Pooled sputum to optimise the efficiency and utility of rapid, point-of-care molecular SARS-CoV-2 testing

BMC Infectious Diseases

Gary W. Davies¹  Alison Burdett²  Adam Mujan²  Maria Karvela²  Tsz-Kin Hon²  Nicola Casali²  Rashmita Sahoo²  Mohammadreza Sohbati²  Judith Bedzo-Nutakor²  Christofer Toumazou³  Graham S. Cooke⁴  Luke S. P. Moore⁵ 

[1] Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, SW10 9NH, London, UK;DnaNudge Ltd, Imperial College White City Campus, The Translation and Innovation Hub, Level 11, 84 Wood Lane, W12 0BZ, London, UK;DnaNudge Ltd, Imperial College White City Campus, The Translation and Innovation Hub, Level 11, 84 Wood Lane, W12 0BZ, London, UK;Department of Electrical and Electronic Engineering, Imperial College London, Exhibition Road, SW7 2AZ, London, UK;North West London Pathology, Imperial College Healthcare NHS Trust, Fulham Palace Road, W6 8RF, London, UK;NIHR Health Protection Research Unit in Healthcare Associated Infections & Antimicrobial Resistance, Imperial College London, Du Cane Road, W12 0NN, London, UK;North West London Pathology, Imperial College Healthcare NHS Trust, Fulham Palace Road, W6 8RF, London, UK;NIHR Health Protection Research Unit in Healthcare Associated Infections & Antimicrobial Resistance, Imperial College London, Du Cane Road, W12 0NN, London, UK;Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, SW10 9NH, London, UK;

关键词: COVID-19;    Coronavirus;    Molecular diagnostics;    PCR;   

DOI  :  10.1186/s12879-021-06316-z

来源: Springer

【 摘 要 】

BackgroundAs SARS-CoV-2 testing expands, particularly to widespread asymptomatic testing, high sensitivity point-of-care PCR platforms may optimise potential benefits from pooling multiple patients’ samples.MethodWe tested patients and asymptomatic citizens for SARS-CoV-2, exploring the efficiency and utility of CovidNudge (i) for detection in individuals’ sputum (compared to nasopharyngeal swabs), (ii) for detection in pooled sputum samples, and (iii) by modelling roll out scenarios for pooled sputum testing.ResultsAcross 295 paired samples, we find no difference (p = 0.1236) in signal strength for sputum (mean amplified replicates (MAR) 25.2, standard deviation (SD) 14.2, range 0–60) compared to nasopharyngeal swabs (MAR 27.8, SD 12.4, range 6–56). At 10-sample pool size we find some drop in absolute strength of signal (individual sputum MAR 42.1, SD 11.8, range 13–60 vs. pooled sputum MAR 25.3, SD 14.6, range 1–54; p < 0.0001), but only marginal drop in sensitivity (51/53,96%). We determine a limit of detection of 250 copies/ml for an individual test, rising only four-fold to 1000copies/ml for a 10-sample pool. We find optimal pooled testing efficiency to be a 12–3-1-sample model, yet as prevalence increases, pool size should decrease; at 5% prevalence to maintain a 75% probability of negative first test, 5-sample pools are optimal.ConclusionWe describe for the first time the use of sequentially dipped sputum samples for rapid pooled point of care SARS-CoV-2 PCR testing. The potential to screen asymptomatic cohorts rapidly, at the point-of-care, with PCR, offers the potential to quickly identify and isolate positive individuals within a population “bubble”.

【 授权许可】

CC BY