Diagnostic, Prognostic, and Therapeutic Value of Droplet Digital PCR (ddPCR) in COVID-19 Patients: A Systematic Review

Abstract

Accurate detection of SARS-CoV-2, the pathogen causing the global pandemic of COVID-19, is essential for disease surveillance and control. Quantitative reverse transcription PCR (RT-qPCR) is considered the reference standard test for the diagnosis of SARS-CoV-2 by the World Health Organization and Centers for Disease Control and Prevention. However, its limitations are a prompt for a more accurate assay to detect SARS-CoV-2, quantify its levels, and assess the prognosis. This article aimed to systematically review the literature and assess the diagnostic performance of droplet digital PCR (ddPCR), also to evaluate its potential role in prognosis and management of COVID-19 patients. PubMed and Scopus databases were searched to identify relevant articles published until 13 July 2021. An additional PubMed search was performed on 21 October 2021. Data from the 39 eligible studies were extracted and an overall 3651 samples from 2825 patients and 145 controls were used for our qualitative analysis. Most studies reported ddPCR was more accurate than RT-qPCR in detecting and quantifying SARS-CoV-2 levels, especially in patients with low viral loads. ddPCR was also found highly effective in quantifying SARS-CoV-2 RNAemia levels in hospitalized patients, monitoring their disease course, and predicting their response to therapy. These findings suggest ddPCR could serve as a complement or alternative SARS-CoV-2 tool with emerging diagnostic, prognostic, and therapeutic value, especially in hospital settings. Additional research is still needed to standardize its laboratory protocols, also to accurately assess its role in monitoring COVID-19 therapy response and in identifying SARS-CoV-2 emerging variants.

A multiplexed, paired-pooled droplet digital PCR assay for detection of SARS-CoV-2 in saliva

“…This is partly explained by the ~4-fold increase in volume of starting sample in the BioRad protocol. Our LOD is lower than that reported for SalivaDirect (6-12 SARS-CoV-2 copies per µL) 24 , which has a similar sample work ow, but relies on the less sensitive RT-qPCR platform 37 . Most other screening assays report LODs within this range as well (0.5-10.6 copies per µl) 12,13,14,15,16,17,18 .…”

Emerging Landscape of SARS-CoV-2 Variants and Detection Technologies

“…Compared with traditional PCR, ddPCR has the advantages of high sensitivity, precision, repeatability, and resistance to inhibitors. It may be that ddPCR is superior to gold standard RT-PCR in the detection and predictive diagnosis of SARS-COV-2 [ 69 ].…”

Emerging clinically tested detection methods for COVID‐19

“…Similar conclusions were obtained in other laboratories, reporting a limit of detection at least 10‐fold better than that of RT‐PCR and a superior performance for the detection of asymptomatic cases of COVID‐19 [ 39 , 40 ]. Amongst others, interesting reviews were published about the use of dPCR in COVID‐19 diagnosis [ 41 ] or in the monitoring of the disease course by correlating the viral RNA plasma levels with the disease severity or progression [ 42 ]. Despite the significant advantages of dPCR over qPCR, there are still some limitations that prevent its universal application in clinical laboratories, such as its higher cost or the unavailability of commercial instruments and master mix reagents.…”