Clinical performance of rapid antigen tests in comparison to RT-PCR for SARS-COV-2 diagnosis in Omicron variant: A systematic review and meta-analysis

Correlation of patient symptoms with SARS-CoV-2 Omicron variant viral loads in nasopharyngeal and saliva samples and their influence on the performance of rapid antigen testing

Evaluating SARS-CoV-2 viral loads in nasopharyngeal (NP) and saliva samples, factors affecting viral loads, and the performance of rapid antigen testing (RAT) have not been comprehensively conducted during SARS-CoV-2 Omicron epidemic. This prospective study included outpatients enrolled during Omicron variant period in Japan. Paired NP swab and saliva samples were collected to measure viral loads by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The correlation between viral loads and clinical symptoms was examined. The performance of an immunochromatography-based RAT kit was also assessed. A total of 153 patients tested within 3 days of symptom onset were included. The mean viral load was 5.60 log10 copies/test and 3.65 log10 copies/test in NP and saliva samples, respectively, resulting in a significant difference (P < 0.0001). Fever over 37°C (axillary temperature) and total number of symptoms other than fever were identified as independent factors positively correlated with the viral loads in both NP and saliva samples. RAT sensitivity using NP and saliva samples was 92% and 68%, respectively, using positive RT-qPCR results as the reference. The sensitivity of RAT using NP and saliva samples was significantly higher in patients with fever ≥37°C and/or at least one symptom than in those with fever <37°C and/or no symptoms (97% vs 83% in NP swabs; 80% vs 50% in saliva). Distinct symptoms, including fever ≥37°C, may reflect high Omicron variant viral loads. Rapid antigen testing, not only using nasopharyngeal swabs but also using saliva, would be useful for COVID-19 diagnosis as point-of-care testing, particularly for symptomatic patients.

IMPORTANCE

We examined nasopharyngeal and salivary viral loads using samples collected from outpatients with SARS-CoV-2 infection during the Omicron epidemic in Japan and explored the outpatient factors correlated with viral loads. In addition, we evaluated the performance of an authorized rapid antigen testing (RAT) kit using nasopharyngeal and saliva samples with RT-PCR testing as the reference. Intriguingly, a correlation between fever and other symptoms and SARS-CoV-2 viral loads in nasopharyngeal and saliva samples was observed based on one COVID-19 outpatient visit. RAT sensitivity was influenced by viral loads. Nevertheless, nasopharyngeal RAT is considered useful for SARS-CoV-2 point-of-care diagnosis. In patients with distinct symptoms, including high-grade fever, salivary RAT could be a practical diagnostic tool because of the higher estimated viral loads. After the Omicron epidemic, outpatients with mild COVID-19 have become the main focus of diagnosis and treatment. Our study provides valuable information regarding the point-of-care diagnosis of these patients.

Comparing the effectiveness of universal admission testing and risk-based testing at emergency admission for preventing nosocomial COVID-19: a multicenter retrospective cohort study in Japan

OBJECTIVE

To compare the effectiveness of universal admission testing (UAT) and risk-based testing (RBT) in preventing nosocomial coronavirus disease 2019 (COVID-19) after the implementation of strict infection control measures.

DESIGN

Retrospective multicenter cohort study.

SETTING

Five community hospitals in Japan.

PATIENTS

14,028 adult patients admitted emergently from June 1, 2022, to January 31, 2023.

METHODS

We calculated crude incidence density rates of community-acquired COVID-19 (positive test ≤4 days postadmission), hospital-acquired COVID-19 (positive test ≥8 days postadmission), total postadmission COVID-19 (all cases of positive test postadmission), and primary cases (sporadic and index cases). A generalized estimating equation model was used to adjust for local incidence (new COVID-19 patients per 100,000 population), single-bed room proportion, and admission proportion of patients older than 65 years.

RESULTS

The weekly local incidence in the study areas was less than 1,800 per 100,000 population (1.8%). Two hospitals implemented RBT and 3 implemented UAT. The median admission testing rate was higher in the UAT group than in the RBT group (95% vs 55%; difference 45.2%, 95% CI, 40.3%-48.8%). Crude and adjusted analyses revealed no significant associations between incidence density rates (IRR; >1 indicates higher incidence with UAT) and admission strategies for any of the outcomes: community-acquired cases (adjusted IRR = 1.23; 95% CI, 0.46-3.31), hospital-acquired cases (1.46; 0.80-2.66), total postadmission COVID-19 (1.22; 0.79-1.87), and primary cases (0.81; 0.59-1.12).

CONCLUSIONS

Compared with risk-based testing, universal admission testing may have limited additional benefits in preventing nosocomial COVID-19 transmission during a period of low-moderate local incidence.

Development and characterization of monoclonal antibodies recognizing nucleocapsid protein of multiple SARS-CoV-2 variants

Rapid antigen test (RAT) is widely used for SARS-CoV-2 infection diagnostics. However, test sensitivity has decreased recently due to the emergence of the Omicron variant and its sublineages. Here we developed a panel of SARS-CoV-2 nucleocapsid protein (NP) specific mouse monoclonal antibodies (mAbs) and assessed their sensitivity and specificity to important SARS-CoV-2 variants. We identified seven mAbs that exhibited strong reactivity to SARS-CoV-2 variants and recombinant NP (rNP) by Western immunoblot or ELISA. Their specificity to SARS-CoV-2 was confirmed by negative or low reactivity to rNPs from SARS-CoV-1, MERS, and common human coronaviruses (HCoV-HKU1, HCoV-CO43, HCoV-NL63, and HCoV-229E). These seven mAbs were further tested by immunoplaque assay against selected variants of concern (VOCs), including two Omicron sublineages, and five mAbs (F461G13, F461G7, F459G7, F457G3, and F461G6), showed strong reactions, warranting further suitability testing for the development of diagnostic assay.

Post-market surveillance of six COVID-19 point-of-care tests using pre-Omicron and Omicron SARS-CoV-2 variants

Post-market surveillance of test performance is a critical function of public health agencies and clinical researchers that ensures tests maintaining diagnostic characteristics following their regulatory approval. Changes in product quality, manufacturing processes over time, or the evolution of new variants may impact product performance. During the COVID-19 pandemic, a plethora of point-of-care tests (POCTs) was released onto the Canadian market. This study evaluated the performance characteristics of several of the most widely distributed POCTs in Canada, including four rapid antigen tests (Abbott Panbio, BTNX Rapid Response, SD Biosensor, and Quidel QuickVue) and two molecular tests (Abbott ID NOW and Lucira Check IT). All tests were challenged with 149 SARS-CoV-2 clinical positives, including multiple variants up to and including Omicron XBB.1.5, as well as 29 clinical negatives. Results were stratified based on whether the isolate was Omicron or pre-Omicron as well as by reverse transcriptase quantitative PCR Ct value. The test performance of each POCT was consistent with the manufacturers' claims and showed no significant decline in clinical performance against any of the variants tested. These findings provide continued confidence in the results of these POCTs as they continue to be used to support decentralized COVID-19 testing. This work demonstrates the essential role of post-market surveillance in ensuring reliability in diagnostic tools.IMPORTANCEPost-market surveillance of diagnostic test performance is critical to ensure their reliability after regulatory approval. This is especially critical in the context of the COVID-19 pandemic as the use of point-of-care tests (POCTs) became widespread. Our study focused on four rapid antigen tests (Abbott Panbio, BTNX Rapid Response, SD Biosensor, and Quidel QuickVue) and two molecular tests (Abbott ID NOW and Lucira Check IT) that were widely distributed across Canada, assessing their performance using many SARS-CoV-2 variants, including up to Omicron subvariant XBB.1.5. Overall, we found no significant difference in performance against any variant, reinforcing confidence in their use. As concerns in test efficacy have been raised by news outlets, particularly regarding the BTNX Rapid Response, this work is even more timely and crucial. Our research offers insights into the performance of widely used COVID-19 POCTs but also highlights the necessity for post-market surveillance.

Impact of Omicron variant sublineage BA.2.75 on the OnSite COVID-19 Ag Rapid Test: the applicability of rapid antigen test with universal transport media

BACKGROUND

Rapid antigen testing (RAT) is one of the most powerful tools for SARS-CoV-2 detection. The OnSite COVID-19 Ag Rapid Test is an antigen-based, point-of-care test approved by the WHO for Emergency Use Listing. The Nucleocapsid (N) gene mutations found in the emerging Omicron sublineages lead to the question of RAT performance.

OBJECTIVE

To ensure the diagnostic performance of the study RAT during rapidly mutated Omicron variants.

RESULTS

We independently evaluated the performance of this assay in 1098 archived samples collected in Thailand during October 2022-February 2023, which were 798 and 300 COVID-19 real-time RT-PCR positive and negative, respectively. The assay performed with 100% sensitivity and 100% specificity using a cycle threshold (Ct) of <20 for the RT-PCR. The sensitivity decreased to 88% when using Ct <30. Most of the SARS-CoV-2 found were Omicron BA.2 (99%), harboring six known N mutations (P13L, E31del, S33del, R203K, G204R and S413R). Eight samples containing hybrid variants (XBB.1*, XBB.2 and XBJ) were detected by the study RAT. This RAT detects all Omicron sublineages known to be circulating in Thailand.

CONCLUSIONS

These results confirmed the good performance of the study RAT for detecting Omicron variants and its appropriateness for individual diagnosis and for genomic surveillance.

Pipette-free field-deployable molecular diagnostic kit for bimodal visual detection of infectious RNA viruses

Here, we developed a field-deployable molecular diagnostic kit for the detection of RNA viruses that operates in a pipette-free manner. The kit is composed of acrylic sticks, PCR tubes, and palm-sized three-dimensional(3D)-printed heaters operated by batteries. The kit performs RNA extraction, reverse transcriptase loop-mediated isothermal amplification (RT-LAMP), and visual detection in one kit. An acrylic stick was engraved with one shallow and one deep cylindrical chamber at each end for the insertion of an FTA card and ethidium homodimer-1 (EthD-1), respectively, to perform RNA extraction/purification and bimodal visual detection of the target amplicons. First, an intercalation of EthD-1 into the target DNA initially produces fluorescence upon UV illumination. Next, the addition of a strong oxidant, in this case sodium (meta) periodate (NaIO4 ), produces intense aggregates in the presence of EthD-1-intercalated DNA, realized by electrostatic interaction. In the absence of the target amplicon, no fluorescence or aggregates are observed. Using this kit, two major infectious viruses-severe fever with thrombocytopenia syndrome virus (SFTSV) and severe acute respiratory syndrome coronavirus (SARS-CoV-2)-were successfully detected in 1 h, and the limits of detection (LOD) were approximately 1 virus μL-1 for SFTSV and 103 copies μL-1 for SARS-CoV-2 RNA. The introduced kit is portable, end-user-friendly, and can be operated in a pipette-free manner, paving the way for simple and convenient virus detection in resource-limited settings.

The Suitability of RNA from Positive SARS-CoV-2 Rapid Antigen Tests for Whole Virus Genome Sequencing and Variant Identification to Maintain Genomic Surveillance

The COVID-19 pandemic has transformed laboratory management, with a surge in demand for diagnostic tests prompting the adoption of new diagnostic assays and the spread of variant surveillance tools. Rapid antigen tests (RATs) were initially used only for screening and later as suitable infection assessment tools. This study explores the feasibility of sequencing the SARS-CoV-2 genome from the residue of the nasopharyngeal swab extraction buffers of rapid antigen tests (RATs) to identify different COVID-19 lineages and sub-lineages.

METHODS

Viral RNA was extracted from the residue of the nasopharyngeal swab extraction buffers of RATs and, after a confirmation of positivity through a reaction of RT-PCR, viral genome sequencing was performed.

RESULTS

Overall, the quality of the sequences obtained from the RNA extracted from the residue of the nasopharyngeal swab extraction buffers of RATs was adequate and allowed us to identify the SARS-CoV-2 variants' circulation and distribution in a period when the use of molecular swabs had been drastically reduced.

CONCLUSIONS

This study demonstrates the potential for genomic surveillance by sequencing SARS-CoV-2 from the residue of the nasopharyngeal swab extraction buffers of RATs, highlighting alternative possibilities for tracking variants.

Standardization and Comparison of Emergency Use Authorized COVID-19 Assays and Testing Laboratories

Motivation

The motivation for this work was the need to establish a predefined cutoff based on genome copies per ml (GE/ml) rather than Ct, which can vary depending on the laboratory and assay used. A GE/ml-based threshold was necessary to define what constituted 'low positives" for samples that were included in data sets submitted to the FDA for emergency use approval for SARS-CoV-2 antigen tests.

Summary

SARS-CoV-2, the causal agent of the global COVID-19 pandemic, made its appearance at the end of 2019 and is still circulating in the population. The pandemic led to an urgent need for fast, reliable, and widely available testing. After December 2020, the emergence of new variants of SARS-CoV-2 led to additional challenges since new and existing tests had to detect variants to the same extent as the original Wuhan strain. When an antigen-based test is submitted to the Food and Drug Administration (FDA) for Emergency Use Authorization (EUA) consideration it is benchmarked against PCR comparator assays, which yield cycle threshold (CT) data as an indirect indicator of viral load - the lower the CT, the higher the viral load of the sample and the higher the CT, the lower the viral load. The FDA mandates that 10-20% of clinical samples used to evaluate the antigen test have to be low positive. Low positive, as defined by the FDA, are clinical samples in which the CT of the SARS-CoV-2 target gene is within 3 CT of the mean CT value of the approved comparator test's Limit of Detection (LOD). While all comparator tests are PCR-based, the results from different PCR assays used are not uniform. Results vary depending on assay platform, target gene, LOD and laboratory methodology. The emergence and dominance of the Omicron variant further challenged this approach as the fraction of low positive clinical samples dramatically increased as compared to earlier SARS-CoV-2 variants. This led to 20-40% of clinical samples having high CT values and therefore assays vying for an EUA were failing to achieve the 80% Percent Positive Agreement (PPA) threshold required. Here we describe the methods and statistical analyses used to establish a predefined cutoff, based on genome copies per ml (GE/ml) to classify samples as low positive (less than the cutoff GE/ml) or high positive (greater than the cutoff GE/mL). CT 30 for the E gene target using Cobas® SARS-CoV-2-FluA/B platform performed at TriCore Reference Laboratories, and this low positive cutoff value was used for two EUA authorizations. Using droplet digital PCR and methods described here, a value 49,447.72 was determined as the GE/ml equivalent for the low positive cutoff. The CT cutoff corresponding to 49447.72 GE/ml was determined across other platforms and laboratories. The methodology and statistical analysis described here can now be used for standardization of all comparators used for FDA submissions with a goal towards establishing uniform criteria for EUA authorization.

Rapid inactivation and sample preparation for SARS-CoV-2 PCR-based diagnostics using TNA-Cifer Reagent E

RT-qPCR remains a key diagnostic methodology for COVID-19/SARS-CoV-2. Typically, nasal or saliva swabs from patients are placed in virus transport media (VTM), RNA is extracted at the pathology laboratory, and viral RNA is measured using RT-qPCR. In this study, we describe the use of TNA-Cifer Reagent E in a pre-clinical evaluation study to inactivate SARS-CoV-2 as well as prepare samples for RT-qPCR. Adding 1 part TNA-Cifer Reagent E to 5 parts medium containing SARS-CoV-2 for 10 min at room temperature inactivated the virus and permitted RT-qPCR detection. TNA-Cifer Reagent E was compared with established column-based RNA extraction and purification methodology using a panel of human clinical nasal swab samples (n = 61), with TNA-Cifer Reagent E showing high specificity (100%) and sensitivity (97.37%). Mixtures of SARS-CoV-2 virus and TNA-Cifer Reagent E could be stored for 3 days at room temperature or for 2 weeks at 4°C without the loss of RT-qPCR detection sensitivity. The detection sensitivity was preserved when TNA-Cifer Reagent E was used in conjunction with a range of VTM for saliva samples but only PBS (Gibco) and Amies Orange for nasal samples. Thus, TNA-Cifer Reagent E improves safety by rapidly inactivating the virus during sample processing, potentially providing a safe means for molecular SARS-CoV-2 testing outside traditional laboratory settings. The reagent also eliminates the need for column-based and/or automated viral RNA extraction/purification processes, thereby providing cost savings for equipment and reagents, as well as reducing processing and handling times.

Efficacy of novel SARS-CoV-2 rapid antigen tests in the era of omicron outbreak

Following the outbreak of Omicron and its subvariants, many of the currently available rapid Ag tests (RATs) showed a decrease in clinical performance. In this study, we evaluated the clinical sensitivity of the SARS-CoV-2 Rapid Antigen Test 2.0 for nasopharyngeal swabs and SARS-CoV-2 Rapid Antigen Test 2.0 Nasal for nasal swabs in 56 symptomatic individuals by comparing the results between RATs, RT-PCR, Omicron RT-PCR, and whole-genome sequencing (WGS). Furthermore, sequences of the Omicron subvariants' spike proteins were subjected to phylogenetic analysis. Both novel RATs demonstrated a high sensitivity of up to 92.86%, (95% CI 82.71%- 98.02%), 94.23%, (95% CI 83.07%- 98.49%), and 97.95% (95% CI 87.76%- 99.89%) compared to the RT-PCR, Omicron RT-PCR, and WGS, respectively. The clinical sensitivity of RATs was at its highest when the Ct value was restricted to 15≤Ct<25, with a sensitivity of 97.05% for RdRp genes. The Omicron RT-PCR analysis revealed subvariants BA.4 or BA.5 (76.8%) and BA.2.75 (16.1%). Subsequently, the WGS analysis identified BA.5 (65.5%) as the dominant subvariant. Phylogenetic analysis of the spike protein of Omicron's subvariants showed a close relationship between BA.4, BA.5, and BA.2.75. These results demonstrated that SARS-CoV-2 Rapid Antigen Test 2.0 and SARS-CoV-2 Rapid Antigen Test 2.0 Nasal are considered useful and efficient RATs for the detection of SARS-CoV-2, particularly during the current Omicron subvariants wave.

Comparing SARS-CoV-2 testing positivity rates and COVID-19 impact among different isolation strategies: a rapid systematic review and a modelling study

Background

The optimal isolation duration for patients with COVID-19 remains unclear. To support an update of World Health Organization (WHO)'s Living Clinical management guidelines for COVID-19 (https://www.who.int/publications/i/item/WHO-2019-nCoV-clinical-2022.2), this rapid systematic review and modelling study addresses the effects of different isolation periods for preventing onward transmission leading to hospitalisation and death among secondary cases.

Methods

We searched the WHO COVID-19 database for studies up to Feb 27, 2023. We included clinical studies of any design with COVID-19 patients confirmed by PCR test or rapid antigen test addressing the impact of any isolation strategy on preventing the spread of COVID-19. There were no restrictions on publication language, publication status, age of patients, severity of COVID-19, variants of SARS-COV-2, comorbidity of patients, isolation location, or co-interventions. We performed random-effects meta-analyses to summarise testing rates of persistent test positivity rates after COVID-19 infection. We performed pre-specified subgroup analyses by symptom status and meta-regression analyses for the proportion of fully vaccinated patients. We developed a model to compare the effects of three isolation strategies on onward transmission leading to hospitalisation and death. The three isolation strategies were (1) 5-day isolation, with no test to release; (2) removal of isolation based on a negative test; and (3) 10-day isolation, with no test to release. The model incorporates estimates of test positivity rates, effective reproduction number, isolation adherence, false negative rate, and hospitalisation rates or case fatality rates. To assess the impact of varying isolation adherence and false negative rates on rapid antigen testing, we conducted some sensitivity analyses. We used the Grading of Recommendations Assessment, Development and Evaluation approach to assess certainty of evidence. The protocol is registered with PROSPERO (CRD42022348626).

Findings

Fifteen studies addressing persistent test positivity rates including 4188 patients proved eligible. Asymptomatic patients (27.1%, 95% CI: 15.8%-40.0%) had a significantly lower rapid antigen test positive rate than symptomatic patients (68.1%, 95% CI: 40.6%-90.3%) on day 5. The rapid antigen test positive rate was 21.5% (95% CI: 0-64.1%; moderate certainty) on day 10. Our modelling study suggested that the risk difference (RD) for asymptomatic patients between 5-day isolation and 10-day isolation in hospitalisations (23 more hospitalisations of secondary cases per 10,000 patients isolated, 95% uncertainty interval (UI) 14 more to 33 more) and mortality (5 more per 10,000 patients, 95% UI 1 to 9 more) of secondary cases proved very small (very low certainty). For symptomatic patients, the potential impact of 5- versus 10-day isolation was much greater in hospitalisations (RD 186 more per 10,000 patients, 95% UI 113 more to 276 more; very low certainty) and mortality (RD 41 more per 10,000 patients, 95% UI 11 more to 73 more; very low certainty). There may be little or no difference between removing isolation based on a negative antigen test and 10-day isolation in the onward transmission leading to hospitalisation or death, but the average isolation period (mean difference -3 days) will be shorter for the removal of isolation based on a negative antigen test (moderate certainty).

Interpretation

5 days versus 10 days of isolation in asymptomatic patients may result in a small amount of onward transmission and negligible hospitalisation and mortality; however, in symptomatic patients, the level of onward transmission is concerning and may lead to high hospitalisation and death rates. The evidence is, however, very uncertain.

Funding

This work was done in collaboration with WHO.

Identification of B-Cell Linear Epitopes in the Nucleocapsid (N) Protein B-Cell Linear Epitopes Conserved among the Main SARS-CoV-2 Variants

The Nucleocapsid (N) protein is highlighted as the main target for COVID-19 diagnosis by antigen detection due to its abundance in circulation early during infection. However, the effects of the described mutations in the N protein epitopes and the efficacy of antigen testing across SARS-CoV-2 variants remain controversial and poorly understood. Here, we used immunoinformatics to identify five epitopes in the SARS-CoV-2 N protein (N_(34-48), N_(89-104), N_(185-197), N_(277-287), and N_(378-390)) and validate their reactivity against samples from COVID-19 convalescent patients. All identified epitopes are fully conserved in the main SARS-CoV-2 variants and highly conserved with SARS-CoV. Moreover, the epitopes N_(185-197) and N_(277-287) are highly conserved with MERS-CoV, while the epitopes N_(34-48), N_(89-104), N_(277-287), and N_(378-390) are lowly conserved with common cold coronaviruses (229E, NL63, OC43, HKU1). These data are in accordance with the observed conservation of amino acids recognized by the antibodies 7R98, 7N0R, and 7CR5, which are conserved in the SARS-CoV-2 variants, SARS-CoV and MERS-CoV but lowly conserved in common cold coronaviruses. Therefore, we support the antigen tests as a scalable solution for the population-level diagnosis of SARS-CoV-2, but we highlight the need to verify the cross-reactivity of these tests against the common cold coronaviruses.