Sensitivity of Reverse Transcription Polymerase Chain Reaction Tests for Severe Acute Respiratory Syndrome Coronavirus 2 Through Time

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.

An alternative method for SARS-CoV-2 detection with use modified fluorescent in situ hybridization

The real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR) tests are the gold standard in detecting SARS-CoV-2 virus infection. However, despite high sensitivity and specificity, they have limitations that in some cases may result in false negative results. Therefore, it is reasonable to search for additional tools that could support microbiological diagnosis of SARS-CoV-2. The aim of the study was to develop a highly specific molecular test capable of detecting and visualizing SARS-CoV-2 infection. A universal probe and a set of 18 specific oligonucleotides with a FLAP sequence attached to them on both sides were designed to visualize SARS-CoV-2 virus infection based on the fluorescence in situ hybridization method (FISH). FISH conditions using the developed kit were standardized on the Vero CCL-81 cell line infected by SARS-CoV-2 virus. The method was tested on 290 nasopharyngeal swabs (collected in a doublet) from patients with clinical symptoms of SARS-CoV-2. Each one swab from the doublet was subjected to RNA isolation and amplification by rRT-PCR. From the second swab, a microscopic preparation was performed for FISH. The use of the rRT-PCR allowed obtaining 200 positive and 90 negative results, while our FISH method allowed for 220 positive results and 70 negative results. The differences obtained using both methods were statistically significant (p = 0.008). The obtained results support the use of FISH as an additional method in microbiological diagnostics of SARS-CoV-2.

Molecular Point-of-Care Assay Development: Design and Considerations

Molecular diagnostic point-of-care (MDx POC) testing is gaining momentum and is increasingly important for infectious disease detection and monitoring, as well as other diagnostic areas such as oncology. Molecular testing has traditionally required high-complexity laboratories. Laboratory testing complexity is determined by utilizing the Clinical Laboratory Improvement Amendments of 1988 (CLIA) Categorization Criteria scorecard, utilizing seven criteria that are scored on a scale of one to three. Previously, most commercially available point-of-care (POC) tests use other analytes and technologies that were not found to be highly complex by the CLIA scoring system. However, during the COVID-19 pandemic, MDx POC testing became much more prominent. Utilization during the COVID-19 pandemic has demonstrated that MDx POC testing applications can have outstanding advantages compared to available non-molecular POC diagnostic tests. This article introduces MDx POC testing to students, technologists, researchers, and others, providing a general algorithm for MDx POC test development. This algorithm is an introductory, step-by-step decision tree for defining a molecular POC diagnostic device meeting the functional requirements for a desired application. The technical considerations driving the decision-making include nucleic acid selection method (DNA, RNA), extraction methods, sample preparation, number of targets, amplification technology, and detection method. The scope of this article includes neither higher-order multiplexing, nor quantitative molecular analysis. This article covers key application considerations, such as sensitivity, specificity, turnaround time, and shipping/storage requirements. This article provides an overall understanding of the best resources and practices to use when developing a MDx POC assay that may be a helpful resource for readers without extensive molecular testing experience as well as for those who are already familiar with molecular testing who want to increase MDx availability at the POC. © 2024 Wiley Periodicals LLC.

Vaccine effectiveness against COVID-19 related hospital admission in the Netherlands by medical risk condition: A test-negative case-control study

INTRODUCTION

Vaccination remains crucial in reducing COVID-19 hospitalizations and mitigating the strain on healthcare systems. We conducted a multicenter study to assess vaccine effectiveness (VE) of primary and booster vaccination against hospitalization and to identify subgroups with reduced VE.

METHODS

From March to July 2021 and October 2021 to January 2022, a test-negative case-control study was conducted in nine Dutch hospitals. The study included adults eligible for COVID-19 vaccination who were hospitalized with respiratory symptoms. Cases tested positive for SARS-CoV-2 within 14 days prior to or 48 h after admission, while controls tested negative. Logistic regression was used to calculate VE, adjusting for calendar week, sex, age, nursing home residency and comorbidity. We explored COVID-19 case characteristics and whether there are subgroups with less effective protection by vaccination against COVID-19 hospitalization.

RESULTS

Between October 2021 to January 2022, when the Delta variant was dominant, 335 cases and 277 controls were included. VE of primary and booster vaccination was 78 % (95 % CI: 65-86), and 89 % (95 % CI: 69-96), respectively. Using data from both study periods, including 700 cases and 511 controls, VE of primary vaccination was significantly reduced in those aged 60+ and patients with malignancy, chronic cardiac disease or an immunocompromising condition.

CONCLUSION

Although VE against hospitalization was 78% and increased to 89% after boosting during the Delta-dominant study period, VE was lower in certain high risk groups, for which indirect protection or other protective measures might be of added importance.

The real-time infection hospitalisation and fatality risk across the COVID-19 pandemic in England

The COVID-19 pandemic led to 231,841 deaths and 940,243 hospitalisations in England, by the end of March 2023. This paper calculates the real-time infection hospitalisation risk (IHR) and infection fatality risk (IFR) using the Office for National Statistics Coronavirus Infection Survey (ONS CIS) and the Real-time Assessment of Community Transmission Survey between November 2020 to March 2023. The IHR and the IFR in England peaked in January 2021 at 3.39% (95% Credible Intervals (CrI): 2.79, 3.97) and 0.97% (95% CrI: 0.62, 1.36), respectively. After this time, there was a rapid decline in the severity from infection, with the lowest estimated IHR of 0.32% (95% CrI: 0.27, 0.39) in December 2022 and IFR of 0.06% (95% CrI: 0.04, 0.08) in April 2022. We found infection severity to vary more markedly between regions early in the pandemic however, the absolute heterogeneity has since reduced. The risk from infection of SARS-CoV-2 has changed substantially throughout the COVID-19 pandemic with a decline of 86.03% (80.86, 89.35) and 89.67% (80.18, 93.93) in the IHR and IFR, respectively, since early 2021. From April 2022 until March 2023, the end of the ONS CIS study, we found fluctuating patterns in the severity of infection with the resumption of more normative mixing, resurgent epidemic waves, patterns of waning immunity, and emerging variants that have shown signs of convergent evolution.

High-Precision Viral Detection Using Electrochemical Kinetic Profiling of Aptamer-Antigen Recognition in Clinical Samples and Machine Learning

High-precision viral detection at point of need with clinical samples plays a pivotal role in the diagnosis of infectious diseases and the control of a global pandemic. However, the complexity of clinical samples that often contain very low viral concentrations makes it a huge challenge to develop simple diagnostic devices that do not require any sample processing and yet are capable of meeting performance metrics such as very high sensitivity and specificity. Herein we describe a new single-pot and single-step electrochemical method that uses real-time kinetic profiling of the interaction between a high-affinity aptamer and an antigen on a viral surface. This method generates many data points per sample, which when combined with machine learning, can deliver highly accurate test results in a short testing time. We demonstrate this concept using both SARS-CoV-2 and Influenza A viruses as model viruses with specifically engineered high-affinity aptamers. Utilizing this technique to diagnose COVID-19 with 37 real human saliva samples results in a sensitivity and specificity of both 100 % (27 true negatives and 10 true positives, with 0 false negative and 0 false positive), which showcases the superb diagnostic precision of this method.

Enhancing Disease Classification with Deep Learning: a Two-Stage Optimization Approach for Monkeypox and Similar Skin Lesion Diseases

Monkeypox (MPox) is an infectious disease caused by the monkeypox virus, presenting challenges in accurate identification due to its resemblance to other diseases. This study introduces a deep learning-based method to distinguish visually similar diseases, specifically MPox, chickenpox, and measles, addressing the 2022 global MPox outbreak. A two-stage optimization approach was presented in the study. By analyzing pre-trained deep neural networks including 71 models, this study optimizes accuracy through transfer learning, fine-tuning, and ensemble learning techniques. ConvNeXtBase, Large, and XLarge models were identified achieving 97.5% accuracy in the first stage. Afterwards, some selection criteria were followed for the models identified in the first stage for use in ensemble learning technique within the optimization approach. The top-performing ensemble model, EM3 (composed of RegNetX160, ResNetRS101, and ResNet101), attains an AUC of 0.9971 in the second stage. Evaluation on unseen data ensures model robustness and enhances the study's overall validity and reliability. The design and implementation of the study have been optimized to address the limitations identified in the literature. This approach offers a rapid and highly accurate decision support system for timely MPox diagnosis, reducing human error, manual processes, and enhancing clinic efficiency. It aids in early MPox detection, addresses diverse disease challenges, and informs imaging device software development. The study's broad implications support global health efforts and showcase artificial intelligence potential in medical informatics for disease identification and diagnosis.

Advancements in Rapid and Affordable Diagnostic Testing for Respiratory Infectious Diseases: Evaluation of Aptamer Beacon Technology for Rapid and Sensitive Detection of SAR-CoV-2 in Breath Condensate

The demand for rapid and efficient diagnostic point-of-care tests for respiratory infectious diseases has become increasingly critical in the current landscape. The emphasis on accessibility has been underscored over the past year, making it crucial to have biological components that exhibit fast and accurate kinetics. The foundation for precise, swift, and effective testing relies on the availability of highly responsive biological agents. Two published aptamer DNA sequences designated Song and MSA52 and their truncated internal stem-loop structures were studied for their potential to serve as aptamer beacons for rapid COVID detection. The candidate beacons were covalently labeled with Atto 633 dye attached to their 5' ends and Iowa Black quencher attached to their 3' ends. The whole aptamer structures exhibited the greatest fluorescence signal intensities and higher fluorescence background than their truncated internal stem-loop beacon structures suggesting that the distance between fluorophores and quenchers was greater for the whole aptamer beacon candidates versus the isolated stem-loop structures. Beacon candidates were tested against two heat- or gamma radiation-killed SARS-CoV-2 Washington 1/2020 virus samples and three different COVID spike (S) proteins to test their effectiveness. Despite the higher background fluorescence, the whole aptamer beacons showed better signal-to-noise ratios and were selected for further investigation. Limit of detection (LOD) studies revealed that both the whole Song and whole MSA52 aptamer beacon candidates had a LOD of 9.61 × 103 genome equivalents in phosphate-buffered saline using the red channel of a Promega Quantus™ fluorometer which correlated well with confirmatory spectrofluorometry. Cross-reactivity studies using numerous COVID variants, related coronaviruses, and other common respiratory pathogens suggested greater COVID selectivity for the whole MSA52 versus the whole Song aptamer beacon candidate, indicating promise for specific COVID detection. Importantly, both whole aptamer beacon candidates exhibited very rapid "bind and detect" fluorescence increases within the first 1-2 min of mixing the beacons with killed SARS-CoV-2 viruses in 100 µl samples. Overall, this work illustrates the strong potential for aptamer beacons for rapid, on-site detection and presumptive diagnosis of COVID in breath condensates or other small liquid samples. This research highlights the strong potential of aptamer beacons for addressing the need for fast and convenient diagnostic tools in global health contexts, especially in resource-limited settings.

Safety of monovalent and bivalent BNT162b2 mRNA COVID-19 vaccine boosters in at-risk populations in Israel: a large-scale, retrospective, self-controlled case series study

BACKGROUND

COVID-19 continues to be a major health threat, particularly among at-risk groups, including individuals aged 60 years or older and people with particular medical conditions. Nevertheless, the absence of sufficient vaccine safety information is one of the key contributors to vaccine refusal. We aimed to assess the short-term safety profile of the BNT162b2 mRNA COVID-19 vaccine booster doses.

METHODS

In this self-controlled case series study, we used a database of members of the largest health-care organisation in Israel. We analysed the medical records of individuals at risk of COVID-19 complications who had received two doses of the monovalent BNT162b2 mRNA COVID-19 vaccine (tozinameran, Pfizer-BioNTech) as their primary course of vaccination and then also received BNT162b2 mRNA COVID-19 vaccine boosters between July 30, 2021, and Nov 28, 2022, as a monovalent first or second booster, or as a bivalent first, second, or third booster, or a combination of these. We included individuals who had active membership of the health-care organisation and who were alive (excluding COVID-19 deaths) throughout the entire study period. We excluded individuals who, during the study period, were either not active Clalit Health Services members or died of non-COVID-19 causes, and those who were infected with COVID-19 during the 7-day period after vaccination. Individuals' at-risk status was assessed on the day before the baseline period started. The primary outcome was non-COVID-19 hospitalisation for 29 adverse events that might be associated with vaccination. For each adverse event, we compared the risk difference of hospitalisation during a 28-day pre-vaccination baseline period versus during a 28-day post-vaccination period, using a non-parametric percentile bootstrap method.

FINDINGS

Of the 3 574 243 members of the health-care organisation, 1 073 110 received a first monovalent booster, 394 251 received a second monovalent booster, and 123 084 received a bivalent first, second, or third booster. Overall, we found no indication of an elevated risk of non-COVID-19 hospitalisation following administration of any of the booster vaccines (risk difference in events per 100 000 individuals: first monovalent booster -37·1 [95% CI -49·8 to -24·2]; second monovalent booster -37·8 [-62·2 to -13·2]; and bivalent booster -18·7 [-53·6 to 15·4]). Except for extremely rare elevated risks after the first monovalent booster-of myocarditis (risk difference 0·7 events per 100 000 individuals [95% CI 0·3-1·3]), seizures (2·2 [0·4-4·1]), and thrombocytopenia (2·6 [0·7-4·7])-we found no safety signals in other adverse events, including ischaemic stroke.

INTERPRETATION

This study provides the necessary vaccine safety assurances for at-risk populations to receive timed roll-out booster vaccinations. These assurances could reduce vaccine hesitancy and increase the number of at-risk individuals who opt to become vaccinated, and thereby prevent the severe outcomes associated with COVID-19.

FUNDING

Israel Science Foundation and Israel Precision Medicine Partnership programme.

Diagnostic performance of GenBody COVID-19 rapid antigen test for laboratory and non-laboratory medical professionals in real practice: A retrospective study

Point-of-care tests for coronavirus disease 2019 (COVID-19) antigen detection have been widely used for rapid diagnosis in various settings. However, research on the diagnostic performance of the COVID-19 antigen test performed by non-laboratory personnel is limited. In this study, we aimed to elucidate the diagnostic performance of GenBody COVID-19 rapid antigen between laboratory professionals and non-laboratory staff. We retrospectively analyzed the data of patients who underwent both GenBody COVID-19 rapid antigen testing and reverse transcription polymerase chain reaction (RT-PCR) between November 01, 2021, and June 30, 2022. The diagnostic performance of the antigen test was compared between laboratory and non-laboratory operators, using RT-PCR as the gold standard. Sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, positive predictive value, negative predictive value, and accuracy were calculated and sensitivity analysis was performed based on the PCR cycle threshold (Ct) value. Of the 11,963 patients, 1273 (10.6%) tested positive using real-time RT-PCR. The sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, positive predictive value, negative predictive value, and accuracy of the GenBody COVID-19 rapid antigen test with 95% confidence interval were 79.92% (77.26%-82.39%), 99.23% (98.73%-99.57%), 103.25 (62.31-171.11), 0.2 (0.18-0.23), 510.18 (299.81-868.18), 98.11% (96.91%-98.85%), 90.75% (89.64%-91.75%) and 92.76% (91.76%-93.67%), respectively, for non-laboratory staff and 79.80% (74.78%-84.22%), 99.99% (99.94%-100.00%), 6983.92 (983.03-49617.00), 0.2 (0.16-0.25), 34566.45 (4770.30-250474.46) 99.58% (97.09%-99.94%), 99.32% (99.15%-99.46%), and 99.33% (99.13%-99.48%), respectively, for laboratory staff. Notably, when the PCR Ct value exceeded 25, the sensitivity of both the groups decreased to < 40%. The diagnostic performance of GenBody COVID-19 rapid antigen performed by non-laboratory staff was comparable to that of laboratory professionals. However, it should be noted that the sensitivity of the antigen tests decreased when the PCR Ct value exceeded 25. Overall, the GenBody COVID-19 antigen test is a viable option for non-laboratory staff during an epidemic.