Viruses (Oct 2020)

Frequency and Duration of SARS-CoV-2 Shedding in Oral Fluid Samples Assessed by a Modified Commercial Rapid Molecular Assay

  • Licia Bordi,
  • Giuseppe Sberna,
  • Eleonora Lalle,
  • Pierluca Piselli,
  • Francesca Colavita,
  • Emanuele Nicastri,
  • Andrea Antinori,
  • Evangelo Boumis,
  • Nicola Petrosillo,
  • Luisa Marchioni,
  • Giulia Minnucci,
  • Elena D’Agostini,
  • Concetta Castilletti,
  • Franco Locatelli,
  • Alimuddin Zumla,
  • Giuseppe Ippolito,
  • Maria Rosaria Capobianchi,
  • on behalf of INMI ReCOVeRI Study Group

DOI
https://doi.org/10.3390/v12101184
Journal volume & issue
Vol. 12, no. 10
p. 1184

Abstract

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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.

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