Review of COVID-19 testing and diagnostic methods

Photoluminescence-based biosensor for the detection of antibodies against SARS-CoV-2 virus proteins by ZnO tetrapod structure integrated within microfluidic system

This paper reports on development of an optical biosensor for the detection of antibodies against SARS-CoV-2 virus proteins in blood serum. ZnO nanotetrapods with high surface area and stable room temperature photoluminescence (PL) were selected as transducers. Structure and optical properties of the ZnO tetrapods have been studied by XRD, SEM and Raman spectroscopy. Crystallinity, dimensions and emission peaks of the ZnO tetrapods were determined. The ZnO tetrapods were fixed on glass chip. Silanization of ZnO tetrapods surface resulted in forming of functional surface groups suitable for the immobilization of bioselective layer. Two types of recombinant proteins (rS and rN) have been used to form bioselective layer on the surface of the ZnO tetrapods. Flow through microfluidic system, integrated with optical system, has been used for the determination of antibodies against SARS-CoV-2 virus proteins present in blood samples. The SARS-CoV-2 probes, prepared in PBS solution, have been injected into the measurement chamber with a constant pumping speed. Steady-state photoluminescence spectra and photoluminescence kinetics have been studied before and after injection of the probes. The biosensor signal has been tested to anti-SARS-CoV-2 antibodies in the range of 0.001 nM-1 nM. Control measurements have been performed with blood serum of healthy person. ZnO-SARS-CoV-2-rS and ZnO-SARS-CoV-2-rN biosensors showed high stability and sensitivity to anti-SARS-CoV-2 antibodies in the range of 0.025-0.5 nM (LOD 0.01 nM) and 0.3-1 nM (LOD 0.3 nM), respectively. Gibbs free energy of interaction between ZnO/SARS-CoV-2-rS and ZnO/SARS-CoV-2-rN bioselective layers with anti-SARS-CoV-2 antibodies showed -35.5 and -21.4 kJ/mol, respectively. Average detection time of biosensor integrated within microfluidic system was 15-20 min. The detection time and pumping speed (50 μL/min) were optimized to make detection faster. The developed system and ZnO-SARS-CoV-2-rS nanostructures have good potential for detection of anti-SARS-CoV-2 antibodies from patient's probes.

COVID-19 Frequency in Hospitalized Psychiatric Patients: A Systematic Review

OBJECTIVE

The COVID-19 pandemic affected individuals in different contexts (e.g. long-term care facilities, schools, communities), including psychiatric hospitals. Thus, the objective of this systematic review, duly registered and approved on PROSPERO (CRD42023427835), is to assess the frequency of positive COVID-19 cases among patients hospitalized in psychiatric hospitals.

METHODS

A total of 4,922 articles were identified in the database searches, and 17 studies conducted in psychiatric hospitals from different regions of the world were selected.

RESULTS

The frequency of positive COVID-19 cases among patients hospitalized in psychiatric hospitals ranged from 1.8% to 98.8%. Out of a total of 19,573 patients hospitalized in psychiatric hospitals, the pooled mean frequency of positive COVID-19 cases was 11.9%. The majority of patients presented COVID-19 symptoms (e.g. cough, fever and others). The COVID-19 diagnosis was primarily conducted through RT-PCR testing in 88.9% of the studies.

CONCLUSION

In conclusion, there is discrepancy in the methodology of the studies assessing the frequency of positive COVID-19 cases in psychiatric hospitals. However, this review allowed us to understand how the COVID-19 pandemic has impacted the population hospitalized in psychiatric hospitals.

Evaluation and comparison of one-step real-time PCR and one-step RT-LAMP methods for detection of SARS-CoV-2

BACKGROUND

There is an increasing disease trend for SARS-COV-2, so need a quick and affordable diagnostic method. It should be highly accurate and save costs compared to other methods. The purpose of this research is to achieve these goals.

METHODS

This study analyzed 342 samples using TaqMan One-Step RT-qPCR and fast One-Step RT-LAMP (Reverse Transcriptase Loop-Mediated Isothermal Amplification). The One-Step LAMP assay was conducted to assess the sensitivity and specificity.

RESULTS

The research reported positive samples using two different methods. In the RT-LAMP method, saliva had 92 positive samples (26.9%) and 250 negative samples (73.09%) and nasopharynx had 94 positive samples (27.4%) and 248 negative samples (72.51%). In the RT-qPCR method, saliva had 86 positive samples (25.1%) and 256 negative samples (74.8%) and nasopharynx had 93 positive samples (27.1%) and 249 negative samples (72.8%). The agreement between the two tests in saliva and nasopharynx samples was 93% and 94% respectively, based on Cohen's kappa coefficient (κ) (P < 0.001). The rate of sensitivity in this technique was reported at a dilution of 1 × 101 and 100% specificity.

CONCLUSIONS

Based on the results of the study the One-Step LAMP assay has multiple advantages. These include simplicity, cost-effectiveness, high sensitivity, and specificity. The One-Step LAMP assay shows promise as a diagnostic tool. It can help manage disease outbreaks, ensure prompt treatment, and safeguard public health by providing rapid, easy-to-use testing.

Advancing COVID-19 Diagnosis: Enhancement in SERS-PCR with 30-nm Au Nanoparticle-Internalized Nanodimpled Substrates

Real-time polymerase chain reaction (RT-PCR) with fluorescence detection is the gold standard for diagnosing coronavirus disease 2019 (COVID-19) However, the fluorescence detection in RT-PCR requires multiple amplification steps when the initial deoxyribonucleic acid (DNA) concentration is low. Therefore, this study has developed a highly sensitive surface-enhanced Raman scattering-based PCR (SERS-PCR) assay platform using the gold nanoparticle (AuNP)-internalized gold nanodimpled substrate (AuNDS) plasmonic platform. By comparing different sizes of AuNPs, it is observed that using 30 nm AuNPs improves the detection limit by approximately ten times compared to 70 nm AuNPs. Finite-difference time-domain (FDTD) simulations show that multiple hotspots are formed between AuNPs and the cavity surface and between AuNPs when 30 nm AuNPs are internalized in the cavity, generating a strong electric field. With this 30 nm AuNPs-AuNDS SERS platform, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ribonucleic acid (RNA)-dependent RNA polymerase (RdRp) can be detected in only six amplification cycles, significantly improving over the 25 cycles required for RT-PCR. These findings pave the way for an amplification-free molecular diagnostic system based on SERS.

Differential privacy preserved federated learning for prognostic modeling in COVID-19 patients using large multi-institutional chest CT dataset

BACKGROUND

Notwithstanding the encouraging results of previous studies reporting on the efficiency of deep learning (DL) in COVID-19 prognostication, clinical adoption of the developed methodology still needs to be improved. To overcome this limitation, we set out to predict the prognosis of a large multi-institutional cohort of patients with COVID-19 using a DL-based model.

PURPOSE

This study aimed to evaluate the performance of deep privacy-preserving federated learning (DPFL) in predicting COVID-19 outcomes using chest CT images.

METHODS

After applying inclusion and exclusion criteria, 3055 patients from 19 centers, including 1599 alive and 1456 deceased, were enrolled in this study. Data from all centers were split (randomly with stratification respective to each center and class) into a training/validation set (70%/10%) and a hold-out test set (20%). For the DL model, feature extraction was performed on 2D slices, and averaging was performed at the final layer to construct a 3D model for each scan. The DensNet model was used for feature extraction. The model was developed using centralized and FL approaches. For FL, we employed DPFL approaches. Membership inference attack was also evaluated in the FL strategy. For model evaluation, different metrics were reported in the hold-out test sets. In addition, models trained in two scenarios, centralized and FL, were compared using the DeLong test for statistical differences.

RESULTS

The centralized model achieved an accuracy of 0.76, while the DPFL model had an accuracy of 0.75. Both the centralized and DPFL models achieved a specificity of 0.77. The centralized model achieved a sensitivity of 0.74, while the DPFL model had a sensitivity of 0.73. A mean AUC of 0.82 and 0.81 with 95% confidence intervals of (95% CI: 0.79-0.85) and (95% CI: 0.77-0.84) were achieved by the centralized model and the DPFL model, respectively. The DeLong test did not prove statistically significant differences between the two models (p-value = 0.98). The AUC values for the inference attacks fluctuate between 0.49 and 0.51, with an average of 0.50 ± 0.003 and 95% CI for the mean AUC of 0.500 to 0.501.

CONCLUSION

The performance of the proposed model was comparable to centralized models while operating on large and heterogeneous multi-institutional datasets. In addition, the model was resistant to inference attacks, ensuring the privacy of shared data during the training process.

Evaluation of the SARS-CoV-2 RNA detection reagent LAMPdirect Genelyzer KIT using nasopharyngeal swab and saliva samples

The LAMPdirect Genelyzer KIT allows for the detection of SARS-CoV-2 RNA in saliva samples with a loop-mediated isothermal amplification (LAMP) method and generates results within 20 min. It has been approved by the Pharmaceuticals and Medical Devices Agency in Japan. In this study, the performance of the LAMPdirect Genelyzer KIT was compared with that of the RT-qPCR reference method using 50 nasopharyngeal swabs and 100 saliva samples. In addition, we evaluated the applicability of an alternative reverse transcriptase and the effects of an inactivation buffer. The total agreement rates were 80.0 % and 82.0 % for nasopharyngeal and saliva samples, respectively. When considering samples at the detection limit (50 copies/reaction) that increases the chance of transmission between humans, the total agreement rates were 100% and 94.1% for nasopharyngeal and saliva samples, respectively. The LAMP method is simple, fast, and inexpensive, making it useful for small medical institutions or rural areas.

Cutting-edge biorecognition strategies to boost the detection performance of COVID-19 electrochemical biosensors: A review

Electrochemical biosensors are known for their high sensitivity, selectivity, and low cost. Recently, they have gained significant attention and became particularly important as promising tools for the detection of COVID-19 biomarkers, since they offer a rapid and accurate means of diagnosis. Biorecognition strategies are a crucial component of electrochemical biosensors and determine their specificity and sensitivity based on the interaction of biological molecules, such as antibodies, enzymes, and DNA, with target analytes (e.g., viral particles, proteins and genetic material) to create a measurable signal. Different biorecognition strategies have been developed to enhance the performance of electrochemical biosensors, including direct, competitive, and sandwich binding, alongside nucleic acid hybridization mechanisms and gene editing systems. In this review article, we present the different strategies used in electrochemical biosensors to target SARS-CoV-2 and other COVID-19 biomarkers, as well as explore the advantages and disadvantages of each strategy and highlight recent progress in this field. Additionally, we discuss the challenges associated with developing electrochemical biosensors for clinical COVID-19 diagnosis and their widespread commercialization.

Effectiveness of interventions to reduce COVID-19 transmission in schools

School reopenings in 2021 and 2022 coincided with the rapid emergence of new SARS-CoV-2 variants in the United States. In-school mitigation efforts varied, depending on local COVID-19 mandates and resources. Using a stochastic age-stratified agent-based model of SARS-CoV-2 transmission, we estimate the impacts of multiple in-school strategies on both infection rates and absenteeism, relative to a baseline scenario in which only symptomatic cases are tested and positive tests trigger a 10-day isolation of the case and 10-day quarantine of their household and classroom. We find that monthly asymptomatic screening coupled with the 10-day isolation and quarantine period is expected to avert 55.4% of infections while increasing absenteeism by 104.3%. Replacing quarantine with test-to-stay would reduce absenteeism by 66.3% (while hardly impacting infection rates), but would require roughly 10-fold more testing resources. Alternatively, vaccination or mask wearing by 50% of the student body is expected to avert 54.1% or 43.1% of infections while decreasing absenteeism by 34.1% or 27.4%, respectively. Separating students into classrooms based on mask usage is expected to reduce infection risks among those who wear masks (by 23.1%), exacerbate risks among those who do not (by 27.8%), but have little impact on overall risk. A combined strategy of monthly screening, household and classroom quarantine, a 50% vaccination rate, and a 50% masking rate (in mixed classrooms) is expected to avert 81.7% of infections while increasing absenteeism by 90.6%. During future public health emergencies, such analyses can inform the rapid design of resource-constrained strategies that mitigate both public health and educational risks.

A universal nucleic acid detection platform combing CRISPR/Cas12a and strand displacement amplification with multiple signal readout

Rapid and sensitive detection of nucleic acids has become crucial in various fields. However, most current nucleic acid detection methods can only be used in specific scenarios, such as RT-qPCR, which relies on fluorometer for signal readout, limiting its application at home or in the field due to its high price. In this paper, a universal nucleic acid detection platform combing CRISPR/Cas12a and strand displacement amplification (CRISPR-SDA) with multiple signal readout was established to adapt to different application scenarios. Nucleocapsid protein gene of SARS-CoV-2 (N gene) and hepatitis B virus (HBV) DNA were selected as model targets. The proposed strategy achieved the sensitivity of 53.1 fM, 0.15 pM, and 1 pM for N gene in fluorescence mode, personal glucose meter (PGM) mode and lateral flow assay (LFA) mode, respectively. It possessed the ability to differentiate single-base mismatch and the presence of salmon sperm DNA with a mass up to 105-fold of the targets did not significantly interfere with the assay signal. The general and modular design idea made CRISPR-SDA as simple as building blocks to construct nucleic acid sensing methods to meet different requirements by simply changing the SDA template and selecting suitable signal report probes, which was expected to find a breadth of applications in nucleic acids detection.

RT-qPCR investigation of post-mortem tissues during COVID-19

In 2020, there were numerous cases in Kazakhstan with clinical symptoms of COVID-19 but negative PCR results in nasopharyngeal and oropharyngeal swabs. The diagnosis was confirmed clinically and by CT scans (computed tomography). The problem with such negative PCR results for SARS-CoV-2 infection confirmation still exists and indicates the need to confirm the diagnosis in the bronchoalveolar lavage in such cases. There is also a lack of information about confirmation of SARS-CoV-2 infection in deceased patients. In this study, various tissue materials, including lungs, bronchi, and trachea, were examined from eight patients who died, presumably from SARS-CoV-2 infection, between 2020 and 2022. Naso/oropharyngeal swabs taken from these patients in hospitals tested PCR negative for SARS-CoV-2. This study presents a modified RNA isolation method based on a comparison of the most used methods for RNA isolation in laboratories: QIAamp Viral RNA Mini Kit and TRIzol-based method. This modified nucleic acid extraction protocol can be used to confirm SARS-CoV-2 infection by RT-qPCR in the tissues of deceased patients in disputed cases. RT-qPCR with RNA of SARS-CoV-2 re-extracted with such method from post-mortem tissues that were stored at -80 °C for more than 32 months still demonstrated high-yielding positive results.

Ultra-sensitive colorimetric detection of SARS-CoV-2 by novel gold nanoparticle (AuNP)-assisted loop-mediated isothermal amplification (LAMP) and freezing methods

Loop-mediated isothermal amplification (LAMP) is a molecular diagnosis technology with the advantages of isothermal reaction conditions and high sensitivity. However, the LAMP reactions are prone to producing false-positive results and thus are usually less reliable. This study demonstrates a gold nanoparticle (AuNP)-assisted colorimetric LAMP technique for diagnosing SARS-CoV-2, which aims to overcome the false-positive results. The AuNPs were functionalized with E gene probes, specifically tailored to bind to the amplified E-gene LAMP product, using the freezing method. Varied salt concentration and AuNP/probe combinations were tested for the highest visual performance. The experiments were conducted on synthetic SARS-CoV-2 RNA (Omicron variant), as well as on clinical samples. The assay showed an exceptional sensitivity of 8.05 fg of LAMP amplicon mixture (0.537 fg/µL). The average reaction time was ~ 30 min. In conclusion, AuNP-assisted LAMP detection will not identify any potential unspecific amplification, which helps to improve the efficiency and reliability of LAMP assays in point-of-care applications. The freezing method to functionalize the AuNPs with probes simplifies the assay, which can be utilized in further diagnostic studies.

Multiplexed detection of eight respiratory viruses based on nanozyme colorimetric microfluidic immunoassay

Pandemics caused by respiratory viruses, such as the SARS-CoV-1/2, influenza virus, and respiratory syncytial virus, have resulted in serious consequences to humans and a large number of deaths. The detection of such respiratory viruses in the early stages of infection can help control diseases by preventing the spread of viruses. However, the diversity of respiratory virus species and subtypes, their rapid antigenic mutations, and the limited viral release during the early stages of infection pose challenges to their detection. This work reports a multiplexed microfluidic immunoassay chip for simultaneous detection of eight respiratory viruses with noticeable infection population, namely, influenza A virus, influenza B virus, respiratory syncytial virus, SARS-CoV-2, human bocavirus, human metapneumovirus, adenovirus, and human parainfluenza viruses. The nanomaterial of the nanozyme (Au@Pt nanoparticles) was optimized to improve labeling efficiency and enhance the detection sensitivity significantly. Nanozyme-binding antibodies were used to detect viral proteins with a limit of detection of 0.1 pg/mL with the naked eye and a microplate reader within 40 min. Furthermore, specific antibodies were screened against the conserved proteins of each virus in the immunoassay, and the clinical sample detection showed high specificity without cross reactivity among the eight pathogens. In addition, the microfluidic chip immunoassay showed high accuracy, as compared with the RT-PCR assay for clinical sample detection, with 97.2%/94.3% positive/negative coincidence rates. This proposed approach thus provides a convenient, rapid, and sensitive method for simultaneous detection of eight respiratory viruses, which is meaningful for the early diagnosis of viral infections. Significantly, it can be widely used to detect pathogens and biomarkers by replacing only the antigen-specific antibodies.

Weight loss treatment for COVID-19 in patients with NCDs: a pilot prospective clinical trial

COVID-19 comorbid with noncommunicable chronic diseases (NCDs) complicates the diagnosis, treatment, and prognosis, and increases the mortality rate. The aim is to evaluate the effects of a restricted diet on clinical/laboratory inflammation and metabolic profile, reactive oxygen species (ROS), and body composition in patients with COVID-19 comorbid with NCDs. We conducted a 6-week open, pilot prospective controlled clinical trial. The study included 70 adult patients with COVID-19 comorbid with type 2 diabetes (T2D), hypertension, or nonalcoholic steatohepatitis (NASH).

INTERVENTIONS

a restricted diet including calorie restriction, hot water drinking, walking, and sexual self-restraint.

PRIMARY ENDPOINTS

COVID-19 diagnosis by detecting SARS-CoV-2 genome by RT-PCR; weight loss in Main group; body temperature; C-reactive protein. Secondary endpoints: the number of white blood cells; erythrocyte sedimentation rate; adverse effects during treatment; fasting blood glucose, glycosylated hemoglobin A1c (HbA1c), systolic/diastolic blood pressure (BP); blood lipids; ALT/AST, chest CT-scan. In Main group, patients with overweight lost weight from baseline (- 12.4%; P < 0.0001); 2.9% in Main group and 7.2% in Controls were positive for COVID-19 (RR: 0.41, CI: 0.04-4.31; P = 0.22) on the 14th day of treatment. Body temperature and C-reactive protein decreased significantly in Main group compared to Controls on day 14th of treatment (P < 0.025). Systolic/diastolic BP normalized (P < 0.025), glucose/lipids metabolism (P < 0.025); ALT/AST normalized (P < 0.025), platelets increased from baseline (P < 0.025), chest CT (P < 0.025) in Main group at 14 day of treatment. The previous antidiabetic, antihypertensive, anti-inflammatory, hepatoprotective, and other symptomatic medications were adequately decreased to completely stop during the weight loss treatment. Thus, the fast weight loss treatment may be beneficial for the COVID-19 patients with comorbid T2D, hypertension, and NASH over traditional medical treatment because, it improved clinical and laboratory/instrumental data on inflammation; glucose/lipid metabolism, systolic/diastolic BPs, and NASH biochemical outcomes, reactive oxygen species; and allowed patients to stop taking medications.

TRIAL REGISTRATION

ClinicalTrials.gov NCT05635539 (02/12/2022): https://clinicaltrials.gov/ct2/show/NCT05635539?term=NCT05635539&draw=2&rank=1 .

A Fast and Sensitive One-Tube SARS-CoV-2 Detection Platform Based on RTX-PCR and Pyrococcus furiosus Argonaute

Since SARS-CoV-2 is a highly transmissible virus, alternative reliable, fast, and cost-effective methods are still needed to prevent virus spread that can be applied in the laboratory and for point-of-care testing. Reverse transcription real-time fluorescence quantitative PCR (RT-qPCR) is currently the gold criteria for detecting RNA viruses, which requires reverse transcriptase to reverse transcribe viral RNA into cDNA, and fluorescence quantitative PCR detection was subsequently performed. The frequently used reverse transcriptase is thermolabile; the detection process is composed of two steps: the reverse transcription reaction at a relatively low temperature, and the qPCR performed at a relatively high temperature, moreover, the RNA to be detected needs to pretreated if they had advanced structure. Here, we develop a fast and sensitive one-tube SARS-CoV-2 detection platform based on Ultra-fast RTX-PCR and Pyrococcus furiosus Argonaute-mediated Nucleic acid Detection (PAND) technology (URPAND). URPAND was achieved ultra-fast RTX-PCR process based on a thermostable RTX (exo-) with both reverse transcriptase and DNA polymerase activity. The URPAND can be completed RT-PCR and PAND to detect nucleic acid in one tube within 30 min. This method can specifically detect SARS-CoV-2 with a low detection limit of 100 copies/mL. The diagnostic results of clinical samples with one-tube URPAND displayed 100% consistence with RT-qPCR test. Moreover, URPAND was also applied to identify SARS-CoV-2 D614G mutant due to its single-nucleotide specificity. The URPAND platform is rapid, accurate, tube closed, one-tube, easy-to-operate and free of large instruments, which provides a new strategy to the detection of SARS-CoV-2 and other RNA viruses.

How do we change our approach to COVID with the changing face of disease?

INTRODUCTION

The emergence of SARS-CoV-2 triggered a global health emergency, causing > 7 million deaths thus far. Limited early knowledge spurred swift research, treatment, and vaccine developments. Implementation of public health measures such as, lockdowns and social distancing, disrupted economies and strained healthcare. Viral mutations highlighted the need for flexible strategies and strong public health infrastructure, with global collaboration crucial for pandemic control.

AREAS COVERED

(i) Revisiting diagnostic strategies, (ii) adapting to the evolving challenge of the virus, (iii) vaccines against new variants, (iv) vaccine hesitancy in the light of the evolving disease, (v) treatment strategies, (vi) hospital preparedness for changing clinical needs, (vii) global cooperation and data sharing, (viii) economic implications, and (ix) education and awareness- keeping communities informed.

EXPERT OPINION

The COVID-19 crisis forced unprecedented adaptation, emphasizing public health readiness, global unity, and scientific advancement. Key lessons highlight the importance of adaptability and resilience against uncertainties. As the pandemic evolves into a 'new normal,' ongoing vigilance, improved understanding, and available vaccines and treatments equip us for future challenges. Priorities now include proactive pandemic strategies, early warnings, supported healthcare, public education, and addressing societal disparities for better health resilience and sustainability.

A high-throughput DNA analysis method based on isothermal amplification on a suspension microarray for detecting mpox virus and viruses with comparable symptoms

BACKGROUND

Mpox is a zoonotic disease caused by mpox virus (MPXV) infection. Since May 2022, there has been a marked increase in human mpox cases in different regions. Rash, fever, and sore throat are typical signs of mpox. However, other viruses, such as the B virus (BV), herpes simplex virus types 1 (HSV-1), herpes simplex virus types 2 (HSV-2), and varicella zoster virus (VZV), can also infect people and cause comparable symptoms. Therefore, clinical symptoms and signs alone make distinguishing MPXV from these viruses difficult.

RESULTS

In this study, we combined suspension microarray technology with recombinase-aided amplification technology (RAA) to establish a high-throughput, sensitive, and quantitative method for detecting MPXV and other viruses that can cause similar symptoms. The experimental results confirmed that the technique has outstanding sensitivity, with a minimum detection limit (LOD) of 0.1 fM and a linear range of 0.3 fM to 20 pM, spanning five orders of magnitude. The approach also exhibits exquisite selectivity, as the amplified signal can only be detected when the target virus nucleic acid is present. Additionally, serum recoveries ranging from 80.52% to 119.09% suggest that the detection outcomes are generally considered reliable. Moreover, the time required for detection using this high-throughput method is very short. After DNA extraction, the detection signal amplified by isothermal amplification on the bead array can be obtained in just 1 h.

SIGNIFICANCE AND NOVELTY

Our research introduces a new technique that utilizes suspension microarray technology and isothermal amplification to create a high-throughput nucleic acid assay. This innovative method offers multiple benefits compared to current techniques, such as being cost-effective, time-efficient, highly sensitive, and having high throughput capabilities. Furthermore, the assay is applicable not only for detecting MPXV and viruses with similar symptoms, but also for clinical diagnostics, food safety, and environmental monitoring, rendering it an effective tool for screening harmful microorganisms.

AIEgens-enhanced rapid sensitive immunofluorescent assay for SARS-CoV-2 with digital microfluidics

BACKGROUND

Sensitive and rapid antigen detection is critical for the diagnosis and treatment of infectious diseases, but conventional ELISAs including chemiluminescence-based assays are limited in sensitivity and require many operation steps. Fluorescence immunoassays are fast and convenient but often show limited sensitivity and dynamic range.

RESULTS

To address the need, an aggregation-induced emission fluorgens (AIEgens) enhanced immunofluorescent assay with beads-based quantification on the digital microfluidic (DMF) platform was developed. Portable DMF devices and chips with small electrodes were fabricated, capable of manipulating droplets within 100 nL and boosting the reaction efficiency. AIEgen nanoparticles (NPs) with high fluorescence and photostability were synthesized to enhance the test sensitivity and detection range. The integration of AIEgen probes, transparent DMF chip design, and the large magnetic beads (10 μm) as capture agents enabled rapid and direct image-taking and signal calculation of the test result. The performance of this platform was demonstrated by point-of-care quantification of SARS-CoV-2 nucleocapsid (N) protein. Within 25 min, a limit of detection of 5.08 pg mL-1 and a limit of quantification of 8.91 pg mL-1 can be achieved using <1 μL sample. The system showed high reproducibility across the wide dynamic range (10-105 pg mL-1), with the coefficient of variance ranging from 2.6% to 9.8%.

SIGNIFICANCE

This rapid, sensitive AIEgens-enhanced immunofluorescent assay on the DMF platform showed simplified reaction steps and improved performance, providing insight into the small-volume point-of-care testing of different biomarkers in research and clinical applications.

Evaluating the Demand for Nucleic Acid Testing in Different Scenarios of COVID-19 Transmission: A Simulation Study

INTRODUCTION

The 2019 novel coronavirus (COVID-19) has been recognized as the most severe human infectious disease pandemic in the past century. To enhance our ability to control potential infectious diseases in the future, this study simulated the influence of nucleic acid testing on the transmission of COVID-19 across varied scenarios. Additionally, it assessed the demand for nucleic acid testing under different circumstances, aiming to furnish a decision-making foundation for the implementation of nucleic acid screening measures, the provision of emergency materials, and the allocation of human resources.

METHODS

Considering the transmission dynamics of COVID-19 and the preventive measures implemented by countries, we explored three distinct levels of epidemic intensity: community transmission, outbreak, and sporadic cases. Integrating the theory of scenario analysis, we formulated six hypothetical epidemic scenarios, each corresponding to possible occurrences during different phases of the pandemic. We developed an improved SEIR model, validated its accuracy using real-world data, and conducted a comprehensive analysis and prediction of COVID-19 infections under these six scenarios. Simultaneously, we assessed the testing resource requirements associated with each scenario.

RESULTS

We compared the predicted number of infections simulated by the modified SEIR model with the actual reported cases in Israel to validate the model. The root mean square error (RMSE) was 350.09, and the R-squared (R2) was 0.99, indicating a well-fitted model. Scenario 4 demonstrated the most effective prevention and control outcomes. Strengthening non-pharmaceutical interventions and increasing nucleic acid testing frequency, even under low testing capacity, resulted in a delayed epidemic peak by 78 days. The proportion of undetected cases decreased from 77.83% to 31.21%, and the overall testing demand significantly decreased, meeting maximum demand even with low testing capacity. The initiation of testing influenced case detection probability. Under high testing capacity, increasing testing frequency elevated the detection rate from 36.40% to 77.83%. Nucleic acid screening proved effective in reducing the demand for testing resources under diverse epidemic prevention and control strategies. While effective interventions and nucleic acid screening measures substantially diminished the demand for testing-related resources, varying degrees of insufficient testing capacity may still persist.

CONCLUSIONS

The nucleic acid detection strategy proves effective in promptly identifying and isolating infected individuals, thereby mitigating the infection peak and extending the time to peak. In situations with constrained testing capacity, implementing more stringent measures can notably decrease the number of infections and alleviate resource demands. The improved SEIR model demonstrates proficiency in predicting both reported and unreported cases, offering valuable insights for future infection risk assessments. Rapid evaluations of testing requirements across diverse scenarios can aptly address resource limitations in specific regions, offering substantial evidence for the formulation of future infectious disease testing strategies.

Improving design features and air bubble manipulation techniques for a single-step sandwich electrochemical ELISA incorporating commercial electrodes into capillary-flow driven immunoassay devices

Integrating electrochemistry into capillary-flow driven immunoassay devices provides unique opportunities for quantitative point-of-care testing. Although custom electrodes can be inexpensive and are tunable, they require skilled fabrication. Here, we report the incorporation of a commercial electrode into a capillary-flow driven immunoassay (iceCaDI) device for a single end-user step sandwich electrochemical enzyme-linked immunosorbent assay (ELISA). The iceCaDI device is a pump-free portable microfluidic device with an integrated commercial screen-printed electrode and flow driven by capillary action. The iceCaDI device is composed of alternating polyester transparency film and double-sided adhesive film layers that are patterned with a laser cutter. This platform was designed to address known limitations of laminated device fabrication methods and operation. First, we developed a foldable laminated device fabrication using hinges for easy assembly and precise alignment. Second, reagent dispersing was achieved by incorporating a 1 mm wide arrow-shaped notch in the middle of the channel that trapped an air bubble and formed a baffle that facilitated reagent spreading to cover the detection area. Third, small vent holes were added to the top layer of the channels to prevent air bubbles from blocking flow. Finally, we fabricated a CRP immunosensor with a detection range of 0.625 to 10.0 μg mL-1 as a proof-of-concept to demonstrate an automatically driven sandwich electrochemical ELISA using the iceCaDI device. Three concentrations of CRP were successfully measured under flow conditions within 8 min. Our proposed device is a promising approach and a step forward in the development of point-of-care (POC) devices for techniques that traditionally require multiple user steps.

Smart and emerging point of care electrochemical sensors based on nanomaterials for SARS-CoV-2 virus detection: Towards designing a future rapid diagnostic tool

In the recent years, researchers from all over the world have become interested in the fabrication of advanced and innovative electrochemical and/or biosensors for respiratory virus detection with the use of nanotechnology. These fabricated sensors demonstrated a number of benefits, including precision, affordability, accessibility, and miniaturization which makes them a promising test method for point-of-care (PoC) screening for SARS-CoV-2 viral infection. In order to comprehend the principles of electrochemical sensing and the role of various types of sensing interfaces, we comprehensively explored the underlying principles of electroanalytical methods and terminologies related to it in this review. In addition, it is addressed how to fabricate electrochemical sensing devices incorporating nanomaterials as graphene, metal/metal oxides, metal organic frameworks (MOFs), MXenes, quantum dots, and polymers. We took an effort to carefully compile current developments, advantages, drawbacks, possible solutions in nanomaterials based electrochemical sensors.

Advances and Challenges in SARS-CoV-2 Detection: A Review of Molecular and Serological Technologies

The urgent need for accurate COVID-19 diagnostics has led to the development of various SARS-CoV-2 detection technologies. Real-time reverse transcriptase polymerase chain reaction (RT-qPCR) remains a reliable viral gene detection technique, while other molecular methods, including nucleic acid amplification techniques (NAATs) and isothermal amplification techniques, provide diverse and effective approaches. Serological assays, detecting antibodies in response to viral infection, are crucial for disease surveillance. Saliva-based immunoassays show promise for surveillance purposes. The efficiency of SARS-CoV-2 antibody detection varies, with IgM indicating recent exposure and IgG offering prolonged detectability. Various rapid tests, including lateral-flow immunoassays, present opportunities for quick diagnosis, but their clinical significance requires validation through further studies. Challenges include variations in specificity and sensitivity among testing platforms and evolving assay sensitivities over time. SARS-CoV-2 antigens, particularly the N and S proteins, play a crucial role in diagnostic methods. Innovative approaches, such as nanozyme-based assays and specific nucleotide aptamers, offer enhanced sensitivity and flexibility. In conclusion, ongoing advancements in SARS-CoV-2 detection methods contribute to the global effort in combating the COVID-19 pandemic.

Analytical and clinical evaluations of SNIBE Maglumi chemiluminescent immunoassay for the detection of SARS-CoV-2 antigen in salivary samples

OBJECTIVES

In this study, we describe the analytical and clinical performances of the SNIBE Maglumi SARS-CoV-2 antigen fully-automated chemiluminescent immunoassay (MAG-CLIA) on salivary samples.

METHODS

Limit of detection (LOD), linearity and precision were tested for values close to or below the declared LOD. Clinical performance of MAG-CLIA was evaluated on leftover salivary samples from the healthcare workers (HCW) surveillance program, at the University-Hospital of Padova. Salivary samples were analyzed by Lumipulse G SARS-CoV-2 Ag, and in case where the values exceeded 0.41 ng/L, further testing was conducted using TaqPathTM COVID-19 RT-PCR (Applied Biosystems, Thermo Fisher Scientific).

RESULTS

The estimated MAG-CLIA LOD was 3 ng/L, with repeatability of 7.5 %. Good linearity was demonstrated by diluting two samples at 52.7 ng/L and 211.4 ng/L. Of the 228 HCW samples, 59/228 (25.9 %) were positive, 169/228 (74.1 %) were negative. MAG-CLIA SARS-CoV-2 sAg median level (and interquartile range [IQR]) was 5.03 ng/L (<0.001-35.8 ng/L) for positive and <0.001 ng/L (<0.001 ng/L) for negative samples. MAG-CLIA AUC was 0.795 (95 % CI: 0.720-0.871). Using the best cut-off, 3.5 ng/L, sensitivity and specificity were 57.1 % (95 % CI: 42.2-71.2 %) and 97.0 % (95 % CI: 93.2-99.0 %), respectively. The agreement with the molecular assay was 88.1 % (Cohen's kappa 0.606 [SE=0.066, p<0.001]).

CONCLUSIONS

The analytical performances of MAG-CLIA are satisfactory, also when values below LOD were tested. In saliva samples, although specificity was elevated, clinical performance was not comparable with that on nasopharyngeal swabs (NPS).

Unraveling the Dynamics of SARS-CoV-2 Mutations: Insights from Surface Plasmon Resonance Biosensor Kinetics

Surface Plasmon Resonance (SPR) technology is known to be a powerful tool for studying biomolecular interactions because it offers real-time and label-free multiparameter analysis with high sensitivity. This article summarizes the results that have been obtained from the use of SPR technology in studying the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations. This paper will begin by introducing the working principle of SPR and the kinetic parameters of the sensorgram, which include the association rate constant (ka), dissociation rate constant (kd), equilibrium association constant (KA), and equilibrium dissociation constant (KD). At the end of the paper, we will summarize the kinetic data on the interaction between angiotensin-converting enzyme 2 (ACE2) and SARS-CoV-2 obtained from the results of SPR signal analysis. ACE2 is a material that mediates virus entry. Therefore, understanding the kinetic changes between ACE2 and SARS-CoV-2 caused by the mutation will provide beneficial information for drug discovery, vaccine development, and other therapeutic purposes.

Access to and utilization of COVID-19 antigen rapid diagnostic tests (Ag-RDTs) among people living with HIV (PLWH): A mixed methods study from Cambodia

Several COVID-19 antigen rapid diagnostic tests have been approved in Cambodia, but no evidence exists about the access to and utilization of these tests. This limits public health interventions to increase testing, especially among vulnerable populations such as people living with HIV (PLWH). We conducted a mixed method study among PLWH in Phnom Penh, Cambodia, between July and August 2022 to understand their current Ag-RDT access and utilization levels, as well as key barriers and drivers. We undertook a cross-sectional survey and focus group discussions among 280 and 10 PLWH, respectively, from five HIV treatment centres using a probability-proportional-to-size and simple random sampling approach. Access was defined as having received a COVID-19 Ag-RDT within the six months and utilization as having administered a COVID-19 Ag-RDT, either to oneself or to others, within the 12 months prior to the study. We calculated means, standard deviations and proportions for continuous and categorical variables, using a linear regression model with random effects to account for clustering. Additionally, we fitted a logistic model with random effects to assess factors associated with Ag-RDT access. For the qualitative data, we used thematic analyses to identify barriers/enablers of Ag-RDT access and utilization. About 35% (n = 101) of PLWH reported having had access to an Ag-RDT test in the past six months. About 11% (n = 32) of the study participants administered the Ag-RDT to themselves, 4% (n = 10) to others and 9% (n = 24) have done both, in the past 12 months. Age and education appeared to be associated with Ag-RDT access in the logistic models. Price and advice from pharmacists were commonly reported to be the main selection criteria for the brand of Ag-RDT chosen. Ag-RDTs are an important diagnostic tool for COVID-19 among PLWH in Cambodia, but familiarity of use and price could hinder better uptake, access and utilization.

Long COVID Symptoms vs. Back Pain and Physical Activity among Students in Poland-Cross-Sectional Study

BACKGROUND

Back pain (BP) is a common condition that affects people of all ages. Moderate- and vigorous-intensity physical activity (PA) is a key element in maintaining health. The purpose of this research was to determine the level of physical activity and back pain (BP) in students with long COVID symptoms and to determine the relationship between the level of PA and BP in students with and without long COVID.

METHODS

A survey was carried out among 402 students from Poland. The inclusion criteria were as follows: student status, age of over 18 years, history of COVID-19, and consent to participate in the study. The International Physical Activity Questionnaire (IPAQ) was used to determine the level of PA. The Oswestry Disability Index (ODI) and the Neck Disability Index (NDI) were used to assess BP.

RESULTS

We found that at least half of the students surveyed did not experience any lumbosacral or cervical spine pain. The authors found no association between the level of PA in women and a history of long COVID symptoms, while there were statistically significant differences in intense PA in men (p = 0.0263), with those who did not report long COVID symptoms being more active. With regard to cervical and lumbar spine pain complaints, in our study, these were statistically significantly stronger in students who were observed to have long COVID symptoms. The difference was not significant only for lumbosacral complaints among men. No strong correlations were found between PA level and the severity of BP.

CONCLUSION

Additional investigation is required to comprehend the complex interaction between long COVID symptoms and levels of PA and BP. Special attention should be paid to the prevention of back pain mainly in the COVID-19 group of students.

Pathogen Discovery in the Post-COVID Era

Pathogen discovery plays a crucial role in the fields of infectious diseases, clinical microbiology, and public health. During the past four years, the global response to the COVID-19 pandemic highlighted the importance of early and accurate identification of novel pathogens for effective management and prevention of outbreaks. The post-COVID era has ushered in a new phase of infectious disease research, marked by accelerated advancements in pathogen discovery. This review encapsulates the recent innovations and paradigm shifts that have reshaped the landscape of pathogen discovery in response to the COVID-19 pandemic. Primarily, we summarize the latest technology innovations, applications, and causation proving strategies that enable rapid and accurate pathogen discovery for both acute and historical infections. We also explored the significance and the latest trends and approaches being employed for effective implementation of pathogen discovery from various clinical and environmental samples. Furthermore, we emphasize the collaborative nature of the pandemic response, which has led to the establishment of global networks for pathogen discovery.

Development of automated microfluidic immunoassays for the detection of SARS-CoV-2 antibodies and antigen

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19) global pandemic. Rapid and sensitive detection of the virus soon after infection is important for the treatment and prevention of transmission of COVID-19, and detection of antibodies is important for epidemiology, assessment of vaccine immunogenicity, and identification of the natural reservoir and intermediate host(s). Patient nasal or oropharyngeal swabs or saliva used in conjunction with polymerase chain reaction (PCR) detect SARS-CoV-2 RNA, whereas lateral flow immunoassays (LFI) detect SARS-CoV-2 proteins. Enzyme-linked immunosorbent assays (ELISA) detect anti-SARS-CoV-2 antibodies in blood. Although effective, these assays have poor sensitivity (e.g., LFI) or are labor intensive and time consuming (PCR and ELISA). Here we describe the development of rapid, automated ELISA-based immunoassays to detect SARS-CoV-2 antigens and antibodies against the virus. The Simple Plex™ platform uses rapid microfluidic reaction kinetics for sensitive analyte detection with small sample volumes. We developed three sensitive <90-min Simple Plex immunoassays that measure either the SARS-CoV-2 antigens or the immune response to SARS-CoV-2, including neutralizing antibodies, in serum from COVID-19 patients.

Recent advances in point-of-care testing of COVID-19

Advances in microfluidic device miniaturization and system integration contribute to the development of portable, handheld, and smartphone-compatible devices. These advancements in diagnostics have the potential to revolutionize the approach to detect and respond to future pandemics. Accordingly, herein, recent advances in point-of-care testing (POCT) of coronavirus disease 2019 (COVID-19) using various microdevices, including lateral flow assay strips, vertical flow assay strips, microfluidic channels, and paper-based microfluidic devices, are reviewed. However, visual determination of the diagnostic results using only microdevices leads to many false-negative results due to the limited detection sensitivities of these devices. Several POCT systems comprising microdevices integrated with portable optical readers have been developed to address this issue. Since the outbreak of COVID-19, effective POCT strategies for COVID-19 based on optical detection methods have been established. They can be categorized into fluorescence, surface-enhanced Raman scattering, surface plasmon resonance spectroscopy, and wearable sensing. We introduced next-generation pandemic sensing methods incorporating artificial intelligence that can be used to meet global health needs in the future. Additionally, we have discussed appropriate responses of various testing devices to emerging infectious diseases and prospective preventive measures for the post-pandemic era. We believe that this review will be helpful for preparing for future infectious disease outbreaks.

Geographical and practical challenges in the implementation of digital health passports for cross-border COVID-19 pandemic management: a narrative review and framework for solutions

The rapid global spread of infectious diseases, epitomized by the recent COVID-19 pandemic, has highlighted the critical need for effective cross-border pandemic management strategies. Digital health passports (DHPs), which securely store and facilitate the sharing of critical health information, including vaccination records and test results, have emerged as a promising solution to enable safe travel and access to essential services and economic activities during pandemics. However, the implementation of DHPs faces several significant challenges, both related to geographical disparities and practical considerations, necessitating a comprehensive approach for successful global adoption. In this narrative review article, we identify and elaborate on the critical geographical and practical barriers that hinder global adoption and the effective utilization of DHPs. Geographical barriers are complex, encompassing disparities in vaccine access, regulatory inconsistencies, differences across countries in data security and users' privacy policies, challenges related to interoperability and standardization, and inadequacies in technological infrastructure and limited access to digital technologies. Practical challenges include the possibility of vaccine contraindications and breakthrough infections, uncertainties surrounding natural immunity, and limitations of standard tests in assessing infection risk. To address geographical disparities and enhance the functionality and interoperability of DHPs, we propose a framework that emphasizes international collaboration to achieve equitable access to vaccines and testing resources. Furthermore, we recommend international cooperation to establish unified vaccine regulatory frameworks, adopting globally accepted standards for data privacy and protection, implementing interoperability protocols, and taking steps to bridge the digital divide. Addressing practical challenges requires a meticulous approach to assessing individual risk and augmenting DHP implementation with rigorous health screenings and personal infection prevention measures. Collectively, these initiatives contribute to the development of robust and inclusive cross-border pandemic management strategies, ultimately promoting a safer and more interconnected global community in the face of current and future pandemics.

The Label-Free Detection and Identification of SARS-CoV-2 Using Surface-Enhanced Raman Spectroscopy and Principal Component Analysis

The World Health Organization (WHO) declared in a May 2023 announcement that the COVID-19 illness is no longer categorized as a Public Health Emergency of International Concern (PHEIC); nevertheless, it is still considered an actual threat to world health, social welfare and economic stability. Consequently, the development of a convenient, reliable and affordable approach for detecting and identifying SARS-CoV-2 and its emerging new variants is crucial. The fingerprint and signal amplification characteristics of surface-enhanced Raman spectroscopy (SERS) could serve as an assay scheme for SARS-CoV-2. Here, we report a machine learning-based label-free SERS technique for the rapid and accurate detection and identification of SARS-CoV-2. The SERS spectra collected from samples of four types of coronaviruses on gold nanoparticles film, fabricated using a Langmuir-Blodgett self-assembly, can provide more spectroscopic signatures of the viruses and exhibit low limits of detection (<100 TCID50/mL or even <10 TCID50/mL). Furthermore, the key Raman bands of the SERS spectra were systematically captured by principal component analysis (PCA), which effectively distinguished SARS-CoV-2 and its variant from other coronaviruses. These results demonstrate that the combined use of SERS technology and PCA analysis has great potential for the rapid analysis and discrimination of multiple viruses and even newly emerging viruses without the need for a virus-specific probe.

Duplex Electrochemical Microfluidic Sensor for COVID-19 Antibody Detection: Natural versus Vaccine-Induced Humoral Response

The rapid transmission and resilience of coronavirus disease 2019 (COVID-19) have led to urgent demands in monitoring humoral response for effective vaccine development, thus a multiplex co-detection platform to discriminate infection-induced from vaccine-induced antibodies is needed. Here a duplex electrochemical immunosensor for co-detection of anti-nucleocapsid IgG (N-IgG) and anti-spike IgG (S-IgG) is developed by using a two-working electrode system, via an indirect immunoassay, with antibody quantification obtained by differential pulse voltammetry. The screen-printed electrodes (SPEs) are modified by carbon black and electrodeposited gold nanoflowers for maximized surface areas, enabling the construction of an immunological chain for S-IgG and N-IgG electrochemical detection with enhanced performance. Using an optimized immunoassay protocol, a wide linear range between 30-750 and 20-1000 ng mL-1 , and a limit of detection of 28 and 15 ng mL-1 are achieved to detect N-IgG and S-IgG simultaneously in serum samples. This duplex immunosensor is then integrated in a microfluidic device to obtain significantly reduced detection time (≤ 7 min) while maintaining its analytical performance. The duplex microfluidic immunosensor can be easily expanded into multiplex format to achieve high throughput screening for the sero-surveillance of COVID-19  and other infectious diseases.

Pneumococcal Vaccine Breakthrough and Failure in Infants and Children: A Narrative Review

Globally, Streptococcus pneumoniae is a leading cause of vaccine-preventable morbidity and mortality in infants and children. In recent decades, large-scale pediatric immunization programs have substantially reduced the incidence of invasive pneumococcal disease. Despite this, residual vaccine-type pneumococcal disease remains in the form of vaccine breakthrough and vaccine failure. This targeted literature review aims to discuss aspects of vaccine breakthrough and failure in infants and children, including disease epidemiology, clinical presentation, risk factors, vaccination schedules, vaccine serotypes, correlates of protection, comorbidities, disease surveillance, and potential implications for future vaccine development.

High prevalence group testing in epidemiology with geometrically inspired algorithms

Demand for mass surveillance during peak times of the SARS-CoV-2 pandemic caused high workload for clinical laboratories. Efficient and cost conserving testing designs by means of group testing can substantially reduce resources during possible future emergency situations. The novel hypercube algorithm proposed by Mutesa et al. 2021 published in Nature provides methodological proof of concept and points out the applicability to epidemiological testing. In this work, the algorithm is explored and expanded for settings with high group prevalence. Numerical studies investigate the limits of the adapted hypercube methodology, allowing to optimize pooling designs for specific requirements (i.e. number of samples and group prevalence). Hyperparameter optimization is performed to maximize test-reduction. Standard deviation is examined to investigate resilience and precision. Moreover, empirical validation was performed by elaborately pooling SARS-CoV-2 virus samples according to numerically optimized pooling designs. Laboratory experiments with SARS-CoV-2 sample groups, ranging from 50 to 200 items, characterized by group prevalence up to 10%, are successfully processed and analysed. Test-reductions from 50 to 72.5% were achieved in the experimental setups when compared to individual testing. Higher theoretical test-reduction is possible, depending on the number of samples and the group prevalence, indicated by simulation results.

A single-molecule RNA electrical biosensor for COVID-19

The COVID-19 pandemic shows a critical need for rapid, inexpensive, and ultrasensitive early detection methods based on biomarker analysis to reduce mortality rates by containing the spread of epidemics. This can be achieved through the electrical detection of nucleic acids at the single-molecule level. In particular, the scanning tunneling microscopic-assisted break junction (STM-BJ) method can be utilized to detect individual nucleic acid molecules with high specificity and sensitivity in liquid samples. Here, we demonstrate single-molecule electrical detection of RNA coronavirus biomarkers, including those of SARS-CoV-2 as well as those of different variants and subvariants. Our target sequences include a conserved sequence in the human coronavirus family, a conserved target specific for the SARS-CoV-2 family, and specific targets at the variant and subvariant levels. Our results demonstrate that it is possible to distinguish between different variants of the COVID-19 virus using electrical conductance signals, as recently suggested by theoretical approaches. Our results pave the way for future miniaturized single-molecule electrical biosensors that could be game changers for infectious diseases and other public health applications.

Screening COVID-19 by Swaasa AI platform using cough sounds: a cross-sectional study

The Advent of Artificial Intelligence (AI) has led to the use of auditory data for detecting various diseases, including COVID-19. SARS-CoV-2 infection has claimed more than six million lives to date and therefore, needs a robust screening technique to control the disease spread. In the present study we created and validated the Swaasa AI platform, which uses the signature cough sound and symptoms presented by patients to screen and prioritize COVID-19 patients. We collected cough data from 234 COVID-19 suspects to validate our Convolutional Neural Network (CNN) architecture and Feedforward Artificial Neural Network (FFANN) (tabular features) based algorithm. The final output from both models was combined to predict the likelihood of having the disease. During the clinical validation phase, our model showed a 75.54% accuracy rate in detecting the likely presence of COVID-19, with 95.45% sensitivity and 73.46% specificity. We conducted pilot testing on 183 presumptive COVID subjects, of which 58 were truly COVID-19 positive, resulting in a Positive Predictive Value of 70.73%. Due to the high cost and technical expertise required for currently available rapid screening methods, there is a need for a cost-effective and remote monitoring tool that can serve as a preliminary screening method for potential COVID-19 subjects. Therefore, Swaasa would be highly beneficial in detecting the disease and could have a significant impact in reducing its spread.

Effectiveness of testing, contact tracing and isolation interventions among the general population on reducing transmission of SARS-CoV-2: a systematic review

We conducted a systematic literature review of general population testing, contact tracing, case isolation and contact quarantine interventions to assess their effectiveness in reducing SARS-CoV-2 transmission, as implemented in real-world settings. We designed a broad search strategy and aimed to identify peer-reviewed studies of any design provided there was a quantitative measure of effectiveness on a transmission outcome. Studies that assessed the effect of testing or diagnosis on disease outcomes via treatment, but did not assess a transmission outcome, were not included. We focused on interventions implemented among the general population rather than in specific settings; these were from anywhere in the world and published any time after 1 January 2020 until the end of 2022. From 26 720 titles and abstracts, 1181 were reviewed as full text, and 25 met our inclusion criteria. These 25 studies included one randomized control trial (RCT) and the remaining 24 analysed empirical data and made some attempt to control for confounding. Studies included were categorized by the type of intervention: contact tracing (seven studies); specific testing strategies (12 studies); strategies for isolating cases/contacts (four studies); and 'test, trace, isolate' (TTI) as a part of a package of interventions (two studies). None of the 25 studies were rated at low risk of bias and many were rated as serious risk of bias, particularly due to the likely presence of uncontrolled confounding factors, which was a major challenge in assessing the independent effects of TTI in observational studies. These confounding factors are to be expected from observational studies during an on-going pandemic, when the emphasis was on reducing the epidemic burden rather than trial design. Findings from these 25 studies suggested an important public health role for testing followed by isolation, especially where mass and serial testing was used to reduce transmission. Some of the most compelling analyses came from examining fine-grained within-country data on contact tracing; while broader studies which compared behaviour between countries also often found TTI led to reduced transmission and mortality, this was not universal. There was limited evidence for the benefit of isolation of cases/contacts away from the home environment. One study, an RCT, showed that daily testing of contacts could be a viable strategy to replace lengthy quarantine of contacts. Based on the scarcity of robust empirical evidence, we were not able to draw any firm quantitative conclusions about the quantitative impact of TTI interventions in different epidemic contexts. While the majority of studies found that testing, tracing and isolation reduced transmission, evidence for the scale of this impact is only available for specific scenarios and hence is not necessarily generalizable. Our review therefore emphasizes the need to conduct robust experimental studies that help inform the likely quantitative impact of different TTI interventions on transmission and their optimal design. Work is needed to support such studies in the context of future emerging epidemics, along with assessments of the cost-effectiveness of TTI interventions, which was beyond the scope of this review but will be critical to decision-making. This article is part of the theme issue 'The effectiveness of non-pharmaceutical interventions on the COVID-19 pandemic: the evidence'.

Emergent Molecular Techniques Applied to the Detection of Porcine Viruses

Molecular diagnostic tests have evolved very rapidly in the field of human health, especially with the arrival of the recent pandemic caused by the SARS-CoV-2 virus. However, the animal sector is constantly neglected, even though accurate detection by molecular tools could represent economic advantages by preventing the spread of viruses. In this regard, the swine industry is of great interest. The main viruses that affect the swine industry are described in this review, including African swine fever virus (ASFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV), and porcine circovirus (PCV), which have been effectively detected by different molecular tools in recent times. Here, we describe the rationale of molecular techniques such as multiplex PCR, isothermal methods (LAMP, NASBA, RPA, and PSR) and novel methods such as CRISPR-Cas and microfluidics platforms. Successful molecular diagnostic developments are presented by highlighting their most important findings. Finally, we describe the barriers that hinder the large-scale development of affordable, accessible, rapid, and easy-to-use molecular diagnostic tests. The evolution of diagnostic techniques is critical to prevent the spread of viruses and the development of viral reservoirs in the swine industry that impact the possible development of future pandemics and the world economy.

Improved protocol for Bst polymerase and reverse transcriptase production and application to a point-of-care diagnostics system

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised awareness in the scientific community about the importance of being prepared for sanitary emergencies. Many measures implemented during the COVID pandemic are now being expanded to other applications. In the field of molecular and immunological diagnostics, the need to massively test the population worldwide resulted in the application of a variety of methods to detect viral infection. Besides gold standard reverse transcription quantitative polymerase chain reaction (RT-qPCR), the use of reverse transcription loop-mediated isothermal amplification (RT-LAMP) arose as an alternative and sensitive method to amplify and detect viral genetic material. We have used openly available protocols and have improved the protein production of RT-LAMP enzymes Bst polymerase and HIV-reverse transcriptase. To optimize enzyme production, we tested different protein tags, and we shortened the protein purification protocol, resulting in reduced processing time and handling of the enzymes and, thus, preserved the protein activity with high purity. The enzymes showed significant stability at 4 °C and 25 °C, over 60 days, and were highly reliable when used as a one-step RT-LAMP reaction in a portable point-of-care device with clinical samples. The enzymes and the reaction setup can be further expanded to detect other infectious diseases agents.

A microfluidic biosensor architecture for the rapid detection of COVID-19

The lack of enough diagnostic capacity to detect severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) has been one of the major challenges in the control the 2019 COVID pandemic; this led to significant delay in prompt treatment of COVID-19 patients or accurately estimate disease situation. Current methods for the diagnosis of SARS-COV-2 infection on clinical specimens (e.g. nasal swabs) include polymerase chain reaction (PCR) based methods, such as real-time reverse transcription (rRT) PCR, real-time reverse transcription loop-mediated isothermal amplification (rRT-LAMP), and immunoassay based methods, such as rapid antigen test (RAT). These conventional PCR methods excel in sensitivity and specificity but require a laboratory setting and typically take up to 6 h to obtain the results whereas RAT has a low sensitivity (typically at least 3000 TCID50/ml) although with the results with 15 min. We have developed a robust micro-electro-mechanical system (MEMS) based impedance biosensor fit for rapid and accurate detection of SARS-COV-2 of clinical samples in the field with minimal training. The biosensor consisted of three regions that enabled concentrating, trapping, and sensing the virus present in low quantities with high selectivity and sensitivity in 40 min using an electrode coated with a specific SARS-COV-2 antibody cross-linker mixture. Changes in the impedance value due to the binding of the SARS-COV-2 antigen to the antibody will indicate positive or negative result. The testing results showed that the biosensor's limit of detection (LoD) for detection of inactivated SARS-COV-2 antigen in phosphate buffer saline (PBS) was as low as 50 TCID50/ml. The biosensor specificity was confirmed using the influenza virus while the selectivity was confirmed using influenza polyclonal sera. Overall, the results showed that the biosensor is able to detect SARS-COV-2 in clinical samples (swabs) in 40 min with a sensitivity of 26 TCID50/ml.

Development and Analytical Evaluation of a Point-of-Care Electrochemical Biosensor for Rapid and Accurate SARS-CoV-2 Detection

The COVID-19 pandemic has underscored the critical need for rapid and accurate screening and diagnostic methods for potential respiratory viruses. Existing COVID-19 diagnostic approaches face limitations either in terms of turnaround time or accuracy. In this study, we present an electrochemical biosensor that offers nearly instantaneous and precise SARS-CoV-2 detection, suitable for point-of-care and environmental monitoring applications. The biosensor employs a stapled hACE-2 N-terminal alpha helix peptide to functionalize an in situ grown polypyrrole conductive polymer on a nitrocellulose membrane backbone through a chemical process. We assessed the biosensor's analytical performance using heat-inactivated omicron and delta variants of the SARS-CoV-2 virus in artificial saliva (AS) and nasal swab (NS) samples diluted in a strong ionic solution, as well as clinical specimens with known Ct values. Virus identification was achieved through electrochemical impedance spectroscopy (EIS) and frequency analyses. The assay demonstrated a limit of detection (LoD) of 40 TCID50/mL, with 95% sensitivity and 100% specificity. Notably, the biosensor exhibited no cross-reactivity when tested against the influenza virus. The entire testing process using the biosensor takes less than a minute. In summary, our biosensor exhibits promising potential in the battle against pandemic respiratory viruses, offering a platform for the development of rapid, compact, portable, and point-of-care devices capable of multiplexing various viruses. The biosensor has the capacity to significantly bolster our readiness and response to future viral outbreaks.

Cost-effectiveness analysis of COVID-19 tests in the unified health system

BACKGROUND

To evaluate the cost-effectiveness ratio and economic impact of the Rapid Antigen Test (TR-Ag) to replace RT-PCR for the detection of the new Coronavirus in the Unified Health System (SUS).

METHODS

This is a cost-effectiveness analysis. Clinical protocols were used for the diagnosis of COVID-19 at the São José Municipal Hospital, located in the city of Itaberá-SP. The Incremental Cost-Effectiveness Ratio (ICER) was divided into two scenarios. In the first, the accuracy reported by the test manufacturers was included, and in the second, the cost resulting from a systematic review. Both were compared with the performance of the RT-PCR test. The increase in diagnoses was chosen as a health outcome and absenteeism was used as a criterion for assessing the economic impact.

RESULTS

The analysis resulted in incremental cost-effectiveness ratios of R$ 42,136.67 and R$ 68,329.73 for every thousand tests, according to the accuracy of the manufacturers' TR-Ag tests and what is reported in the literature in relation to RT-PCR, respectively. The average value found for the RT-PCR test (R$ 202.87) represents an increase of 165.32% in cost in relation to the value found for the TR-Ag. 4,305 tests were performed between April 2020 and December 2021 at the referral hospital. Also, maintaining the use of RT-PCR as the first choice for diagnosing COVID-19 and regulating absenteeism in the economically active population could have an impact of up to R$ 1,022,779.68 on municipal management.

CONCLUSION

It is concluded that the TR-Ag are configured as a cost-effective alternative for the SUS in the detection of the new Coronavirus. The strategy becomes economically favorable for the expansion of testing, combating the COVID-19 pandemic and reducing the impact on the local economy. However, studies are needed to validate the accuracy of the tests so that economic evaluations on the subject are more assertive.

Seroprevalence of SARS-CoV-2 antibodies in Republic of Congo, February 2022

In resource-limited countries, the lack of widespread screening masks the true situation of COVID-19. We conducted this study to assess SARS-CoV-2 spread by detection of specific antibodies and to determine associated factors. A population-based cross-sectional study was conducted. Subjects were tested for the presence of two antibodies (IgM and IgG) specific to SARS-CoV-2. Data collection was done using a smartphone with the KoboCollect application. Prevalence of antibodies was estimated with 95% confidence intervals. Logistic regression was used to determine factors associated with positive serological test. A total of 9,094 persons were tested in 4,340 households. The mean age was 30.18 ± 18.65 years, 46.5% male. The overall seroprevalence (prevalence, 95% CI) of SARS-CoV-2 antibodies was (48.2% [47.2%-49.2%]). Being vaccinated, having been in contact with a COVID-19 patient, being older than 50 years, living in a union, having secondary education and having tertiary education were factors independently associated with the likelihood of having anti-sars-CoV-2. We estimate in February 2022 that 48% persons had antibodies against the COVID-19 virus, more among those vaccinated. Vaccination intensification in low prevalence departments will reduce the risk of new outbreaks.

COVID-19 and Laboratory Markers from Romanian Patients-A Narrative Review

COVID-19 has significantly impacted the whole world, and Romania was no exception. Biomarkers play a crucial role in understanding and managing the disease. However, research regarding laboratory analyses for patients with COVID-19 is fairly limited. For detection, PCR testing is still considered the golden standard, while antibodies are still useful for monitoring both patients and their vaccination status. In our country, biomarkers such as CRP, LDH, transaminases, cardiac, and iron markers have been used to assess the status of patients and even predict illness outcome. CRP, IL-6, LDH, FER, fibrinogen, creatinine, and vitamin D levels have been associated with increased severity, risk of ICU admission, and death. Cardiac markers and D-dimers are also good predictors, but their role seems more important in patients with complications. HDL cholesterol and BUN levels were also suggested as potential biomarkers. Hematological issues in SARS-CoV-2 infections include neutrophilia, lymphopenia and their ratio, while PCT, which is a marker of bacterial infections, is better to be used in patients with co- or supra-infections. The current research is a narrative review that focuses on the laboratory results of Romanian COVID-19 patients. The goal of this article is to provide an update on the research on biomarkers and other laboratory tests conducted inside the borders of Romania and identify gaps in this regard. Secondly, options for further research are discussed and encouraged.

Diagnostic Efficacy of Chest Computed Tomography with a Dual-Reviewer Approach in Patients Diagnosed with Pneumonia Secondary to Severe Acute Respiratory Syndrome Coronavirus 2

To compare the diagnostic effectiveness of chest computed tomography (CT) utilizing a single- versus a dual-reviewer approach in patients with pneumonia secondary to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we conducted a retrospective observational study of data from a cross-section of 4809 patients with probable SARS-CoV-2 from March to November 2020. All patients had a CT radiological report and reverse-transcription polymerase chain reaction (PCR) results. A dual-reviewer approach was applied to two groups while conducting a comparative examination of the data. Reviewer 1 reported 108 patients negative and 374 patients positive for coronavirus disease 2019 (COVID-19) in group A, and 266 negative and 142 positive in group B. Reviewer 2 reported 150 patients negative and 332 patients positive for COVID-19 in group A, and 277 negative and 131 positive in group B. The consensus result reported 87 patients negative and 395 positive for COVID-19 in group A and 274 negative and 134 positive in group B. These findings suggest that a dual-reviewer approach improves chest CT diagnosis compared to a conventional single-reviewer approach.

Evaluation of Rapid Multiplex Reverse Transcription-Quantitative Polymerase Chain Reaction Assays for SARS-CoV-2 Detection in Individual and Pooled Samples

Although coronavirus disease 2019 (COVID-19) is no longer a Public Health Emergency of International Concern (PHEIC), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has had a vast impact to date. Hence, continuous management is required, given the uncertainty caused by the potential evolution of SARS-CoV-2. Reverse transcription-quantitative PCR (RT-qPCR) diagnosis has been fundamental in overcoming this issue. In this study, the performances of two rapid RT-qPCR assays (Real-Q Direct SARS-CoV-2 Detection Kit and Allplex™ SARS-CoV-2 fast PCR Assay) with short PCR times were comparatively evaluated using a STANDARD M nCoV Real-Time Detection Kit (STANDARD M, conventional RT-qPCR assay). All kits showed a limit of detection values (102-103 copies/reaction). The evaluation showed that the two rapid assay tests had ≥97.89% sensitivity and ≥99.51% specificity (κ = 0.98) for individual samples and ≥97.32% sensitivity and ≥97.67% specificity for pooled samples compared to STANDARD M. These results indicate that the two rapid RT-qPCR kits, which showed significant time reduction in performance, are as effective as a conventional RT-qPCR assay. They are likely to increase not only the number of tests that can be performed but also the efficiency of sustainable management of COVID-19 in the long term.

Impact of the COVID-19 Pandemic on the US healthcare system

The COVID-19 epidemic had an enormous effect on the health of millions of individuals worldwide and the global economy. A shortage of doctors, nurses, personal protective equipment, and medicines was seen globally. The pandemic drew attention to limitations in the healthcare sector of the United States of America. The massive rise in the daily number of cases, more usage of ICU facilities and all the treatment modalities, and increased overtime compensation for the staff negatively impacted the hospital’s finances. This also affected the mental and physical health of all the healthcare workers. Through additional funding from federal relief legislation and the relaxation of many regulatory requirements, the federal, state, and local governments took significant steps to address the need for prevention and treatment services that arose from COVID-19 and the disruptions in healthcare delivery and finances resulting from the pandemic. Congress enacted the Coronavirus Aid, Relief, and Economic Security Act, or CARES Act, on March 27th, 2020. This measure appropriated $2.2 trillion to offer immediate and direct economic assistance to Americans affected by the COVID-19 outbreak.

The spike protein of SARS-CoV-2 can be detected by electrochemical impedance spectroscopy using antibody desorption from iron magnetic nanoparticles

SARS-CoV-2 is a matter of concern. Here, biosensors were prepared using iron magnetic nanoparticles containing antibodies against the receptor binding domain (RBD) of the spike protein. Antibodies were adsorbed to nanoparticles in three configurations, including direct adsorption without functionalization (DANPs). Nanoparticles were added to a glassy carbon electrode and connected to an electrochemical cell. Electrochemical impedance spectroscopy and ELISA experiments indicated that antibodies were desorbed from the DANPs upon the addition of the RBD. DANPs-based biosensors produced linear curves with decreasing charge transfer resistance due to the removal of antibodies. Thus, a detection method can be based on antibody desorption.

SERS immuno- and apta-assays in biosensing/bio-detection: Performance comparison, clinical applications, challenges

Surface Enhanced Raman Spectroscopy is increasingly used as a sensitive bioanalytical tool for detection of variety of analytes ranging from viruses and bacteria to cancer biomarkers and toxins, etc. This comprehensive review describes principles of operation and compares the performance of immunoassays and aptamer assays with Surface Enhanced Raman scattering (SERS) detection to each other and to some other bioassay methods, including ELISA and fluorescence assays. Both immuno- and aptamer-based assays are categorized into assay on solid substrates, assays with magnetic nanoparticles and assays in laminar flow or/and strip assays. The best performing and recent examples of assays in each category are described in the text and illustrated in the figures. The average performance, particularly, limit of detection (LOD) for each of those methods reflected in 9 tables of the manuscript and average LODs are calculated and compared. We found out that, on average, there is some advantage in terms of LOD for SERS immunoassays (0.5 pM median LOD of 88 papers) vs SERS aptamer-based assays (1.7 pM median LOD of 51 papers). We also tabulated and analyzed the clinical performance of SERS immune and aptamer assays, where selectivity, specificity, and accuracy are reported, we summarized the best examples. We also reviewed challenges to SERS bioassay performance and real-life application, including non-specific protein binding, nanoparticle aggregation, limited nanotag stability, sometimes, relatively long time to results, etc. The proposed solutions to those challenges are also discussed in the review. Overall, this review may be interesting not only to bioanalytical chemist, but to medical and life science researchers who are interested in improvement of bioanalyte detection and diagnostics.

Diagnostic value and characteristic analysis of serum nucleocapsid antigen in COVID-19 patients

Background

To date, several types of laboratory tests for coronavirus disease 2019 (COVID-19) diagnosis have been developed. However, the clinical importance of serum severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid antigen (N-Ag) remains to be fully elucidated. In this study, we sought to investigate the value of serum SARS-CoV-2 N-Ag for COVID-19 diagnosis and to analyze N-Ag characteristics in COVID-19 individuals.

Methods

Serum samples collected from 215 COVID-19 patients and 65 non-COVID-19 individuals were used to quantitatively detect N-Ag via chemiluminescent immunoassay according to the manufacturer's instructions.

Results

The sensitivity and specificity of the N-Ag assay were 64.75% (95% confidence interval (95% CI) [55.94-72.66%]) and 100% (95% CI [93.05-100.00%]), respectively, according to the cut-off value recommended by the manufacturer. The receiver operating characteristic (ROC) curve showed a sensitivity of 100.00% (95% CI [94.42-100.00%]) and a specificity of 71.31% (95% CI [62.73-78.59%]). The positive rates and levels of serum SARS-CoV-2 N-Ag were not related to sex, comorbidity status or disease severity of COVID-19 (all P < 0.001). Compared with RT‒PCR, there was a lower positive rate of serum N-Ag for acute COVID-19 patients (P < 0.001). The positive rate and levels of serum SARS-CoV-2 N-Ag in acute patients were significantly higher than those in convalescent patients (all P < 0.001). In addition, the positive rate of serum SARS-CoV-2 N-Ag in acute COVID-19 patients was higher than that of serum antibodies (IgM, IgG, IgA and neutralizing antibodies (Nab)) against SARS-CoV-2 (all P < 0.001). However, the positive rate of serum SARS-CoV-2 N-Ag in convalescent COVID-19 patients was significantly lower than that of antibodies (all P < 0.001).

Conclusion

Serum N-Ag can be used as a biomarker for early COVID-19 diagnosis based on appropriate cut-off values. In addition, our study also demonstrated the relationship between serum N-Ag and clinical characteristics.

A review of current effective COVID-19 testing methods and quality control

COVID-19 is a highly infectious disease caused by the SARS-CoV-2 virus, which primarily affects the respiratory system and can lead to severe illness. The virus is extremely contagious, early and accurate diagnosis of SARS-CoV-2 is crucial to contain its spread, to provide prompt treatment, and to prevent complications. Currently, the reverse transcriptase polymerase chain reaction (RT-PCR) is considered to be the gold standard for detecting COVID-19 in its early stages. In addition, loop-mediated isothermal amplification (LMAP), clustering rule interval short palindromic repeats (CRISPR), colloidal gold immunochromatographic assay (GICA), computed tomography (CT), and electrochemical sensors are also common tests. However, these different methods vary greatly in terms of their detection efficiency, specificity, accuracy, sensitivity, cost, and throughput. Besides, most of the current detection methods are conducted in central hospitals and laboratories, which is a great challenge for remote and underdeveloped areas. Therefore, it is essential to review the advantages and disadvantages of different COVID-19 detection methods, as well as the technology that can enhance detection efficiency and improve detection quality in greater details.