Sensitivity assessment of droplet digital PCR for SARS-CoV-2 detection

Falzone,Luca; Musso,Nicolò; Gattuso,Giuseppe; Bongiorno,Dafne; Palermo,Concetta Ilenia; Scalia,Guido; Libra,Massimo; Stefani,Stefania

doi:10.3892/ijmm.2020.4673

Sensitivity assessment of droplet digital PCR for SARS-CoV-2 detection

Authors:
- Luca Falzone
- Nicolò Musso
- Giuseppe Gattuso
- Dafne Bongiorno
- Concetta Ilenia Palermo
- Guido Scalia
- Massimo Libra
- Stefania Stefani
View Affiliations

Affiliations: Epidemiology Unit, IRCCS Istituto Nazionale Tumori ‘Fondazione G. Pascale’, I‑80131 Naples, Italy, Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, I‑95123 Catania, Italy, Department of Biomedical and Biotechnological Sciences, Section of General Pathology, University of Catania, I‑95123 Catania, Italy, U.O.C. Laboratory Analysis Unit, A.O.U. ‘Policlinico‑Vittorio Emanuele’, I‑95123 Catania, Italy
Published online on: July 13, 2020 https://doi.org/10.3892/ijmm.2020.4673
Pages: 957-964
Copyright: © Falzone et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )

Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )

Cited By (CrossRef): 0 citations Loading Articles...

Abstract

Reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) is the gold standard method for the diagnosis of COVID‑19 infection. Due to pre‑analytical and technical limitations, samples with low viral load are often misdiagnosed as false‑negative samples. Therefore, it is important to evaluate other strategies able to overcome the limits of RT‑qPCR. Blinded swab samples from two individuals diagnosed positive and negative for COVID‑19 were analyzed by droplet digital PCR (ddPCR) and RT‑qPCR in order to assess the sensitivity of both methods. Intercalation chemistries and a World Health Organization (WHO)/Center for Disease Control and Prevention (CDC)‑approved probe for the SARS‑CoV‑2 N gene were used. SYBR‑Green RT‑qPCR is not able to diagnose as positive samples with low viral load, while, TaqMan Probe RT‑qPCR gave positive signals at very late Ct values. On the contrary, ddPCR showed higher sensitivity rate compared to RT‑qPCR and both EvaGreen and probe ddPCR were able to recognize the sample with low viral load as positive even at 10‑fold diluted concentration. In conclusion, ddPCR shows higher sensitivity and specificity compared to RT‑qPCR for the diagnosis of COVID‑19 infection in false‑negative samples with low viral load. Therefore, ddPCR is strongly recommended in clinical practice for the diagnosis of COVID‑19 and the follow‑up of positive patients until complete remission.

View Figures

View References

1	Chakraborty I and Maity P: COVID-19 outbreak: Migration, effects on society, global environment and prevention. Sci Total Environ. 728:1388822020. View Article : Google Scholar : PubMed/NCBI
2	Docea AO, Tsatsakis A, Albulescu D, Cristea O, Zlatian O, Vinceti M, Moschos SA, Tsoukalas D, Goumenou M, Drakoulis N, et al: A new threat from an old enemy: Re-emergence of coronavirus (Review). Int J Mol Med. 45:1631–1643. 2020.PubMed/NCBI
3	Mackenzie JS and Smith DW: COVID-19-A novel zoonotic disease: A review of the disease, the virus, and public health measures. Asia Pac J Public Health. May 30–2020.Epub ahead of print. View Article : Google Scholar : PubMed/NCBI
4	Goumenou M, Sarigiannis D, Tsatsakis A, Anesti O, Docea AO, Petrakis D, Tsoukalas D, Kostoff R, Rakitskii V, Spandidos DA, et al: COVID-19 in Northern Italy: An integrative overview of factors possibly influencing the sharp increase of the outbreak (Review). Mol Med Rep. 22:20–32. 2020.PubMed/NCBI
5	Calina D, Docea AO, Petrakis D, Egorov AM, Ishmukhametov AA, Gabibov AG, Shtilman MI, Kostoff R, Carvalho F, Vinceti M, et al: Towards effective COVID-19 vaccines: Updates, perspectives and challenges (Review). Int J Mol Med. 46:3–16. 2020.PubMed/NCBI
6	Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, Bleicker T, Brünink S, Schneider J, Schmidt ML, et al: Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 25:20000452020. View Article : Google Scholar :
7	World Health Organization (WHO): All technical guidance on COVID-19 - select topic from drop down menu. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/laboratory-guidance.
8	Won J, Lee S, Park M, Kim TY, Park MG, Choi BY, Kim D, Chang H, Kim VN and Lee CJ: Development of a Laboratory-safe and low-cost detection protocol for SARS-CoV-2 of the Coronavirus Disease 2019 (COVID-19). Exp Neurobiol. 29:107–119. 2020. View Article : Google Scholar : PubMed/NCBI
9	Wang X, Yao H, Xu X, Zhang P, Zhang M, Shao J, Xiao Y and Wang H: Limits of detection of six approved RT-PCR kits for the novel SARS-coronavirus-2 (SARS-CoV-2). Clin Chem. 66:977–979. 2020. View Article : Google Scholar : PubMed/NCBI
10	Tahamtan A and Ardebili A: Real-time RT-PCR in COVID-19 detection: Issues affecting the results. Expert Rev Mol Diagn. 20:453–454. 2020. View Article : Google Scholar : PubMed/NCBI
11	Lippi G, Simundic AM and Plebani M: Potential preanalytical and analytical vulnerabilities in the laboratory diagnosis of coronavirus disease 2019 (COVID-19). Clin Chem Lab Med. 58:1070–1076. 2020. View Article : Google Scholar : PubMed/NCBI
12	Tang YW, Schmitz JE, Persing DH and Stratton CW: Laboratory diagnosis of COVID-19: Current issues and challenges. J Clin Microbiol. 58:e00512–e00520. 2020. View Article : Google Scholar : PubMed/NCBI
13	Taylor SC, Carbonneau J, Shelton DN and Boivin G: Optimization of Droplet Digital PCR from RNA and DNA extracts with direct comparison to RT-qPCR: Clinical implications for quantification of Oseltamivir-resistant subpopulations. J Virol Methods. 224:58–66. 2015. View Article : Google Scholar : PubMed/NCBI
14	Hindson CM, Chevillet JR, Briggs HA, Gallichotte EN, Ruf IK, Hindson BJ, Vessella RL and Tewari M: Absolute quantification by droplet digital PCR versus analog real-time PCR. Nat Methods. 10:1003–1005. 2013. View Article : Google Scholar : PubMed/NCBI
15	Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, Bright IJ, Lucero MY, Hiddessen AL, Legler TC, et al: High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem. 83:8604–8610. 2011. View Article : Google Scholar : PubMed/NCBI
16	Filetti V, Falzone L, Rapisarda V, Caltabiano R, Eleonora Graziano AC, Ledda C and Loreto C: Modulation of microRNA expression levels after naturally occurring asbestiform fibers exposure as a diagnostic biomarker of mesothelial neoplastic transformation. Ecotoxicol Environ Saf. 198:1106402020. View Article : Google Scholar : PubMed/NCBI
17	Salemi R, Falzone L, Madonna G, Polesel J, Cinà D, Mallardo D, Ascierto PA, Libra M and Candido S: MMP-9 as a candidate marker of response to BRAF inhibitors in melanoma patients with BRAFV600E mutation detected in circulating-free DNA. Front Pharmacol. 9:8562018. View Article : Google Scholar :
18	Battaglia R, Palini S, Vento ME, La Ferlita A, Lo Faro MJ, Caroppo E, Borzì P, Falzone L, Barbagallo D, Ragusa M, et al: Identification of extracellular vesicles and characterization of miRNA expression profiles in human blastocoel fluid. Sci Rep. 9:842019. View Article : Google Scholar : PubMed/NCBI
19	Whale AS, Huggett JF, Cowen S, Speirs V, Shaw J, Ellison S, Foy CA and Scott DJ: Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation. Nucleic Acids Res. 40:e822012. View Article : Google Scholar : PubMed/NCBI
20	Department of Health and Human Services, Public Health Service, Centres for Disease Control and Prevention (CDC): 2019-Novel Coronavirus (2019-nCoV) Real-time rRT-PCR Panel. Primers and Probes. Division of Viral Diseases. CDC; Atlanta, GA: 2020, https://www.who.int/docs/default-source/coronaviruse/uscdcrt-pcr-panel-primer-probes.pdf?sfvrsn=fa29cb4b_2. Accessed March 15, 2020.
21	Fresta CG, Fidilio A, Lazzarino G, Musso N, Grasso M, Merlo S, Amorini AM, Bucolo C, Tavazzi B, Lazzarino G, et al: Modulation of pro-oxidant and pro-inflammatory activities of M1 macrophages by the natural dipeptide carnosine. Int J Mol Sci. 21:E7762020. View Article : Google Scholar : PubMed/NCBI
22	Musso N, Caronia FP, Castorina S, Lo Monte AI, Barresi V and Condorelli DF: Somatic loss of an EXT2 gene mutation during malignant progression in a patient with hereditary multiple osteochondromas. Cancer Genet. 208:62–67. 2015. View Article : Google Scholar : PubMed/NCBI
23	World Health Organization (WHO): Emergencies diseases novel coronavirus 2019. https://www.who.int/.
24	Carter LJ, Garner LV, Smoot JW, Li Y, Zhou Q, Saveson CJ, Sasso JM, Gregg AC, Soares DJ, Beskid TR, et al: Assay techniques and test development for COVID-19 diagnosis. ACS Cent Sci. 6:591–605. 2020. View Article : Google Scholar : PubMed/NCBI
25	Xiao AT, Tong YX and Zhang S: False-negative of RT-PCR and prolonged nucleic acid conversion in COVID-19 Rather than recurrence. J Med Virol. https://doi.org/10.1002/jmv.25855.
26	Li Y, Yao L, Li J, Chen L, Song Y, Cai Z and Yang C: Stability issues of RT-PCR testing of SARS-CoV-2 for hospitalized patients clinically diagnosed with COVID-19. J Med Virol. 92:903–908. 2020. View Article : Google Scholar : PubMed/NCBI
27	Dingle TC, Sedlak RH, Cook L and Jerome KR: Tolerance of droplet-digital PCR vs real-time quantitative PCR to inhibitory substances. Clin Chem. 59:1670–1672. 2013. View Article : Google Scholar : PubMed/NCBI
28	Dong L, Wang X, Wang S, Du M, Niu C, Yang J, Li L, Zhang G, Fu B, Gao Y, et al: Interlaboratory assessment of droplet digital PCR for quantification of BRAF V600E mutation using a novel DNA reference material. Talanta. 207:1202932020. View Article : Google Scholar
29	Pinheiro LB, O'Brien H, Druce J, Do H, Kay P, Daniels M, You J, Burke D, Griffiths K and Emslie KR: Interlaboratory reproducibility of Droplet Digital Polymerase Chain Reaction using a new DNA reference material format. Anal Chem. 89:11243–11251. 2017. View Article : Google Scholar : PubMed/NCBI
30	Rutsaert S, Bosman K, Trypsteen W, Nijhuis M and Vandekerckhove L: Digital PCR as a tool to measure HIV persistence. Retrovirology. 15:162018. View Article : Google Scholar : PubMed/NCBI
31	Yucha RW, Hobbs KS, Hanhauser E, Hogan LE, Nieves W, Ozen MO, Inci F, York V, Gibson EA, Thanh C, et al: High-throughput characterization of HIV-1 reservoir reactivation using a single-cell-in-Droplet PCR assay. EBioMedicine. 20:217–229. 2017. View Article : Google Scholar : PubMed/NCBI
32	Trypsteen W, Kiselinova M, Vandekerckhove L and De Spiegelaere W: Diagnostic utility of droplet digital PCR for HIV reservoir quantification. J Virus Erad. 2:162–169. 2016.PubMed/NCBI