SARS-CoV-2 Omicron Variant, Lineage BA.1, Is Associated with Lower Viral Load in Nasopharyngeal Samples Compared to Delta Variant

  1. Célia Sentis
  2. Geneviève Billaud
  3. Antonin Bal
  4. Emilie Frobert
  5. Maude Bouscambert
  6. Gregory Destras
  7. Laurence Josset
  8. Bruno Lina
  9. Florence Morfin
  10. Alexandre Gaymard
  11. the COVID-Diagnosis HCL Study Group

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Abstract

Objectives: High viral load in upper respiratory tract specimens observed for Delta cases might contribute to its increased infectivity compared to the other variant. However, it is not yet documented if the Omicron variant’s enhanced infectivity is also related to a higher viral load. Our aim was to determine if the Omicron variant’s spread is also related to higher viral loads compared to the Delta variant. Methods: Nasopharyngeal swabs, 129 (Omicron) and 85 (Delta), from Health Care Workers were collected during December 2021 at the University Hospital of Lyon, France. Cycle threshold (Ct) for the RdRp target of cobas® 6800 SARS-CoV-2 assay was used as a proxy to evaluate SARS-CoV-2 viral load. Variant identification was performed using a screening panel and confirmed by whole genome sequencing. Results: Herein, we showed that the RT-PCR Ct values in Health Care Workers sampled within 5 days after symptom onset were significantly higher for Omicron cases than Delta cases (21.7 for Delta variant and 23.8 for Omicron variant, p = 0.008). This difference was also observed regarding patient with complete vaccination. Conclusions: This result supports the studies showing that the increased transmissibility of Omicron is related to other mechanisms than higher virus excretion.

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  1. Version published to 10.3390/v14050919
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    SciScore for 10.1101/2022.02.02.22269653: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.

    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: We detected the following sentences addressing limitations in the study:
    The present study has several limitations as viral load was estimated by Ct without specific quantification and normalization. Only BA.1 lineage were circulating in France during the study period and results for other Omicron lineage such as BA.2 could differ. Our results were also impacted by the vaccination strategy. Omicron viral load was lower for patients with complete vaccination but the inverse trend was observed for boosted patients. This might be related to a lower susceptibility to neutralizing antibodies for Omicron variant compared to Delta variant. Boosted patients infected by Delta variant might be more protected than patients infected by Omicron, which would explain the lower viral load in Delta group (8,15,16). These results should be taken carefully as more patients with boosted vaccination were observed in the Omicron infection group and counterwise more patients with complete vaccination were observed in the Delta infection group (Table 1). This observation has to be related to the National vaccination strategy, as French government announced a mandatory third dose vaccination to health care workers during December. In addition, most of positive samples for Delta variant were collected at the beginning of December. Omicron variant began to be detected in France mid-December 2021 and overthrow Delta variant during the last week of December (Figure 1A). A more in-depth study taking into account vaccination status, time since the last injection and antibody le...

    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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  3. Version published to 10.1101/2022.02.02.22269653 on medRxiv