Performance of novel digital real-time PCR for detection of SARS-CoV-2, respiratory syncytial viruses, and influenza viruses in Ghana.

UNLABELLED

Digital PCR (dPCR) systems offer high sensitivity and reproducibility without requiring external control standards. However, their performance against real-time reverse transcription-PCR (rRT-PCR) for detecting respiratory viruses remains unexplored in Ghana. We therefore evaluated the performance of a novel dPCR, Lab-On-An-Array (LOAA), for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respiratory syncytial virus (RSV), and influenza viruses type A (Flu A) and B (Flu B). A cross-sectional hospital-based study was conducted between August 2022 and January 2023 in Ghana's Ashanti and Savannah Regions. Oropharyngeal swabs from 356 participants with a median age of 19 years, presenting with suspected respiratory illness, were tested using LOAA and rRT-PCR. Viral RNA was extracted using a Qiagen Viral Mini Kit (Qiagen Diagnostics GmbH, Germany). LOAA and rRT-PCR tests were performed using Genoplexor COVID-19/Flu/RSV Detection Kit (Optolane Technologies Inc, South Korea) and FluoroType SARS-CoV-2/Flu/RSV kits (Hain Lifescience GmbH, Germany), respectively. LOAA's performance metrics were assessed using rRT-PCR as the gold standard. Overall positivity rates were 29.78% and 30.90% for LOAA and rRT-PCR, respectively. Compared to rRT-PCR, LOAA's sensitivity was 87.76% for RSV, 91.30% for SARS-CoV-2, 86.21% for Flu B, and 88.89% for Flu A. Positive predictive value was the highest for RSV (97.73%) and lowest for Flu A (61.54%); negative predictive values were ≥98.00% for all respiratory viruses. LOAA recorded an "almost perfect" agreement (κ ≥0.88) with rRT-PCR for RSV, SARS-CoV-2, and Flu B and good agreement for Flu A (κ = 0.72). LOAA is sensitive in detecting SARS-CoV-2, RSV, and Flu B infections; however, minor improvements for Flu A are required.

IMPORTANCE

This study presents the potential of a digital PCR as a highly sensitive and reproducible tool for detecting respiratory viruses in Ghana, where robust diagnostic methods are essential for managing public health challenges. By evaluating the novel Lab-On-An-Array (LOAA) system, we provide its critical operational performance against the gold-standard rRT-PCR for detecting severe acute respiratory syndrome coronavirus 2, respiratory syncytial virus, and influenza viruses. Our findings show that LOAA demonstrates excellent agreement with rRT-PCR for most viruses, offering a promising alternative for respiratory virus surveillance and diagnosis. This research is particularly significant for resource-limited settings, as it supports the adoption of advanced molecular diagnostics to improve early detection and response to respiratory infections. Minor refinements for specific viruses, such as influenza A, could further enhance its utility in clinical and epidemiological applications.