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

BMC Infectious Diseases

Gary W. Davies¹  Judith Bedzo-Nutakor²  Christofer Toumazou²  Adam Mujan²  Nicola Casali²  Mohammadreza Sohbati²  Tsz-Kin Hon²  Rashmita Sahoo²  Alison Burdett²  Maria Karvela²  Graham S. Cooke³  Luke S. P. Moore³ 

[1] Chelsea and Westminster NHS Foundation Trust;DnaNudge Ltd, Imperial College White City Campus, The Translation and Innovation Hub;North West London Pathology, Imperial College Healthcare NHS Trust;

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

DOI  :  10.1186/s12879-021-06316-z

来源: DOAJ

【 摘 要 】

Abstract Background As 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. Method We 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. Results Across 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. Conclusion We 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】

Unknown