Top 5 Takeaways

  1. Omicron BA.1 Shows Higher Ct Values: The Omicron BA.1 sublineage exhibited higher cycle threshold (Ct) values compared to pre-Omicron variants, indicating lower RNA levels in nasal swabs.
  2. Culturable Virus in Omicron Infections: Despite higher Ct values, culturable SARS-CoV-2 virus was still detected in Omicron BA.1 infections, challenging the consistency of Ct values as a proxy for infectiousness.
  3. Study Methodology: The study involved longitudinal nasal swab specimen collection from a cohort of nonhospitalized, SARS-CoV-2 positive participants in the San Francisco Bay Area, with specimen analysis comparing Omicron and pre-Omicron infections.
  4. Variant-Specific Viral Dynamics: The findings highlight variant-specific differences in viral dynamics, particularly in the relationship between RNA levels and shedding of infectious virus.
  5. Public Health Implications: The study supports CDC guidance that Ct values are not a consistent indicator of infectiousness across different SARS-CoV-2 variants.

Original Article Author and Citation

Corresponding Author

J. Daniel Kelly,

Suggested Citation

Tassetto M, Garcia-Knight M, Anglin K, et al. Detection of Higher Cycle Threshold Values in Culturable SARS-CoV-2 Omicron BA.1 Sublineage Compared with Pre-Omicron Variant Specimens — San Francisco Bay Area, California, July 2021—March 2022. MMWR Morb Mortal Wkly Rep 2022;71:1151–1154. DOI:


The MMWR article focuses on a study that analyzed nasal swab specimens from a cohort in the San Francisco Bay Area, comparing SARS-CoV-2 Omicron BA.1 sublineage with pre-Omicron variants. The key observation was that Omicron BA.1 infections exhibited higher cycle threshold (Ct) values, suggesting lower RNA levels, but still maintained the presence of culturable virus.


Participants with confirmed SARS-CoV-2 infection self-collected nasal swabs daily for two weeks. The specimens were analyzed using real-time RT-PCR to determine Ct values, whole genome sequencing for variant identification, and tissue culture for assessing culturable virus.


The study highlights the inconsistency of using Ct values as indicators of infectiousness across SARS-CoV-2 variants. The presence of culturable virus in Omicron BA.1 specimens despite higher Ct values suggests variant-specific differences in the relationship between RNA levels and infectious virus shedding.


This study underscores the need for caution in using Ct values as a proxy for infectiousness in SARS-CoV-2 infections, especially considering variant-specific dynamics. The findings support CDC guidance and add to the understanding of how different SARS-CoV-2 variants behave.

This has been your booster shot of MMWR Info! Please check back for more MMWR, Public Health, and Programming Tutorial content daily.

Leave a Reply

Your email address will not be published. Required fields are marked *

You may use these HTML tags and attributes:

<a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <s> <strike> <strong>