Saliva molecular testing bypassing RNA extraction is suitable for monitoring and diagnosing SARS-CoV-2 infection in children

Abstract

IMPORTANCE Adults are being vaccinated against SARS-CoV-2 worldwide, but the longitudinal protection of these vaccines is uncertain, given the ongoing appearance of SARS-CoV-2 variants. Children are susceptible to infection, and some studies reported that they actively transmit the virus even when asymptomatic, thus affecting the community. Methods to easily test infected children and track the virus they carry are in demand. OBJECTIVE To determine if saliva is an effective sample for detecting SARS-CoV-2 RNA and antibodies in children aged 10 years and under, and associate viral RNA levels to infectivity. DESIGN, SETTING, AND PARTICIPANTS In this cross-sectional study, saliva SARS-CoV-2 RT-qPCR tests, with and without RNA extraction, were validated in 49 hospitalized adults. The test was then applied to 85 children, aged 10 years and under, admitted to the hospital regardless of COVID-19 symptomatology. Amongst 85 children, 29 (63.0%) presented at least one COVID-19 symptom, 46 (54.1%) were positive for SARS-CoV-2 infection, 28 (32.9%) were under the age of 1 and the mean (SD) age was 3.8 (3.4) years. Saliva samples were collected up to 48 h after a positive test by nasopharyngeal (NP) swab-RT-qPCR. EXPOSURE Infection by SARS-COV-2 in adults up to 8 days post-symptom onset. Children admitted to hospital for any reason and therefore with unclear onset of SARS-CoV-2 infection. MAIN OUTCOMES AND MEASURES Saliva RT-qPCR up to CT<37 accurately identifies SARS-CoV-2 infected children, with viral infectivity in tissue culture restricted to CT<26. RESULTS In adults, the accuracy of the saliva SARS-CoV-2 RT-qPCR test was 98.0% (95% confidence intervals [CI]: 89.3%-100%) as compared to NP-RT-qPCR. In children, the sensitivity, specificity, and accuracy of saliva-RT-qPCR tests compared to NP swab-RT-qPCR were, respectively, 84.8% (71.8%-92.4%), 100% (91.0%-100%), and 91.8% (84.0%-96.6%) with RNA extraction and 81.8% (68.0%-90.5%), 100% (91.0%-100%), and 90.4% (82.1%-95.0%) without RNA extraction. The threshold for rescuing infectious particles from saliva was CT<26. There were significant IgM positive responses to the spike protein and its receptor-binding domain (RBD) among children positive for SARS-CoV-2 by NP swab and negative by saliva compared to other groups, indicating late infection onset (>7-10 days). CONCLUSIONS AND RELEVANCE Saliva-molecular testing is suitable in children aged 10 years and under, including infants aged <1 year, even bypassing RNA extraction methods. Importantly, the detected viral RNA levels were significantly above the infectivity threshold in several samples. Further investigation is required to understand how SARS-CoV-2 RNA levels correlate with viral transmission.