Comparison of SARS-CoV-2 Reverse Transcriptase Polymerase Chain Reaction and BinaxNOW Rapid Antigen Tests at a Community Site During an Omicron Surge : A Cross-Sectional Study

Testing for SARS-CoV-2: lessons learned and current use cases

SUMMARYThe emergence and worldwide dissemination of SARS-CoV-2 required both urgent development of new diagnostic tests and expansion of diagnostic testing capacity on an unprecedented scale. The rapid evolution of technologies that allowed testing to move out of traditional laboratories and into point-of-care testing centers and the home transformed the diagnostic landscape. Four years later, with the end of the formal public health emergency but continued global circulation of the virus, it is important to take a fresh look at available SARS-CoV-2 testing technologies and consider how they should be used going forward. This review considers current use case scenarios for SARS-CoV-2 antigen, nucleic acid amplification, and immunologic tests, incorporating the latest evidence for analytical/clinical performance characteristics and advantages/limitations for each test type to inform current debates about how tests should or should not be used.

Comparative Performance of COVID-19 Test Methods in Healthcare Workers during the Omicron Wave

The COVID-19 pandemic presents unique requirements for accessible, reliable testing, and many testing platforms and sampling techniques have been developed over the course of the pandemic. Not all test methods have been systematically compared to each other or a common gold standard, and the performance of tests developed in the early epidemic have not been consistently re-evaluated in the context of new variants. We conducted a repeated measures study with adult healthcare workers presenting for SARS-CoV-2 testing. Participants were tested using seven testing modalities. Test sensitivity was compared using any positive PCR test as the gold standard. A total of 325 individuals participated in the study. PCR tests were the most sensitive (saliva PCR 0.957 ± 0.048, nasopharyngeal PCR 0.877 ± 0.075, oropharyngeal PCR 0.849 ± 0.082). Standard nasal rapid antigen tests were less sensitive but roughly equivalent (BinaxNOW 0.613 ± 0.110, iHealth 0.627 ± 0.109). Oropharyngeal rapid antigen tests were the least sensitive (BinaxNOW 0.400 ± 0.111, iHealth brands 0.311 ± 0.105). PCR remains the most sensitive testing modality for the diagnosis of COVID-19 and saliva PCR is significantly more sensitive than oropharyngeal PCR and equivalent to nasopharyngeal PCR. Nasal AgRDTs are less sensitive than PCR but have benefits in convenience and accessibility. Saliva-based PCR testing is a viable alternative to traditional swab-based PCR testing for the diagnosis of COVID-19.

Screening Strategies to Reduce COVID-19 Mortality in Nursing Homes

Importance

Nursing home residents continue to bear a disproportionate share of COVID-19 morbidity and mortality, accounting for 9% of all US COVID-19 deaths in 2023, despite comprising only 0.4% of the population.

Objective

To evaluate the cost-effectiveness of screening strategies in reducing COVID-19 mortality in nursing homes.

Design and Setting

An agent-based model was developed to simulate SARS-CoV-2 transmission in the nursing home setting. Parameters were determined using SARS-CoV-2 virus data and COVID-19 data from the Centers for Medicare & Medicaid Services and US Centers for Disease Control and Prevention that were published between 2020 and 2023, as well as data on nursing homes published between 2010 and 2023. The model used in this study simulated interactions and SARS-CoV-2 transmission between residents, staff, and visitors in a nursing home setting. The population used in the simulation model was based on the size of the average US nursing home and recommended staffing levels, with 90 residents, 90 visitors (1 per resident), and 83 nursing staff members.

Exposure

Screening frequency (none, weekly, and twice weekly) was varied over 30 days against varying levels of COVID-19 community incidence, booster uptake, and antiviral use.

Main Outcomes and Measures

The main outcomes were SARS-CoV-2 infections, detected cases per 1000 tests, and incremental cost of screening per life-year gained.

Results

Nursing home interactions were modeled between 90 residents, 90 visitors, and 83 nursing staff over 30 days, completing 4000 to 8000 simulations per parameter combination. The incremental cost-effectiveness ratios of weekly and twice-weekly screening were less than $150 000 per resident life-year with moderate (50 cases per 100 000) and high (100 cases per 100 000) COVID-19 community incidence across low-booster uptake and high-booster uptake levels. When COVID-19 antiviral use reached 100%, screening incremental cost-effectiveness ratios increased to more than $150 000 per life-year when booster uptake was low and community incidence was high.

Conclusions and Relevance

The results of this cost-effectiveness analysis suggest that screening may be effective for reducing COVID-19 mortality in nursing homes when COVID-19 community incidence is high and/or booster uptake is low. Nursing home administrators can use these findings to guide planning in the context of widely varying levels of SARS-CoV-2 transmission and intervention measures across the US.

Comparison of RT-PCR and antigen test sensitivity across nasopharyngeal, nares, and oropharyngeal swab, and saliva sample types during the SARS-CoV-2 omicron variant

Limited data highlight the need to understand differences in SARS-CoV-2 omicron (B.1.1.529) variant viral load between the gold standard nasopharyngeal (NP) swab, mid-turbinate (MT)/anterior nasal swabs, oropharyngeal (OP) swabs, and saliva. MT, OP, and saliva samples from symptomatic individuals in Atlanta, GA, in January 2022 and longitudinal samples from a small familial cohort were tested by both RT-PCR and ultrasensitive antigen assays. Higher concentrations in the nares were observed in the familial cohort, but a dominant sample type was not found among 39 cases in the cross-sectional cohort. The composite of positive MT or OP assay for both RT-PCR and antigen assay trended toward higher diagnostic yield but did not achieve significant difference. Our data did not identify a singular preferred sample type for SARS-CoV-2 testing, but higher levels of saliva nucleocapsid, a trend toward higher yield of composite OP/MT result, and association of apparent MT or OP predominance with symptoms warrant further study.

Accuracy of Rapid Antigen Screening Tests for SARS-CoV-2 Infection at Correctional Facilities in Korea: March - May 2022

BACKGROUND

The number of confirmed cases of individuals with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection increased rapidly due to the Omicron variant. Correctional facilities are vulnerable to infectious diseases, and they introduced rapid antigen tests (RATs) to allow for early detection and rapid response. We aimed to evaluate the diagnostic performance and usefulness of SARS-CoV-2 RATs in newly incarcerated people.

MATERIALS AND METHODS

We conducted a cross-sectional study at correctional facilities in Korea from 9 March to 22 May 2022. The study population was newly incarcerated people who were divided into two groups. In one group, 799 paired SARS-CoV-2 RATs and real-time polymerase chain reaction (RT-PCR) were conducted simultaneously in 522 individuals in March 2022. In the other group, 4,034 paired RATs and RT-PCR consecutively in 4,034 participants; only individuals with negative RATs results underwent RT-PCR from April to May 2022. We analyzed data using descriptive statistics and a logistic regression model.

RESULTS

Among the 799 specimens in March, RT-PCR was positive in 72 (9.0%), and among the 4,034 specimens in April - May 2022, RT-PCR was positive in 40 (1.0%). Overall, the RATs had a sensitivity of 58.3%, specificity of 100.0%, positive predictive value (PPV) of 100.0%, and negative predictive value (NPV) of 96.0%. Asymptomatic individuals constituted 98.2% of the study group, and symptomatic individuals 1.8%. In asymptomatic cases, the sensitivity of RATs was 52.5%, specificity was 100.0%, PPV was 100.0%, and NPV was 96.3%. In symptomatic cases, the sensitivity of RATs was 84.6%, specificity was 100.0%, PPV was 100.0%, and NPV was 33.3%. Sensitivity (P = 0.034) and NPV (P = 0.004) differed significantly according to the presence and absence of symptoms, and the F1 score was the highest at 0.9 in symptomatic individuals in March. There was a positive linear trend in the proportion of false-negative RATs in newly incarcerated people following the weekly incidence of SARS-CoV-2 (P = 0.033). The best-associated predictors of RATs for SARS-CoV-2 infection involved symptoms, timing of sample collection, and repeat testing.

CONCLUSION

Sensitivity and NPV significantly depend on whether symptoms are present, and the percentage of false negatives is correlated with the incidence. Thus, using RATs should be adjusted according to the presence or absence of symptoms and the incidence of SARS-CoV-2 infection in the community. RATs could be a useful screening tool as an effective first-line countermeasure because they can rapidly identify infectious patients and minimize SARS-CoV-2 transmission in correctional facilities.

COVID-19 Rapid Antigen Tests With Self-Collected vs Health Care Worker-Collected Nasal and Throat Swab Specimens: A Randomized Clinical Trial

Importance

Self- or health care worker (HCW)-collected nasal swab specimens are the preferred sampling method to perform rapid antigen testing for COVID-19, but it is debated whether throat specimens can improve test sensitivity.

Objective

To compare the diagnostic accuracy of self- and HCW-collected nasal vs throat swab specimens for COVID-19 rapid antigen testing.

Design, Setting, and Participants

This per-protocol multicenter randomized clinical trial was conducted from February 15 through March 25, 2022. The participants, individuals aged 16 years or older requesting a COVID-19 test for diagnostic or screening purposes, had 4 specimens collected for individual testing at 1 of 2 urban COVID-19 outpatient test centers in Copenhagen, Denmark.

Interventions

Participants were randomized 1:1 to self-collected or HCW-collected nasal and throat swab specimens for rapid antigen testing. Additional HCW-collected nasal and throat swab specimens for reverse transcriptase-polymerase chain reaction (RT-PCR) were used as the reference standard.

Main Outcomes and Measures

The primary outcome was sensitivity to diagnose COVID-19 of a self- vs HCW-collected nasal and throat specimen for rapid antigen testing compared with RT-PCR.

Results

Of 2941 participants enrolled, 2674 (90.9%) had complete test results and were included in the final analysis (1535 [57.4%] women; median age, 40 years [IQR, 28-55 years]); 1074 (40.2%) had COVID-19 symptoms, and 827 (30.9%) were positive for SARS-CoV-2 by RT-PCR. Health care worker-collected throat specimens had higher mean sensitivity than HCW-collected nasal specimens for rapid antigen testing (69.4% [95% CI, 65.1%-73.6%] vs 60.0% [95% CI, 55.4%-64.5%]). However, a subgroup analysis of symptomatic participants found that self-collected nasal specimens were more sensitive than self-collected throat specimens for rapid antigen testing (mean sensitivity, 71.5% [95% CI, 65.3%-77.6%] vs 58.0% [95% CI, 51.2%-64.7%]; P < .001). Combining nasal and throat specimens increased sensitivity for HCW- and self-collected specimens by 21.4 and 15.5 percentage points, respectively, compared with a single nasal specimen (both P < .001).

Conclusions and Relevance

This randomized clinical trial found that a single HCW-collected throat specimen had higher sensitivity for rapid antigen testing for SARS-CoV-2 than a nasal specimen. In contrast, the self-collected nasal specimens had higher sensitivity than throat specimens for symptomatic participants. Adding a throat specimen to the standard practice of collecting a single nasal specimen could improve sensitivity for rapid antigen testing in health care and home-based settings.

Trial Registration

ClinicalTrials.gov Identifier: NCT05209178.

Assessment of the detection accuracy of SARS-CoV-2 rapid antigen test in children and adolescents: An updated meta-analysis

BACKGROUND

Real-time and appropriate antigen tests play a pivotal role in preventing severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. However, a previous meta-analysis reported that the antigen test had lower sensitivity for the detection of SARS-CoV-2 in children. To provide a comprehensive evaluation of diagnostic efficiency, we performed an updated meta-analysis to assess the detection accuracy of SARS-CoV-2 antigen tests stratified by days after symptom onset and specimen type in children and adolescents.

METHODS

We comprehensively searched for appropriate studies in the PubMed, Embase, and Cochrane Library databases. Studies on the diagnostic accuracy of antigen tests for SARS-CoV-2 in children and adolescents were included. The relevant data of the included studies were extracted to construct a 2 × 2 table on a per-patient basis. The overall sensitivity and specificity of the SARS-CoV-2 antigen tests were estimated using a bivariate random-effects model.

RESULTS

Seventeen studies enrolling 10 912 patients were included in the present meta-analysis. For the detection accuracy of SARS-CoV-2 antigen tests, the meta-analysis generated a pooled sensitivity of 77.9% (95% confidence interval [CI]: 67.3%-85.8%) and a pooled specificity of 99.6% (95% CI: 98.9%-99.8%). The subgroup analysis of studies that examined antigen tests in symptomatic participants ≦7 days after symptom onset generated a pooled sensitivity of 79.4% (95% CI: 47.6%-94.2%) and a pooled specificity of 99.4% (95% CI: 98.2%-99.8%). Another subgroup analysis of studies that evaluated nasal swab specimens demonstrated a pooled sensitivity of 80.1% (95% CI: 65.0%-89.7%) and a pooled specificity of 98.5% (95% CI: 97.3%-9.2%).

CONCLUSION

Our findings demonstrated that the antigen test performed using nasal swab specimens exhibited high sensitivity for the detection of SARS-CoV-2 within 7 days after symptom onset. Therefore, antigen testing using nasal swabs may be effective in blocking SARS-CoV-2 transmission in children.

The diversification of SARS-CoV-2 Omicron variants and evaluation of their detection with molecular and rapid antigen assays

BACKGROUND

The SARS-CoV-2 pandemic saw the rapid rise, global spread, and diversification of the omicron variant in 2022. Given the overwhelming dominance of this variant globally and its diverse lineages, there is an urgent need to ensure that diagnostic assays are capable of detecting widely circulating omicron sub-lineages.

STUDY DESIGN

Remnant clinical VTM samples from SARS-CoV-2 PCR confirmed infections (n = 733) collected in Wisconsin (n = 94), New York (n = 267), and South Carolina (n = 372) throughout 2022 were sequenced, classified, and tested with m2000 RealTime SARS-CoV-2, Alinity m SARS-CoV-2, ID NOW COVID-19 v2.0, BinaxNOW COVID-19 Ag Card, and Panbio COVID-19 Rapid Test Device assays.

RESULTS

Sequences and lineage classifications were obtained for n = 641/733 (87.4%) samples and included delta (n = 6) and representatives from all major SARS-CoV-2 omicron variants circulating in 2022 (BA.1, BA.2, BA.3, BA.4, BA.5, BE, BF, BQ.1, and XBB). Panels of diverse omicron lineages were tested by molecular assays RealTime (n = 624), Alinity m (n = 80), and ID NOW v2.0 (n = 88) with results showing 100% detection for all samples. BinaxNOW and Panbio had sensitivities of 494/533 (92.7%) and 416/469 (88.7%), respectively for specimens with >4 log10 copies/test, consistent with expected performance for frozen specimens. Furthermore, BinaxNOW demonstrated SARS-CoV-2 detection in clinical samples 1-4 days, and up to 18 days post-symptom onset in BA.1 infected patients with >4 log10 copies/test.

CONCLUSIONS

This data highlights the rise and diversification of SARS-CoV-2 omicron variants over the course of 2022 and demonstrate that each of the 5 tested assays can detect the breadth of omicron variants circulating globally.

Reviewing methods of deep learning for diagnosing COVID-19, its variants and synergistic medicine combinations

The COVID-19 pandemic has necessitated the development of reliable diagnostic methods for accurately detecting the novel coronavirus and its variants. Deep learning (DL) techniques have shown promising potential as screening tools for COVID-19 detection. In this study, we explore the realistic development of DL-driven COVID-19 detection methods and focus on the fully automatic framework using available resources, which can effectively investigate various coronavirus variants through modalities. We conducted an exploration and comparison of several diagnostic techniques that are widely used and globally validated for the detection of COVID-19. Furthermore, we explore review-based studies that provide detailed information on synergistic medicine combinations for the treatment of COVID-19. We recommend DL methods that effectively reduce time, cost, and complexity, providing valuable guidance for utilizing available synergistic combinations in clinical and research settings. This study also highlights the implication of innovative diagnostic technical and instrumental strategies, exploring public datasets, and investigating synergistic medicines using optimised DL rules. By summarizing these findings, we aim to assist future researchers in their endeavours by providing a comprehensive overview of the implication of DL techniques in COVID-19 detection and treatment. Integrating DL methods with various diagnostic approaches holds great promise in improving the accuracy and efficiency of COVID-19 diagnostics, thus contributing to effective control and management of the ongoing pandemic.

Aptamer-Based Strategies to Address Challenges in COVID-19 Diagnosis and Treatments

Coronavirus disease (COVID-19), a highly contagious and rapidly spreading disease with significant fatality in the elderly population, has swept across the world since 2019. Since its first appearance, the causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has undergone multiple mutations, with Omicron as the predominant circulating variant of concern at the moment. The gold standard for diagnosis of COVID-19 by real-time polymerase chain reaction (RT-PCR) to detect the virus is laborious and requires well-trained personnel to perform sophisticated procedures. Also, the genetic variants of SARS-CoV-2 that arise regularly could result in false-negative detection. Meanwhile, the current COVID-19 treatments such as conventional medicine, complementary and alternative medicine, passive antibody therapy, and respiratory therapy are associated with adverse effects. Thus, there is an urgent need to discover novel diagnostic and therapeutic approaches against SARS-CoV-2 and its variants. Over the past 30 years, nucleic acid-based aptamers have gained increasing attention and serve as a promising alternative to the antibodies in the diagnostic and therapeutic fields with their uniqueness of being small, nonimmunogenicity, and thermally stable. Aptamer targeting the SARS-CoV-2 structural proteins or the host receptor proteins represent a powerful tool to control COVID-19 infection. In this review, challenges faced by currently available diagnostic and therapeutic tools for COVID-19 are underscored, along with how aptamers can shed a light on the current COVID-19 pandemic, focusing on the critical factors affecting the discovery of high-affinity aptamers and their potential applications to control COVID-19 infection.

COVID-19 Antigen Results Correlate with the Quantity of Replication-Competent SARS-CoV-2 in a Cross-Sectional Study of Ambulatory Adults during the Delta Wave

Appropriate interpretation of various diagnostic tests for COVID-19 is critical, yet the association among rapid antigen tests, reverse transcription (RT)-PCR, and viral culture has not been fully defined. To determine whether rapid antigen testing correlates with the presence and quantity of replication-competent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in ambulatory adults, 626 adult participants were enrolled in a cross-sectional diagnostic study. Each participant had two anterior nasal swabs obtained for rapid antigen and RT-PCR testing and SARS-CoV-2 viral culture. The primary outcomes were the presence and quantification of SARS-CoV-2 growth in VeroE6-ACE2-TMPRSS2 cells in asymptomatic and symptomatic ambulatory adults. In this cross-sectional study of 626 adult outpatients, the sensitivity of a single positive antigen test to identify replication-competent SARS-CoV-2 was 63.6% in asymptomatic and 91.0% in symptomatic participants. Viral culture titers were the highest at the onset of symptoms and rapidly declined by 7 days after symptom onset. The positive agreement of the rapid antigen test with RT-PCR at a cycle threshold CT less than 30 was 66.7% in asymptomatic and 90.7% in symptomatic participants. Among symptomatic participants a with a CT less than 30, a single antigen test had a positive agreement of 90.7% (95% confidence interval [CI], 84.8% to 94.8%). There was 100% negative agreement as all 425 RT-PCR-negative participants had a negative antigen test. A positive antigen test in symptomatic adults with COVID-19 has a strong correlation with replication-competent SARS-CoV-2. Rapid antigen test results may be a suitable proxy for infectiousness. IMPORTANCE Do rapid antigen test results correlate with replication-competent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (i.e., infectious) virus? In this cross-sectional diagnostic study of 626 adults, the sensitivity of the antigen test to identify replication-competent SARS-CoV-2 was 63.6% in asymptomatic and 91.0% in symptomatic participants. Viral culture titers were the highest at the onset of symptoms and rapidly declined by 7 days after symptom onset. The positive agreement of the rapid antigen test with reverse transcription (RT)-PCR at a CT of less than 30 was 66.7% in asymptomatic participants and 90.7% in symptomatic participants. A positive antigen test may be an appropriate surrogate for identifying replication-competent virus in symptomatic individuals with COVID-19.

Update of ESCMID COVID-19 guidelines: diagnostic testing for SARS-CoV-2

SCOPE

Since the onset of coronavirus disease 2019 (COVID-19), several assays have been deployed for the diagnosis of SARS-CoV-2. The European Society of Clinical Microbiology and Infectious Diseases (ESCMID) published the first set of guidelines on SARS-CoV-2 in-vitro diagnosis in February 2022. Since the COVID-19 landscape is rapidly evolving, the relevant ESCMID guidelines panel releases an update of the previously published recommendations on diagnostic testing for SARS-CoV-2. This update aims to delineate the best diagnostic approach for SARS-CoV-2 in different populations based on current evidence.

METHODS

An ESCMID COVID-19 guidelines task force was established by the ESCMID Executive Committee. A small group was established, half appointed by the chair, and the remaining selected with an open call. The panel met virtually once a week. For all decisions, a simple majority vote was used. A list of clinical questions using the PICO (population, intervention, comparison, and outcome) format was developed at the beginning of the process. For each PICO, two panel members performed a literature search focusing on systematic reviews with a third panellist involved in case of inconsistent results. The panel reassessed the PICOs previously defined as priority in the first set of guidelines and decided to address 49 PICO questions, as 6 of them were discarded as outdated/non-clinically relevant. The "Grading of Recommendations Assessment, Development and Evaluation(GRADE)-adoption, adaptation, and de novo development of recommendations (ADOLOPMENT)" evidence-to-decision framework was utilized to produce the guidelines.

QUESTIONS ADDRESSED BY THE GUIDELINE AND RECOMMENDATIONS

After literature search, we updated 16 PICO questions; these PICOs address the use of antigen-based assays among symptomatic and asymptomatic patients with different ages, COVID-19 severity status or risk for severe COVID-19, time since onset of symptoms/contact with an infectious case, and finally, types of biomaterials used.

Performance of 20 rapid antigen detection tests to detect SARS-CoV-2 B.1.617.2 (Delta) and B.1.1.529 (Omicron) variants using a clinical specimen panel from January 2022, Berlin, Germany

BackgroundThere are conflicting reports on the performance of rapid antigen detection tests (RDT) in the detection of the SARS-CoV-2 Omicron (B.1.1.529) variant; however, these tests continue to be used frequently to detect potentially contagious individuals with high viral loads.AimThe aim of this study was to investigate comparative detection of the Delta (B.1.617.2) and Omicron variants by using a selection of 20 RDT and a limited panel of pooled combined oro- and nasopharyngeal clinical Delta and Omicron specimens.MethodsWe tested 20 CE-marked RDT for their performance to detect SARS-CoV-2 Delta and Omicron by using a panel of pooled clinical specimens collected in January 2022 in Berlin, Germany.ResultsWe observed equivalent detection performance for Delta and Omicron for most RDT, and sensitivity was widely in line with our previous pre-Delta/Omicron evaluation. Some variation for individual RDT was observed either for Delta vs Omicron detection, or when compared with the previous evaluation, which may be explained both by different panel sizes resulting in different data robustness and potential limitation of batch-to-batch consistency. Additional experiments with three RDT using non-pooled routine clinical samples confirmed comparable performance to detect Delta vs Omicron. Overall, RDT that were previously positively evaluated retained good performance also for Delta and Omicron variants.ConclusionOur findings suggest that currently available RDT are sufficient for the detection of SARS-CoV-2 Delta and Omicron variants.

Attitudes towards booster, testing and isolation, and their impact on COVID-19 response in winter 2022/2023 in France, Belgium, and Italy: a cross-sectional survey and modelling study

Background

European countries are focusing on testing, isolation, and boosting strategies to counter the 2022/2023 winter surge due to SARS-CoV-2 Omicron subvariants. However, widespread pandemic fatigue and limited compliance potentially undermine mitigation efforts.

Methods

To establish a baseline for interventions, we ran a multicountry survey to assess respondents’ willingness to receive booster vaccination and comply with testing and isolation mandates. Integrating survey and estimated immunity data in a branching process epidemic spreading model, we evaluated the effectiveness and costs of current protocols in France, Belgium, and Italy to manage the winter wave.

Findings

The vast majority of survey participants (N = 4594) was willing to adhere to testing (>91%) and rapid isolation (>88%) across the three countries. Pronounced differences emerged in the declared senior adherence to booster vaccination (73% in France, 94% in Belgium, 86% in Italy). Epidemic model results estimate that testing and isolation protocols would confer significant benefit in reducing transmission (17–24% reduction, from R = 1.6 to R = 1.3 in France and Belgium, to R = 1.2 in Italy) with declared adherence. Achieving a mitigating level similar to the French protocol, the Belgian protocol would require 35% fewer tests (from 1 test to 0.65 test per infected person) and avoid the long isolation periods of the Italian protocol (average of 6 days vs. 11). A cost barrier to test would significantly decrease adherence in France and Belgium, undermining protocols’ effectiveness.

Interpretation

Simpler mandates for isolation may increase awareness and actual compliance, reducing testing costs, without compromising mitigation. High booster vaccination uptake remains key for the control of the winter wave.

Funding

The 10.13039/501100000780European Commission, ANRS–Maladies Infectieuses Émergentes, the Agence Nationale de la Recherche, the Chaires Blaise Pascal Program of the Île-de-France region.

Performance of High Throughput SARS-CoV-2 Antigen Testing Compared to Nucleic Acid Testing

OBJECTIVE

Independent assessment of SARS-CoV-2 antigen (COV2Ag) tests remains important as varying performance between assays is common. We assessed the performance of a new high-throughput COV2Ag test compared to SARS-CoV-2 nucleic acid amplification tests (NAAT).

METHODS

A total of 347 nasopharyngeal samples collected from January to October 2021 were assessed by NAAT as part of standard-of-care testing (CDC LDT or GeneXpert System, Cepheid) and COV2Ag using the ADVIA Centaur CoV2Ag assay (Siemens Healthineers).

RESULTS

Among NAAT positive specimens we found 82.4% agreement and in NAAT negative specimens we found 97.3% agreement (overall agreement 85.6%). In symptomatic persons, COV2Ag agreed with NAAT 90.0% (n = 291), and in asymptomatic persons, 62.5% (n = 56). Agreement between positive NAAT and COV2Ag increased at lower cycle threshold (Ct) values.

CONCLUSION

The COV2Ag assay exceeded the World Health Organization minimum performance requirements of ≥ 80% sensitivity and ≥ 97% specificity. The COV2Ag assay is helpful for large scale screening efforts due to high-throughput and reduced wait times.

Combined Diagnosis of SARS-CoV-2: Rapid Antigen Detection as an Adjunct to Nucleic Acid Detection

Coronavirus disease 2019 is a serious threat to human life, and early diagnosis and screening can help control the COVID-19 pandemic. The high sensitivity of reverse transcriptase-polymerase chain reaction (RT-PCR) assay is the gold standard for the diagnosis of COVID-19, but there are still some false-negative results. Rapid antigen detection (RAD) is recommended by the World Health Organization (WHO) as a screening method for COVID-19. This review analyzed the characteristics of RDT and found that although the overall sensitivity of RAD was not as high as that of RT-PCR, but RAD was more sensitive in COVID-19 patients within 5 days of the onset of symptoms and in COVID-19 patients with Ct ≤ 25. Therefore, RAD can be used as an adjunct to RT-PCR for screening patients with early COVID-19. Finally, this review provides a combined diagnostic protocol for RAD and nucleic acid testing with the aim of providing a feasible approach for COVID-19 screening.

The Potential of Nanobodies for COVID-19 Diagnostics and Therapeutics

The infectious severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent for coronavirus disease 2019 (COVID-19). Globally, there have been millions of infections and fatalities. Unfortunately, the virus has been persistent and a contributing factor is the emergence of several variants. The urgency to combat COVID-19 led to the identification/development of various diagnosis (polymerase chain reaction and antigen tests) and treatment (repurposed drugs, convalescent plasma, antibodies and vaccines) options. These treatments may treat mild symptoms and decrease the risk of life-threatening disease. Although these options have been fairly beneficial, there are some challenges and limitations, such as cost of tests/drugs, specificity, large treatment dosages, intravenous administration, need for trained personal, lengthy production time, high manufacturing costs, and limited availability. Therefore, the development of more efficient COVID-19 diagnostic and therapeutic options are vital. Nanobodies (Nbs) are novel monomeric antigen-binding fragments derived from camelid antibodies. Advantages of Nbs include low immunogenicity, high specificity, stability and affinity. These characteristics allow for rapid Nb generation, inexpensive large-scale production, effective storage, and transportation, which is essential during pandemics. Additionally, the potential aerosolization and inhalation delivery of Nbs allows for targeted treatment delivery as well as patient self-administration. Therefore, Nbs are a viable option to target SARS-CoV-2 and overcome COVID-19. In this review we discuss (1) COVID-19; (2) SARS-CoV-2; (3) the present conventional COVID-19 diagnostics and therapeutics, including their challenges and limitations; (4) advantages of Nbs; and (5) the numerous Nbs generated against SARS-CoV-2 as well as their diagnostic and therapeutic potential.

Analytical performance of the rapid qualitative antigen kit for the detection of SARS-CoV-2 during widespread circulation of the Omicron variant

INTRODUCTION

Rapid qualitative antigen testing is essential in the clinical management of COVID-19. However, most evaluations of antigen tests have been performed before the emergence of the Omicron variant.

METHODS

This prospective observational study evaluated QuickNavi-COVID19 Ag, a rapid antigen detection test between December 2021 and February 2022 in Japan, using real-time reverse transcription (RT)-PCR as a reference. Two nasopharyngeal samples were simultaneously collected for antigen testing and for RT-PCR. Variant analysis of the SARS-CoV-2 genomic sequencing was also performed.

RESULTS

In total, nasopharyngeal samples were collected from 1073 participants (417 positive; 919 symptomatic; 154 asymptomatic) for analysis. Compared with those of RT-PCR, the sensitivity, specificity, positive predictive value, and negative predictive value were 94.2% (95% CI: 91.6%-96.3%), 99.5% (95% CI: 98.7%-99.9%), 99.2% (95% CI: 97.8%-99.8%), and 96.5% (95% CI: 94.8%-97.7%), respectively. The sensitivity among symptomatic individuals was 94.3% (95% CI: 91.5%-96.4%). Overall, 85.9% of sequences were classified as Omicron sublineage BA.1, 12.4% were Omicron sublineage BA.2, and 1.6% were Delta B.1.617.2. (Delta variant). Most of the samples (87.1%) had Ct values of <25, and the sensitivity was 47.4% for low viral load samples (Ct ≥ 30); a similar trend has been observed in both symptomatic and asymptomatic groups.

CONCLUSIONS

The QuickNavi-COVID19 Ag test showed sufficient diagnostic performance for the detection of the SARS-CoV-2 Omicron sublineages BA.1 and BA.2 from nasopharyngeal samples. However, the current study was mainly performed in symptomatic patients and the results are not sufficiently applicable for asymptomatic patients.

Diagnostic accuracy of SARS-CoV-2 rapid antigen self-tests in asymptomatic individuals in the omicron period: a cross-sectional study

OBJECTIVES

To assess the performances of three commonly used antigen rapid diagnostic tests used as self-tests in asymptomatic individuals in the Omicron period.

METHODS

We performed a cross-sectional diagnostic test accuracy study in the Omicron period in three public health service COVID-19 test sites in the Netherlands, including 3600 asymptomatic individuals aged ≥ 16 years presenting for SARS-CoV-2 testing for any reason except confirmatory testing after a positive self-test. Participants were sampled for RT-PCR (reference test) and received one self-test (either Acon Flowflex [Flowflex], MP Biomedicals (MPBio), or Siemens-Healthineers CLINITEST [CLINITEST]) to perform unsupervised at home. Diagnostic accuracies of each self-test were calculated.

RESULTS

Overall sensitivities were 27.5% (95% CI, 21.3-34.3%) for Flowflex, 20.9% (13.9-29.4%) for MPBio, and 25.6% (19.1-33.1%) for CLINITEST. After applying a viral load cut-off (≥5.2 log10 SARS-CoV-2 E-gene copies/mL), sensitivities increased to 48.3% (37.6-59.2%), 37.8% (22.5-55.2%), and 40.0% (29.5-51.2%), respectively. Specificities were >99% for all tests in most analyses.

DISCUSSION

The sensitivities of three commonly used SARS-CoV-2 antigen rapid diagnostic tests when used as self-tests in asymptomatic individuals in the Omicron period were very low. Antigen rapid diagnostic test self-testing in asymptomatic individuals may only detect a minority of infections at that point in time. Repeated self-testing in case of a negative self-test is advocated to improve the diagnostic yield, and individuals should be advised to re-test when symptoms develop.

Sensitivity of Rapid Antigen Tests Against SARS-CoV-2 Omicron and Delta Variants

Rapid Antigen Tests (RAT) have become an invaluable tool for combating the COVID-19 pandemic. However, concerns have been raised regarding the ability of existing RATs to effectively detect emerging SARS-CoV-2 variants. We compared the performance of eight commercially available, emergency use authorized RATs against the Delta and Omicron SARS-CoV-2 variants using individual patient and serially diluted pooled clinical samples. The RATs exhibited lower sensitivity for Omicron samples when using PCR Cycle threshold (C T ) value (a proxy for RNA concentration) as the comparator. Interestingly, however, they exhibited similar sensitivity for Omicron and Delta samples when using quantitative antigen concentration as the comparator. We further found that the Omicron samples had lower ratios of antigen to RNA, which offers a potential explanation for the apparent lower sensitivity of RATs for that variant when using C T value as a reference. Our findings underscore the complexity in assessing RAT performance against emerging variants and highlight the need for ongoing evaluation in the face of changing population immunity and virus evolution.

Longitudinal observation of viral load in patients infected with Omicron variant and its relationship with clinical symptoms

Objective

In 2022, a new coronavirus variant (Omicron) infection epidemic broke out in Shanghai, China. However, it is unclear whether the duration of this omicron variant is different from that of the prototype strain.

Methods

We retrospectively analyzed 157 cases of Omicron variant infection in Taizhou Public Health Center from March 29, 2022, to April 18, 2022, and observed the dynamics of nucleic acid Ct values during the admission and discharge of patients. Clinical and laboratory indicators of these patients were also obtained.

Results

Compared to the prototype strain, the Omicron variant showed a broad population susceptibility in infected individuals (regardless of age and presence of underlying disease) and had slight damage to the immune system and renal function; the viral loads peaked was 2-3 days from disease onset; the median duration of omicron variant was 15-18 days; the nucleic acid Ct value of nasopharyngeal swabs of infected patients is lower than that of throat swabs, and the Ct value of oropharyngeal swabs is unstable during the recovery period.

Conclusion

Therefore, we found that the time to peak viral load of this Omicron variant was 2-3 days after the onset of the disease, and the duration was 15-18 days; symptomatic patients had higher viral load and longer hospitalization time. This finding will provide a basis for understanding omicron variants and formulating the national prevention and control strategy.

Clinical Performance of Direct RT-PCR Testing of Raw Saliva for Detection of SARS-CoV-2 in Symptomatic and Asymptomatic Individuals

RT-PCR tests based on RNA extraction from nasopharyngeal swabs (NPS) are promoted as the "gold standard" for SARS-CoV-2 detection. However, the use of saliva samples offers noninvasive self-collection more suitable for high-throughput testing. This study evaluated performance of the TaqPath COVID-19 Fast PCR Combo kit 2.0 assay for detection of SARS-CoV-2 in raw saliva relative to a lab-developed direct RT-PCR test (SalivaDirect-based PCR, SDB-PCR) and an RT-PCR test based on RNA extraction from NPS. Saliva and NPS samples were collected from symptomatic and asymptomatic individuals (N = 615). Saliva samples were tested for SARS-CoV-2 using the TaqPath COVID-19 Fast PCR Combo kit 2.0 and the SDB-PCR, while NPS samples were tested by RT-PCR in RNA extracts according to the Irish national testing system. TaqPath COVID-19 Fast PCR Combo kit 2.0 detected SARS-CoV-2 in 52 saliva samples, of which 51 were also positive with the SDB-PCR. Compared to the NPS "gold standard" biospecimen method, 49 samples displayed concordant results, while three samples (35 Collapse

Key Words

• COVID-19
• RT-PCR
• SARS-CoV-2
• asymptomatic
• d
• saliva
• surveillance
• symptomatic

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MESH Headings

• Humans
• Reverse Transcriptase Polymerase Chain Reaction
• SARS-CoV-2/genetics
• Pandemics
• Saliva
• COVID-19/diagnosis
• RNA
• Specimen Handling

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Grants

• Science Foundation Ireland (SFI)

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Affiliation(s)

Rosa Castillo-Bravo Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
Noel Lucca Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
Linyi Lai Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
Killian Marlborough Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
Galina Brychkova Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
Maryam Shideh Sakhteh Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
Charlie Lonergan Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
Justin O’Grady Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom
Nabil-Fareed Alikhan Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom
Alexander J. Trotter Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom
Andrew J. Page Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom
Breda Smyth College of Medicine, Nursing and Health Sciences, National University of Ireland Galway, Ireland Health Service Executive (HSE) West, Merlin Park University Hospital, Galway, Ireland
Peter C. McKeown Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland
Jelena D. M. Feenstra Thermo Fisher Scientific, South San Francisco, California, USA
Camilla Ulekleiv Thermo Fisher Scientific, South San Francisco, California, USA
Oceane Sorel Thermo Fisher Scientific, South San Francisco, California, USA
Manoj Gandhi Thermo Fisher Scientific, South San Francisco, California, USA
Charles Spillane Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland

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Clinical practice of rapid antigen tests for SARS-CoV-2 Omicron variant: A single-center study in China

Responding to the fast-spreading SARS-CoV-2 Omicron variant, to improve screening efficiency, rapid antigen tests (RATs) were first added as a supplementary detection method in China in mid-March, 2022. What and how big a role RATs should play need to be supported by clinical data. Here, RAT performance and relevant factors in comparison with nucleic acid amplification tests (NAATs) were assessed in Omicron-infected inpatients. From the NAAT results, nasopharyngeal swabs (NPs) performed better than oropharyngeal swabs (OPs). RATs tested on NAAT positive NPs performed better than those with OP-positive samples. The RAT positivity rate was strongly associated with high levels of N and OFR1ab genes, especially in NPs where patients also had significantly longer hospital stays and shorter days from symptom onset to RAT testing. Self-performed RATs had a detection accuracy that was comparable to professionally performed RATs when the subjects were well guided. The antigen negative rate of the studied patients was 100% at discharge. These findings suggest that, in addition to a supplementary detection role, RATs can be an important strategy for evaluating the disease progression of Omicron-infected inpatients. This study provides important clinical data to support better rules regarding RATs under China's COVID-19 prevention and control policy.

The Performance of Lateral Flow Tests in the Age of the Omicron: A Rapid Systematic Review

Prompt detection and isolation of COVID-19 cases is vital for preventing further viral transmission, and lateral flow or rapid antigen tests have been an important diagnostic tool in this pandemic. However, concerns have emerged regarding the sensitivity of these devices for the new BA.1, BA.2, and BA.4/5 omicron variants, which have greater transmissibility and extensive mutations in its spike (S) and nucleocapsid (N) proteins. N protein is an important target protein for existing lateral flow devices. This paper therefore aimed to provide a rapid review of available literature on the performance of the lateral flow tests for detecting the omicron coronavirus variant. A systematic literature search of PubMed, EMBASE, OVID Medline, and Google Scholar found six published studies and four preprints investigating the performance of existing lateral flow devices for the omicron variant, as compared to the B.1.617.2 (Delta) variant. Overall, it appears that the devices have poorer performance for the omicron variant and when testing samples with cycle threshold (Ct) values greater than 25 and in asymptomatic individuals. As most available data were preliminary and had small sample sizes, it is recommended that these data be further studied to better inform and adapt our public health responses.

Prevalence of Positive Rapid Antigen Tests After 7-Day Isolation Following SARS-CoV-2 Infection in College Athletes During Omicron Variant Predominance

IMPORTANCE

The US Centers for Disease Control and Prevention shortened the recommended isolation period for SARS-CoV-2 infection from 10 days to 5 days in December 2021. It is unknown whether an individual with the infection may still have a positive result to a rapid antigen test and potentially be contagious at the end of this shortened isolation period.

OBJECTIVE

To estimate the proportion of individuals with SARS-CoV-2 infection whose rapid antigen test is still positive starting 7 days postdiagnosis.

DESIGN, SETTING, AND PARTICIPANTS

This case series analyzed student athletes at a National Collegiate Athletic Association Division I university campus who tested positive for SARS-CoV-2 between January 3 and May 6, 2022. Individuals underwent rapid antigen testing starting 7 days postdiagnosis to determine whether they could end their isolation period.

EXPOSURES

Rapid antigen testing 7 days after testing positive for SARS-CoV-2.

MAIN OUTCOMES AND MEASURES

Rapid antigen test results, symptom status, and SARS-CoV-2 variant identification via campus wastewater analysis.

RESULTS

A total of 264 student athletes (140 [53%] female; mean [SD] age, 20.1 [1.2] years; range, 18-25 years) representing 268 infections (177 [66%] symptomatic, 91 [34%] asymptomatic) were included in the study. Of the 248 infections in individuals who did a day 7 test, 67 (27%; 95% CI, 21%-33%) tests were still positive. Patients with symptomatic infections were significantly more likely to test positive on day 7 vs those who were asymptomatic (35%; 95% CI, 28%-43% vs 11%; 95% CI, 5%-18%; P < .001). Patients with the BA.2 variant were also significantly more likely to test positive on day 7 compared with those with the BA.1 variant (40%; 95% CI, 29%-51% vs 21%; 95% CI, 15%-27%; P = .007).

CONCLUSIONS AND RELEVANCE

In this case series, rapid antigen tests remained positive in 27% of the individuals after 7 days of isolation, suggesting that the Centers for Disease Control and Prevention-recommended 5-day isolation period may be insufficient in preventing ongoing spread of disease. Further studies are needed to determine whether these findings are present in a more heterogeneous population and in subsequent variants.

COVID-19 Symptoms and Duration of Rapid Antigen Test Positivity at a Community Testing and Surveillance Site During Pre-Delta, Delta, and Omicron BA.1 Periods

Importance

Characterizing the clinical symptoms and evolution of community-based SARS-CoV-2 infections may inform health practitioners and public health officials in a rapidly changing landscape of population immunity and viral variants.

Objectives

To compare COVID-19 symptoms among people testing positive with a rapid antigen test (RAT) during the Omicron BA.1 variant period (December 1, 2021, to January 30, 2022) with the pre-Delta (January 10 to May 31, 2021) and Delta (June 1 to November 30, 2021) variant periods and to assess the duration of RAT positivity during the Omicron BA.1 surge.

Design, Setting, and Participants

This cross-sectional study was conducted from January 10, 2021, to January 31, 2022, at a walk-up community COVID-19 testing site in San Francisco, California. Participants included children and adults seeking COVID-19 testing with an RAT, regardless of age, vaccine status, or symptoms.

Main Outcomes and Measures

Fisher exact tests or χ2 tests were used to compare COVID-19 symptoms during the Omicron BA.1 period with the pre-Delta and Delta periods for vaccination status and age group. Among people returning for repeated testing during the Omicron period, the proportion with a positive RAT between 4 and 14 days from symptom onset or since first positive test if asymptomatic was estimated.

Results

Among 63 277 persons tested (median [IQR] age, 32 [21-44] years, with 12.0% younger than 12 years; 52.0% women; and 68.5% Latinx), a total of 18 301 people (28.9%) reported symptoms, of whom 4565 (24.9%) tested positive for COVID-19. During the Omicron BA.1 period, 3032 of 7283 symptomatic participants (41.6%) tested positive, and the numbers of these reporting cough and sore throat were higher than during pre-Delta and Delta periods (cough: 2044 [67.4%] vs 546 [51.3%] of 1065 participants, P < .001 for pre-Delta, and 281 [60.0%] of 468 participants, P = .002, for Delta; sore throat: 1316 [43.4%] vs 315 [29.6%] of 1065 participants, P < .001 for pre-Delta, and 136 [29.1%] of 468 participants, P < .001, for Delta). Compared with the 1065 patients with positive test results in the pre-Delta period, congestion among the 3032 with positive results during the Omicron BA.1 period was more common (1177 [38.8%] vs 294 [27.6%] participants, P < .001), and loss of taste or smell (160 [5.3%] vs 183 [17.2%] participants, P < .001) and fever (921 [30.4%] vs 369 [34.7%] participants, P = .01) were less common. In addition, during the Omicron BA.1 period, fever was less common among the people with positive test results who had received a vaccine booster compared with those with positive test results who were unvaccinated (97 [22.5%] of 432 vs 42 [36.2%] of 116 participants, P = .003), and fever and myalgia were less common among participants who had received a booster compared with those with positive results who had received only a primary series (fever: 97 [22.5%] of 432 vs 559 [32.8%] of 1705 participants, P < .001; myalgia: 115 [26.6%] of 432 vs 580 [34.0%] of 1705 participants, P = .003). During the Omicron BA.1 period, 5 days after symptom onset, 507 of 1613 people (31.1%) with COVID-19 stated that their symptoms were similar, and 95 people (5.9%) reported worsening symptoms. Among people testing positive, 80.2% of participants who were symptomatic and retested remained positive 5 days after symptom onset.

Conclusions and Relevance

In this cross-sectional study, COVID-19 upper respiratory tract symptoms were more commonly reported during the Omicron BA.1 period than during the pre-Delta and Delta periods, with differences by vaccination status. Rapid antigen test positivity remained high 5 days after symptom onset, supporting guidelines requiring a negative test to inform the length of the isolation period.

Estimate of undetected severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection in acute-care hospital settings using an individual-based microsimulation model

Objective:

Current guidance states that asymptomatic screening for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) prior to admission to an acute-care setting is at the facility’s discretion. This study’s objective was to estimate the number of undetected cases of SARS-CoV-2 admitted as inpatients under 4 testing approaches and varying assumptions.

Design and setting:

Individual-based microsimulation of 104 North Carolina acute-care hospitals

Patients:

All simulated inpatient admissions to acute-care hospitals from December 15, 2021, to January 13, 2022 [ie, during the SARS-COV-2 ο (omicron) variant surge].

Interventions:

We simulated (1) only testing symptomatic patients, (2) 1-stage antigen testing with no confirmatory polymerase chain reaction (PCR) test, (3) 1-stage antigen testing with a confirmatory PCR for negative results, and (4) serial antigen screening (ie, repeat antigen test 2 days after a negative result).

Results:

Over 1 month, there were 77,980 admissions: 13.7% for COVID-19, 4.3% with but not for COVID-19, and 82.0% for non–COVID-19 indications without current infection. Without asymptomatic screening, 1,089 (credible interval [CI], 946–1,253) total SARS-CoV-2 infections (7.72%) went undetected. With 1-stage antigen screening, 734 (CI, 638–845) asymptomatic infections (67.4%) were detected, with 1,277 false positives. With combined antigen and PCR screening, 1,007 (CI, 875–1,159) asymptomatic infections (92.5%) were detected, with 5,578 false positives. A serial antigen testing policy detected 973 (CI, 845–1,120) asymptomatic infections (89.4%), with 2,529 false positives.

Conclusions:

Serial antigen testing identified >85% of asymptomatic infections and resulted in fewer false positives with less cost per identified infection compared to combined antigen plus PCR testing.

Analytical Sensitivity of Eight Different SARS-CoV-2 Antigen-Detecting Rapid Tests for Omicron-BA.1 Variant

The emergence of each novel SARS-CoV-2 variant of concern (VOC) requires investigation of its potential impact on the performance of diagnostic tests in use, including antigen-detecting rapid diagnostic tests (Ag-RDTs). Although anecdotal reports have been circulating that the newly emerged Omicron-BA.1 variant is in principle detectable by Ag-RDTs, few data on sensitivity are available. We have performed (i) analytical sensitivity testing with cultured virus in eight Ag-RDTs and (ii) retrospective testing in duplicates with clinical samples from vaccinated individuals with Omicron-BA.1 (n = 59) or Delta (n = 54) breakthrough infection on seven Ag-RDTs. Overall, in our analytical study we have found heterogenicity between Ag-RDTs for detecting Omicron-BA.1. When using cultured virus, we observed a trend toward lower endpoint sensitivity for Omicron-BA.1 detection than for earlier circulating SARS-CoV-2 and the other VOCs. In our retrospective study, the detection of Delta and Omicron-BA.1 was assessed in a comparable set of stored clinical samples using seven Ag-RDTs. Four hundred ninety-seven of all 826 tests (60.17%) performed on Omicron-BA.1 samples were positive, compared to 489/756 (64.68%) for Delta samples. In the analytical study, the sensitivity for both Omicron-BA.1 and Delta between the Ag-RDTs was variable. All seven Ag-RDTs showed comparable sensitivities to detect Omicron-BA.1 and Delta in the retrospective study. IMPORTANCE Sensitivity for detecting Omicron-BA.1 shows high heterogenicity between Ag-RDTs, necessitating a careful consideration when using these tests to guide infection prevention measures. Analytical and retrospective testing is a proxy and timely solution to generate rapid performance data, but it is not a replacement for clinical evaluations, which are urgently needed. Biological and technical reasons for detection failure by some Ag-RDTs need to be further investigated.

A mixed methods study evaluating acceptability of a daily COVID-19 testing regimen with a mobile-app connected, at-home, rapid antigen test: Implications for current and future pandemics

BACKGROUND

Widespread use of at-home rapid COVID-19 antigen tests has been proposed as an important public health intervention to interrupt chains of transmission. Antigen tests may be preferred over PCR because they provide on-demand results for relatively low cost and can identify people when they are most likely to be infectious, particularly when used daily. Yet the extent to which a frequent antigen testing intervention will result in a positive public health impact for COVID-19 will depend on high acceptability and high adherence to such regimens.

METHODS

We conducted a mixed-methods study assessing acceptability of and adherence to a daily at-home mobile-app connected rapid antigen testing regimen among employees of a US-based media company. Acceptability was assessed across seven domains of the Theoretical Framework of Acceptability.

RESULTS

Among 31 study participants, acceptability of the daily testing intervention was generally high, with participants reporting high perceived effectiveness, intervention coherence, and self-efficacy; positive affective attitude; acceptable degree of burden and opportunity cost; and assessing the intervention as ethical. 71% reported a preference to test daily using an at-home antigen test than weekly employment-based PCR. Mean adherence to the 21-day testing regimen was 88% with 43% of participants achieving 100% adherence, 48% testing at least every other day, and 10% testing less than every other day.

CONCLUSIONS

Despite overall high acceptability and adherence, we identified three implementation challenges that must be addressed for frequent serial testing for COVID-19 to be implemented at scale and have a positive public health impact. First, users need guidance on how and when to adapt testing frequencies to different epidemiological conditions. Second, users and institutions need guidelines for how to safely store and share test results. Third, implementation of serial testing strategies must prioritize health equity and protect those most vulnerable to COVID-19.

Clinical Performance of Rapid and Point-of-Care Antigen Tests for SARS-CoV-2 Variants of Concern: A Living Systematic Review and Meta-Analysis

Rapid antigen tests (RATs) for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are widely used in the Coronavirus disease 2019 (COVID-19) pandemic caused by diverse variants. Information on the real-world performance of RATs for variants is urgently needed for decision makers. Systematic searches of the available literature and updates were conducted in PubMed, Ovid-MEDLINE, Ovid-EMBASE, CENTRAL, and KMBASE for articles evaluating the accuracy of instrument-free RATs for variants up until 14 March 2022. A bivariate random effects model was utilized to calculate pooled diagnostic values in comparison with real-time reverse transcription-polymerase chain reaction as the reference test. A total of 7562 samples from six studies were available for the meta-analysis. The overall pooled sensitivity and specificity of RATs for variants were 69.7% (95% confidence interval [CI] = 62.5% to 76.1%) and 100.0% (95% CI = 98.8% to 100.0%), respectively. When an additional 2179 samples from seven studies reporting sensitivities only were assessed, the pooled sensitivity dropped to 50.0% (95% CI = 44.0% to 55.0%). These findings suggest reassessment and monitoring of the diagnostic utility of RATs for variants, especially for the sensitivity aspect, to facilitate appropriate diagnosis and management of COVID-19 patients.

Comparison of Home Antigen Testing With RT-PCR and Viral Culture During the Course of SARS-CoV-2 Infection

IMPORTANCE

As self-collected home antigen tests become widely available, a better understanding of their performance during the course of SARS-CoV-2 infection is needed.

OBJECTIVE

To evaluate the diagnostic performance of home antigen tests compared with reverse transcription-polymerase chain reaction (RT-PCR) and viral culture by days from illness onset, as well as user acceptability.

DESIGN, SETTING, AND PARTICIPANTS

This prospective cohort study was conducted from January to May 2021 in San Diego County, California, and metropolitan Denver, Colorado. The convenience sample included adults and children with RT-PCR-confirmed infection who used self-collected home antigen tests for 15 days and underwent at least 1 nasopharyngeal swab for RT-PCR, viral culture, and sequencing.

EXPOSURES

SARS-CoV-2 infection.

MAIN OUTCOMES AND MEASURES

The primary outcome was the daily sensitivity of home antigen tests to detect RT-PCR-confirmed cases. Secondary outcomes included the daily percentage of antigen test, RT-PCR, and viral culture results that were positive, and antigen test sensitivity compared with same-day RT-PCR and cultures. Antigen test use errors and acceptability were assessed for a subset of participants.

RESULTS

This study enrolled 225 persons with RT-PCR-confirmed infection (median [range] age, 29 [1-83] years; 117 female participants [52%]; 10 [4%] Asian, 6 [3%] Black or African American, 50 [22%] Hispanic or Latino, 3 [1%] Native Hawaiian or Other Pacific Islander, 145 [64%] White, and 11 [5%] multiracial individuals) who completed 3044 antigen tests and 642 nasopharyngeal swabs. Antigen test sensitivity was 50% (95% CI, 45%-55%) during the infectious period, 64% (95% CI, 56%-70%) compared with same-day RT-PCR, and 84% (95% CI, 75%-90%) compared with same-day cultures. Antigen test sensitivity peaked 4 days after illness onset at 77% (95% CI, 69%-83%). Antigen test sensitivity improved with a second antigen test 1 to 2 days later, particularly early in the infection. Six days after illness onset, antigen test result positivity was 61% (95% CI, 53%-68%). Almost all (216 [96%]) surveyed individuals reported that they would be more likely to get tested for SARS-CoV-2 infection if home antigen tests were available over the counter.

CONCLUSIONS AND RELEVANCE

The results of this cohort study of home antigen tests suggest that sensitivity for SARS-CoV-2 was moderate compared with RT-PCR and high compared with viral culture. The results also suggest that symptomatic individuals with an initial negative home antigen test result for SARS-CoV-2 infection should test again 1 to 2 days later because test sensitivity peaked several days after illness onset and improved with repeated testing.

Accuracy of Rapid Antigen vs Reverse Transcriptase-Polymerase Chain Reaction Testing for SARS-CoV-2 Infection in College Athletes During Prevalence of the Omicron Variant

This case series evaluates the performance of rapid antigen tests in detecting SARS-CoV-2 infection in college athletes during prevalence of a dominant Omicron variant.

Accuracy of rapid point-of-care antigen-based diagnostics for SARS-CoV-2: An updated systematic review and meta-analysis with meta-regression analyzing influencing factors

BACKGROUND

Comprehensive information about the accuracy of antigen rapid diagnostic tests (Ag-RDTs) for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is essential to guide public health decision makers in choosing the best tests and testing policies. In August 2021, we published a systematic review and meta-analysis about the accuracy of Ag-RDTs. We now update this work and analyze the factors influencing test sensitivity in further detail.

METHODS AND FINDINGS

We registered the review on PROSPERO (registration number: CRD42020225140). We systematically searched preprint and peer-reviewed databases for publications evaluating the accuracy of Ag-RDTs for SARS-CoV-2 until August 31, 2021. Descriptive analyses of all studies were performed, and when more than 4 studies were available, a random-effects meta-analysis was used to estimate pooled sensitivity and specificity with reverse transcription polymerase chain reaction (RT-PCR) testing as a reference. To evaluate factors influencing test sensitivity, we performed 3 different analyses using multivariable mixed-effects meta-regression models. We included 194 studies with 221,878 Ag-RDTs performed. Overall, the pooled estimates of Ag-RDT sensitivity and specificity were 72.0% (95% confidence interval [CI] 69.8 to 74.2) and 98.9% (95% CI 98.6 to 99.1). When manufacturer instructions were followed, sensitivity increased to 76.3% (95% CI 73.7 to 78.7). Sensitivity was markedly better on samples with lower RT-PCR cycle threshold (Ct) values (97.9% [95% CI 96.9 to 98.9] and 90.6% [95% CI 88.3 to 93.0] for Ct-values <20 and <25, compared to 54.4% [95% CI 47.3 to 61.5] and 18.7% [95% CI 13.9 to 23.4] for Ct-values ≥25 and ≥30) and was estimated to increase by 2.9 percentage points (95% CI 1.7 to 4.0) for every unit decrease in mean Ct-value when adjusting for testing procedure and patients' symptom status. Concordantly, we found the mean Ct-value to be lower for true positive (22.2 [95% CI 21.5 to 22.8]) compared to false negative (30.4 [95% CI 29.7 to 31.1]) results. Testing in the first week from symptom onset resulted in substantially higher sensitivity (81.9% [95% CI 77.7 to 85.5]) compared to testing after 1 week (51.8%, 95% CI 41.5 to 61.9). Similarly, sensitivity was higher in symptomatic (76.2% [95% CI 73.3 to 78.9]) compared to asymptomatic (56.8% [95% CI 50.9 to 62.4]) persons. However, both effects were mainly driven by the Ct-value of the sample. With regards to sample type, highest sensitivity was found for nasopharyngeal (NP) and combined NP/oropharyngeal samples (70.8% [95% CI 68.3 to 73.2]), as well as in anterior nasal/mid-turbinate samples (77.3% [95% CI 73.0 to 81.0]). Our analysis was limited by the included studies' heterogeneity in viral load assessment and sample origination.

CONCLUSIONS

Ag-RDTs detect most of the individuals infected with SARS-CoV-2, and almost all (>90%) when high viral loads are present. With viral load, as estimated by Ct-value, being the most influential factor on their sensitivity, they are especially useful to detect persons with high viral load who are most likely to transmit the virus. To further quantify the effects of other factors influencing test sensitivity, standardization of clinical accuracy studies and access to patient level Ct-values and duration of symptoms are needed.