This is a summary, written by members of the CITF Secretariat, of:

Matic N, Lowe CF, Ritchie G, Young M, Lawson T, Romney MG. Omicron (B. 1.1. 529) SARS-CoV-2 viral load among nasopharyngeal and oral samples compared to other Variants of Concern and impact on diagnostic testing strategy. Clinical Microbiology and Infection. 2022 May 11. doi:

The results and/or conclusions contained in the research do not necessarily reflect the views of all CITF members.

A letter published in Clinical Microbiology and Infection reported that either a nasopharyngeal swab or an oral rinse is able to detect the Omicron variant in those who were infected, even if the amount of virus detectable by the former is ten times greater than the latter. This is important because sometimes the oral rinse may be the only acceptable method of testing for SARS-CoV-2 infection. The study was led by CITF-funded researcher Dr. Marc Romney from the University of British Columbia.

Omicron replicates more proficiently in the upper respiratory tract compared to other VOCs and the original strain of SARS-CoV-21. As such, it is suggested that oral fluids such as saliva may be adept at detecting these COVID variants compared to nasal fluids. These results indicate that nasopharyngeal collection is still very effective at detecting Omicron.

Key findings:

  • Among over 8,000 SARS-CoV-2 positive samples tested, viral loads were on average 10 times greater in nasopharyngeal swabs compared to oral rinses (also known as ‘saliva gargles’).
  • While nasopharyngeal swabs exhibited higher viral loads and therefore led to more sensitive detection, oral rinses remain a suitable option for detecting SARS-CoV-2, especially in settings where nasopharyngeal collection is not available or is less acceptable/palatable.
  • Omicron viral loads were not significantly different than those from other VOCs, even when accounting for timing of sample collection.

Included in the analyses were 6,456 nasopharyngeal swabs and 1,603 oral rinses that were positive for Alpha, Delta, Gamma, or Omicron. Samples were submitted for diagnostic PCR testing between February 2021 and mid-January 2022 in British Columbia and the Yukon. Nasal swab rapid antigen tests were not assessed in this study.

1 Hui KP, Ho JC, Cheung MC, Ng KC, Ching RH, Lai KL, Kam TT, Gu H, Sit KY, Hsin MK, Au TW. SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo. Nature. 2022 Feb 1. Doi: 10.1038/s41586-022-04479-6