Change in Saliva RT-PCR Sensitivity Over the Course of SARS-CoV-2 Infection

While real-time reverse transcriptase-polymerase chain reaction (RT-PCR) on nasopharyngeal swabs is the current standard for SARS-CoV-2 detection, saliva is an attractive alternative for diagnosis and screening due to ease of collection and minimal supply requirements.1,2 Studies on the sensitivity of saliva-based SARS-CoV-2 molecular testing have shown considerable variability.3 We conducted a prospective, longitudinal study to investigate the testing time frame that optimizes saliva sensitivity for SARS-CoV-2 detection. Between June 17,2020, and February 15,2021, a convenience sample of individuals exposed to a household member with RT-PCR-confirmed SARS-CoV-2 within 2 weeks were recruited from Children's Hospital Los Angeles and nearby community testing sites into the Household Exposure and Respiratory Virus Transmission and Immunity Study (HEARTS). Paired nasopharyngeal and saliva samples were collected every 3 to 7 days for up to 4 weeks or until 2 negative nasopharyngeal test results. RT-PCR for SARS-CoV-2 N1 and N2 genes was performed; cycle threshold less than 40 defined a positive result. A nasopharyngeal N1 cycle threshold of 34 or less was defined as high viral load. Detailed specimen collection and RT-PCR methods are reported in the eMethods in the Supplement.