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

The relationship of SARS-CoV-2 antigen testing results, viral load, and viral culture detection remains to be fully defined. Presumptively, viral culture can provide a surrogate measure for infectivity of sampled individuals, and thereby inform how and where to most appropriately deploy available diagnostic testing modalities. We therefore determined the relationship of antigen testing results from three lateral flow and one microfluidics assay to viral culture performed in parallel in 181 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. We found that antigen tests were predictive of viral culture positivity, with the LumiraDx method showing enhanced sensitivity (90%; 95% confidence interval (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 (ROCs) of 0.94-0.97 and 0.92, respectively. In particular, 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. Taken together, the detection of SARS-CoV-2 antigen identified highly infectious individuals, some of whom may harbor 10,000-fold more virus in their samples than those with any detectable infectious virus. As such, our data support use of antigen testing in defining infectivity status at the time of sampling.

Limit of Detection for Rapid Antigen Testing of the SARS-CoV-2 Omicron and Delta Variants of Concern Using Live-Virus Culture

“…The titers of the Omicron lh01 (NCBI accession number OL719310 ), Delta (BEI Resources catalog number NR-55671, isolate hCoV-19/USA/MD-HP05285/2021; Johns Hopkins University), and WA1 ( 10 ) viruses were determined by a plaque assay ( 10 ) and further calibrated with the Abbott RealTime SARS-CoV-2 assay (Abbott Molecular, Inc., Des Plaines, IL) ( 15 ). The genomes of the Omicron, Delta, and WA1 viral stocks used in our analysis were also sequenced using the NEBNext ARTIC SARS-CoV-2 companion kit (New England BioLabs, Ipswich, MA) and MinION (Oxford Nanopore Technologies, Oxford, UK) technology ( 16 – 20 ), confirming the lack of mutation acquisition during propagation.…”

“…2 ) suggest that this represents a true reduction in analytical sensitivity for Delta rather than an artifact of enhanced plaquing efficiencies for Delta relative to antigen levels and associated levels of genome copies. We previously found that the CareStart and LumiraDx antigen tests were excellent in the detection of presumptively WA1-infected individuals ( 15 ). We expect, however, that the observed magnitude of the loss in Delta sensitivity could result in a >20% loss in the detection of potentially infectious individuals based on our previous examination of the effect of LoD on clinical sensitivity ( 21 ).…”

“… Correlation of PFU per milliliter and viral load in genome copies per milliliter. Stocks of each strain were serially diluted 10-fold in PBS and analyzed by PFU ( 10 ) and calibrated reverse transcription-quantitative PCR (RT-qPCR) assays ( 15 ). Both axes are on a log 10 scale.…”

Why Daily SARS-CoV-2 Nasal Rapid Antigen Testing Poorly Detects Infected and Infectious Individuals

“…However, an approximate 1000-fold difference between RNA viral load and viral titer is reasonably expected. 38…”

Modelling the impact of repeat asymptomatic testing policies for staff on SARS-CoV-2 transmission potential

“…The probability of testing positive is also assumed to be deterministically linked to RNA viral load. Note that we assume this because of the data available on LFD test sensitivity as a function of RNA viral load measured by PCR, however several studies have suggested that LFD test sensitivity is actually more closely linked to infectious viral load or culture positive probability [29,30,31,32]. Furthermore, the sensitivity relationships used here imply that the outcomes of subsequent tests are independent.…”