Rapid, point-of-care antigen and molecular-based tests for diagnosis of SARS-CoV-2 infection

Tutorial on Multiple Mediation Analysis Using Causal Networks: Application to Diagnosing COVID-19 From Its Early and Late Symptoms

BACKGROUND AND OBJECTIVES

There are two methods of studying multiple mediation: network-based and analysis of coefficients in regression equations.

This tutorial shows how multiple mediation analysis can be conducted through first constructing causal networks; and then evaluating the direct and mediated impact within the network. The proposed method is demonstrated in the context of diagnosing COVID-19 from its symptoms.

METHODS

822 individuals who had completed a COVID-19 test were recruited through listservs and via employees and patients of Virginia Commonwealth University Health Center. Participants reported their symptoms and which symptom(s) occurred first. A Causal Network model was established through a repeated chain of regressions in four steps: First, we identified the order of occurrence of symptoms. Second, COVID-19 test results were LASSO regressed on symptoms and demographic variables, establishing direct effects. Third, the direct effects were LASSO regressed on prior symptoms and demographic variables, establishing indirect effects. Fourth, the joint distribution of the variables in the network was simulated by evaluating regression equations at factorial combinations of their direct effects. Fifth, the mediated effect was calculated through twin modeling, where the model derived from the real data was compared to the counterfactual model that represented 'what if' there was no mediation.

RESULTS

The 10-fold cross-validated area under the receiver curve for the network model was 0.82, which is a moderate to high level of accuracy. The network model identified later symptoms (e.g., chills) mediated the effect of earlier symptoms (e.g. fever).

CONCLUSIONS

A network-based multiple mediation analysis led to new insights by integrating findings of 19 separate regressions into a single network model. The procedure showed how artificial intelligence can help in triage of COVID-19 patients from their symptoms, before any home or laboratory tests.

The COVID-19 pandemic and critical laboratory functions. Can fast-track molecular testing reduce work absence in the laboratory?

Background

Amid the SARS-CoV-2 pandemic, laboratories faced the challenge of maintaining diagnostic operations while adhering to infection prevention and control (IPC) guidelines. We investigated the impact of implementing rapid molecular testing of employees of a large medical laboratory to prevent workplace transmission.

Aim/objective

To evaluate if fast-track PCR diagnostics, alongside local infection control measures, could reduce internal transmission and workplace sickness absence.

Methods

Employees with respiratory symptoms, but testing negative for SARS-CoV-2, were allowed to work if clinically healthy. All included employees completed a questionnaire and underwent SARS-CoV-2 antibody testing post-pandemic. Data on sickness absence were retrieved from local human resources systems, and comparative analyses were conducted between the pre-pandemic and pandemic periods.

Findings/results

Of 153 participants, 84 (55%) reported having had COVID-19, with 12 (14%) suspecting workplace transmission. Six (4%) tested positive for SARS-CoV-2 IgG nucleocapsid despite no COVID-19 diagnosis. Among 101 (66%) reporting respiratory symptoms and negative SARS-CoV-2 tests, 80 (79%) were allowed to return to the workplace. Mean workplace sickness absence during the pandemic 2020 (3.74%) and 2021 (4.19%) was significant lower compared with sickness absence in the laboratory before the pandemic in 2019 (4.54%). No larger outbreaks in the laboratory were recorded.

Discussion

SARS-CoV-2 infections in the laboratory were mostly symptomatic and acquired outside the workplace. The combination of local IPC and rapid and frequent testing of employees facilitated an effective infection control and minimized workplace absence, maintain diagnostic operations.

Serological surveillance for SARS-CoV-2 antibodies among students, faculty and staff within a large university system during the pandemic

BACKGROUND

At the end of December 2019, the world faced severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which led to the outbreak of coronavirus disease 2019 (COVID-19), associated with respiratory issues. This virus has shown significant challenges, especially for senior citizens, patients with other underlying illnesses, or those with a sedentary lifestyle. Serological tests conducted early on have helped identify how the virus is transmitted and how to curb its spread. The study hypothesis was that the rapid serological test for SARS-CoV-2 antibodies could indicate the immunoreactive profile during the COVID-19 pandemic in a university population.

AIM

To conduct active surveillance for serological expression of anti-SARS-CoV-2 antibodies in individuals within a university setting during the COVID-19 pandemic.

METHODS

This sectional study by convenience sampling was conducted in a large university in Niteroi-RJ, Brazil, from March 2021 to July 2021. The study population consisted of students, faculty, and administrative staff employed by the university. A total of 3433 faculty members, 60703 students, and 3812 administrative staff were invited to participate. Data were gathered through rapid serological tests to detect immunoglobulin (Ig) M and IgG against SARS-CoV-2. The χ² or Fisher's exact test was used to conduct statistical analysis. A 0.20 significance level was adopted for variable selection in a multiple logistic regression model to evaluate associations.

RESULTS

A total of 1648 individuals were enrolled in the study. The proportion of COVID-19 positivity was 164/1648 (9.8%). The adjusted logistic model indicate a positive association between the expression of IgM or IgG and age [odds ratio (OR) = 1.16, 95%CI: 1.02-1.31] (P < 0.0024), individuals who had been in contact with a COVID-19-positive case (OR = 3.49, 95%CI: 2.34-5.37) (P < 0.001), those who had received the COVID-19 vaccine (OR = 2.33, 95%CI: 1.61-3.35) (P < 0.001) and social isolation (OR = 0.59, 95%CI: 0.41-0.84) (P < 0.004). The likelihood of showing a positive result increased by 16% with every ten-year increment. Conversely, adherence to social distancing measures decreased the likelihood by 41%.

CONCLUSION

These findings evidenced that the population became more exposed to the virus as individuals discontinued social distancing practices, thereby increasing the risk of infection for themselves.

Immuno-μSARS2 Chip: A Peptide-Based Microarray to Assess COVID-19 Prognosis Based on Immunological Fingerprints

A multiplexed microarray chip (Immuno-μSARS2) aiming at providing information on the prognosis of the COVID-19 has been developed. The diagnostic technology records information related to the profile of the immunological response of patients infected by the SARS-CoV-2 virus. The diagnostic technology delivers information on the avidity of the sera against 28 different peptide epitopes and 7 proteins printed on a 25 mm2 area of a glass slide. The peptide epitopes (12-15 mer) derived from structural proteins (Spike and Nucleocapsid) have been rationally designed, synthesized, and used to develop Immuno-μSARS2 as a multiplexed and high-throughput fluorescent microarray platform. The analysis of 755 human serum samples (321 from PCR+ patients; 288 from PCR- patients; 115 from prepandemic individuals and classified as hospitalized, admitted to intensive-care unit (ICU), and exitus) from three independent cohorts has shown that the chips perform with a 98% specificity and 91% sensitivity identifying RT-PCR+ patients. Computational analysis utilized to correlate the immunological signatures of the samples analyzed indicate significant prediction rates against exitus conditions with 82% accuracy, ICU admissions with 80% accuracy, and 73% accuracy over hospitalization requirement compared to asymptomatic patients' fingerprints. The miniaturized microarray chip allows simultaneous determination of 96 samples (24 samples/slide) in 90 min and requires only 10 μL of sera. The diagnostic approach presented for the first time here could have a great value in assisting clinicians in decision-making based on the information provided by the Immuno-μSARS2 regarding progression of the disease and could be easily implemented in diagnostics of other infectious diseases.

One-Step Immunoassay for Biomarker Quantification in Complex Mixtures Based on Phase-Separated Antifouling Coacervates

We develop and present a one-pot sandwich immunoassay (termed oneSTEP) to detect target biomolecules in complex biological fluids based on programmable zwitterionic polymer coacervates. We design these coacervates to selectively recruit target analytes with ultralow nonspecific adsorption. We show that dynamic compartmentalization combined with local target enrichment delivers a rapid and wash-free sandwich immunoassay with high specificity and a high signal-to-noise ratio. The fluorescence-based readout is performed using standard microscopy methods and flow cytometry. We demonstrate the capabilities of the oneSTEP assay by detecting complement component 5 in human serum and the spike protein of severe acute respiratory syndrome coronavirus 2 in artificial saliva with a limit of detection of 300 pM. The results highlight the potential of the oneSTEP sandwich immunoassay as complementary to bead-based approaches in high-throughput screening studies as well as clinical diagnostics.

Potential biases in test-negative design studies of COVID-19 vaccine effectiveness arising from the inclusion of asymptomatic individuals

The test-negative design (TND) is a popular method for evaluating vaccine effectiveness (VE). A "classical" TND study includes symptomatic individuals tested for the disease targeted by the vaccine to estimate VE against symptomatic infection. However, recent applications of the TND have attempted to estimate VE against infection by including all tested individuals, regardless of their symptoms. In this article, we use directed acyclic graphs and simulations to investigate potential biases in TND studies of COVID-19 VE arising from the use of this "alternative" approach, particularly when applied during periods of widespread testing. We show that the inclusion of asymptomatic individuals can potentially lead to collider stratification bias, uncontrolled confounding by health and healthcare-seeking behaviors (HSBs), and differential outcome misclassification. While our focus is on the COVID-19 setting, the issues discussed here may also be relevant in the context of other infectious diseases. This may be particularly true in scenarios where there is either a high baseline prevalence of infection, a strong correlation between HSBs and vaccination, different testing practices for vaccinated and unvaccinated individuals, or settings where both the vaccine under study attenuates symptoms of infection and diagnostic accuracy is modified by the presence of symptoms.

A modeling study to define guidelines for antigen screening in schools and workplaces to mitigate COVID-19 outbreaks

BACKGROUND

In-person interaction offers invaluable benefits to people. To guarantee safe in-person activities during a COVID-19 outbreak, effective identification of infectious individuals is essential. In this study, we aim to analyze the impact of screening with antigen tests in schools and workplaces on identifying COVID-19 infections.

METHODS

We assess the effectiveness of various screening test strategies with antigen tests in schools and workplaces through quantitative simulations. The primary outcome of our analyses is the proportion of infected individuals identified. The transmission process at the population level is modeled using a deterministic compartmental model. Infected individuals are identified through screening tests or symptom development. The time-varying sensitivity of antigen tests and infectiousness is determined by a viral dynamics model. Screening test strategies are characterized by the screening schedule, sensitivity of antigen tests, screening duration, timing of screening initiation, and available tests per person.

RESULTS

Here, we show that early and frequent screening is the key to maximizing the effectiveness of the screening program. For example, 44.5% (95% CI: 40.8-47.5) of infected individuals are identified by daily testing, whereas it is only 33.7% (95% CI: 30.5-37.3) when testing is performed at the end of the program duration. If high sensitivity antigen tests (Detection limit: 6.3 × 10 4 copies/mL) are deployed, it reaches 69.3% (95% CI: 66.5-72.5).

CONCLUSIONS

High sensitivity antigen tests, high frequency screening tests, and immediate initiation of screening tests are important to safely restart educational and economic activities in-person. Our computational framework is useful for assessing screening programs by incorporating situation-specific factors.

Implementation and User Satisfaction of a Comprehensive Telemedicine Approach for SARS-CoV-2 Self-Sampling: Monocentric, Prospective, Interventional, Open-Label, Controlled, Two-Arm Feasibility Study

Background

The universal availability of smartphones has created new opportunities for innovative telemedicine applications in health care. The COVID-19 pandemic has heightened the demand for contactless health care services, making SARS-CoV-2 polymerase chain reaction (PCR) testing a crucial component of pandemic containment.

Objective

This feasibility study aimed to examine a comprehensive telemedicine approach for SARS-CoV-2 testing, focusing on the practicality, user satisfaction, and economic implications of self-sampling guided by a telemedicine platform.

Methods

The study process involved shipping self-sampling kits, providing instructions for at-home sample collection, processing biomaterials (swabs and capillary blood), communicating test results, and providing interoperable data for clinical routine and research through a medical mobile app. A total of 100 individuals were randomly assigned to either the conventional health care professional (HCP)-performed SARS-CoV-2 testing group (conventional testing group, CG) or the telemedicine-guided SARS-CoV-2 self-sampling approach (telemedicine group, TG). Feasibility of the TG approach, user satisfaction, user-centered outcomes, and economic aspects were assessed and compared between the groups.

Results

In the TG group, 47 out of 49 (95%) individuals received a self-sampling kit via mail, and 37out of 49 (76%) individuals successfully returned at least one sample for diagnostics. SARS-CoV-2 PCR tests were conducted in 95% (35/37) of TG cases compared with 88% (44/50) in the CG. Users in the TG reported high satisfaction levels with ease of use (5.2/7), interface satisfaction (5.2/7), and usefulness (4.3/7). A microcosting model indicated a slightly higher cost for the TG approach than the CG approach. The TG demonstrated the potential to facilitate interoperable data transmission by providing anonymized, standardized datasets for extraction using Health Level 7-Fast Healthcare Interoperability Resources. This supports the national COVID-19 Data Exchange Platform and facilitates epidemiological evaluation based on the German COVID Consensus dataset.

Conclusions

These preliminary findings suggest that a telemedicine-based approach to SARS-CoV-2 testing is feasible and could be integrated into existing hospital data infrastructures. This model has the potential for broader application in medical care, offering a scalable solution that could improve user satisfaction and treatment quality in the future.

Performance of self-performed SARS-CoV-2 rapid antigen test: a systematic review and meta-analysis

Background

The aim of this study was to investigate the accuracy of self-tested SARS-CoV-2 rapid antigen tests.

Methods

Databases of Pubmed, Embase, and Cochrane Library were searched for original studies investigating accuracy of self-tested SARS-CoV-2 rapid antigen tests, with RT-PCR as "gold standard."

Results

Forty-five eligible studies were found after database searching and screening using pre-defined criteria. The accuracy results from 50,897 suspected COVID-19 patients were pooled, and the overall sensitivity, specificity and diagnostic odds ratio were 0.77, 1.00, and 625.95, respectively. Subgroup analysis showed higher sensitivity of rapid antigen tests in subgroups of Abbott Panbio, self-collected nasal swab samples, and use of nasopharyngeal or oropharyngeal swab and lower Ct cutoff value in RT-PCR.

Conclusion

Fully self-performed SARS-CoV-2 rapid antigen tests showed overall high accuracy compared to "gold standard," and are reliable surrogates for the standard test of COVID-19 using nasopharyngeal or oropharyngeal samples and RT-PCR.

Laboratory-based molecular test alternatives to RT-PCR for the diagnosis of SARS-CoV-2 infection

BACKGROUND

Diagnosing people with a SARS-CoV-2 infection played a critical role in managing the COVID-19 pandemic and remains a priority for the transition to long-term management of COVID-19. Initial shortages of extraction and reverse transcription polymerase chain reaction (RT-PCR) reagents impaired the desired upscaling of testing in many countries, which led to the search for alternatives to RNA extraction/purification and RT-PCR testing. Reference standard methods for diagnosing the presence of SARS-CoV-2 infection rely primarily on real-time reverse transcription-polymerase chain reaction (RT-PCR). Alternatives to RT-PCR could, if sufficiently accurate, have a positive impact by expanding the range of diagnostic tools available for the timely identification of people infected by SARS-CoV-2, access to testing and the use of resources.

OBJECTIVES

To assess the diagnostic accuracy of alternative (to RT-PCR assays) laboratory-based molecular tests for diagnosing SARS-CoV-2 infection.

SEARCH METHODS

We searched the COVID-19 Open Access Project living evidence database from the University of Bern until 30 September 2020 and the WHO COVID-19 Research Database until 31 October 2022. We did not apply language restrictions.

SELECTION CRITERIA

We included studies of people with suspected or known SARS-CoV-2 infection, or where tests were used to screen for infection, and studies evaluating commercially developed laboratory-based molecular tests for the diagnosis of SARS-CoV-2 infection considered as alternatives to RT-PCR testing. We also included all reference standards to define the presence or absence of SARS-CoV-2, including RT-PCR tests and established clinical diagnostic criteria.

DATA COLLECTION AND ANALYSIS

Two authors independently screened studies and resolved disagreements by discussing them with a third author. Two authors independently extracted data and assessed the risk of bias and applicability of the studies using the QUADAS-2 tool. We presented sensitivity and specificity, with 95% confidence intervals (CIs), for each test using paired forest plots and summarised results using average sensitivity and specificity using a bivariate random-effects meta-analysis. We illustrated the findings per index test category and assay brand compared to the WHO's acceptable sensitivity and specificity threshold for diagnosing SARS-CoV-2 infection using nucleic acid tests.

MAIN RESULTS

We included data from 64 studies reporting 94 cohorts of participants and 105 index test evaluations, with 74,753 samples and 7517 confirmed SARS-CoV-2 cases. We did not identify any published or preprint reports of accuracy for a considerable number of commercially produced NAAT assays. Most cohorts were judged at unclear or high risk of bias in more than three QUADAS-2 domains. Around half of the cohorts were considered at high risk of selection bias because of recruitment based on COVID status. Three quarters of 94 cohorts were at high risk of bias in the reference standard domain because of reliance on a single RT-PCR result to determine the absence of SARS-CoV-2 infection or were at unclear risk of bias due to a lack of clarity about the time interval between the index test assessment and the reference standard, the number of missing results, or the absence of a participant flow diagram. For index tests categories with four or more evaluations and when summary estimations were possible, we found that: a) For RT-PCR assays designed to omit/adapt RNA extraction/purification, the average sensitivity was 95.1% (95% CI 91.1% to 97.3%), and the average specificity was 99.7% (95% CI 98.5% to 99.9%; based on 27 evaluations, 2834 samples and 1178 SARS-CoV-2 cases); b) For RT-LAMP assays, the average sensitivity was 88.4% (95% CI 83.1% to 92.2%), and the average specificity was 99.7% (95% CI 98.7% to 99.9%; 24 evaluations, 29,496 samples and 2255 SARS-CoV-2 cases); c) for TMA assays, the average sensitivity was 97.6% (95% CI 95.2% to 98.8%), and the average specificity was 99.4% (95% CI 94.9% to 99.9%; 14 evaluations, 2196 samples and 942 SARS-CoV-2 cases); d) for digital PCR assays, the average sensitivity was 98.5% (95% CI 95.2% to 99.5%), and the average specificity was 91.4% (95% CI 60.4% to 98.7%; five evaluations, 703 samples and 354 SARS-CoV-2 cases); e) for RT-LAMP assays omitting/adapting RNA extraction, the average sensitivity was 73.1% (95% CI 58.4% to 84%), and the average specificity was 100% (95% CI 98% to 100%; 24 evaluations, 14,342 samples and 1502 SARS-CoV-2 cases). Only two index test categories fulfil the WHO-acceptable sensitivity and specificity requirements for SARS-CoV-2 nucleic acid tests: RT-PCR assays designed to omit/adapt RNA extraction/purification and TMA assays. In addition, WHO-acceptable performance criteria were met for two assays out of 35 when tests were used according to manufacturer instructions. At 5% prevalence using a cohort of 1000 people suspected of SARS-CoV-2 infection, the positive predictive value of RT-PCR assays omitting/adapting RNA extraction/purification will be 94%, with three in 51 positive results being false positives, and around two missed cases. For TMA assays, the positive predictive value of RT-PCR assays will be 89%, with 6 in 55 positive results being false positives, and around one missed case.

AUTHORS' CONCLUSIONS

Alternative laboratory-based molecular tests aim to enhance testing capacity in different ways, such as reducing the time, steps and resources needed to obtain valid results. Several index test technologies with these potential advantages have not been evaluated or have been assessed by only a few studies of limited methodological quality, so the performance of these kits was undetermined. Only two index test categories with enough evaluations for meta-analysis fulfil the WHO set of acceptable accuracy standards for SARS-CoV-2 nucleic acid tests: RT-PCR assays designed to omit/adapt RNA extraction/purification and TMA assays. These assays might prove to be suitable alternatives to RT-PCR for identifying people infected by SARS-CoV-2, especially when the alternative would be not having access to testing. However, these findings need to be interpreted and used with caution because of several limitations in the evidence, including reliance on retrospective samples without information about the symptom status of participants and the timing of assessment. No extrapolation of found accuracy data for these two alternatives to any test brands using the same techniques can be made as, for both groups, one test brand with high accuracy was overrepresented with 21/26 and 12/14 included studies, respectively. Although we used a comprehensive search and had broad eligibility criteria to include a wide range of tests that could be alternatives to RT-PCR methods, further research is needed to assess the performance of alternative COVID-19 tests and their role in pandemic management.

Development and Diagnosis Performance of IgM-Based Rapid Antigen Test for Early Detection of SARS-CoV-2 Infection in a Large Cohort of Suspected COVID-19 Cases - USA, Poland, and Sweden, 2021-2022

Introduction

Antigen testing has been crucial in effectively managing the coronavirus disease 2019 (COVID-19) pandemic. This study evaluated the clinical performance of a nasopharyngeal swab (NPS)-based antigen rapid diagnostic test (Ag-RDT) compared to the gold standard real-time reverse transcription-polymerase chain reaction (RT-PCR) for early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Methods

We developed an IgM-based rapid antigen test for early detection of SARS-CoV-2 infection. Between July 2021 and January 2022, we analyzed 1,030 NPS samples from participants at three centers in different countries, using both antigen rapid diagnostic tests (Ag-RDT) and RT-PCR.

Results

The Ag-RDT demonstrated minimal detection limits as low as 0.1 ng/mL for recombinant N antigen and 100 TCID50/mL for heat-inactivated SARS-CoV-2 virus. Specificity assessments involving four human coronaviruses and 13 other respiratory viruses showed no cross-reactivity. The Ag-RDT assay (ALLtest) exhibited high sensitivity (93.18%-100%) and specificity (99.67%-100%) across all centers. Factors such as cycle threshold (Ct) values and the timing of symptoms since onset were influential, with sensitivity increasing at lower Ct values (<30) and within the first week of symptoms.

Conclusion

The ALLtest Ag-RDT demonstrated high reliability and significant potential for diagnosing suspected COVID-19 cases.

Diagnostic accuracy of Savanna RVP4 (QuidelOrtho) for the detection of Influenza A virus, RSV, and SARS-CoV-2

Seasonal increase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus A/B (Flu A/B), and respiratory syncytial virus (RSV) require rapid diagnostic test methods for the management of respiratory tract infections. In this study, we compared the diagnostic accuracy of Savanna RVP4 (RVP4, QuidelOrtho) with Xpert Xpress Plus SARS-CoV-2/Flu/RSV (Xpert, Cepheid). Nasopharyngeal swabs from patients treated at a tertiary care hospital (Germany) were tested for SARS-CoV-2, Flu A/B, and RSV by RVP4 to assess diagnostic accuracy (reference standard: Xpert). The intra and inter assay precision of Ct-values was assessed by repeated test in triplicates (on day 1) and duplicates (days 2-3). All patients with a physician's order for a multiplex test for SARS-CoV-2, Flu, and RSV test were included. Duplicate swabs from the same patient, samples with a total volume ≤1 mL, or inappropriate shipment/storage were excluded. In total, 229 swabs were included between September 2023 and February 2024. The concordance between both tests was 96.5% (SARS-CoV-2), 98.7% (Flu A), and 99.6% (RSV). Flu B was not detected by both tests. The RVP4 test had a sensitivity of 85%-95% and a specificity of 100% for the detection of SARS-CoV-2, Flu A, and RSV. The intra and inter assay precision of Ct-values from RVP4 was 3% and 2% (SARS-CoV-2), 5% and 4% (Flu A), and 0% and 3% (RSV), respectively. The Savanna RVP4 has a favorable diagnostic accuracy for the detection of SARS-CoV-2, Flu A, and RSV.

IMPORTANCE

We assessed the diagnostic accuracy of a new point-of-care test for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus A/B (Flu A/B), and respiratory syncytial virus (RSV). The new test has a concordance with the reference standard of 96.5% (SARS-CoV-2), 98.7% (Flu A), and 99.1% (RSV). The sensitivity of 85%-95% and specificity of 100% for the detection of SARS-CoV-2, Flu A, and RSV is comparable with similar nucleic acid amplification-based point of care tests but at lower costs.

Biosensors for Public Health and Environmental Monitoring: The Case for Sustainable Biosensing

Climate change is a profound crisis that affects every aspect of life, including public health. Changes in environmental conditions can promote the spread of pathogens and the development of new mutants and strains. Early detection is essential in managing and controlling this spread and improving overall health outcomes. This perspective article introduces basic biosensing concepts and various biosensors, including electrochemical, optical, mass-based, nano biosensors, and single-molecule biosensors, as important sustainability and public health preventive tools. The discussion also includes how the sustainability of a biosensor is crucial to minimizing environmental impacts and ensuring the long-term availability of vital technologies and resources for healthcare, environmental monitoring, and beyond. One promising avenue for pathogen screening could be the electrical detection of biomolecules at the single-molecule level, and some recent developments based on single-molecule bioelectronics using the Scanning Tunneling Microscopy-assisted break junctions (STM-BJ) technique are shown here. Using this technique, biomolecules can be detected with high sensitivity, eliminating the need for amplification and cell culture steps, thereby enhancing speed and efficiency. Furthermore, the STM-BJ technique demonstrates exceptional specificity, accurately detects single-base mismatches, and exhibits a detection limit essentially at the level of individual biomolecules. Finally, a case is made here for sustainable biosensors, how they can help, the paradigm shift needed to achieve them, and some potential applications.

A high throughput immuno-affinity mass spectrometry method for detection and quantitation of SARS-CoV-2 nucleoprotein in human saliva and its comparison with RT-PCR, RT-LAMP, and lateral flow rapid antigen test

OBJECTIVES

Many reverse transcription polymerase chain reaction (RT-PCR) methods exist that can detect SARS-CoV-2 RNA in different matrices. RT-PCR is highly sensitive, although viral RNA may be detected long after active infection has taken place. SARS-CoV-2 proteins have shorter detection windows hence their detection might be more meaningful. Given salivary droplets represent a main source of transmission, we explored the detection of viral RNA and protein using four different detection platforms including SISCAPA peptide immunoaffinity liquid chromatography-mass spectrometry (SISCAPA-LC-MS) using polyclonal capture antibodies.

METHODS

The SISCAPA-LC MS method was compared to RT-PCR, RT-loop-mediated isothermal amplification (RT-LAMP), and a lateral flow rapid antigen test (RAT) for the detection of virus material in the drool saliva of 102 patients hospitalised after infection with SARS-CoV-2. Cycle thresholds (Ct) of RT-PCR (E gene) were compared to RT-LAMP time-to-positive (TTP) (NE and Orf1a genes), RAT optical densitometry measurements (test line/control line ratio) and to SISCAPA-LC-MS for measurements of viral protein.

RESULTS

SISCAPA-LC-MS showed low sensitivity (37.7 %) but high specificity (89.8 %). RAT showed lower sensitivity (24.5 %) and high specificity (100 %). RT-LAMP had high sensitivity (83.0 %) and specificity (100.0 %). At high initial viral RNA loads (<20 Ct), results obtained using SISCAPA-LC-MS correlated with RT-PCR (R2 0.57, p-value 0.002).

CONCLUSIONS

Detection of SARS-CoV-2 nucleoprotein in saliva was less frequent than the detection of viral RNA. The SISCAPA-LC-MS method allowed processing of multiple samples in <150 min and was scalable, enabling high throughput.

Faster detection of asymptomatic COVID-19 cases among care home staff in England through the combination of SARS-CoV-2 testing technologies

To detect SARS-CoV-2 amongst asymptomatic care home staff in England, a dual-technology weekly testing regime was introduced on 23 December 2020. A lateral flow device (LFD) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) test were taken on the same day (day 0) and a midweek LFD test was taken three to four days later. We evaluated the effectiveness of using dual-technology to detect SARS-CoV-2 between December 2020 to April 2021. Viral concentrations derived from qRT-PCR were used to determine the probable stage of infection and likely level of infectiousness. Day 0 PCR detected 1,493 cases of COVID-19, of which 53% were in the early stages of infection with little to no risk of transmission. Day 0 LFD detected 83% of cases that were highly likely to be infectious. On average, LFD results were received 46.3 h earlier than PCR, enabling removal of likely infectious staff from the workplace quicker than by weekly PCR alone. Demonstrating the rapidity of LFDs to detect highly infectious cases could be combined with the ability of PCR to detect cases in the very early stages of infection. In practice, asymptomatic care home staff were removed from the workplace earlier, breaking potential chains of transmission.

The Role and Value of Professional Rapid Testing of Acute Respiratory Infections (ARIs) in Europe: A Special Focus on the Czech Republic, Poland, and Romania

This review aims to explore the role of professional diagnostic rapid testing of acute respiratory infections (ARIs), especially COVID-19 and influenza, ensuring proper disease management and treatment in Europe, and particularly in Czech Republic, Poland, and Romania. The paper was constructed based on a review of scientific evidence and national and international policies and recommendations, as well as a process of validation by four experts. The development of new testing technologies, treatment options, and increased awareness of the negative multidimensional impact of ARI profiles transformed differential diagnosis into a tangible and desirable reality. This review covers the following topics: (1) the multidimensional impact of ARIs, (2) ARI rapid diagnostic testing platforms and their value, (3) the policy landscape, (4) challenges and barriers to implementation, and (5) a set of recommendations illustrating a path forward. The findings indicate that rapid diagnostic testing, including at the point of care (POC), can have a positive impact on case management, antimicrobial and antibiotic stewardship, epidemiological surveillance, and decision making. Integrating this strategy will require the commitment of governments and the international and academic communities, especially as we identified room for improvement in the access and expansion of POC rapid testing in the focus countries and the inclusion of rapid testing in relevant policies.

Self-administered versus clinician-performed BinaxNOW COVID rapid test: a comparison of accuracy

We conducted a single-center study at a free community testing site in Baltimore City to assess the accuracy of self-performed rapid antigen tests (RATs) for COVID-19. Self-administered BinaxNOW RATs were compared with clinician-performed RATs and against a reference lab molecular testing as the gold standard. Of the 953 participants, 14.9% were positive for SARS- CoV-2 as determined by RT-PCR. The sensitivity and specificity were similar for both self- and clinician-performed RATs (sensitivity: 83.9% vs 88.2%, P = 0.40; specificity: 99.8% vs 99.6%, P = 0.6). Subgroup comparisons based on age and race yielded similar results. Notably, 5.2% (95% CI: 1.5% to 9.5%) of positive results were potentially missed due to participant misinterpretation of the self-test card. However, the false-positive rate for RATs was reassuringly comparable in accuracy to clinician-administered tests. These findings hold significant implications for physicians prescribing treatment based on patient-reported, self-administered positive test results. Our study provides robust evidence supporting the reliability and utility of patient-performed RATs, underscoring their comparable accuracy to clinician-performed RATs, and endorsing their continued use in managing COVID-19. Further studies using other rapid antigen test brands are warranted.IMPORTANCEAccurate and accessible COVID-19 testing is crucial for effective disease control and management. A recent single-center study conducted in Baltimore City examined the reliability of self-performed rapid antigen tests (RATs) for COVID-19. The study found that self-administered RATs yielded similar sensitivity and specificity to clinician-performed tests, demonstrating their comparable accuracy. These findings hold significant implications for physicians relying on patient-reported positive test results for treatment decisions. The study provides robust evidence supporting the reliability and utility of patient-performed RATs, endorsing their continued use in managing COVID-19. Furthermore, the study highlights the need for further research using different rapid antigen test brands to enhance generalizability. Ensuring affordable and widespread access to self-tests is crucial, particularly in preparation for future respiratory virus seasons and potential waves of reinfection of SARS-CoV-2 variants such as the Omicron variant.

Implementing a pilot study of COVID-19 self-testing in high-risk populations and remote locations: results and lessons learnt

BACKGROUND

Rapid antigen-detection tests for SARS-CoV-2 self-testing represent a useful tool for pandemic control and expanding access to community-level case screening. COVID-19 self-tests have been extensively used in high-income countries since 2021; however, their introduction and programmatic implementation in low- and middle-income countries was delayed. We aimed to identify and continuously improve a weekly COVID-19 self-testing model among staff at healthcare facilities and schools.

METHODS

This mixed-methods, observational prospective study was conducted in 5 healthcare centres and 24 schools in Georgia, between June and December 2022. The study comprised the integration of COVID-19 self-testing into the national mandatory testing programme for high-risk groups, with primary distribution of self-tests among staff performed weekly, plus secondary distribution to their household members. These use cases were selected because NCDC was seeking to strengthen their already strong weekly testing programme, by investigating self-testing to ease the burden of testing in the healthcare system. Online surveys and semi-structured interviews were used for data collection.

RESULTS

In total, 2156 participants were enrolled (1963 female, 72%). At baseline and mid- and end-points, 88%, 97% and 99%, respectively, of participants agreed/strongly agreed they would self-test. Similarly, the majority were willing to report their self-testing results (88%, 98% and 96% at baseline and mid- and end-points, respectively). Weekly reporting of test results to the national COVID-19 database was high during all the implementation. There were 622 COVID-19 positive results reported, and linked to care, from 601 individuals (282 participants and 319 household members). Findings from qualitative interviews showed great satisfaction with self-testing for its convenience, ease of use, trust in the results, no need to travel for diagnostics, and increased perception of safety.

CONCLUSIONS

Our findings contribute to the evidence-base regarding self-testing strategies conducted via workplaces and secondary distribution to households. Willingness to perform a COVID-19 self-test increased after implementation. This pilot enhanced pandemic preparedness through expansion of the national self-testing reporting system, development of communications materials, changes in the national legal framework and coordination mechanisms, and improved perceptions around self-care in the community. The lessons learnt can inform operational aspects of the introduction and scale-up of self-care strategies.

Access to Methotrexate Monitoring in Latin America: A Multicountry Survey of Supportive Care Capacity

High-dose methotrexate (HDMTX) is used to treat a broad spectrum of cancers. Methotrexate (MTX) monitoring and adequate supportive care are critical for safe drug administration; however, MTX level timing is not always possible in low- and middle-income countries. The aim of this study was to evaluate HDMTX supportive care capacity and MTX monitoring practices in Latin America (LATAM) to identify gaps and opportunities for improvement. A multicenter survey was conducted among LATAM pediatric oncologists. Twenty healthcare providers from 20 institutions answered the online questionnaire. HDMTX was used to treat acute lymphoblastic leukemia (ALL; 100%), non-Hodgkin lymphoma (84.2%), diffuse large B-cell lymphoma (47.4%), osteosarcoma (78.9%), and medulloblastoma (31.6%). Delays in starting HDMTX infusion were related to bed shortages (47.4%) and MTX shortages (21.1%). MTX monitoring was performed at an in-hospital laboratory in 52%, at an external/nearby laboratory in 31.6%, and was not available in 10.5%. Median interval between sampling and obtaining MTX levels was ≤ 2 h in 45% and ≥ 6 h in 30%, related to laboratory location. Sites without access to MTX monitoring reduced the MTX dose for patients with high-risk ALL or did not include MTX in the treatment of patients with osteosarcoma. Respondents reported that implementation of point-of-care testing of MTX levels is feasible. In LATAM, highly variable supportive care capacity may affect the safe administration of MTX doses. Improving accessibility of MTX monitoring and the speed of obtaining results should be prioritized to allow delivery of full doses of MTX required by the current protocols.

Clinical Performance of the Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for the Diagnosis of COVID-19 in a Thai Community Hospital at the Thailand-Myanmar Border

INTRODUCTION

Coronavirus disease 2019 (COVID-19) continues to be a global health threat and is a public health issue in Thailand and other countries. The extensive cross-border between Thailand and Myanmar is considered to be at a potentially high risk for COVID-19 distribution in this region. In this instance, simple and cost-effective tests for rapid and early detection of COVID-19 would be useful for effective patient management and control of the disease.

METHODS

This study was conducted at Mae Sot Hospital on the border of Thailand-Myanmar to evaluate the diagnostic performance of a simple colorimetric reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay developed recently for the rapid detection of SARS-CoV-2. Nasopharyngeal specimens were routinely collected and processed through automated nucleic acid extraction followed by real-time reverse transcription-polymerase chain reaction (rRT-PCR) using the Molaccu® COVID-19 Detection Kit. The RT-LAMP assay was further performed on remnant RNA samples, and the visual results were compared to those of rRT-PCR as a reference.

RESULTS

Of the 727 samples tested, the RT-LAMP assay could detect 322 out of 374 samples positive for SARS-CoV-2 by rRT-PCR with 100% (n = 353/353) negative agreement. The comparative analysis demonstrated the overall accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of the RT-LAMP at 92.85% (n = 675/727, 95% CI: 90.73-94.61), 86.10% (n = 322/374, 95% CI: 82.17-89.44), 100% (n = 353/353, 95% CI: 98.96-100), 100% (n = 322/322, 95% CI: 98.86-100), and 87.16% (n = 353/405, 95% CI: 84.06-89.73), respectively.

CONCLUSION

This RT-LAMP assay showed good diagnostic performance in the hospital setting. It can increase laboratory capacity for rapid SARS-CoV-2 testing and has the potential for use as an alternative or a backup assay at the point of need, especially where alternatives are unavailable for any reason, such as a decline in COVID-19 cases.

COVID-19 lateral flow test image classification using deep CNN and StyleGAN2

Introduction

Artificial intelligence (AI) in healthcare can enhance clinical workflows and diagnoses, particularly in large-scale operations like COVID-19 mass testing. This study presents a deep Convolutional Neural Network (CNN) model for automated COVID-19 RATD image classification.

Methods

To address the absence of a RATD image dataset, we crowdsourced 900 real-world images focusing on positive and negative cases. Rigorous data augmentation and StyleGAN2-ADA generated simulated images to overcome dataset limitations and class imbalances.

Results

The best CNN model achieved a 93% validation accuracy. Test accuracies were 88% for simulated datasets and 82% for real datasets. Augmenting simulated images during training did not significantly improve real-world test image performance but enhanced simulated test image performance.

Discussion

The findings of this study highlight the potential of the developed model in expediting COVID-19 testing processes and facilitating large-scale testing and tracking systems. The study also underscores the challenges in designing and developing such models, emphasizing the importance of addressing dataset limitations and class imbalances.

Conclusion

This research contributes to the deployment of large-scale testing and tracking systems, offering insights into the potential applications of AI in mitigating outbreaks similar to COVID-19. Future work could focus on refining the model and exploring its adaptability to other healthcare scenarios.

Public health-focused use of COVID-19 rapid antigen and PCR tests

During the Covid-19 pandemic, accurate PCR tests were augmented by the cheap, rapid, and logistically convenient, yet less sensitive antigen tests. In Israel, a testing policy shift was implemented due to limited availability of PCR tests during the Omicron surge. Thus, both PCR and antigen tests were used, as this was the only alternative for mass testing and surveillance at the time. Yet, evidence-based surveillance requires a robust understanding of the expected consequences of changing the testing policy. Using 41,065 paired tests performed by trained staff between January and April 2022 in Israel, we estimate how the sensitivity of antigen tests changes as a function of Ct value and other key covariates. The results reveal a logarithmic relationship between antigen detection probability and viral load, as quantified by Ct-values of the PCR tests. Further analysis shows a statistically significant association with an odds ratio of approximately 0.76 with each unit of Ct-value. The analysis suggests that in spite of their compromised sensitivity, antigen tests are a natural solution for routine use, while PCR tests should be considered in situations where a false negative result could have serious consequences. These findings are the foundations of policies that will utilize the strengths of the different tests, and achieve enhanced hybrid surveillance.

Validation of 12 Rapid Antigen Tests for the Detection of SARS-CoV-2

The rapid identification SARS-CoV-2 virus has become the basis for the control of the COVID-19 outbreak. The rapid antigen tests for SARS-CoV-2 are quick, widely available, and inexpensive. Rapid antigen tests have gradually replaced the time-consuming and costly RT-PCR. Currently, although several RAT kits have been extensively used for the diagnosis of COVID-19, validity data are limited due to the inconsistent sensitivity and poor reproducibility. Meanwhile, WHO does not recommend specific commercial RAT kits. Therefore, it is crucial to establish a method to evaluate the effectiveness of different rapid antigen tests kits. This study aimed to develop an evaluation system for rapid antigen tests to provide an efficient and accurate technique for screening SARS-CoV-2 antigen detection kits. Given large number of rapid antigen tests kits available, this study only focused on those that are representative and commonely used in China. By minimzing biases through randomization, concealment, and blinding, we eventually found that the Test 1 had the lowest sensitivity and the Test VI had the highest sensitivity. This study provided an evaluation platform that can potentially serve as a reference for COVID-19 diagnostic strategies.

Exploring Post-COVID-19 Functional Outcomes in Residents in Long-Term Care Homes in British Columbia, Canada

Research on functional outcomes in long-term care (LTC) home residents after COVID-19 infection is limited. In the current study, we examined outcomes in 1,310 LTC residents with a positive COVID-19 test in the period from March 2020 to April 2022 ("COVID" group). We also reviewed outcomes in residents in the same LTC homes without a history of COVID-19 during the same period ("No-COVID" group, n = 2,301). In a retrospective longitudinal design, we explored activities of daily living (ADLs), cognitive function, and clinical care needs over time. Change was assessed from the last assessment before contracting COVID-19 to three assessments subsequent to COVID-19, over on average seven months after infection. We found deterioration over time in ADLs and cognitive performance in both groups. The change in ADLs and clinical care needs was slightly greater in the COVID than the No-COVID group from baseline to the first follow-up assessment; in subsequent assessments, the change was similar in both groups. Overall, we observed similar functional outcomes among surviving residents in the two groups, with initially greater deterioration in ADLs and clinical care needs in residents with a history of COVID-19 followed by a trajectory resembling the one in the No-COVID residents.

Molecular diagnostic approaches for SARS-CoV-2 detection and pathophysiological consequences

SARS-CoV-2, a novel coronavirus within the Coronaviridae family, is the causative agent behind the respiratory ailment referred to as COVID-19. Operating on a global scale, COVID-19 has led to a substantial number of fatalities, exerting profound effects on both public health and the global economy. The most frequently reported symptoms encompass fever, cough, muscle or body aches, loss of taste or smell, headaches, and fatigue. Furthermore, a subset of individuals may manifest more severe symptoms, including those consistent with viral pneumonitis, which can be so profound as to result in fatalities. Consequently, this situation has spurred the rapid advancement of disease diagnostic technologies worldwide. Predominantly employed in diagnosing COVID-19, the real-time quantitative reverse transcription PCR has been the foremost diagnostic method, effectively detecting SARS-CoV-2 viral RNA. As the pandemic has evolved, antigen and serological tests have emerged as valuable diagnostic tools. Antigen tests pinpoint specific viral proteins of SARS-CoV-2, offering swift results, while serological tests identify the presence of antibodies in blood samples. Additionally, there have been notable strides in sample collection methods, notably with the introduction of saliva-based tests, presenting a non-invasive substitute to nasopharyngeal swabs. Given the ongoing mutations in SARS-CoV-2, there has been a continuous need for genomic surveillance, encompassing full genome sequencing and the identification of new variants through Illumina technology and, more recently, nanopore metagenomic sequencing (SMTN). Consequently, while diagnostic testing methods for COVID-19 have experienced remarkable progress, no test is flawless, and there exist limitations with each technique, including sensitivity, specificity, sample collection, and the minimum viral load necessary for accurate detection. These aspects are comprehensively addressed within this current review.

Performance evaluation of SARS-CoV-2 antigen detection in the post-pandemic era: multi-laboratory assessment

OBJECTIVES

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen detection is an indispensable tool for epidemic surveillance in the post-pandemic era. Faced with irregular performance, a comprehensive external quality assessment (EQA) scheme was conducted by the National Center for Clinical Laboratories (NCCL) to evaluate the analytical performance and status of SARS-CoV-2 antigen tests.

METHODS

The EQA panel included ten lyophilized samples containing serial 5-fold dilutions of inactivated SARS-CoV-2-positive supernatants of the Omicron BA.1 and BA.5 strains and negative samples, which were classified into "validating" samples and "educational" samples. Data were analyzed according to qualitative results for each sample.

RESULTS

A total of 339 laboratories in China participated in this EQA scheme, and 378 effective results were collected. All validating samples were correctly reported by 90.56 % (307/339) of the participants and 90.21 % (341/378) of the datasets. The positive percent agreement (PPA) was >99 % for samples with concentrations of 2 × 107 copies/mL but was 92.20 % (697/756) for 4 × 106 copies/mL and 25.26 % (382/1,512) for 8 × 105 copies/mL samples. Colloidal gold was the most frequently used (84.66 %, 320/378) but showed the lowest PPAs (57.11 %, 1,462/2,560) for positive samples compared with fluorescence immunochromatography (90 %, 36/40) and latex chromatography (79.01 %, 335/424). Among 11 assays used in more than 10 clinical laboratories, ACON showed a higher sensitivity than other assays.

CONCLUSIONS

The EQA study can help to validate whether it's necessary to update antigen detection assays for manufacturers and provide participants with information about the performance of assays to take the first step toward routine post-market surveillance.

Assessing the real-world effectiveness of five SARS-CoV-2 vaccines in a cohort of Mexican pensioners: a nationwide nested test-negative design study

Background

Despite the extensive distribution of COVID-19 vaccines across Latin America, research on their real-world performance remains limited. We aimed to evaluate the effectiveness of five vaccines (BNT162b2, AZD1222, CoronaVac, Gam-COVID-Vac, and Ad5-nCoV) in a cohort of 2,559,792 pensioners covered by the Mexican Institute of Social Security.

Methods

We conducted a nested test-negative design study on 28,271 individuals tested for SARS-CoV-2 infection between April and November 2021, accounting for 29,226 separate episodes. We used mixed-effects logistic regression models to estimate the vaccine effectiveness (VE) in fully vaccinated individuals for symptomatic infection, hospitalization, severe disease, and death.

Findings

The median age of the study population was 70 years (interquartile range 65-76) and 76.4% (21,598/28,271) were male. VE rates were 56.3%, 75.3%, 79.7%, and 79.8% against symptomatic infection (95% confidence interval [CI]: 53.5-59.0), hospitalization (95% CI: 73.4-77.0), severe disease (95% CI: 78.0-81.3), and death (95% CI: 78.1-81.4), respectively. When evaluating vaccines individually, all showed moderate to high VE, with the best being BNT162b2 (symptomatic infection, 69.8%, 95% CI: 67.3-72.0; hospitalization, 84.1%, 95% CI: 82.5-85.6; severe disease, 88.2%, 95% CI: 86.7-89.5; and death, 88.3%, 95% CI: 86.9-89.6) and Gam-COVID-Vac (symptomatic infection, 70.0%, 95% CI: 64.8-74.4; hospitalization, 86.8%, 95% CI: 83.7-89.3; severe disease, 91.9%, 95% CI: 89.4-93.9; and death, 92.0%, 95% CI: 89.5-93.9).

Interpretation

All five SARS-CoV-2 vaccines available for this population showed moderate to high levels of protection against COVID-19 and its progression to severe outcomes.

Funding

Fundación IMSS, México.

COVID-19 scent dog research highlights and synthesis during the pandemic of December 2019-April 2023

CONTEXT

This review was undertaken to provide information concerning the advancement of research in the area of COVID-19 screening and testing during the worldwide pandemic from December 2019 through April 2023. In this review, we have examined the safety, effectiveness, and practicality of utilizing trained scent dogs in clinical and public situations for COVID-19 screening. Specifically, results of 29 trained scent dog screening peer-reviewed studies were compared with results of real-time reverse-transcription polymerase chain reaction (RT-PCR) and rapid antigen (RAG) COVID-19 testing methods.

OBJECTIVES

The review aims to systematically evaluate the strengths and weaknesses of utilizing trained scent dogs in COVID-19 screening.

METHODS

At the time of submission of our earlier review paper in August 2021, we found only four peer-reviewed COVID-19 scent dog papers: three clinical research studies and one preprint perspective paper. In March and April 2023, the first author conducted new literature searches of the MEDLINE/PubMed, Google Scholar, and Cochrane Library websites. Again, the keyword phrases utilized for the searches included "COVID detection dogs," "COVID scent dogs," and "COVID sniffer dogs." The Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) 2020 Checklist was followed to ensure that our review adhered to evidence-based guidelines for reporting. Utilizing the results of the reviewed papers, we compiled statistics to intercompare and summarize basic information concerning the scent dogs and their training, the populations of the study participants, the types of sampling methods, the comparative tests utilized, and the effectiveness of the scent dog screening.

RESULTS

A total of 8,043 references were identified through our literature search. After removal of duplicates, there were 7,843 references that were screened. Of these, 100 were considered for full-text eligibility, 43 were included for qualitative synthesis, and 29 were utilized for quantitative analysis. The most relevant peer-reviewed COVID-19 scent dog references were identified and categorized. Utilizing all of the scent dog results provided for this review, we found that 92.3 % of the studies reached sensitivities exceeding 80 and 32.0 % of the studies exceeding specificities of 97 %. However, 84.0 % of the studies reported specificities above 90 %. Highlights demonstrating the effectiveness of the scent dogs include: (1) samples of breath, saliva, trachea-bronchial secretions and urine as well as face masks and articles of clothing can be utilized; (2) trained COVID-19 scent dogs can detect presymptomatic and asymptomatic patients; (3) scent dogs can detect new SARS-CoV-2 variants and Long COVID-19; and (4) scent dogs can differentiate SARS-CoV-2 infections from infections with other novel respiratory viruses.

CONCLUSIONS

The effectiveness of the trained scent dog method is comparable to or in some cases superior to the real-time RT-PCR test and the RAG test. Trained scent dogs can be effectively utilized to provide quick (seconds to minutes), nonintrusive, and accurate results in public settings and thus reduce the spread of the COVID-19 virus or other viruses. Finally, scent dog research as described in this paper can serve to increase the medical community's and public's knowledge and acceptance of medical scent dogs as major contributors to global efforts to fight diseases.

The importance of prevalence and pre-test probability on the microbiological diagnosis of SARS-CoV-2: the case of Spain in 2020

OBJECTIVE

The aim of this work was to estimate the conditioned probability for the diagnosis of SARS-CoV-2 infection with reverse transcription polymerase chain reaction (RT-PCR), viral antigen rapid diagnostic tests (Ag-RDT), and antibody detection tests depending on the prevalence in the specific healthcare settings in Spain in 2020, and on the pre-test probability (PTP) according to the clinical situation, age and unknown or close contacts of the patient.

METHODS

Performance parameters of tests were obtained from literature. Prevalence data and PTP were obtained from Spanish sources and a survey, respectively. The post-test probability is the positive predictive value (PPV) when test is positive. For negative result, we also calculated the probability of having the infection (false negatives).

RESULTS

For both RT-PCR and viral Ag-RDT, the lowest PPV values were for the population screenings. This strategy proved to be useful in ruling out infection but generates a high number of false positives. At individual level, both tools provided high PPV (≥ 97%) when the PTP values are over 35%. In seroprevalence studies, though the specificity of IgG alone tests is high, under low seroprevalence, false positives cannot be avoided. Total antibodies tests are useful for diagnosis of COVID-19 in those doubtful cases with RT-PCR or Ag-RDT tests being repeatedly negative.

CONCLUSIONS

The interpretating of results depends not only on the accuracy of the test, but also on the prevalence of the infection in different settings, and the PTP associated to the patient before performing the test.

Analysis of the Factors That Affect the Detection Duration of SARS-CoV-2 in Loop Mediated Isothermal Amplification among COVID-19 Inpatients

In COVID-19 patients who are immunocompromised or have severe COVID-19, the duration of infectious viral shedding may be longer, and a longer isolation duration is recommended. At the National Sagamihara Hospital, a decline in the viral load to end the isolation of hospitalized patients with COVID-19 was confirmed using loop-mediated isothermal amplification (LAMP). However, a subset of patients displayed LAMP positivity for more than 20 days after symptom onset. Therefore, we conducted a retrospective observational study to investigate the factors that affect the persistence of LAMP positivity. This study included a total of 102 participants. The severity of COVID-19 was mild (25.5%), moderate (67.6%), or severe (6.9%). The median number (interquartile range) of days until negative LAMP results from symptom onset were 16 (14-19) days. Multivariate logistic regression analysis showed that patients ≥55 years and/or those with the delta variant were correlated with persistent LAMP positivity for more than 20 days after symptom onset. This study identified age, the delta variant, and oxygen requirement as factors that contribute to persistently positive LAMP results. Therefore, it is posited that in these patients, the implementation of LAMP for deisolation would result in a prolonged isolation duration.

Efficient Selective Adsorption of SARS-CoV-2 via the Recognition of Spike Proteins Using an Affinity Spongy Monolith

Since the outbreak of COVID-19, SARS-CoV-2, the infection has been spreading to date. The rate of false-negative result on a polymerase chain reaction (PCR) test considered the gold standard is roughly 20%. Therefore, its accuracy poses a question as well as needs improvement in the test. This study reports fabrication of a substrate of an anti-spike protein (AS)-immobilized porous material having selective adsorption toward a spike protein protruding from the surface of SARS-CoV-2. We have employed an organic polymer substrate called spongy monolith (SPM). The SPM has through-pores of about 10 μm and is adequate for flowing liquid containing virus particles. It also involves an epoxy group on the surface, enabling arbitrary proteins such as antibodies to immobilize. When antibodies of the spike protein toward receptor binding domain were immobilized, selective adsorption of the spike protein was observed. At the same time, when mixed analytes of spike proteins, lysozymes and amylases, were flowed into an AS-SPM, selective adsorption toward the spike proteins was observed. Then, SARS-CoV-2 was flowed into the BSA-SPM or AS-SPM, amounts of SARS-CoV-2 adsorption toward the AS-SPM were much larger compared to the ones toward the BSA-SPM. Furthermore, rotavirus was not adsorbed to the AS-SPM at all. These results show that the AS-SPM recognizes selectively the spike proteins of SARS-CoV-2 and may be possible applications for the purification and concentration of SARS-CoV-2.

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).

Diagnostic accuracy of Panbio™ rapid antigen test for SARS-CoV-2 in paediatric population

BACKGROUND

Rapid antigen-detection tests (Ag-RDTs) are used to diagnose SARS-CoV-2 infection. Real-world studies of Ag-RDTs are necessary to evaluate their diagnostic yield in paediatric patients. Our aim was to evaluate the accuracy of the Panbio™ Rapid Antigen Test for SARS-CoV-2 in the setting of a primary health care centre (PHC), with use of the Reverse Transcription-Polymerase Chain Reaction (RT-PCR) as gold standard.

METHODS

This prospective diagnostic study was conducted at PHCs in Mallorca, Spain. Patients were ≤ 18 years-old that attended sites for RT-PCR testing due to symptoms suggestive of infection (fever, headache, nasal congestion and dry cough, among others) or epidemiological exposure (close contacts). Two samples were collected: a nasal mid-turbinate sample for Ag-RDTs and a nasopharyngeal swab for RT-PCR testing. The sensitivity, specificity, and predictive values of the AgRDT were calculated using the RT-PCR results as the reference.

RESULTS

We examined 1142 participants from 0 to 18 years (47.5% female, mean age 8.9 ± 4.8 years, median 9.0 [5.0-13.0]). There were 84 positive RT-PCR results (pre-test probability of 7.3%) and 52 positive Ag-RDT results. The sensitivity of the Ag-RDT was 59.5% (95% Confidence Interval (CI): 48.2-69.9%), the specificity was 99.8% (95%CI: 99.2-99.9%), the positive predictive value was 96.1% (95%CI: 85.6-99.4%), and the negative predictive value was 96.8% (95%CI: 95.6-97.7%). The sensitivity for individuals referred by a general practitioner (GP) or paediatrician due to symptoms was 71.4% (95%CI: 51.5-86.0%) and for asymptomatic individuals was 50.0% (95%CI: 9.1-90.8%). The specificity was greater than 98.9% overall and in all subgroups. The sensitivity was 73.0% (95%CI: 52.0-87.5%) for referred patients due to symptoms and who were tested within 5 days since symptom onset. No significant statistical differences between any groups were found. There were 34 false-negative Ag-RDT results (40.5%) and 2 false-positive Ag-RDT results (0.2%).

CONCLUSION

The sensitivity of the Panbio™ Test in paediatric individuals is below the minimum of 80% recommended by the World Health Organization for Ag-RDTs. This test had better accuracy in individuals referred by a GP or paediatrician due to symptoms, rather than those who were asymptomatic or referred due to epidemiological exposure. The RT-PCR test using a nasopharyngeal swab is accurate, but a less invasive alternative that has better sensitivity than the Panbio™ Test is needed for paediatric populations.

Point-of-care testing in private pharmacy and drug retail settings: a narrative review

BACKGROUND

Point-of-care testing (POCT) using rapid diagnostic tests for infectious disease can potentially guide appropriate use of antimicrobials, reduce antimicrobial resistance, and economise use of healthcare resources. POCT implementation in private retail settings such as pharmacies and drug shops could lessen the burden on public healthcare. We performed a narrative review on studies of POCTs in low- and middle-income countries (LMICs), and explored uptake, impact on treatment, and feasibility of implementation.

METHODS

We searched MEDLINE/PubMed for interventional studies on the implementation of POCT for infectious diseases performed by personnel in private retail settings. Data were extracted and analysed by two independent reviewers.

RESULTS

Of the 848 studies retrieved, 23 were included in the review. Studies were on malaria (19/23), malaria and pneumonia (3/23) or respiratory tract infection (1/23). Nine randomised controlled studies, four controlled, non-randomised studies, five uncontrolled interventions, one interventional pre-post study, one cross-over interventional study and three retrospective analyses of RCTs were included. Study quality was poor. Overall, studies showed that POCT can be implemented successfully, leading to improvements in appropriate treatment as measured by outcomes like adherence to treatment guidelines. Despite some concerns by health workers, customers and shop providers were welcoming of POCT implementation in private retail settings. Main themes that arose from the review included the need for well-structured training with post-training certification covering guidelines for test-negative patients, integrated waste management, community sensitization and demand generation activities, financial remuneration and pricing schemes for providers, and formal linkage to healthcare and support.

CONCLUSION

Our review found evidence that POCT can be implemented successfully in private retail settings in LMICs, but comprehensive protocols are needed. High-quality randomised studies are needed to understand POCTs for infectious diseases other than malaria.

Accuracy of Expired BinaxNOW Rapid Antigen Tests

The widespread existence of expired antigen testing kits in households and potential coronavirus outbreaks necessitates evaluating the reliability of these expired kits. Our study examined BinaxNOW COVID-19 rapid antigen tests 27 months postmanufacture and 5 months past their FDA extended expiration dates, using SARS-CoV-2 variant XBB.1.5 viral stock. We conducted testing at two concentrations, the limit of detection (LOD) and 10 times the LOD. One hundred expired and unexpired kits were tested at each concentration for a total of 400 antigen tests. At the LOD (2.32 × 102 50% tissue culture infective dose/mL [TCID50/mL]), both expired and unexpired tests displayed 100% sensitivity (95% confidence interval [CI], 96.38% to 100%), with no statistical difference (95% CI, -3.92% to 3.92%). Similarly, at 10 times the LOD, unexpired tests retained 100% sensitivity (95% CI, 96.38% to 100%), while expired tests exhibited 99% sensitivity (95% CI, 94.61% to 99.99%), demonstrating a statistically insignificant 1% difference (95% CI, -2.49% to 4.49%; P = 0.56). Expired rapid antigen tests had fainter lines than the unexpired tests at each viral concentration. The expired rapid antigen tests at the LOD were only just visible. These findings carry significant implications for waste management, cost efficiency, and supply chain resilience in pandemic readiness efforts. They also provide critical insights for formulating clinical guidelines for interpreting results from expired kits. In light of expert warnings of a potential outbreak of a severity rivaling the Omicron variant, our study underscores the importance of maximizing the utility of expired antigen testing kits in managing future health emergencies. IMPORTANCE The study examining the reliability of expired antigen testing kits in the context of COVID-19 has significant real-world implications. By demonstrating that these expired kits retain their sensitivity in detecting the virus, this work provides evidence that expired kits can still be utilized, reducing waste and optimizing resources in health care systems. These findings are especially crucial in light of potential future coronavirus outbreaks and the need to be prepared. The study's outcomes have the potential to contribute to waste management efforts, cost efficiency, and supply chain resilience, ensuring that diagnostic tests remain readily available for effective public health interventions. Furthermore, it provides critical insights for formulating clinical guidelines on interpreting results from expired kits, enhancing the accuracy of testing outcomes, and supporting informed decision-making. Ultimately, this work holds great importance in maximizing the utility of expired antigen testing kits, safeguarding public health, and enhancing pandemic readiness on a global scale.

The relationship between sublingual immunotherapy for allergic rhinitis and the risk of symptoms in patients with COVID-19 infection

To evaluated the risk ratio of Allergic rhinitis (AR) people on the symptoms after COVID-19 infection, and explored the relationship between AR and the symptoms after COVID-19 infection. An observational study was performed of people from outpatient department of the Hospital of Chengdu University of Chinese Medicine. Participants completed an electronic survey and between January 10 to January 20, 2023. We divided the participants into three groups according to the disease information of the population: non-AR people group (AR-N), AR patients with sublingual immunotherapy group (AR-S), and AR patients with conventional therapy group (AR-C). A total of 1116 participants were included in the study, with an average age of 21.76 ± 8.713, women accounted for 62.5%, men accounted for 37.5%. The final results showed that the risk of most symptoms after AR-C infection was not different from that of AR-N, except for sore throat, dry and itchy, chest distress, shortness of breath, and dyspnea. AR-S could effectively reduce the risk of post-infection symptoms including: dry and itchy (OR = 0.484, 95%CI: 0.335-0.698), pain (OR = 0.513, 95%CI:0.362-0.728), cough (OR = 0.506, 95% CI:0.341-0.749), expectoration (OR = 0.349, 95% CI:0.244-0.498), fever (OR = 0.569, 95% CI:0.379-0.853), head and body pain (OR = 0.456, 95% CI:0.323-0.644), fatigue (OR = 0.256, 95% CI:0.177-0.371), cold limbs (OR = 0.325, 95%CI:0.227-0.465), diarrhea (OR = 0.246, 95% CI:0.132-0.457), constipation (OR = 0.227, 95%CI:0.100-0.513), hyposmia (OR = 0.456, 95% CI:0.296-0.701), hypogeusia (OR = 0.397, 95% CI:0.259-0.607), chest distress (OR = 0.534, 95% CI:0.343-0.829), shortness of breath (OR = 0.622, 95% CI:0.398-0.974), palpitations (OR = 0.355, 95% CI:0.206-0.613). The risk of symptoms after COVID-19 infection in allergic rhinitis population receiving sublingual immunotherapy is lower.

To PCR or not? The impact of shifting policy from PCR to rapid antigen tests to diagnose COVID-19 during the omicron epidemic: a nationwide surveillance study

Background

Coronavirus disease 2019 (COVID-19) had caused huge impacts worldwide. Polymerase chain reaction (PCR) is the mainstay diagnostic modality. In most hospitals in Taiwan, samples for PCR are collected at emergency department (ER) or outdoor clinics to avoid virus spread inside hospitals. Home rapid antigen test (RAT) is a feasible, low-cost, and convenient tool with moderate sensitivity and high specificity, which can be performed at home to reduce hospital visits. Due to comparably low severity of omicron variant and high vaccine coverage (~80% residents fully vaccinated with AstraZeneca, Moderna, or Pfizer BioNTech COVID-19 vaccines as of March 2022), the policy was shifted from containment to co-existing with COVID-19 in Taiwan. Virus spread rapidly in the community after the ease of social restrictive measurements. To acquire a confirmed diagnosis, PCR testing was requested for people with suspected COVID-19 infection. As a consequence, people with respiratory symptoms or contact history surged into hospitals for PCR testing, thus, the medical capacity was challenged. The diagnostic policy was altered from PCR to RAT, but the impact of diagnostic policy change remains unclear.

Objectives

We conducted this study to investigate the number of COVID-19 cases, PCR testing, hospitalizations, mortalities, and hospital visits during the epidemic and evaluate the impact of diagnostic policy change on hospital visits.

Methods

The diagnostic policy change was implemented in late May 2022. We used nationwide and hospital-based data of COVID-19 cases, PCR testing, hospitalizations, mortalities, and hospital visits before and after policy change as of 31 Jul 2022.

Results

During the omicron epidemic, significant and synchronous increase of COVID-19 patients, PCR testing, hospital visits were observed. COVID-19 cases increased exponentially since April 2022 and the COVID-19 patients peaked in June (1,943, 55,571, and 61,511 average daily new cases in April, May, and June, respectively). The PCR testing peaked in May (85,788 daily tests) with high positive rate (81%). The policy of RAT as confirmatory diagnosis was implemented on 26 May 2022 and a substantial decline of PCR testing numbers occurred (85,788 and 83,113 daily tests in May and June). People hospitalized for COVID-19 peaked in June (821.8 patients per day) and decreased in July (549.5 patients). The mortality cases also peaked in June (147 cases/day). This trend was also validated by the hospital-based data with a significant decrease of emergency department visits (11,397 visits in May while 8,126 visits in June) and PCR testing (21,314 in May and 6,158 in June). The proportion of people purely for PCR testing also decreased (10-26 vs. 5-14%, before and after policy change, respectively).

Conclusions

The impact of diagnostic policy change was a complicated issue and our study demonstrated the huge impact of diagnostic policy on health seeking behavior. The PCR testing numbers and emergency department visits had substantial decrease after diagnostic policy change, and the plateau of epidemic peak eased gradually in ~1 month later. Widespread RAT application may contribute to the decreased hospital visits and preserve medical capacity. Our study provides some evidences for policy maker's reference.

Severe Acute Respiratory Syndrome Associated Infections

Viral infections are some of the most common sources of respiratory illness in pediatric and adult populations worldwide. Influenza and coronaviruses are viral pathogens that could lead to severe respiratory illness and death. More recently, respiratory illness from coronaviruses, accounts for more than 1 million deaths in the United States alone. This article will explore the epidemiology, pathogenesis, diagnosis, treatment, and prevention of severe acute respiratory syndrome caused by coronavirus-2, and Middle Eastern respiratory syndrome.

Evaluation of Abbott ID NOW COVID-19 POC test performance characteristics and integration in the regional health network workflows to improve health care delivery

With the recent global surge of SARS-CoV-2 Delta variant, there continues to be high demand for COVID-19 diagnostic testing. Abbott ID NOW is a rapid, CLIA-waived, COVID-19 diagnostic test ideally suited for use in urgent care settings or where access to diagnostic testing is limited. In this study we describe the results of rigorous validation of ID NOW and post-implementation study of POC test utilization patterns within community hospitals and clinics. Performance of ID NOW was validated by comparison of the results from 207 consecutive, paired, specimens tested on the ID NOW and on the m2000/Alinity m platforms. Once validated, ID NOW devices were placed for clinical use at four regional hospitals and clinics. We found that the ID NOW and m2000/Alinity m positive and negative percent agreement were 94.5% (95% CI, 85.1% to 98.1%) and 99.3% (95% CI, 96.4% to 99.9%), respectively. As of August 2021, a total of 2,301 tests were performed by ID NOW at individual regional network sites. The population tested consisted of 55.5% White and 42.9% Black patients, with Black patients presenting predominantly in the hospitals, while White patients were more evenly distributed between hospital and clinic sites. Disease prevalence observed among patients tested by ID NOW (12.3%) was aligned with overall prevalence seen at regional sites (11.3%). In summary, the ID NOW test can provide rapid and accurate results in a variety of near-to-patient and POC settings. If used correctly, it could serve as a valuable diagnostic tool to enable equal access to care and improve healthcare delivery within large health network systems.

The QuantuMDx Q-POC SARS-CoV-2 RT-PCR assay for rapid detection of COVID-19 at point-of-care: preliminary evaluation of a novel technology

Accurate and rapid point-of-care (PoC) diagnostics are critical to the control of the COVID-19 pandemic. The current standard for accurate diagnosis of SARS-CoV-2 is laboratory-based reverse transcription polymerase chain reaction (RT-PCR) assays. Here, a preliminary prospective performance evaluation of the QuantuMDx Q-POC SARS-CoV-2 RT-PCR assay is reported. Between November 2020 and March 2021, 49 longitudinal combined nose/throat (NT) swabs from 29 individuals hospitalised with RT-PCR confirmed COVID-19 were obtained at St George's Hospital, London. In addition, 101 mid-nasal (MN) swabs were obtained from healthy volunteers in June 2021. These samples were used to evaluate the Q-POC SARS-CoV-2 RT-PCR assay. The primary analysis was to compare the sensitivity and specificity of the Q-POC test against a reference laboratory-based RT-PCR assay. The overall sensitivity of the Q-POC test compared with the reference test was 96.88% (83.78- 99.92% CI) for a cycle threshold (Ct) cut-off value for the reference test of 35 and 80.00% (64.35-90.95% CI) without altering the reference test's Ct cut-off value of 40. The Q-POC test is a sensitive, specific and rapid PoC test for SARS-CoV-2 at a reference Ct cut-off value of 35. The Q-POC test provides an accurate option for RT-PCR at PoC without the need for sample pre-processing and laboratory handling, enabling rapid diagnosis and clinical triage in acute care and other settings.

Multicenter Diagnostic Evaluation of OnSite COVID-19 Rapid Test (CTK Biotech) among Symptomatic Individuals in Brazil and the United Kingdom

The COVID-19 pandemic has given rise to numerous commercially available antigen rapid diagnostic tests (Ag-RDTs). To generate and to share accurate and independent data with the global community requires multisite prospective diagnostic evaluations of Ag-RDTs. This report describes the clinical evaluation of the OnSite COVID-19 rapid test (CTK Biotech, CA, USA) in Brazil and the United Kingdom. A total of 496 paired nasopharyngeal (NP) swabs were collected from symptomatic health care workers at Hospital das Clínicas in São Paulo, Brazil, and 211 NP swabs were collected from symptomatic participants at a COVID-19 drive-through testing site in Liverpool, United Kingdom. Swabs were analyzed by Ag-RDT, and results were compared to quantitative reverse transcriptase PCR (RT-qPCR). The clinical sensitivity of the OnSite COVID-19 rapid test in Brazil was 90.3% (95% confidence interval [CI], 75.1 to 96.7%) and in the United Kingdom was 75.3% (95% CI, 64.6 to 83.6%). The clinical specificity in Brazil was 99.4% (95% CI, 98.1 to 99.8%) and in the United Kingdom was 95.5% (95% CI, 90.6 to 97.9%). Concurrently, analytical evaluation of the Ag-RDT was assessed using direct culture supernatant of SARS-CoV-2 strains from wild-type (WT), Alpha, Delta, Gamma, and Omicron lineages. This study provides comparative performance of an Ag-RDT across two different settings, geographical areas, and populations. Overall, the OnSite Ag-RDT demonstrated a lower clinical sensitivity than claimed by the manufacturer. The sensitivity and specificity from the Brazil study fulfilled the performance criteria determined by the World Health Organization, but the performance obtained from the UK study failed to do. Further evaluation of Ag-RDTs should include harmonized protocols between laboratories to facilitate comparison between settings. IMPORTANCE Evaluating rapid diagnostic tests in diverse populations is essential to improving diagnostic responses as it gives an indication of the accuracy in real-world scenarios. In the case of rapid diagnostic testing within this pandemic, lateral flow tests that meet the minimum requirements for sensitivity and specificity can play a key role in increasing testing capacity, allowing timely clinical management of those infected, and protecting health care systems. This is particularly valuable in settings where access to the test gold standard is often restricted.

SARS-CoV-2 Testing Strategies in the Diagnosis and Management of COVID-19 Patients in Low-Income Countries: A Scoping Review

The accuracy of diagnostic laboratory tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can impact downstream clinical procedures in managing and controlling the outbreak of coronavirus disease 2019 (COVID-19). To assess the effectiveness of laboratory tools for managing COVID-19 patients in low-income countries (LICs), we systematically searched the PubMed, Embase, Scopus and CINHAL databases for reports published between January 2020 and June 2022. We found that 22 of 1303 articles reported the performance of various SARS-CoV-2 detection tools across 10 LICs. These tools were (1) real-time reverse transcriptase polymerase chain reaction (RT-PCR); (2) reverse transcription loop-mediated isothermal amplification (RT-LAMP); (3) rapid diagnostic tests (RDTs); (4) enzyme-linked immunosorbent assay (ELISA); and (5) dot-blot immunoassay. The detection of COVID-19 is largely divided into two main streams-direct virus (antigen) detection and serology (immunoglobulin)-based detection. Point-of-care testing using antigen-based RDTs is preferred in LICs because of cost effectiveness and simplicity in the test procedures. The nucleic acid amplification technology (RT-PCR and RT-LAMP) has the highest diagnostic performance among the available tests, but it is not broadly used in this context due to costs and shortage of facilities/trained staff. The serology-based test method is affected by antibody interferences and varying amounts of SARS-CoV-2 immunoglobulins expressed at different stages of disease onset. We further discuss the effectiveness and shortcomings of each of these tools in the diagnosis and management of COVID-19. Using the LICs as the study model, our findings highlight ways to improve the quality and turnaround time of COVID-19 testing in resource-constrained settings, notably through local/international collaborative efforts to refine the molecular-based or immunoassay-based testing technologies.

Diagnosis, treatment protocols, and outcomes of liver transplant recipients infected with COVID-19

Several cases of fatal pneumonia during November 2019 were linked initially to severe acute respiratory syndrome coronavirus 2, which the World Health Organization later designated as coronavirus disease 2019 (COVID-19). The World Health Organization declared COVID-19 as a pandemic on March 11, 2020. In the general population, COVID-19 severity can range from asymptomatic/mild symptoms to seriously ill. Its mortality rate could be as high as 49%. The Centers for Disease Control and Prevention have acknowledged that people with specific underlying medical conditions, among those who need immunosuppression after solid organ transplantation (SOT), are at an increased risk of developing severe illness from COVID-19. Liver transplantation is the second most prevalent SOT globally. Due to their immunosuppressed state, liver transplant (LT) recipients are more susceptible to serious infections. Therefore, comorbidities and prolonged immunosuppression among SOT recipients enhance the likelihood of severe COVID-19. It is crucial to comprehend the clinical picture, immunosuppressive management, prognosis, and prophylaxis of COVID-19 infection because it may pose a danger to transplant recipients. This review described the clinical and laboratory findings of COVID-19 in LT recipients and the risk factors for severe disease in this population group. In the following sections, we discussed current COVID-19 therapy choices, reviewed standard practice in modifying immunosuppressant regimens, and outlined the safety and efficacy of currently licensed drugs for inpatient and outpatient management. Additionally, we explored the clinical outcomes of COVID-19 in LT recipients and mentioned the efficacy and safety of vaccination use.

Is self-testing the next paradigm for diagnostics?

The study estimates the usability and attitude assessment of users for India's first approved rapid antigen self-test kit; the CoviSelf™. India approved its first AI-powered self-test for Covid-19 in April 2021 a few weeks after the first approval in the US. We present here a study on usability and attitude assessment of users of India's first approved rapid antigen self-test kit; the CoviSelf™. The study evaluates participants' understanding of and performance of test procedure and interprets the results. Analysis revealed that more than 90% study participants followed steps correctly as illustrated in the user's manual. Age group and gender-based analysis showed comparable scores for usability of the test kit suggesting users of different age groups has same ease in using the test kit. What we learnt from this study could be start of self-test revolution, where rapid tests could expand the access of diagnostics for hundreds of diseases including HIV, HPV, and dengue to millions of people who could not get access to diagnostics because we lacked manpower or facility to conduct tests. Self-testing could break the barriers for diagnostics that Internet did for information.

Advances in Diagnosis and Treatment for SARS-CoV-2 Variants

The COVID-19 pandemic’s epidemiological and clinical characteristics have been affected in recent months by the introduction of SARS-CoV-2 variants with unique spikes of protein alterations. These variations can lessen the protection provided by suppressing monoclonal antibodies and vaccines, as well as enhance the frequencies of transmission of the virus and/or the risk of contracting the disease. Due to these mutations, SARS-CoV-2 may be able to proliferate despite increasing levels of vaccination coverage while preserving and enhancing its reproduction efficiency. This is one of the main strategies in tackling the COVID-19 epidemics, the accessibility of precise and trustworthy biomarkers for the SARS-CoV-2 genetic material and also its nucleic acids is important to investigate the disease in suspect communities, start making diagnoses and management in symptomatic or asymptomatic persons, and evaluate authorization of the pathogen after infection. Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) for virus nucleic acid identification is still the most effective method for such uses due to its sensitivity, quickness, high-throughput sequencing capacity, and trustworthiness. It is essential to update the primer and probe sequences to maintain the recognition of recently emerging variations. Concerning viral variations could develop that are dangerously resistant to the immunization induced by the present vaccinations in coronavirus disease 2019. Additionally, the significance of effective public health interventions and vaccination programs will grow if some variations of concern exhibit an increased risk of transmission or toxicity. The international reaction must’ve been immediate and established in science. These results supported ongoing efforts to prevent and identify infection, as well as to describe mutations in vaccine recipients, and they suggest a potential risk of illness following effective immunization and transmission of pathogens with a mutant viral.

A fast RT-qPCR system significantly shortens the time for SARS-CoV-2 nucleic acid test

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious threat to global development. Rapid and accurate diagnosis is critical for containing the pandemic and treating patients in time. As the gold standard for SARS-CoV-2 diagnosis, the qualitative reverse transcription-PCR (RT-qPCR) test has long been criticized for its long detection time. In this study, we optimized the primers and probes targeting SARS-CoV-2 ORF1ab and N gene designed by the Chinese Center for Disease Control and Preventions (CDC) to increase their Tm values to meet the optimal elongation temperature of Taq DNA polymerase, thus greatly shortened the elongation time. The higher elongation temperature in turn narrowed the temperature range of the reaction and saved more time. In addition, by shortening the distance between the fluorophore at the 5' end and the quencher in the middle we got a probe with higher signal-to-noise ratio. Finally, by using all these measures and optimized RT-qPCR program we successfully reduced the time (nucleic acid extraction step is not included) for nucleic acid test from 74 min to 26 min.

Sniffer dogs performance is stable over time in detecting COVID-19 positive samples and agrees with the rapid antigen test in the field

Rapid antigen diagnostic (RAD) tests have been developed for the identification of the SARS-CoV-2 infection. However, they require nasopharyngeal or nasal swab, which is invasive, uncomfortable, and aerosolising. The use of saliva test was also proposed but has not yet been validated. Trained dogs may efficiently smell the presence of SARS-CoV-2 in biological samples of infected people, but further validation is needed both in laboratory and in field. The present study aimed to (1) assess and validate the stability over a specific time period of COVID-19 detection in humans' armpit sweat by trained dogs thanks to a double-blind laboratory test-retest design, and (2) assess this ability when sniffing people directly. Dogs were not trained to discriminate against other infections. For all dogs (n. 3), the laboratory test on 360 samples yielded 93% sensitivity and 99% specificity, an 88% agreement with the Rt-PCR, and a moderate to strong test-retest correlation. When sniffing people directly (n. 97), dogs' (n. 5) overall sensitivity (89%) and specificity (95%) were significantly above chance level. An almost perfect agreement with RAD results was found (kappa 0.83, SE 0.05, p = 0.001). Therefore, sniffer dogs met appropriate criteria (e.g., repeatability) and WHO's target product profiles for COVID-19 diagnostics and produced very promising results in laboratory and field settings, respectively. These findings support the idea that biodetection dogs could help reduce the spread of the virus in high-risk environments, including airports, schools, and public transport.

Application of ultrasensitive assay for SARS-CoV-2 antigen in nasopharynx in the management of COVID-19 patients with comorbidities during the peak of 2022 Shanghai epidemics in a tertiary hospital

OBJECTIVES

Various comorbidities associated with COVID-19 add up in severity of the disease and obviously prolonged the time for viral clearance. This study investigated a novel ultrasensitive MAGLUMI^® SARS-CoV-2 Ag chemiluminescent immunoassay assay (MAG-CLIA) for diagnosis and monitoring the infectivity of COVID-19 patients with comorbid conditions during the pandemic of 2022 Shanghai.

METHODS

Analytical performances of the MAG-CLIA were evaluated, including precision, limit of quantitation, linearity and specificity. Nasopharyngeal specimens from 232 hospitalized patients who were SARS-CoV-2 RT-qPCR positive and from 477 healthy donors were included. The longitudinal studies were performed by monitoring antigen concentrations alongside with RT-qPCR results in 14 COVID-19 comorbid participants for up to 22 days. The critical antigen concentration in determining virus infectivity was evaluated at the reference cycle threshold (Ct) of 35.

RESULTS

COVID-19 patients were well-identified using an optimal threshold of 0.64 ng/L antigen concentration, with sensitivity and specificity of 95.7% (95% CI: 92.2-97.9%) and 98.3% (95% CI: 96.7-99.3%), respectively, while the Wondfo LFT exhibited those of 34.9% (95% CI: 28.8-41.4%) and 100% (95% CI: 99.23-100%), respectively. The sensitivity of MAG-CLIA remained 91.46% (95% CI: 83.14-95.8%) for the samples with Ct values between 35 and 40. Close dynamic consistence was observed between MAG-CLIA and viral load time series in the longitudinal studies. The critical value of 8.82 ng/L antigen showed adequate sensitivity and specificity in evaluating the infectivity of hospitalized convalescent patients with comorbidities.

CONCLUSIONS

The MAG-CLIA SARS-CoV-2 Ag detection is an effective and alternative approach for rapid diagnosis and enables us to evaluate the infectivity of hospitalized convalescent patients with comorbidities.

Quantitative Analysis of the Effectiveness of Antigen- and Polymerase Chain Reaction-Based Combination Strategies for Containing COVID-19 Transmission in a Simulated Community

The number of coronavirus disease 2019 (COVID-19) cases continues to surge, overwhelming healthcare systems and causing excess mortality in many countries. Testing of infectious populations remains a key strategy to contain the COVID-19 outbreak, delay the exponential spread of the disease, and flatten the epidemic curve. Using the Omicron variant outbreak as a background, this study aimed to evaluate the effectiveness of testing strategies with different test combinations and frequencies, analyze the factors associated with testing effectiveness, and optimize testing strategies based on these influencing factors. We developed a stochastic, agent-based, discrete-time susceptible-latent-infectious-recovered model simulating a community to estimate the association between three levels of testing strategies and COVID-19 transmission. Antigen testing and its combination strategies were more efficient than polymerase chain reaction (PCR)-related strategies. Antigen testing also showed better performance in reducing the demand for hospital beds and intensive care unit beds. The delay in the turnaround time of test results had a more significant impact on the efficiency of the testing strategy compared to the detection limit of viral load and detection-related contacts. The main advantage of antigen testing strategies is the short turnaround time, which is also a critical factor to be optimized to improve PCR strategies. After modifying the turnaround time, the strategies with less frequent testing were comparable to daily testing. The choice of testing strategy requires consideration of containment goals, test efficacy, community prevalence, and economic factors. This study provides evidence for the selection and optimization of testing strategies in the post-pandemic era and provides guidance for optimizing healthcare resources.