Sars-Cov-2 antigen tests predict infectivity based on viral culture: comparison of antigen, PCR viral load, and viral culture testing on a large sample cohort

Abstract

Objective: To define the relationship of SARS-CoV-2 antigen, viral load determined by RT-qPCR, and viral culture detection. Presumptively, viral culture can provide a surrogate measure for infectivity of sampled individuals and thereby inform how and where to most appropriately deploy antigen and nucleic acid amplification-based diagnostic testing modalities.

Methods: We compared the antigen testing results from three lateral flow and one microfluidics assay to viral culture detection and viral load determination performed in parallel in up to 189 nasopharyngeal swab samples positive for SARS-CoV-2. Sample viral loads, determined by RT-qPCR, were distributed across the range of viral load values observed in our testing population.

Results: Antigen tests were predictive of viral culture positivity, with the LumiraDx microfluidics method showing enhanced sensitivity (90%; 95% CI 83-94%) compared with the BD Veritor (74%, 95% CI 65-81%), CareStart (74%, 95% CI 65-81%) and Oscar Corona (74%, 95% CI 65-82%) lateral flow antigen tests. Antigen and viral culture positivity were also highly correlated with sample viral load, with areas under the receiver operator characteristic curves of 0.94 to 0.97 and 0.92, respectively. A viral load threshold of 100 000 copies/mL was 95% sensitive (95% CI, 90-98%) and 72% specific (95% CI, 60-81%) for predicting viral culture positivity. Adjusting for sample dilution inherent in our study design, sensitivities of antigen tests were ≥95% for detection of viral culture positive samples with viral loads >106 genome copies/mL, although specificity of antigen testing was imperfect.

Discussion: Antigen testing results and viral culture were correlated. For culture positive samples, the sensitivity of antigen tests was high at high viral loads that are likely associated with significant infectivity. Therefore, our data provides support for use of antigen testing in ruling out infectivity at the time of sampling.

Keywords: Infectivity; Laboratory diagnostics; SARS-CoV-2 antigen test; SARS-CoV-2 viral culture; SARS-CoV-2 viral load.

Copyright © 2022 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Figures

Fig. 1

Quantitative relationship between culturable virus and sample viral load. Day 3 viral culture supernatant from each cultured sample and its corresponding respiratory sample were each analysed by RT-qPCR to determine respective viral loads (n = 181). The viral load in genome copies/mL (logarithmic scale) of culture supernatant is plotted against the genome copies/mL (logarithmic scale) of the original patient sample. Linear regression (solid line) with 95% CIs (dashed lines) is shown. R2 = 0.55. Samples with negative viral cultures (see Materials and Methods) for representation are assigned a y-axis, value of 100, and are demarcated as coloured brown dots.

Fig. 2

Antigen testing results compared with viral load. Viral load in genome copies/mL (logarithmic scale).

Fig. 3

Receiver operator characteristic curves (ROC) comparing SARS-CoV-2 sample viral load levels as a predictor of viral culture and antigen detection. For each plot, sensitivity versus 1-specificity was plotted for each viral load value (genome/copies/mL) determined by RT-qPCR for each sample in our study when used as a lower limit threshold for scoring positive and negative detection for all other viral load results with qualitative viral culture or antigen test determinations, respectively, as the comparators. (a) Viral load in genome copies/mL versus detection by viral culture. (b) Viral load versus LumiraDx antigen detection. (c) Viral load versus BD Veritor antigen detection. (d) Viral load versus Oscar Corona antigen detection. (e) Viral load versus CareStart antigen detection. Viral load values along the ROC curves are labeled in power of 10 logarithmic intervals and demarcated in colour as indicated in accompany heatmap legend bar. Area under the curve for each ROC curve is denoted on respective plots.

Fig. 4

Model of infectious risk versus SARS-CoV-2 detection by RT-qPCR and antigen tests. Both LumiraDx and lateral flow-based antigen tests (e.g. BD Veritor, CareStart, and Oscar Corona) were able to detect individuals with viable, culturable virus and who therefore pose an immediate infectious risk to others. Dotted lines indicate reliable detection threshold predicted for each method. Presumptively, infectious risk is proportional to the amount of culturable virus, which is roughly proportional to the viral load in samples. Antigen tests were excellent in detecting patients with the highest viral loads, which may be 104- to 105-fold greater than viral loads detected at the lowest levels where virus can be consistently cultured. The PCR and, to a lesser extent, the LumiraDx test can detect individuals before and after the expected infectious period and therefore may be more appropriate for screening programs where regular testing is performed at longer time intervals. The viral load curve shown is for representational purposes and may not reflect viral load kinetics in any specific individual.