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

• DOI: 10.1093/jalm/jfae095
• Publication Date: 2024-09-09T06:51:29Z
• Authors: Jason S Chwa; Yunho Shin; Yesun Lee; Thomas Fabrizio; Zion Congrave-Wilson; Wesley A Cheng; Jaycee Jumarang; Minjun Kim; Richard Webby; Jeffrey M Bender; Pia S Pannaraj

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