Background: RT-PCR on nasopharyngeal (NPS)/oropharyngeal swabs is the gold standard
for diagnosis of SARS-CoV-2 infection and viral load monitoring. Oral fluid (OF) is an alternate
clinical sample, easy and safer to collect and could be useful for COVID-19 diagnosis, monitoring viral
load and shedding. Methods: Optimal assay conditions and analytical sensitivity were established
for the commercial Simplexa™ COVID-19 Direct assay adapted to OF matrix. The assay was
used to test 337 OF and NPS specimens collected in parallel from 164 hospitalized patients;
50 bronchoalveolar lavage (BAL) specimens from a subgroup of severe COVID-19 cases were
also analysed. Results: Using Simplexa™ COVID-19 Direct on OF matrix, 100% analytical detection
down to 1 TCID50/mL (corresponding to 4 × 103
copies (cp)/mL) was observed. No crossreaction
with other viruses transmitted through the respiratory toute was observed. Parallel testing of 337 OF
and NPS samples showed highly concordant results (κ = 0.831; 95 % CI = 0.771–0.891), and high
correlation of Ct values (r = 0.921; p < 0.0001). High concordance and elevated correlation was
observed also between OF and BAL. Prolonged viral RNA shedding was observed up to 100 days
from symptoms onset (DSO), with 32% and 29% positivity observed in OF and NPS samples,
respectively, collected between 60 and 100 DSO. Conclusions: Simplexa™ COVID-19 Direct assays on
OF have high sensitivity and specificity to detect SARS-CoV-2 RNA and provide an alternative to
NPS for diagnosis and monitoring SARS-CoV-2 shedding
