Björn Reinius

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Abstract

Throughout the SARS-CoV-2 pandemic, multiple waves of variants of concern have swept across populations, leading to a chain of new and yet more contagious lineages dominating COVID-19 cases. Here, we tracked the remarkably rapid shift from Omicron BA.1 to BA.2 sub-variant dominance in the Swedish population during January–March 2022. By analysis of 174,933 clinical nasopharyngeal swab samples using a custom variant-typing RT-PCR assay, we uncover nearly two-fold higher levels of viral RNA in cases with Omicron BA.2. Importantly, increased viral load in the upper pharynx upon BA.2 infection may provide part of the explanation why Omicron BA.2 is more transmissible and currently outcompetes the BA.1 variant across populations.

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  1. Rapid Reviews Infectious Diseases

    Firdausi Qadri

    Review 2: "Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 Variant Transition in the Swedish Population Reveals Higher Viral Quantity in BA.2 Cases"

    In general, reviewers believe this preprint sets useful groundwork for future research, though somewhat lacking in explanation of the methods used to choose the analyzed sample and other details.

  2. Rapid Reviews Infectious Diseases

    Jianfa Bai

    Review 1: "Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 Variant Transition in the Swedish Population Reveals Higher Viral Quantity in BA.2 Cases"

    In general, reviewers believe this preprint sets useful groundwork for future research, though somewhat lacking in explanation of the methods used to choose the analyzed sample and other details.

  4. ScreenIT

    SciScore for 10.1101/2022.03.26.22272984: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Informed consent for the use of anonymized CT values or samples obtained in routine clinical diagnostics was not obtained and is not required, and is in accordance with the study permit obtained by the Swedish Ethical Review Authority (Dnr 2020-01945 and 2022-01139-02, Etikprövningsmyndigheten).
    Sex as a biological variablenot detected.
    RandomizationFor the purpose and analyses of the current study, sample identities were anonymised, and IDs were replaced by a randomized code (i.e., those listed in supplementary tables).
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    In the parallel genotyping of 133 SARS-CoV-2-positive samples, performed using Thermo Fisher TaqMan SARS-CoV-2 Mutation Panel Assay (according to the manufacturers instructions) and our SARS-CoV-2 N1/RP/SBA1 assay, all Omicron samples were of the BA.1 lineage as demonstrated by WGS.
    Thermo Fisher TaqMan
    suggested: None
    WGS
    suggested: None
    SARS-CoV-2 One-Step RT-PCR Kit, RdRp and N Genes, IVD (NZYTech) was performed according to the manufacturer’s instructions (Version 13/2021, December 2021).
    NZYTech
    suggested: (NZYTech, RRID:SCR_016772)
    Sequencing data analysis: Raw data was quality trimmed using fastp10 v0.20.0 and de novo assembled using MEGAHIT11 v1.2.9 [--min-contig-len 5000]
    MEGAHIT11
    suggested: None
    Disjoint contigs were scaffolded against the SARS-CoV-2 reference genome [ASM985889v3] using RagTag12 v2.1.0 and SARS-CoV-2 lineage was assigned using pangolin13 v3.1.20 [lineages version 2022-02-28].
    RagTag12
    suggested: None
    Alignment statistics was obtained using Minimap214 v2.24-r1122 [-ax sr Sars_cov_2.ASM985889v3.dna_sm.toplevel.fa.gz] and samtools15 v1.10 [stats] [coverage].
    Minimap214
    suggested: None
    samtools15
    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

    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.

  5. Version published to 10.1101/2022.03.26.22272984v1 on medRxiv