SARS-CoV-2 Variants May Affect Saliva RT-PCR Assay Sensitivity

Area of Science:

• Virology
• Infectious Diseases
• Diagnostic Testing

Background:

• Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants exhibit varied tropism within the respiratory tract.
• Saliva-based reverse transcription-polymerase chain reaction (RT-PCR) offers a convenient and cost-effective alternative to nasopharyngeal swabs (NPS).
• Limited research exists on saliva testing sensitivity across different SARS-CoV-2 variants of concern.

Purpose of the Study:

• To investigate the sensitivity of saliva-based RT-PCR for detecting SARS-CoV-2 across different variants.
• To compare saliva sensitivity between symptomatic and asymptomatic individuals.
• To identify factors influencing the accuracy of saliva-based SARS-CoV-2 detection.

Main Methods:

• Paired NPS and saliva specimens from symptomatic or exposed individuals were tested using SARS-CoV-2 RT-PCR.
• Viral genome sequencing identified the infecting SARS-CoV-2 variant.
• Saliva sensitivity was determined relative to NPS-positive RT-PCR results, with statistical analyses performed.

Main Results:

• Overall saliva sensitivity was 61.7%, with higher sensitivity observed during Delta variant infections (79.6%) compared to pre-Delta (58.5%) and Omicron (61.5%) variants.
• Saliva sensitivity was significantly higher in symptomatic individuals across all variants (e.g., 78.7% for Omicron) versus asymptomatic cases (e.g., 51.2% for Omicron).
• Delta variant infection, presence of symptoms, and high NPS viral load were independently associated with increased odds of positive saliva RT-PCR results.

Conclusions:

• Saliva-based RT-PCR sensitivity for SARS-CoV-2 varies by variant and symptom status.
• The Delta variant and symptomatic infection are linked to higher saliva test sensitivity.
• Continuous evaluation of saliva testing is essential for effective SARS-CoV-2 detection as new variants emerge.