Impact of antigen test target failure and testing strategies on the transmission of SARS-CoV-2 variants

A novel immunoassay technique using principal component analysis for enhanced detection of emerging viral variants

Rapid diagnostics are critical infectious disease tools that are designed to detect a known biomarker using antibodies specific to that biomarker. However, a way to detect unknown disease variants has not yet been achieved in a paper test format. We describe here a route to make an adaptable paper immunoassay that can detect an unknown biomarker, demonstrating it on SARS-CoV-2 variants. The immunoassay repurposes cross reactive antibodies raised against the alpha variant. Gold nanoparticles of two different colors conjugated to two different antibodies create a colorimetric signal, and machine learning of the resulting colorimetric pattern is used to train the assay to discriminate between variants of alpha and Omicron BA.5. By using principal component analysis, the colorimetric test patterns can pick up and discriminate an unknown variant that it has not encountered before, Omicron BA.1. The test has an accuracy of 100% and a potential calculated discriminatory power of 900. We show that it can be used adaptively and that it can be used to pick up emerging variants without the need to raise new antibodies.

Opportunities for Enhanced Public Health Surveillance via Molecular Detection and Sequencing of Diverse Respiratory Viruses From Self-collected SARS-CoV-2 Antigen Test Swabs

We sequenced and genotyped severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza, adenovirus, and respiratory syncytial virus, among other pathogens, from residual anterior nasal swabs self-collected for rapid SARS-CoV-2 antigen testing at the US Naval Academy. This is a key proof-of-concept for an acute respiratory infection surveillance approach, which could leverage prevalent SARS-CoV-2 antigen self-testing.

Monitoring epidemic processes under political measures

Statistical modeling of epidemiological curves to capture the course of epidemic processes and to implement a signaling system for detecting significant changes in the process is a challenging task, especially when the process is affected by political measures. As previous monitoring approaches are subject to various problems, we develop a practical and flexible tool that is well suited for monitoring epidemic processes under political measures. This tool enables monitoring across different epochs using a single statistical model that constantly adapts to the underlying process, and therefore allows both retrospective and on-line monitoring of epidemic processes. It is able to detect essential shifts and to identify anomaly conditions in the epidemic process, and it provides decision-makers a reliable method for rapidly learning from trends in the epidemiological curves. Moreover, it is a tool to evaluate the effectivity of political measures and to detect the transition from pandemic to endemic. This research is based on a comprehensive COVID-19 study on infection rates under political measures in line with the reporting of the Robert Koch Institute covering the entire period of the pandemic in Germany.

Development of Detection Antibody Targeting the Linear Epitope in SARS-CoV-2 Nucleocapsid Protein with Ultra-High Sensitivity

The COVID-19 pandemic caused by SARS-CoV-2 highlighted the importance of reliable detection methods for disease control and surveillance. Optimizing detection antibodies by rational screening antigens would improve the sensitivity and specificity of antibody-based detection methods such as colloidal gold immunochromatography. In this study, we screened three peptide antigens with conserved sequences in the N protein of SARS-CoV-2 using bioinformatical and structural biological analyses. Antibodies that specifically recognize these peptides were prepared. The epitope of the peptide that had the highest binding affinity with its antibody was located on the surface of the N protein, which was favorable for antibody binding. Using the optimal antibody that can recognize this epitope, we developed colloidal gold immunochromatography, which can detect the N protein at 10 pg/mL. Importantly, this antibody could effectively recognize both the natural peptide antigen and mutated peptide antigen in the N protein, showing the feasibility of being applied in the large-scale population testing of SARS-CoV-2. Our study provides a platform with reference significance for the rational screening of detection antibodies with high sensitivity, specificity, and reliability for SARS-CoV-2 and other pathogens.

Is It Possible to Test for Viral Infectiousness?: The Use Case of (SARS-CoV-2)

Identifying and managing individuals with active or chronic disease, implementing appropriate infection control measures, and mitigating the spread of the COVID-19 pandemic highlighted the need for tests of infectiousness. The gold standard for assessing infectiousness has been the recovery of infectious virus in cell culture. Using cycle threshold values, antigen testing, and SARS-CoV-2, replication intermediate strands were used to assess infectiousness, with many limitations. Infectiousness can be influenced by host factors (eg, preexisting immune responses) and virus factors (eg, evolution).

Universal masking during COVID-19 outbreaks in aged care settings: A systematic review and meta-analysis

Aged care facilities (ACF) are a high-risk COVID-19 transmission setting, and older residents are at greater risk of severe outcomes. This systematic review and meta-analysis assessed whether universal masking and COVID-19 vaccination reduce SARS-CoV-2 attack rates (ARs) in ACF. Articles published between 1 December 2019 and 28 February 2022 were screened across five databases (Medline, Embase, PubMed, Scopus, Web of Science and Cumulative Index to Nursing and Allied Health Literature (CINAHL)). Risk of bias was assessed using relevant Joanna Briggs Institute critical appraisal tools. Meta-analysis of single proportions, subgroup analysis, and meta-regression were performed to compare the effects of universal masking and vaccine doses on pooled SARS-CoV-2 ARs. Of 99 included articles, SARS-CoV-2 ARs for residents were available in 86 studies (representing 139 outbreaks), and for staff in 49 studies (78 outbreaks). Universal masking was associated with lower SARS-CoV-2 ARs in ACF outbreaks (AR = 34.9% [95% CI: 27.2-42.6%]) compared to facilities without universal masking (67.3% [54.2-80.4%], p < .0001). In ACF with universal masking prior to outbreak onset, facility-wide testing, and documentation of asymptomatic infection, the asymptomatic AR at time of testing was 11.4% (6.5-17.4%) in residents. Receipt of zero, one and two vaccination doses were associated with ARs of 64.9% (49.6-80.2%), 54.9% (33.7-76.1%) and 45.2% (29.2-61.3%), respectively. To protect residents from COVID-19, ACF should provide vaccination of residents and staff, universal masking for staff, and facility-wide testing during times of heightened community transmission.

A population-based study of the trend in SARS-CoV-2 diagnostic modalities from the beginning of the pandemic to the Omicron surge in Kyoto City, Kyoto, Japan

BACKGROUND

The coronavirus disease 2019 (COVID-19) presents critical diagnostic challenges for managing the pandemic. We investigated the 30-month changes in COVID-19 testing modalities and functional testing sites from the early period of the pandemic to the most recent Omicron surge in 2022 in Kyoto City, Japan.

METHODS

This is a retrospective-observational study using a local anonymized population database that included patients' demographic and clinical information, testing methods and facilities from January 2020 to June 2022, a total of 30 months. We computed the distribution of symptomatic presentation, testing methods, and testing facilities among cases. Differences over time were tested using chi-square tests of independence.

RESULTS

During the study period, 133,115 confirmed COVID-19 cases were reported, of which 90.9% were symptomatic. Although nucleic acid amplification testing occupied 68.9% of all testing, the ratio of lateral flow devices (LFDs) rapidly increased in 2022. As the pandemic continued, the testing capability was shifted from COVID-19 designated facilities to general practitioners, who became the leading testing providers (57.3% of 99,945 tests in 2022).

CONCLUSIONS

There was a dynamic shift in testing modality during the first 30 months of the pandemic in Kyoto City. General practitioners increased their role substantially as the use of LFDs spread dramatically in 2022. By comprehending and documenting the evolution of testing methods and testing locations, it is anticipated that this will contribute to the establishment of an even more efficient testing infrastructure for the next pandemic.

Antibody- and aptamer-free SERS substrate for ultrasensitive and anti-interference detection of SARS-CoV-2 spike protein in untreated saliva

Sensitive and anti-interference detection of targeted signal(s) in body fluids is one of the paramount tasks in biosensing. Overcoming the complication and high cost of antibody/aptamer-modification, surface-enhanced Raman spectroscopy (SERS) based on antibody/aptamer-free (AAF) substrates has shown great promise, yet with rather limited detection sensitivity. Herein, we report ultrasensitive and anti-interference detection of SARS-CoV-2 spike protein in untreated saliva by an AAF SERS substrate, applying the evanescent field induced by the high-order waveguide modes of well-defined nanorods for SERS for the first time. A detection limit of 3.6 × 10-17 M and 1.6 × 10-16 M are obtained in phosphate buffered saline and untreated saliva, respectively; the detection limits are three orders of magnitude improved than the best records from AAF substrates. This work unlocks an exciting path to design AAF SERS substrates for ultrasensitive biosensing, not limited to detection of viral antigens.

Rapid antigen tests for SARS-CoV-2-a synopsis of the medical evidence

SARS-CoV-2, the causative agent of the COVID-19 pandemic, continues to influence health, economy, and stability worldwide. Diagnostic testing for SARS-CoV-2 is important to contain the COVID-19 pandemic. With the commercial availability of certified antigen (Ag) rapid diagnostic tests (RDTs), which can be used to identify an infection with SARS-CoV-2 an easy-to-use tool was introduced. Self-tests can offer advantages to complement professionally administered rapid antigen detection or nucleic acid amplification testing (NAAT). Compared to real-time polymerase chain reaction (RT-PCR), Ag-RDTs are cost inexpensive, do not need specialized laboratory equipment, facilitating high-throughput testing. However, Ag-RDT sensitivities are strongly dependent on the viral load within the specimen, which has limited their application in clinical settings so far. The methodical limitations of Ag-RDTs may produce false negative test results, particularly when specimens with low viral loads are examined. This may facilitate viral transmissions if protective measurements are lifted mistakenly.

Rapid point-of-care detection of SARS-CoV-2 infection in exhaled breath using ion mobility spectrometry: a pilot study

BACKGROUND

An effective testing strategy is essential for pandemic control of the novel Coronavirus disease 2019 (COVID-19) caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Breath gas analysis can expand the available toolbox for diagnostic tests by using a rapid, cost-beneficial, high-throughput point-of-care test. We conducted a bi-center clinical pilot study in Germany to evaluate breath gas analysis using multi-capillary column ion mobility spectrometry (MCC-IMS) to detect SARS-CoV-2 infection.

METHODS

Between September 23, 2020, and June 11, 2021, breath gas measurements were performed on 380 patients (SARS-CoV-2 real-time polymerase chain reaction (PCR) positive: 186; PCR negative: 194) presenting to the emergency department (ED) with respiratory symptoms.

RESULTS

Breath gas analysis using MCC-IMS identified 110 peaks; 54 showed statistically significant differences in peak intensity between the SARS-CoV-2 PCR-negative and PCR-positive groups. A decision tree analysis classification resulted in a sensitivity of 83% and specificity of 86%, but limited robustness to dataset changes. Modest values for the sensitivity (74%) and specificity (52%) were obtained using linear discriminant analysis. A systematic search for peaks led to a sensitivity of 77% and specificity of 67%; however, validation by transferability to other data is questionable.

CONCLUSIONS

Despite identifying several peaks by MCC-IMS with significant differences in peak intensity between PCR-negative and PCR-positive samples, finding a classification system that allows reliable differentiation between the two groups proved to be difficult. However, with some modifications to the setup, breath gas analysis using MCC-IMS may be a useful diagnostic toolbox for SARS-CoV-2 infection.

TRIAL REGISTRATION

This study was registered at ClinicalTrials.gov on September 21, 2020 (NCT04556318; Study-ID: HC-N-H-2004).

Analytical sensitivity of COVID-19 rapid antigen tests: A case for a robust reference standard

Aggressive diagnostic testing remains an indispensable strategy for health and aged care facilities to prevent the transmission of SARS-CoV-2 in vulnerable populations. The preferred diagnostic platform has shifted towards COVID-19 rapid antigen tests (RATs) to identify the most infectious individuals. As such, RATs are being manufactured faster than at any other time in our history yet lack the relevant quantitative analytics required to inform on absolute analytical sensitivity enabling manufacturers to maintain high batch-to-batch reproducibility, and end-users to accurately compare brands for decision making. Here, we describe a novel reference standard to measure and compare the analytical sensitivity of RATs using a recombinant GFP-tagged nucleocapsid protein (NP-GFP). Importantly, we show that the GFP tag does not interfere with NP detection and provides several advantages affording streamlined protein expression and purification in high yields as well as faster, cheaper and more sensitive quality control measures for post-production assessment of protein solubility and stability. Ten commercial COVID-19 RATs were evaluated and ranked using NP-GFP as a reference standard. Analytical sensitivity data of the selected devices as determined with NP-GFP did not correlate with those reported by the manufacturers using the median tissue culture infectious dose (TCID₅₀) assay. Of note, TCID₅₀ discordance has been previously reported. Taken together, our results highlight an urgent need for a reliable reference standard for evaluation and benchmarking of the analytical sensitivity of RAT devices. NP-GFP is a promising candidate as a reference standard that will ensure that RAT performance is accurately communicated to healthcare providers and the public.

A non-enzymatic test for SARS-CoV-2 RNA using DNA nanoswitches

The emergence of a highly contagious novel coronavirus in 2019 led to an unprecedented need for large scale diagnostic testing. The associated challenges including reagent shortages, cost, deployment delays, and turnaround time have all highlighted the need for an alternative suite of low-cost tests. Here, we demonstrate a diagnostic test for SARS-CoV-2 RNA that provides direct detection of viral RNA and eliminates the need for costly enzymes. We employ DNA nanoswitches that respond to segments of the viral RNA by a change in shape that is readable by gel electrophoresis. A new multi-targeting approach samples 120 different viral regions to improve the limit of detection and provide robust detection of viral variants. We apply our approach to a cohort of clinical samples, positively identifying a subset of samples with high viral loads. Since our method directly detects multiple regions of viral RNA without amplification, it eliminates the risk of amplicon contamination and renders the method less susceptible to false positives. This new tool can benefit the COVID-19 pandemic and future emerging outbreaks, providing a third option between amplification-based RNA detection and protein antigen detection. Ultimately, we believe this tool can be adapted both for low-resource onsite testing as well as for monitoring viral loads in recovering patients.

SARS-CoV-2 and animals, a long story that doesn't have to end now: What we need to learn from the emergence of the Omicron variant

OIE, the world organization for animal health, recently released an update on the state of the art of knowledge regarding SARS-CoV-2 in animals. For farmed animals, ferrets and minks were found to be highly susceptible to the virus and develop symptomatic disease both in natural conditions and in experimental infections. Lagomorphs of the species Oryctolagus cuniculus are indicated as highly susceptible to the virus under experimental conditions, but show no symptoms of the disease and do not transmit the virus between conspecifics, unlike raccoon dogs (Nyctereutes procyonoides), which in addition to being highly susceptible to the virus under experimental conditions, can also transmit the virus between conspecifics. Among felines, the circulation of the virus has reached a level of cases such as sometimes suggests the experimental use of vaccines for human use or treatments with monoclonal antibodies. But even among wild animals, several species (White-tailed deer, Egyptian rousettes, and minks) have now been described as potential natural reservoirs of the virus. This proven circulation of SARS-CoV-2 among animals has not been accompanied by the development of an adequate surveillance system that allows following the evolution of the virus among its natural hosts. This will be all the more relevant as the surveillance system in humans inevitably drops and we move to surveillance by sentinels similar to the human flu virus. The lesson that we can draw from the emergence of Omicron and, more than likely, its animal origin must not be lost, and in this mini-review, we explain why.