Diagnostic Performance of Automated SARS-CoV-2 Antigen Assay in Nasal Swab during COVID-19 Vaccination Campaign

Correlation of COVID-19 vaccination and RT-PCR ct value among cases in Addis Ababa, Ethiopia: implication for future preparedness

BACKGROUND

The COVID-19 disease requires accurate diagnosis to effectively manage infection rates and disease progression. The study aims to assess the relationship between vaccination status and RT-PCR cycle threshold (Ct) values by comparing clinical, RDT and RT-PCR results.

METHODS

A total of 453 suspected COVID-19 cases were included in this study. Nasopharyngeal swabs were collected for both RDT and RT-PCR testing, with RDTs conducted on-site and RT-PCR at the Ethiopian Public Health Institute (EPHI) genomics laboratory. Detailed clinical, RDT, and RT-PCR results were analyzed. Data analysis included descriptive statistics, cross-tabulation, and Chi-Square tests to investigate the connections between diagnostic outcomes and vaccination status, with a focusing on Ct values.

RESULTS

RDT results showed 34.0% negative and 65.8% positive, while RT-PCR results indicated 35.8% negative and 64.2% positive cases. The discrepancies between RDT and RT-PCR results emphasize the importance of thorough testing. No significant association was found between vaccination status and viral load, as indicated by Ct values. Among RT-PCR positive cases, 49.8% had been vaccinated, suggesting challenges in interpreting results among vaccinated individuals. Further analysis revealed that vaccination (first or second dose) had minimal impact on Ct values, indicating limited influence of vaccination status on viral load dynamics in infected individuals.

CONCLUSIONS

The study highlights the significant differences between RDT and RT-PCR outcomes, underscoring the need for a comprehensive testing approach. Additionally, the findings suggest that vaccination status does not significantly impact RT-PCR Ct values, complicating the interpretation of diagnostic results in vaccinated individuals, especially in breakthrough infections and potential false positives.

Influences of 23 different equations used to calculate gene copies of SARS-CoV-2 during wastewater-based epidemiology

Following the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, the use of wastewater-based surveillance (WBS) has increased dramatically along with associated infrastructure globally. However, due to the global nature of its application, and various workflow adaptations (e.g., sample collection, water concentration, RNA extraction kits), numerous methods for back-calculation of gene copies per volume (gc/L) of sewage have also emerged. Many studies have considered the comparability of processing methods (e.g., water concentration, RNA extraction); however, for equations used to calculate gene copies in a wastewater sample and subsequent influences on monitoring viral trends in a community and its association with epidemiological data, less is known. Due to limited information on how many formulas exist for the calculation of SARS-CoV-2 gene copies in wastewater, we initially attempted to quantify how many equations existed in the referred literature. We identified 23 unique equations, which were subsequently applied to an existing wastewater dataset. We observed a range of gene copies based on use of different equations, along with variability of AUC curve values, and results from correlation and regression analyses. Though a number of individual laboratories appear to have independently converged on a similar formula for back-calculation of viral load in wastewater, and share similar relationships with epidemiological data, differential influences of various equations were observed for variation in PCR volumes, RNA extraction volumes, or PCR assay parameters. Such observations highlight challenges when performing comparisons among WBS studies when numerous methodologies and back-calculation methods exist. To facilitate reproducibility among studies, the different gc/L equations were packaged as an R Shiny app, which provides end users the ability to investigate variability within their datasets and support comparisons among studies.

Does the COVID-19 Vaccination Reduce the Risk to Transmit SARS-CoV-2 to Others?

It has been assumed that the COVID-19 vaccination reduces the risk of transmission to others. Results during the delta predominance show that the viral load in the vaccinated population is not consistently lower compared to the unvaccinated, and during the omicron predominance, the viral load was even somewhat higher. Levels of infectious SARS-CoV-2 were partly lower in the vaccinated population. Viral loads were mostly lower in re-infections compared to breakthrough infections. Viral clearance including the detection of infectious virus has mostly been described to be faster in the vaccinated population suggesting a shorter duration as a possible source for transmission. The epidemiological relevance of this finding remains uncertain. Approximately half of the transmission studies found lower secondary attack rates from the fully vaccinated population, but the results are probably best explained by the vaccination status of the contact population. Public health data from the UK show that the number of COVID-19 cases is higher among the fully vaccinated and boosted population who might be possible sources, in contrast to lower case numbers within the first three months among the vaccinated obtained in phase 3 trials on symptomatic cases. Overall, there is no convincing evidence that the COVID-19 vaccination significantly reduces the risk to transmit SARS-CoV-2 to others.

Automated antigen assays display a high heterogeneity for the detection of SARS-CoV-2 variants of concern, including several Omicron sublineages

Diagnostic tests for direct pathogen detection have been instrumental to contain the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic. Automated, quantitative, laboratory-based nucleocapsid antigen (Ag) tests for SARS-CoV-2 have been launched alongside nucleic acid-based test systems and point-of-care (POC) lateral-flow Ag tests. Here, we evaluated four commercial Ag tests on automated platforms for the detection of different sublineages of the SARS-CoV-2 Omicron variant of concern (VoC) (B.1.1.529) in comparison with "non-Omicron" VoCs. A total of 203 Omicron PCR-positive respiratory swabs (53 BA.1, 48 BA.2, 23 BQ.1, 39 XBB.1.5 and 40 other subvariants) from the period February to March 2022 and from March 2023 were examined. In addition, tissue culture-expanded clinical isolates of Delta (B.1.617.2), Omicron-BA.1, -BF.7, -BN.1 and -BQ.1 were studied. These results were compared to previously reported data from 107 clinical "non-Omicron" samples from the end of the second pandemic wave (February to March 2021) as well as cell culture-derived samples of wildtype (wt) EU-1 (B.1.177), Alpha VoC (B.1.1.7) and Beta VoC (B.1.351)). All four commercial Ag tests were able to detect at least 90.9% of Omicron-containing samples with high viral loads (Ct < 25). The rates of true-positive test results for BA.1/BA.2-positive samples with intermediate viral loads (Ct 25-30) ranged between 6.7% and 100.0%, while they dropped to 0 to 15.4% for samples with low Ct values (> 30). This heterogeneity was reflected also by the tests' 50%-limit of detection (LoD50) values ranging from 44,444 to 1,866,900 Geq/ml. Respiratory samples containing Omicron-BQ.1/XBB.1.5 or other Omicron subvariants that emerged in 2023 were detected with enormous heterogeneity (0 to 100%) for the intermediate and low viral load ranges with LoD50 values between 23,019 and 1,152,048 Geq/ml. In contrast, detection of "non-Omicron" samples was more sensitive, scoring positive in 35 to 100% for the intermediate and 1.3 to 32.9% of cases for the low viral loads, respectively, corresponding to LoD50 values ranging from 6181 to 749,792 Geq/ml. All four assays detected cell culture-expanded VoCs Alpha, Beta, Delta and Omicron subvariants carrying up to six amino acid mutations in the nucleocapsid protein with sensitivities comparable to the non-VoC EU-1. Overall, automated quantitative SARS-CoV-2 Ag assays are not more sensitive than standard rapid antigen tests used in POC settings and show a high heterogeneity in performance for VoC recognition. The best of these automated Ag tests may have the potential to complement nucleic acid-based assays for SARS-CoV-2 diagnostics in settings not primarily focused on the protection of vulnerable groups. In light of the constant emergence of new Omicron subvariants and recombinants, most recently the XBB lineage, these tests' performance must be regularly re-evaluated, especially when new VoCs carry mutations in the nucleocapsid protein or immunological and clinical parameters change.

Comparison of performance of LIAISON SARS-CoV-2 antigen assay with RT-PCR during the Omicron wave

Due to the newly emerging Omicron variant, there is a need to re-evaluate the performance of automated antigen tests. Our study aim was to evaluate the performance of the automated Liaison SARS-CoV-2 antigen assay against reverse transcriptase polymerase chain reaction (RT-PCR) in samples with Omicron variant.A prospective study was performed on 373 combined oro-nasopharyngeal samples (NPS) randomly collected from symptomatic patients. NPS were tested with Liaison SARS-CoV-2 Ag test (DiaSorin, Italy) and DS Coronex COVID-19 Multiplex RT-PCR Diagnosis Kit (DS BioTechnology, Ankara, Turkey).Of 373 samples, 124 (33.2%) were found to be RT-PCR positive and 249 (66.8%) RT-PCR negative. Taking RT-PCR as a reference, the sensitivity and specificity of the Liaison SARS-CoV-2 Ag assay were found as 84.6% (95%CI 77.3%-90%) and 100% (95%CI 98.5%-100%), respectively. For samples with a cycle threshold (Ct) value <25 (high viral load), the sensitivity increased to 100%. When antigen concentration and Ct values were compared, a strong negative correlation between antigen and Ct values was determined (P < 0.001).The Liaison antigen test met the performance criteria recommended by the WHO for samples with the Omicron variant. In addition, it showed excellent sensitivity and specificity in patients with high viral load. Therefore, Liaison antigen test can be a reliable and useful alternative in the diagnosis of SARS-CoV-2 infection, particularly in resource-constrained laboratories.

Analysis of diagnostic performance and factors causing nonspecific reactions in SARS-CoV-2 rapid antigen detection tests

INTRODUCTION

Early diagnosis and appropriate infection control are important to prevent the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, we aimed to assess the diagnostic performance of SARS-CoV-2 rapid antigen detection (RAD) tests and the factors that cause nonspecific reactions.

METHODS

Nasopharyngeal swab specimens (n = 100), sputum specimens (n = 10), and lithium-heparin plasma samples (n = 100) were collected. We evaluated Espline®SARS-CoV-2 (Espline) and SARS-CoV-2 Rapid Antigen Test that also known as STANDARD Q® (STANDARD Q), with reverse transcription-polymerase chain reaction (RT-PCR) and Lumipulse® Presto SARS-CoV-2 Ag as reference tests. In addition, we investigated the effects of inadequate pretreatment methods and five potential causes of nonspecific reactions.

RESULTS

The sensitivities of Espline and STANDARD Q were 60% and 57%, respectively, and their specificity was 100%. It was confirmed that the judgment line for the positive insufficiently mixed specimens was faint. A false-positive result was observed with STANDARD Q when sputum was used as a specimen to investigate judgment the effect of viscosity.

CONCLUSIONS

Espline and STANDARD Q show good sensitivity for specimens with Ct values less than 25, but specimens collected within 9 days of symptom onset may still give false negatives. The test should be performed carefully, and the results should be judged comprehensively, taking into account clinical symptoms and patient background.

High performance of the automated ADVIA Centaur Systems SARS-CoV-2 Antigen Assay in nasopharyngeal samples with high viral load

ADVIA Centaur SARS-CoV-2 Antigen (COV2Ag) Assay (Siemens Healthineers) was evaluated for SARS-CoV-2 detection. A total of 141 nasopharyngeal samples were analyzed by this technique and results were compared with those obtained by quantitative reverse-transcription polymerase chain reaction (RT-PCR). The overall sensitivity and specificity of the test were 68.70% and 70%, respectively. Regarding cycle threshold (Ct) values, the COV2Ag test showed a sensitivity of 93.75% and 100% for nasopharyngeal samples with Ct < 25 and < 20, respectively. ADVIA Centaur COV2Ag Assay is a useful, automated, and rapid technique for early SARS-CoV-2 diagnosis and isolation of the infected individuals, avoiding its transmission.

Systematic Review of Diagnostic Accuracy of DiaSorin Liaison SARS-CoV-2 Antigen Immunoassay

Background

Quantification of SARS-CoV-2 antigens by means of rapid, high-throughput and fully-automated techniques has been proposed as a feasible alternative to overcome the current shortage of resources for routine molecular diagnostics. To this end, we provide here a systematic review of diagnostic accuracy of DiaSorin Liaison SARS-CoV-2 antigen immunoassay.

Methods

An electronic search was conduced in Medline and Scopus, with no language or date restrictions (up to January 20, 2022), for identifying all published studies articles in which the diagnostic performance of the DiaSorin Liaison SARS-CoV-2 antigen immunoassay was compared with molecular diagnostic techniques.

Results

The electronic search identified a final number of 11 studies, totalling 4449 oro- and naso-pharyngeal specimens. The pooled diagnostic sensitivity, specificity and area under the curve (AUC) of the Liaison SARS-CoV-2 antigen immunoassay in all samples were 0.51 (95%CI, 0.49-0.54), 1.00 (95%CI, 1.00-1.00) and 0.994 (95%CI, 0.990-0.998), respectively, whilst the overall concordance with molecular diagnostics was 82.1%. The pooled diagnostic sensitivity, specificity and AUC of the Liaison SARS-CoV-2 antigen immunoassay in specimens with high viral load (i.e., cycle threshold values <25-30) were 0.79 (95%CI, 0.75-0.82), 1.00 (95%CI, 0.99-1.00) and 0.911 (95%CI, 0.879-0.943), respectively, whilst the overall concordance with molecular diagnostics in such samples increased to 94.2%.

Conclusion

The results of this systematic literature review suggest that there is sufficient accuracy of the DiaSorin Liaison SARS-CoV-2 antigen immunoassay in samples with high viral loads that would enable its reliable usage for identifying superspreaders, who are responsible for the vast majority of transmission events.