Journal Article

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

Cheng, Wesley A, Fabrizio, Thomas, Shin, Yunho, Pannaraj, Pia S, Webby, Richard, Bender, Jeffrey M, Chwa, Jason S, Lee, Yesun, Kim, Minjun, Jumarang, Jaycee, Congrave-Wilson, Zion

2024

Overview

Abstract Background Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants demonstrate predilection for different regions of the respiratory tract. While saliva-based reverse transcription-polymerase chain reaction (RT-PCR) testing is a convenient, cost-effective alternative to nasopharyngeal swabs (NPS), few studies to date have investigated whether saliva sensitivity differs across variants of concern. Methods SARS-CoV-2 RT-PCR was performed on paired NPS and saliva specimens collected from individuals with acute coronavirus disease 2019 (COVID-19) symptoms or exposure to a COVID-19 household contact. Viral genome sequencing of NPS specimens and Los Angeles County surveillance data were used to determine the variant of infection. Saliva sensitivity was calculated using NPS-positive RT-PCR as the reference standard. Factors contributing to the likelihood of saliva SARS-CoV-2 RT-PCR positivity were evaluated with univariate and multivariable analyses. Results Between June 2020 and December 2022, 548 saliva samples paired with SARS-CoV-2 positive NPS samples were tested by RT-PCR. Overall, saliva sensitivity for SARS-CoV-2 detection was 61.7% (95% CI, 57.6%–65.7%). Sensitivity was highest with Delta infection (79.6%) compared to pre-Delta (58.5%) and Omicron (61.5%) (P = 0.003 and 0.01, respectively). Saliva sensitivity was higher in symptomatic individuals across all variants compared to asymptomatic cases [pre-Delta 80.6% vs 48.3% (P < 0.001), Delta 100% vs 72.5% (P = 0.03), Omicron 78.7% vs 51.2% (P < 0.001)]. Infection with Delta, symptoms, and high NPS viral load were independently associated with 2.99-, 3.45-, and 4.0-fold higher odds of SARS-CoV-2 detection by saliva-based RT-PCR (P = 0.004, <0.001, and <0.001), respectively. Conclusions As new variants emerge, evaluating saliva-based testing approaches may be crucial to ensure effective virus detection.

• Publisher: Oxford University Press
• Subject: Adolescent / Adult / Aged / Coronaviruses / COVID-19 / COVID-19 - diagnosis / COVID-19 - virology / COVID-19 Nucleic Acid Testing - methods / Female / Humans / Infections / Male / Middle Aged / Nasopharynx - virology / Polymerase chain reaction / Respiratory tract / Reverse Transcriptase Polymerase Chain Reaction - methods / Reverse transcription / RNA, Viral - analysis / RNA, Viral - genetics / RNA, Viral - isolation & purification / Saliva / Saliva - virology / SARS-CoV-2 - genetics / SARS-CoV-2 - isolation & purification / Sensitivity and Specificity / Severe acute respiratory syndrome coronavirus 2 / Young Adult