ABSTRACT
Background: Saliva is an attractive sample for detecting SARS-CoV-2 because it is easy to collect and minimally invasive. However, contradictory reports exist concerning the sensitivity of saliva versus nasal swabs. Methods: We recruited and followed close contacts of COVID-19 cases for up to 14 days from their last exposure and collected self-reported symptoms, mid-turbinate swabs (MTS) and saliva every two or three days. Ct values and frequency of viral detection by MTS and saliva were compared. Logistic regression was used to estimate the probability of detection by days since symptom onset for the two sample types. Results: We enrolled 58 contacts who provided a total of 200 saliva and MTS sample pairs; 14 contacts (13 with symptoms) had one or more positive samples. Overall, saliva and MTS had similar rates of viral detection (p=0.78). Although Ct values for saliva were significantly greater than for MTS (p=0.014), Cohen's Kappa demonstrated substantial agreement ({kappa}=0.83). However, sensitivity varied significantly with time relative to symptom onset. Early in the course of infection (days -3 to 2), saliva had 12 times (95%CI: 1.2, 130) greater likelihood of detecting viral RNA compared to MTS. After day 2, there was a non-significant trend to greater sensitivity using MTS samples. Conclusion: Saliva and MTS specimens demonstrated high agreement, making saliva a suitable alternative to MTS nasal swabs for COVID-19 detection. Furthermore, saliva was more sensitive than MTS early in the course of infection, suggesting that it may be a superior and cost-effective screening tool for COVID-19.