Saliva Swabs Are The Preferred Sample For Omicron Detection
Regardless of the impact of vaccination, accurate diagnostics remain critical to the COVID-19 pandemic response. With the emergence of the Omicron variant, we are now facing with an upsurge in the number of cases worldwide, along with an increased risk of reinfection and vaccine breakthrough infections. The Omicron variant is characterized by more than 50 mutations, most which are located in the spike protein. The significance of these mutations regarding viral transmission, tissue tropism and diagnostic testing is yet to be fully discovered. Recent studies suggest that these mutations might have altered the tissue tropism of the virus, altering the tissues the virus may prefer to infect. Indeed, current data indicate that unlike previous variants, Omicron exhibits higher levels of viral shedding in saliva specimen relative to nasal specimen, signifying that saliva swabs may be more accurate at detecting the Omicron variant than nasal swabs. Here’s what to know about the current findings on the issue.
Saliva-Based COVID-19 Testing May Be More Accurate at Detecting the Omicron Variant
Recent research demonstrates that as the Omicron variant displays higher replication rates in the upper respiratory tract than the Delta variant, while nasal swabs were more accurate with the Delta variant, saliva swabs may be more accurate for the PCR-based detection of the omicron variant. Indeed, Relative to previous variants, preliminary data shows that Omicron exhibits higher viral loads in the mouth, throat, and saliva compared to the nose. Along with higher accuracy, studies suggest that saliva-based tests could detect the presence of the virus days earlier than its appearance in the nasal swab.
A study from the University of Cape Town has analyzed the relative performance of saliva-based tests and mid-turbinate tests for the PCR-based identification of delta and omicron variants. To this end, the team collected saliva specimen and mid-turbinate specimen from 382 symptomatic, non-hospitalized patients who came in to get tested for COVID-19 between August and December 2021. The detection of SARS-CoV-2 RNA in either specimen was considered a positive infection. To evaluate the positive percent agreement of each swab, the results derived from the test samples and composite standards were compared. For the Delta variant, the positive percent agreement of swabs to the composite standard was 71% for saliva and 100% for the nasal swabs. In the case of Omicron, however, the rates were reversed, with 100% for saliva and 86% for nasal swabs.
Viral Load in Saliva Samples
Although the study is yet to be peer reviewed, these findings showcase that the saliva specimen contain more SARS-CoV-2 RNA than nasal specimen and supports the existing data on altered tissue tropism for the Omicron variant. Consequently, the researchers conclude that presumably due to altered tissue tropism and viral shredding pattern of the Omicron variant, PCR tests based on nasal specimen are less effective at detecting the variant than saliva-based tests.
Still, this may be especially true at the early onset of the infection. Another study from the USA suggests that in the early phase of the infection, compared to the nasal specimen, saliva specimen is 12 times more likely to test positive for SARS-CoV-2. However, after around three days, the viral load in the nose seemed to grow, and the difference in accuracy between the specimen decreased.
Can nasal at-home tests be used on throat specimen?
Recently a health official from Israel recommended antigen test users to swab their throat along with their nose when self-testing for COVID-19. Some professionals in the US have also claimed that people should swab the throat before swabbing the nose. Although many people have reportedly started modifying their at-home tests to swab both the back of their throat and their nose, for the time being, experts are advising tests to be used as instructed. Many tests are either specifically designed and authorized for throat swabs or for nasal swabs. Moreover, the existing data demonstrates that collecting an adequate throat sample may be more challenging than a nasal sample, leading to more sampling errors and false negative results.
Points to consider when taking a saliva-based test
When it comes to saliva-based tests, eating, drinking, smoking, or chewing anything before the test could affect the results. Many tests do advise that you wait for at least thirty minutes after you consume something to perform the test. It is also recommended to swab the inside of the mouth, including above and below the tongue, insides of both cheeks, the gums, and the hard palate for at least 30 minutes to get the best results.
As the Omicron variant becomes the dominant variant worldwide, early findings of recent studies suggest that the reassessment of current diagnostic sampling methods and testing standards may be necessary. Although these findings indicate that nasal or nasopharyngeal specimen alone may result in “suboptimal diagnoses”, most tests for at-home and healthcare use are formulated for nasal swabs. In many countries, saliva-based tests are not authorized or commercially available. Moreover, many diagnostic laboratories are not equipped to analyze saliva samples. On the other hand, the next variant may not exhibit similar characteristics. Perhaps future tests should be designed to process both mouth and nasal specimen. Overall, the need to adjust to new variants and upcoming data requires higher flexibility regarding our response to the pandemic.
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- Adamson, B., Sikka, R., Wyllie, A. L., & Premsrirut, P. (2022). Discordant SARS-CoV-2 PCR and rapid antigen test results when infectious: A December 2021 occupational case series. medRxiv. https://doi.org/10.1101/2022.01.04.22268770
- Marais, G., Hsiao, N. Y., Iranzadeh, A., Doolabh, D., Enoch, A., Chu, C. Y., Williamson, C., Brink, A., & Hardie, D. (2021). Saliva swabs are the preferred sample for Omicron detection. medRxiv. https://doi.org/10.1101/2021.12.22.21268246