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

Alison Burdett,Christofer Toumazou,Mohammadreza Sohbati,Rashmita Sahoo,Nicola Casali,Judith Bedzo-Nutakor,Tsz-Kin Hon,Luke S P Moore,Adam Mujan,Graham S Cooke,Gary W Davies,Maria Karvela

doi:10.1186/s12879-021-06316-z

Abstract

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”.

Highlights

As SARS-CoV-2 testing expands, to widespread asymptomatic testing, high sensitivity point-of-care PCR platforms may optimise potential benefits from pooling multiple patients’ samples
Sputum sampling To investigate whether sputum samples are compatible with the CovidNudge platform, we undertook a comparative analysis of nasopharyngeal swab samples with sputum
Sputum sampling Paired nasopharyngeal and sputum samples were obtained from symptomatic [8] and asymptomatic hospital patients admitted through the emergency department diagnosed as SARS-CoV-2 positive (n = 74) or negative (n = 103), and asymptomatic screening from members of the London Symphony Orchestra (n = 118). 295 paired samples were obtained

Summary

Introduction

As SARS-CoV-2 testing expands, to widespread asymptomatic testing, high sensitivity point-of-care PCR platforms may optimise potential benefits from pooling multiple patients’ samples. The platform comprises a single-use DnaCartridge and a processing unit (the NudgeBox) with six viral targets (RdRp-IP2, RdRpIP4, e-gene, n1, n2, n3) and one host gene as a sample adequacy control (Ribonuclease P, RNaseP) (supplementary Fig. 1a, supplementary Table 1), generating positive, negative, or indeterminate results (supplementary Table 2) [3]. The sensitivity of this assay compared with laboratory-based PCR using nasopharyngeal swab samples was found to be 97% (95% CI 89.6–99.6) with a specificity of 100% (95% CI 98.5–100) [3]

Methods

Results

Discussion

Conclusion