With the emergence of the Omicron variant, determining the most effective testing methods for SARS-CoV-2 became crucial. Researchers aimed to understand how different sampling methods—nasopharyngeal (NP), nasal, oropharyngeal (OP), and saliva—compare in detecting Omicron using RT-PCR and antigen tests.

As self-testing gained popularity and debates over sampling methods intensified, this study aimed to fill in the knowledge gaps surrounding viral load differences and diagnostic effectiveness.

Research Overview: Two Cohorts, Multiple Sample Types

The study took place in Atlanta during Omicron’s peak in January 2022, involving two cohorts: a family cohort that self-collected nasal, OP, and saliva samples, and a larger, cross-sectional cohort of 121 symptomatic individuals whose samples were collected by trained staff. Both cohorts’ samples were tested using RT-PCR and ultrasensitive antigen testing to assess viral loads across different sample types.

Family Cohort Findings: Nasal-Predominant Viral Load

For the family cohort, self-collected nasal swabs consistently showed higher viral antigen levels and lower cycle threshold (Ct) values, indicating a larger quantity of viral RNA compared to OP and saliva samples. This result suggested that nasal swabs might consistently capture a “nasal-predominant” viral load across various timepoints of infection, providing useful insights into testing strategies.

Cross-Sectional Findings: Mixed Viral Load Phenotypes

In contrast, the cross-sectional cohort displayed mixed viral load phenotypes. There was no clear dominance of any sample type across 39 confirmed positive cases. While some individuals showed a “MT-predominant” viral load, others exhibited an “OP-predominant” phenotype. Interestingly, saliva consistently showed higher antigen levels than both MT and OP, although it did not correlate with improved diagnostic performance.

Diagnostic Performance: RT-PCR and Antigen Sensitivity

The study assessed diagnostic accuracy using RT-PCR and antigen tests. RT-PCR testing showed high positive percent agreement (PPA) ranging from 89.7% to 94.4% across MT, OP, and saliva samples, with minor overlap. Antigen tests, however, had a lower PPA, from 64.9% to 91.4%, depending on the clinical cutoff. Combining MT and OP samples slightly increased sensitivity but did not provide a statistically significant improvement over MT alone.

Symptom Correlations and Viral Load

In subgroup analyses, symptoms like sore throat and rhinorrhea appeared to influence viral loads in specific sample types. Participants with sore throats had higher OP viral antigen levels, while those with rhinorrhea showed higher MT antigen levels. This suggests that symptom-based selection of sample types could help optimize testing strategies.

Factors Affecting Viral Load

Statistical modeling revealed that sample type played a significant role in antigen concentration, but not in cycle threshold (Ct) values. Interestingly, factors like the duration of symptoms and vaccination status did not significantly impact the Ct or antigen levels, highlighting the variability of viral load across different sample types.

Key Takeaways and Future Implications

This research did not identify a single best sample type for SARS-CoV-2 detection during Omicron’s prevalence. However, the findings suggest that combining MT and OP samples might increase sensitivity. The potential role of symptoms in predicting the most effective sample types also warrants further investigation. While saliva showed high antigen levels, the lack of validated saliva rapid tests limits its clinical utility. Ultimately, more extensive studies are needed to confirm these trends and refine testing strategies.

For accurate and reliable sample collection, consider using Yousuto OP swabs, designed for optimal viral detection and improved diagnostic results.

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References:
Comparison of RT-PCR and antigen test sensitivity across nasopharyngeal, nares, and oropharyngeal swab, and saliva sample types during the SARS-CoV-2 Omicron variant.