Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Direct Quantitation of SARS-CoV-2 Using Droplet Digital PCR in Suspected Samples With Very Low Viral Load

Version 1 : Received: 23 April 2021 / Approved: 26 April 2021 / Online: 26 April 2021 (20:09:26 CEST)

How to cite: Deiana, M.; Piubelli, C.; Mori, A.; Chiecchi, G.P.; La Marca, G.; Leonardi, M.; Treggiari, D.; Beltrame, A.; Moro, L.; Bisoffi, Z.; Pomari, E. Direct Quantitation of SARS-CoV-2 Using Droplet Digital PCR in Suspected Samples With Very Low Viral Load. Preprints 2021, 2021040688 (doi: 10.20944/preprints202104.0688.v1). Deiana, M.; Piubelli, C.; Mori, A.; Chiecchi, G.P.; La Marca, G.; Leonardi, M.; Treggiari, D.; Beltrame, A.; Moro, L.; Bisoffi, Z.; Pomari, E. Direct Quantitation of SARS-CoV-2 Using Droplet Digital PCR in Suspected Samples With Very Low Viral Load. Preprints 2021, 2021040688 (doi: 10.20944/preprints202104.0688.v1).

Abstract

Background: The reference test for SARS-CoV-2 detection is the reverse transcriptase real time PCR (real time RT-PCR). However, evidences reported that real time RT-PCR has a lower sensitivity compared with the droplet digital PCR (ddPCR) leading to possible false negative in low viral load cases. Methods: We used ddPCR for viral genes N1 and N2 on 20 negative (no detection) samples from symptomatic hospitalized COVID-patients presenting fluctuating real time RT-PCR results and 10 suspected samples (Ct value>35) from asymptomatic not hospitalized subjects. Results: ddPCR performed on RNA revealed 65% of positivity for at least one viral target in the hospitalized patients group of samples (35% for N1 and N2, 10% only for N1 and 20% only for N2) and 50% in the suspected cases (30% for N1 and N2, while 20% only for N2). On hospitalized patients’ samples, we applied also a direct ddPCR approach on the swab material, achieving an overall positivity of 83%. Conclusion: ddPCR, in particular the direct quantitation on swabs, shows a sensitivity advantage for the SARS-CoV-2 identification and may be useful to reduce the false negative diagnosis, especially for low viral load suspected samples.

Subject Areas

droplet digital PCR; real time RT-PCR; SARS-CoV-2; false negative; viral load; diagnosis

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