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. 2022 Apr 28;14(5):919.
doi: 10.3390/v14050919.

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

Célia Sentis  1   2 , Geneviève Billaud  1 , Antonin Bal  1   2   3 , Emilie Frobert  1   2 , Maude Bouscambert  1 , Gregory Destras  1   2   3 , Laurence Josset  1   2   3 , Bruno Lina  1   2 , Florence Morfin  1   2 , Alexandre Gaymard  1   2 , The Covid-Diagnosis Hcl Study Group
Affiliations

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

Célia Sentis et al. Viruses. .

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.

Keywords: COVID-19; Delta variant; Omicron variant; SARS-CoV-2; viral load.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
RT-PCR cycle threshold values for Delta or Omicron. (A): Cycle threshold of Delta or Omicron variant according to symptoms. Global analysis included all samples (Delta, n = 85, Omicron, n = 129). Asymptomatic patients (Delta, n = 28 and Omicron, n = 34), symptoms appearing less than 5 days prior sampling (Delta, n = 51 and Omicron, n = 74) and symptoms appearing more than 5 days prior sampling (Delta, n = 6 and Omicron, n = 21). (B): Cycle threshold of Omicron or Delta variant by age. Ct was analyzed for patients under 40 years old (Delta, n = 61 and Omicron, n = 90) and patients over 40 years old (Delta, n = 24 and Omicron, n = 39). (C): Cycle threshold of Delta or Omicron variant according to vaccination status. Vaccination was considered complete when patient received 2 doses or 1 dose and 1 infection or less than 7 days after the third dose (Delta, n = 52 and Omicron, n = 43) and boosted when patients received 3 doses or 2 doses and 1 infection (Delta, n = 18 and Omicron, n = 58). p-value was calculated with Student’s t-test. ns = not significant, * = <0.05, ** = <0.01, *** = <0.001.
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Supplementary concepts