Performance of RT-PCR on saliva specimens compared to nasopharyngeal swabs for the detection of SARS-CoV-2 in children: A prospective comparative clinical trial

ABSTRACT Background Saliva RT-PCR is an attractive alternative for the detection of SARS-CoV-2 in adults with much less known in children. Methods Children and adolescents with symptoms suggestive of COVID-19 were prospectively enrolled in a comparative clinical trial of saliva and nasopharyngeal (NP) RT-PCR between November and December 2020. Detection rates and sensitivities of saliva and NP RT-PCR were compared. Participants with discordant NP and saliva RT-PCR results including viral load (VL) were also analyzed. Result Out of 405 patients enrolled, 397 patients had two tests performed. Mean age was 12.7 years (range 1.2-17.9). Detection rates were 22.9% (95%CI 18.8-27.1%) by saliva RT-PCR, 25.4% (21.2-29.7%) by NP RT-PCR, and 26.7% (22.4-31.1%) by any test. The sensitivity of saliva was 85.2% (78.2-92.1%) when using NP as the gold standard; in contrast, when saliva was considered the gold standard, the sensitivity of NP was 94.5% (89.8-99.2%).For a NP RT-PCR VL threshold of ≥10 3 and ≥10 4 copies/ml, sensitivity of saliva increases to 88.7% and 95.2% respectively. Sensitivity of saliva and NP swabs was respectively 89.5% and 95.3% in patient with symptoms less than 4 days (p=0.249) and 70.0% and 95.0% in those with symptoms ≥ 4 to 7 days (p=0.096). The 15 patients who had an isolated positive NP RT-PCR were significantly younger (p=0.034), had a lower NP VL (median 5.6×10 3 vs 3.9×10 7 , p<0.001), and were not able to drool saliva at the end of the sampling (p=0.002). VLs were significantly lower with saliva PCR than with NP RT-PCR (median 8.7 cp/ml x10 4 ; IQR 1.2×10 4 -5.2×10 5 ; vs median 4.0×10 7 cp/ml; IQR 8.6×10 5 -1.x10 8 ; p<0.001). Conclusion Saliva PCR shows diagnostic performances close to NP RT-PCR for SARS-CoV2 detection in most symptomatic outpatient children and adolescents.