Investigation of Discordant SARS-CoV-2 RT-PCR Results Using Neat Saliva

Saliva is an attractive sample for coronavirus disease 2019 testing due its ease of collection and amenability to detect viral RNA without processing. Using a direct-to-RT-PCR method with saliva self-collected from confirmed COVID-19 positive volunteers, we observed 32% false negative results. Confirmed negative and healthy volunteer samples spiked with 10⁶ genome copies/mL of heat-inactivated severe acute respiratory syndrome coronavirus 2 showed false negative results of 10% and 13%, respectively. Additional sample heating or dilution of the false negative samples conferred modest improvement. These results highlight the potential to significantly underdiagnose COVID-19 infections when testing directly from heterogeneous neat saliva samples.