Review of Current COVID-19 Diagnostics and Opportunities for Further Development

Population-Level SARS-CoV-2 RT-PCR Cycle Threshold Values and Their Relationships with COVID-19 Transmission and Outcome Metrics: A Time Series Analysis Across Pandemic Years

This study investigates the relationship between SARS-CoV-2 RT-PCR cycle threshold (Ct) values and key COVID-19 transmission and outcome metrics across five years of the pandemic in Jalisco, Mexico. Utilizing a comprehensive time-series analysis, we evaluated weekly median Ct values as proxies for viral load and their temporal associations with positivity rates, reproduction numbers (Rt), hospitalizations, and mortality. Cross-correlation and lagged regression analyses revealed significant lead-lag relationships, with declining Ct values consistently preceding surges in positivity rates and hospitalizations, particularly during the early phases of the pandemic. Granger causality tests and vector autoregressive modeling confirmed the predictive utility of Ct values, highlighting their potential as early warning indicators. The study further observed a weakening association in later pandemic stages, likely influenced by the emergence of new variants, hybrid immunity, changes in human behavior, and diagnostic shifts. These findings underscore the value of Ct values as scalable tools for public health surveillance and highlight the importance of contextualizing their analysis within specific epidemiological and temporal frameworks. Integrating Ct monitoring into surveillance systems could enhance pandemic preparedness, improve outbreak forecasting, and strengthen epidemiological modeling.

Epidemiology of respiratory viruses according to age group, 2023-24 winter season, Kyoto, Japan

The seasonality and epidemiology of viral acute respiratory infections (ARIs) have changed since the coronavirus disease 2019 pandemic. However, molecular-based ARI surveillance has not been conducted in Japan. We developed a regional surveillance program to define the local epidemiology of ARIs. Between December 2023 and March 2024, 2,992 upper respiratory samples collected from patients suspected of having ARIs at five facilities in Kyoto City, Japan, were tested for SARS-CoV-2, influenza virus, and respiratory syncytial virus (RSV) using RT‒PCR. Samples negative for these viruses were randomly selected for testing with the FilmArray Respiratory Panel, and the detection rates of other viruses were estimated. SARS-CoV-2, influenza virus, and RSV were detected in 598 (20.3%), 165 (5.6%), and 40 (1.4%) of the 2,949 samples with valid RT‒PCR results, respectively. The most prevalent viruses in the < 6, 6-17, 18-64, and ≥ 65 year age groups were rhinovirus/enterovirus, RSV, and SARS-CoV-2; influenza virus, seasonal coronavirus, and rhinovirus/enterovirus; SARS-CoV-2, seasonal coronavirus, and influenza virus; and SARS-CoV-2, seasonal coronavirus, and influenza virus, respectively. Significant differences in the detection rates of these viruses were detected between the age groups. This study highlights the importance of age-stratified molecular-based surveillance for a comprehensive understanding of the epidemiology of ARIs.

2D Materials-Based Field-Effect Transistor Biosensors for Healthcare

The need for accurate point-of-care (POC) tools, driven by increasing demands for precise medical diagnostics and monitoring, has accelerated the evolution of biosensor technology. Integrable 2D materials-based field-effect transistor (2D FET) biosensors offer label-free, rapid, and ultrasensitive detection, aligning perfectly with current biosensor trends. Given these advancements, this review focuses on the progress, challenges, and future prospects in the field of 2D FET biosensors. The distinctive physical properties of 2D materials and recent achievements in scalable synthesis are highlighted that significantly improve the manufacturing process and performance of FET biosensors. Additionally, the advancements of 2D FET biosensors are investigated in fatal disease diagnosis and screening, chronic disease management, and environmental hazards monitoring, as well as their integration in flexible electronics. Their promising capabilities shown in laboratory trials accelerate the development of prototype products, while the challenges are acknowledged, related to sensitivity, stability, and scalability that continue to impede the widespread adoption and commercialization of 2D FET biosensors. Finally, current strategies are discussed to overcome these challenges and envision future implications of 2D FET biosensors, such as their potential as smart and sustainable POC biosensors, thereby advancing human healthcare.

The first report on detecting SARS-CoV-2 inside bacteria of the human gut microbiome: A case series on asymptomatic family members and a child with COVID-19

Many studies report the importance of using feces as source sample for detecting SARS-CoV-2 in patients with COVID-19 symptoms but who are negative to oropharyngeal/ nasopharyngeal tests. Here, we report the case of an asymptomatic child whose family members had negative results with the rapid antigen nasopharyngeal swab tests. The 21-month-old child presented with fever, diarrhea, bilateral conjunctivitis, and conspicuous lacrimation. In this study, analysis for the presence of SARS-CoV-2 in fecal samples by using Luminex technology allowed accurate detection of the presence of the viral RNA in the feces of the child and of all her relatives, which thus resulted to be positive but asymptomatic. It is the first time that SARS-CoV-2- is observed inside the bacteria of the human gut microbiome and outside a matrix resembling extracellular bacterial lysates, in agreement with a bacteriophage mechanism with the images obtained by transmission electron microscopy (TEM), post-embedding immunogold, and by fluorescence microscope. In addition to the typical observations of respiratory symptoms, accurate evaluation of clinical gastrointestinal and neurological symptoms, combined with efficient highly sensitive molecular testing on feces, represent an efficient approach for detecting SARS-CoV-2, and for providing the correct therapy in challenging COVID-19 cases, like the one here reported.

Assessment of the Effective Sensitivity of SARS-CoV-2 Sample Pooling Based on a Large-Scale Screening Experience: Retrospective Analysis

BACKGROUND

The development of new large-scale saliva pooling detection strategies can significantly enhance testing capacity and frequency for asymptomatic individuals, which is crucial for containing SARS-CoV-2.

OBJECTIVE

This study aims to implement and scale-up a SARS-CoV-2 screening method using pooled saliva samples to control the virus in critical areas and assess its effectiveness in detecting asymptomatic infections.

METHODS

Between August 2020 and February 2022, our laboratory received a total of 928,357 samples. Participants collected at least 1 mL of saliva using a self-sampling kit and registered their samples via a smartphone app. All samples were directly processed using AutoMate 2550 for preanalytical steps and then transferred to Microlab STAR, managed with the HAMILTON Pooling software for pooling. The standard pool preset size was 20 samples but was adjusted to 5 when the prevalence exceeded 2% in any group. Real-time polymerase chain reaction (RT-PCR) was conducted using the Allplex SARS-CoV-2 Assay until July 2021, followed by the Allplex SARS-CoV-2 FluA/FluB/RSV assay for the remainder of the study period.

RESULTS

Of the 928,357 samples received, 887,926 (95.64%) were fully processed into 56,126 pools. Of these pools, 4863 tested positive, detecting 5720 asymptomatic infections. This allowed for a comprehensive analysis of pooling's impact on RT-PCR sensitivity and false-negative rate (FNR), including data on positive samples per pool (PPP). We defined Ctref as the minimum cycle threshold (Ct) of each data set from a sample or pool and compared these Ctref results from pooled samples with those of the individual tests (ΔCtP). We then examined their deviation from the expected offset due to dilution [ΔΔCtP = ΔCtP - log2]. In this work, the ΔCtP and ΔΔCtP were 2.23 versus 3.33 and -0.89 versus 0.23, respectively, comparing global results with results for pools with 1 positive sample per pool. Therefore, depending on the number of genes used in the test and the size of the pool, we can evaluate the FNR and effective sensitivity (1 - FNR) of the test configuration. In our scenario, with a maximum of 20 samples per pool and 3 target genes, statistical observations indicated an effective sensitivity exceeding 99%. From an economic perspective, the focus is on pooling efficiency, measured by the effective number of persons that can be tested with 1 test, referred to as persons per test (PPT). In this study, the global PPT was 8.66, reflecting savings of over 20 million euros (US $22 million) based on our reagent prices.

CONCLUSIONS

Our results demonstrate that, as expected, pooling reduces the sensitivity of RT-PCR. However, with the appropriate pool size and the use of multiple target genes, effective sensitivity can remain above 99%. Saliva pooling may be a valuable tool for screening and surveillance in asymptomatic individuals and can aid in controlling SARS-CoV-2 transmission. Further studies are needed to assess the effectiveness of these strategies for SARS-CoV-2 and their application to other microorganisms or biomarkers detected by PCR.

Prevalence of COVID-19 in prison population: a meta-analysis of 35 studies

PURPOSE

COVID-19 is an infectious disease caused by the SARS-CoV-2 virus. Considering the restricted and enclosed nature of prisons and closed environments and the prolonged and close contact between individuals, COVID-19 is more likely to have a higher incidence in these settings. This study aims to assess the prevalence of COVID-19 among prisoners.

DESIGN/METHODOLOGY/APPROACH

Papers published in English from 2019 to July 7, 2023, were identified using relevant keywords such as prevalence, COVID-19 and prisoner in the following databases: PubMed/MEDLINE, Scopus and Google Scholar. For the meta-analysis of the prevalence, Cochrane's Q statistics were calculated. A random effect model was used due to the heterogeneity in COVID-19 prevalence across included studies in the meta-analysis. All analyses were performed in STATA-13.

FINDINGS

The pooled data presented a COVID-19 prevalence of 20% [95%CI: 0.13, 0.26] and 24% [95%CI: 0.07, 0.41], respectively, in studies that used PCR and antibody tests. Furthermore, two study designs, cross-sectional and cohort, were used. The results of the meta-analysis showed studies with cross-sectional and cohort designs reported 20% [95%CI: 0.11, 0.29] and 25% [95%CI: 0.13, 0.38], respectively.

ORIGINALITY/VALUE

Through more meticulous planning, it is feasible to reduce the number of individuals in prison cells, thereby preventing the further spread of COVID-19.

Use of high-resolution fluorescence in situ hybridization for fast and robust detection of SARS-CoV-2 RNAs

Early, rapid, and accurate diagnostic tests play critical roles not only in the identification/management of individuals infected by SARS-CoV-2, but also in fast and effective public health surveillance, containment, and response. Our aim has been to develop a fast and robust fluorescence in situ hybridization (FISH) detection method for detecting SARS-CoV-2 RNAs by using an HEK 293 T cell culture model. At various times after being transfected with SARS-CoV-2 E and N plasmids, HEK 293 T cells were fixed and then hybridized with ATTO-labeled short DNA probes (about 20 nt). At 4 h, 12 h, and 24 h after transfection, SARS-CoV-2 E and N mRNAs were clearly revealed as solid granular staining inside HEK 293 T cells at all time points. Hybridization time was also reduced to 1 h for faster detection, and the test was completed within 3 h with excellent results. In addition, we have successfully detected 3 mRNAs (E mRNA, N mRNA, and ORF1a (-) RNA) simultaneously inside the buccal cells of COVID-19 patients. Our high-resolution RNA FISH might significantly increase the accuracy and efficiency of SARS-CoV-2 detection, while significantly reducing test time. The method can be conducted on smears containing cells (e.g., from nasopharyngeal, oropharyngeal, or buccal swabs) or smears without cells (e.g., from sputum, saliva, or drinking water/wastewater) for detecting various types of RNA viruses and even DNA viruses at different timepoints of infection.

An optimization framework for large-scale screening under limited testing capacity with application to COVID-19

We consider the problem of targeted mass screening of heterogeneous populations under limited testing capacity. Mass screening is an essential tool that arises in various settings, e.g., ensuring a safe supply of blood, reducing prevalence of sexually transmitted diseases, and mitigating the spread of infectious disease outbreaks. The goal of mass screening is to classify whole population groups as positive or negative for an infectious disease as efficiently and accurately as possible. Under limited testing capacity, it is not possible to screen the entire population and hence administrators must reserve testing and target those among the population that are most in need or most susceptible. This paper addresses this decision problem by taking advantage of accessible population-level risk information to identify the optimal set of sub-populations to target for screening. We conduct a comprehensive analysis that considers the two most commonly adopted schemes: Individual testing and Dorfman group testing. For both schemes, we formulate an optimization model that aims to minimize the number of misclassifications under a testing capacity constraint. By analyzing the formulations, we establish key structural properties which we use to construct efficient and accurate solution techniques. We conduct a case study on COVID-19 in the United States using geographic-based data. Our results reveal that the considered proactive targeted schemes outperform commonly adopted practices by substantially reducing misclassifications. Our case study provides important managerial insights with regards to optimal allocation of tests, testing designs, and protocols that dictate the optimality of schemes. Such insights can inform policy-makers with tailored and implementable data-driven recommendations.

Graphene transistor-based biosensors for rapid detection of SARS-CoV-2

Field-effect transistor (FET) biosensors use FETs to detect changes in the amount of electrical charge caused by biomolecules like antigens and antibodies. COVID-19 can be detected by employing these biosensors by immobilising bio-receptor molecules that bind to the SARS-CoV-2 virus on the FET channel surface and subsequent monitoring of the changes in the current triggered by the virus. Graphene Field-effect Transistor (GFET)-based biosensors utilise graphene, a two-dimensional material with high electrical conductivity, as the sensing element. These biosensors can rapidly detect several biomolecules including the SARS-CoV-2 virus, which is responsible for COVID-19. GFETs are ideal for real-time infectious illness diagnosis due to their great sensitivity and specificity. These graphene transistor-based biosensors could revolutionise clinical diagnostics by generating fast, accurate data that could aid pandemic management. GFETs can also be integrated into point-of-care (POC) diagnostic equipment. Recent advances in GFET-type biosensors for SARS-CoV-2 detection are discussed here, along with their associated challenges and future scope.

SARS-CoV-2 recombinase polymerase amplification assay with lateral flow readout and duplexed full process internal control

Nucleic acid amplification tests for the detection of SARS-CoV-2 have been an important testing mechanism for the COVID-19 pandemic. While these traditional nucleic acid diagnostic methods are highly sensitive and selective, they are not suited to home or clinic-based uses. Comparatively, rapid antigen tests are cost-effective and user friendly but lack in sensitivity and specificity. Here we report on the development of a one-pot, duplexed reverse transcriptase recombinase polymerase amplification SARS-CoV-2 assay with MS2 bacteriophage as a full process control. Detection is carried out with either real-time fluorescence or lateral flow readout with an analytical sensitivity of 50 copies per reaction. Unlike previously published assays, the RNA-based MS2 bacteriophage control reports on successful operation of lysis, reverse transcription, and amplification. This SARS-CoV-2 assay features highly sensitive detection, visual readout through an LFA strip, results in less than 25 minutes, minimal instrumentation, and a useful process internal control to rule out false negative test results.

Lessons from the pandemic: new best practices in selecting molecular diagnostics for point-of-care testing of infectious diseases in sub-Saharan Africa

INTRODUCTION

Point-of-care molecular diagnostics offer solutions to the limited diagnostic availability and accessibility in resource-limited settings. During the COVID-19 pandemic, molecular diagnostics became essential tools for accurate detection and monitoring of SARS-CoV-2. The unprecedented demand for molecular diagnostics presented challenges and catalyzed innovations which may provide lessons for the future selection of point-of-care molecular diagnostics.

AREAS COVERED

We searched PubMed from January 2020 to August 2023 to identify lessons learned from the COVID-19 pandemic which may impact the selection of point-of-care molecular diagnostics for future use in sub-Saharan Africa. We evaluated this in the context of REASSURED criteria (Real-time connectivity; Ease of specimen collection; Affordable; Sensitive; Specific; User-friendly; Rapid and robust; Equipment free; and Deliverable to users at the point of need) for point-of-care diagnostics for resource-limited settings.

EXPERT OPINION

The diagnostic challenges and successes during the COVID-19 pandemic affirmed the importance of the REASSURED criteria but demonstrated that these are not sufficient to ensure new diagnostics will be appropriate for public health emergencies. Capacity for rapid scale-up of diagnostic testing and transferability of assays, data, and technology are also important, resulting in updated REST-ASSURED criteria. Few diagnostics will meet all criteria, and trade-offs between criteria will need to be context-specific.

Multiplexed DNA and Protease Detection with Orthogonal Energy Transfer on a Single Quantum Dot Scaffolded Biosensor

Almost all pathogens, whether viral or bacterial, utilize key proteolytic steps in their pathogenesis. The ability to detect a pathogen's genomic material along with its proteolytic activity represents one approach to identifying the pathogen and providing initial evidence of its viability. Here, we report on a prototype biosensor design assembled around a single semiconductor quantum dot (QD) scaffold that is capable of detecting both nucleic acid sequences and proteolytic activity by using orthogonal energy transfer (ET) processes. The sensor consists of a central QD assembled via peptidyl-PNA linkers with multiple DNA sequences that encode complements to genomic sequences originating from the Ebola, Influenza, and COVID-19 viruses, which we use as surrogate targets. These are hybridized to complement strands labeled with a terbium (Tb) chelate, AlexaFluor647 (AF647), and Cy5.5 dyes, giving rise to two potential FRET cascades: the first includes Tb → QD → AF647 → Cy5.5 (→ = ET step), which is detected in a time-gated modality, and QD → AF647 → Cy5.5, which is detected from direct excitation. The labeled DNA-displaying QD construct is then further assembled with a RuII-modified peptide, which quenches QD photoluminescence by charge transfer and is recognized by a protease to yield the full biosensor. Each of the labeled DNAs and peptides can be ratiometrically assembled to the QD in a controllable manner to tune each of the ET pathways. Addition of a given target DNA displaces its labeled complement on the QD, disrupting that FRET channel, while protease addition disrupts charge transfer quenching of the central QD scaffold and boosts its photoluminescence and FRET relay capabilities. Along with characterizing the ET pathways and verifying biosensing in both individual and multiplexed formats, we also demonstrate the ability of this construct to function in molecular logic and perform Boolean operations; this highlights the construct's ability to discriminate and transduce signals between different inputs or pathogens. The potential application space for such a sensor device is discussed.

Re-testing as a method of implementing external quality assessment program for COVID-19 real time PCR testing in Uganda

BACKGROUND

Significant milestones have been made in the development of COVID19 diagnostics Technologies. Government of the republic of Uganda and the line Ministry of Health mandated Uganda Virus Research Institute to ensure quality of COVID19 diagnostics. Re-testing was one of the methods initiated by the UVRI to implement External Quality assessment of COVID19 molecular diagnostics.

METHOD

participating laboratories were required by UVRI to submit their already tested and archived nasopharyngeal samples and corresponding meta data. These were then re-tested at UVRI using the WHO Berlin protocol, the UVRI results were compared to those of the primary testing laboratories in order to ascertain performance agreement for the qualitative & quantitative results obtained. Ms Excel window 12 and GraphPad prism ver 15 was used in the analysis. Bar graphs, pie charts and line graphs were used to compare performance agreement between the reference Laboratory and primary testing Laboratories.

RESULTS

Eleven (11) Ministry of Health/Uganda Virus Research Institute COVID19 accredited laboratories participated in the re-testing of quality control samples. 5/11 (45%) of the primary testing laboratories had 100% performance agreement with that of the National Reference Laboratory for the final test result. Even where there was concordance in the final test outcome (negative or positive) between UVRI and primary testing laboratories, there were still differences in CT values. The differences in the Cycle Threshold (CT) values were insignificant except for Tenna & Pharma Laboratory and the UVRI(p = 0.0296). The difference in the CT values were not skewed to either the National reference Laboratory(UVRI) or the primary testing laboratory but varied from one laboratory to another. In the remaining 6/11 (55%) laboratories where there were discrepancies in the aggregate test results, only samples initially tested and reported as positive by the primary laboratories were tested and found to be false positives by the UVRI COVID19 National Reference Laboratory.

CONCLUSION

False positives were detected from public, private not for profit and private testing laboratories in almost equal proportion. There is need for standardization of molecular testing platforms in Uganda. There is also urgent need to improve on the Laboratory quality management systems of the molecular testing laboratories in order to minimize such discrepancies.

Prospective, clinical comparison of self-collected throat-bilateral nares swabs and saline gargle compared to health care provider collected nasopharyngeal swabs among symptomatic outpatients with potential SARS-CoV-2 infection

Background

In British Columbia (BC), self-collected saline gargle (SG) is the only alternative to health care provider (HCP)-collected nasopharyngeal (NP) swabs to detect SARS-CoV-2 in an outpatient setting by polymerase chain reaction (PCR). However, some individuals cannot perform a SG. Our study aimed to assess combined throat-bilateral nares (TN) swabbing as a swab-based alternative.

Methods

Symptomatic individuals greater than 12 years of age seeking a COVID-19 PCR test at one of two COVID-19 collection centres in Metro Vancouver were asked to participate in this study. Participants provided a HCP-collected NP sample and a self-collected SG and TN sample for PCR testing, which were either HCP observed or unobserved.

Results

Three-hundred and eleven individuals underwent all three collections. Compared against HCP-NP, SG was 99% sensitive and 98% specific (kappa 0.97) and TN was 99% sensitive and 99% specific (kappa 0.98). Using the final clinical test interpretation as the reference standard, NP was 98% sensitive and 100% specific (kappa 0.98), and both SG and TN were 99% sensitive and 100% specific (both kappa 0.99). Mean cycle threshold values for each viral target were higher in SG specimens compared to the other sample types; however, this did not significantly impact the clinical performance, because the positivity rates were similar. The clinical performance of all specimen types was comparable within the first 7 days of symptom onset, regardless of the observation method. SG self-collections were rated the most acceptable, followed by TN.

Conclusions

TN provides another less invasive self-collection modality for symptomatic outpatient SARS-CoV-2 PCR testing.

DNAzyme Nanomachine with Fluorogenic Substrate Delivery Function: Advancing Sensitivity in Nucleic Acid Detection

We have developed a hook-equipped DNA nanomachine (HDNM) for the rapid detection of specific nucleic acid sequences without a preamplification step. HDNM efficiently unwinds RNA structures and improves the detection sensitivity. Compared to the hookless system, HDNM offers an 80-fold and 13-fold enhancement in DNA and RNA detection, respectively, reducing incubation time from 3 to 1 h.

Development and evaluation of the automated multipurpose molecular testing system PCRpack for high-throughput SARS-CoV-2 testing

IMPORTANCE

Accurate and fast molecular testing is important for the diagnosis and control of COVID-19. During patient surges in the COVID-19 pandemic, laboratories were challenged by a higher demand for molecular testing under skilled staff shortages. We developed an automated multipurpose molecular testing system, named PCRpack, for the rapid, high-throughput testing of infectious pathogens, including SARS-CoV-2. The system is provided in an all-in-one package, including a liquid handling instrument, a laboratory information management system, and other materials needed for testing operation; is highly customizable; and is easily implemented. PCRpack showed robust liquid handling performance, high clinical diagnostic performance, a shorter turn-around time with minimal hands-on time, and a high testing capacity. These features contribute to the rapid implementation of the high-performance and high-throughput molecular testing environment at any phase of the pandemic caused by SARS-CoV-2 or future emerging pathogens.

From Archipelago to Pandemic Battleground: Unveiling Indonesia's COVID-19 Crisis

The coronavirus disease 2019 (COVID-19) pandemic has posed unprecedented challenges to countries worldwide, including Indonesia. With its unique archipelagic geography consisting of more than 17,000 thousand islands, Indonesia faces unique complexities in managing the spread of the virus. Based on existing literature, this review article elaborates on key issues that have shaped Indonesia's COVID-19 response. The article begins by examining the early stages of the COVID-19 pandemic in Indonesia, along with the implementation of various preventive measures and the impact of the virus on public health. This article examines how Indonesia's socio-economic factors have generally influenced its healthcare system and further delves into the COVID-19 response strategies implemented by the Indonesian government and public health authorities as well as overall crisis preparedness. It discusses the actions taken to control the spread of the virus, including testing strategies and vaccination efforts. The difficulties encountered in implementing these measures are presented. In conclusion, this review article provides a comprehensive understanding of the COVID-19 crisis in Indonesia, covering facts on multiple dimensions ranging from the timeline of the pandemic to vaccination efforts, epidemiology, socio-economic implications, testing strategies, mobility patterns, public holidays, the impact of working from home, and the utilization of complementary and alternative medicine in addition to the standard of care for COVID-19. The insights gained from this article can complement future strategies for pandemic management and response in Indonesia and other countries facing similar challenges.

Detection of viral RNAs at ambient temperature via reporter proteins produced through the target-splinted ligation of DNA probes

Nucleic acid assays are not typically deployable in point-of-care settings because they require costly and sophisticated equipment for the control of the reaction temperature and for the detection of the signal. Here we report an instrument-free assay for the accurate and multiplexed detection of nucleic acids at ambient temperature. The assay, which we named INSPECTR (for internal splint-pairing expression-cassette translation reaction), leverages the target-specific splinted ligation of DNA probes to generate expression cassettes that can be flexibly designed for the cell-free synthesis of reporter proteins, with enzymatic reporters allowing for a linear detection range spanning four orders of magnitude and peptide reporters (which can be mapped to unique targets) enabling highly multiplexed visual detection. We used INSPECTR to detect a panel of five respiratory viral targets in a single reaction via a lateral-flow readout and ~4,000 copies of viral RNA via additional ambient-temperature rolling circle amplification of the expression cassette. Leveraging synthetic biology to simplify workflows for nucleic acid diagnostics may facilitate their broader applicability at the point of care.

VIDIIA Hunter diagnostic platform: a low-cost, smartphone connected, artificial intelligence-assisted COVID-19 rapid diagnostics approved for medical use in the UK

Introduction: Accurate and rapid diagnostics paired with effective tracking and tracing systems are key to halting the spread of infectious diseases, limiting the emergence of new variants and to monitor vaccine efficacy. The current gold standard test (RT-qPCR) for COVID-19 is highly accurate and sensitive, but is time-consuming, and requires expensive specialised, lab-based equipment. Methods: Herein, we report on the development of a SARS-CoV-2 (COVID-19) rapid and inexpensive diagnostic platform that relies on a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay and a portable smart diagnostic device. Automated image acquisition and an Artificial Intelligence (AI) deep learning model embedded in the Virus Hunter 6 (VH6) device allow to remove any subjectivity in the interpretation of results. The VH6 device is also linked to a smartphone companion application that registers patients for swab collection and manages the entire process, thus ensuring tests are traced and data securely stored. Results: Our designed AI-implemented diagnostic platform recognises the nucleocapsid protein gene of SARS-CoV-2 with high analytical sensitivity and specificity. A total of 752 NHS patient samples, 367 confirmed positives for coronavirus disease (COVID-19) and 385 negatives, were used for the development and validation of the test and the AI-assisted platform. The smart diagnostic platform was then used to test 150 positive clinical samples covering a dynamic range of clinically meaningful viral loads and 250 negative samples. When compared to RT-qPCR, our AI-assisted diagnostics platform was shown to be reliable, highly specific (100%) and sensitive (98-100% depending on viral load) with a limit of detection of 1.4 copies of RNA per µL in 30 min. Using this data, our CE-IVD and MHRA approved test and associated diagnostic platform has been approved for medical use in the United Kingdom under the UK Health Security Agency's Medical Devices (Coronavirus Test Device Approvals, CTDA) Regulations 2022. Laboratory and in-silico data presented here also indicates that the VIDIIA diagnostic platform is able to detect the main variants of concern in the United Kingdom (September 2023). Discussion: This system could provide an efficient, time and cost-effective platform to diagnose SARS-CoV-2 and other infectious diseases in resource-limited settings.

Development of a loop-mediated isothermal amplification (LAMP)-based electrochemical test for rapid detection of SARS-CoV-2

Rapid, reliable, sensitive, portable, and accurate diagnostics are required to control disease outbreaks such as COVID-19 that pose an immense burden on human health and the global economy. Here we developed a loop-mediated isothermal amplification (LAMP)-based electrochemical test for the detection of SARS-CoV-2 that causes COVID-19. The test is based on the oxidation-reduction reaction between pyrophosphates (generated from positive LAMP reaction) and molybdate that is detected by cyclic voltammetry using inexpensive and disposable carbon screen printed electrodes. Our test showed higher sensitivity (detecting as low as 5.29 RNA copies/μL) compared to the conventional fluorescent reverse transcriptase (RT)-LAMP. We validated our tests using human serum and saliva spiked with SARS-CoV-2 RNA and clinical (saliva and nasal-pharyngeal) swab samples demonstrating 100% specificity and 93.33% sensitivity. Our assay provides a rapid, specific, and sensitive test with an electrochemical readout in less than 45 min that could be adapted for point-of-care settings.

Integrated point-of-care RT-PCR methods during and after COVID-19 pandemic

The COVID-19 pandemic has taken the world by surprise and people and organisations worldwide worked in some way or the other to combat the spread; isolate from the infected and get back to normal life, as it was before the pandemic hit. In this regard, the diagnosis of COVID-19 was at the centre of control and prevention and have seen a vehement change in every aspect, especially development of point-of-care testing for better and quick diagnosis. Among different types of techniques developed, the most important was the RT-PCR method of detection which detects nucleic acid of the virus in samples. RT-PCR is a laboratory-based method requiring trained professionals and precise steps for accurate testing. With the advent and spread of the pandemic, number of RT-PCR diagnostic centres rose significantly, and the detection process became less cumbersome, easy to use, ability to handle large volume of samples, more accurate, less time-consuming, and cost-effective. Different industries developed RT-PCR kits, reducing the efforts to prepare laboratory samples. Machines were employed for labour-driven tasks in PCR testing. In addition, new age technologies such as artificial intelligence, IoT, digital systems were combined with RT-PCR for accurate and easy testing. In this review, point-of-care RT-PCR methods, when the COVID-19 started, and the methods now, has been compared on the basis of technological advancements.

Antigen concentration, viral load, and test performance for SARS-CoV-2 in multiple specimen types

The relationship between N-antigen concentration and viral load within and across different specimens guides the clinical performance of rapid diagnostic tests (RDT) in different uses. A prospective study was conducted in Porto Velho, Brazil, to investigate RDT performance in different specimen types as a function of the correlation between antigen concentration and viral load. The study included 214 close contacts with recent exposures to confirmed cases, aged 12 years and older and with various levels of vaccination. Antigen concentration was measured in nasopharyngeal swab (NPS), anterior nares swab (ANS), and saliva specimens. Reverse transcriptase (RT)-PCR was conducted on the NPS and saliva specimens, and two RDTs were conducted on ANS and one RDT on saliva. Antigen concentration correlated well with viral load when measured in the same specimen type but not across specimen types. Antigen levels were higher in symptomatic cases compared to asymptomatic/oligosymptomatic cases and lower in saliva compared to NPS and ANS samples. Discordant results between the RDTs conducted on ANS and the RT-PCR on NPS were resolved by antigen concentration values. The analytical limit-of-detection of RDTs can be used to predict the performance of the tests in populations for which the antigen concentration is known. The antigen dynamics across different sample types observed in SARS-CoV-2 disease progression support use of RDTs with nasal samples. Given lower antigen concentrations in saliva, rapid testing using saliva is expected to require improved RDT analytical sensitivity to achieve clinical sensitivity similar to rapid testing of nasal samples.

Sequencing the SARS-CoV-2 Genome from Stool Samples of Post-acute Cases Implicates a Novel Mutation Associated with Reduced Antibody Neutralization

Whole-genome SARS-CoV-2 sequencing tools are crucial for tracking the COVID-19 pandemic. However, current techniques require sampling of actively infectious patients following COVID-19 testing to recover enough SARS-CoV-2 RNA from the nasopharyngeal passage, which rapidly clears during the first few weeks of infection. A prospective assessment of the viral genome sourced from recovered non-infectious patients would greatly facilitate epidemiological tracking. Thus, we developed a protocol to isolate and sequence the genome of SARS-CoV-2 from stool samples of post-acute SARS-CoV-2 patients, at timepoints ranging from 10-120 days after onset of symptoms. Stool samples were collected from patients at varying timepoints post-convalescence, and viral DNA was isolated and sequenced using the QIAamp Viral RNA Mini Kit (Qiagen Inc.) and Ion Ampliseq^™ Library Kit Plus (Life Technologies Corporation). Capacity of neutralizing antibodies in patient plasma was tested using a Luminex panel (Coronavirus Ig Total Human 11-Plex ProcartaPlex^™ Panel, ThermoFisher). Of 64 samples obtained from post-acute patients, 21 (32.8%) yielded sufficient material for whole-genome sequencing. This allowed us to identify widely divergent phylogenetic relativity of the SARS-CoV-2 genome from post-acute patients living in the same households and infected around the same time. Additionally, we observed that individuals who recovered from infection expressed varying degrees of antibodies against SARS-CoV-2 structural proteins that corresponded to distinct variants. Interestingly, we identified a novel point mutation in the viral genome where infected patients expressed antibodies with a significantly reduced capacity to neutralize the virus in vitro relative to that of those infected with the wild-type strain. Altogether, we demonstrate a protocol to successfully sequence the SARS-CoV-2 genome from stool samples from patients up to 4 months post-infection, which can be applied to studies that assess the relationship between variants and immune response post-hoc and safe monitoring of the SARS-CoV-2 genome during the pandemic.

Challenges of SARS-CoV-2 genomic surveillance in India during low positivity rate scenario

Being the second most populous country in the world, India presents valuable lessons for the world about dealing with the SARS-CoV-2 pandemic. From this perspective, we attempted a retrospective evaluation of India's SARS-CoV-2 genomic surveillance strategy and also gave some recommendations for undertaking effective genomic surveillance. The dynamics of the COVID-19 pandemic are continuously evolving, and there is a dire need to modulate the genomic surveillance strategy accordingly. The pandemic is now settling towards a low positivity rate scenario, so it is required to revise the practices and policies formulated for a high positivity rate scenario. The perspective also recommends adopting a decentralised approach for SARS-CoV-2 genomic surveillance with a focus on optimising the workflow of SARS-CoV-2 genomic surveillance to ensure early detection of emerging variants, especially in the low positivity rate scenario. The perspective emphasises a key observation that the SARS-CoV-2 genomic surveillance is an important mitigation effort during the pandemic, the guards of such mitigation efforts should not be lowered during the low positivity rate scenario. We attempt to highlight the limitations faced by the Indian healthcare administration during the SARS-CoV-2 genomic surveillance and, simultaneously, suggest policy interventions derived from our first-hand experience, which may be implementable in a vast, populated country like India.

Comparison of C-reactive protein with distinct hyperinflammatory biomarkers in association with COVID-19 severity, mortality and SARS-CoV-2 variants

C-reactive protein (CRP) has been one of the most investigated inflammatory-biomarkers during the ongoing COVID-19 pandemics caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The severe outcome among patients with SARS-CoV-2 infection is closely related to the cytokine storm and the hyperinflammation responsible for the acute respiratory distress syndrome and multiple organ failure. It still remains a challenge to determine which of the hyperinflammatory biomarkers and cytokines are the best predictors for disease severity and mortality in COVID-19 patients. Therefore, we evaluated and compared the outcome prediction efficiencies between CRP, the recently reported inflammatory modulators (suPAR, sTREM-1, HGF), and the classical biomarkers (MCP-1, IL-1β, IL-6, NLR, PLR, ESR, ferritin, fibrinogen, and LDH) in patients confirmed with SARS-CoV-2 infection at hospital admission. Notably, patients with severe disease had higher serum levels of CRP, suPAR, sTREM-1, HGF and classical biomarkers compared to the mild and moderate cases. Our data also identified CRP, among all investigated analytes, to best discriminate between severe and non-severe forms of disease, while LDH, sTREM-1 and HGF proved to be excellent mortality predictors in COVID-19 patients. Importantly, suPAR emerged as a key molecule in characterizing the Delta variant infections.

Predicting SARS-CoV-2 infection among hemodialysis patients using multimodal data

Background

The coronavirus disease 2019 (COVID-19) pandemic has created more devastation among dialysis patients than among the general population. Patient-level prediction models for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are crucial for the early identification of patients to prevent and mitigate outbreaks within dialysis clinics. As the COVID-19 pandemic evolves, it is unclear whether or not previously built prediction models are still sufficiently effective.

Methods

We developed a machine learning (XGBoost) model to predict during the incubation period a SARS-CoV-2 infection that is subsequently diagnosed after 3 or more days. We used data from multiple sources, including demographic, clinical, treatment, laboratory, and vaccination information from a national network of hemodialysis clinics, socioeconomic information from the Census Bureau, and county-level COVID-19 infection and mortality information from state and local health agencies. We created prediction models and evaluated their performances on a rolling basis to investigate the evolution of prediction power and risk factors.

Result

From April 2020 to August 2020, our machine learning model achieved an area under the receiver operating characteristic curve (AUROC) of 0.75, an improvement of over 0.07 from a previously developed machine learning model published by Kidney360 in 2021. As the pandemic evolved, the prediction performance deteriorated and fluctuated more, with the lowest AUROC of 0.6 in December 2021 and January 2022. Over the whole study period, that is, from April 2020 to February 2022, fixing the false-positive rate at 20%, our model was able to detect 40% of the positive patients. We found that features derived from local infection information reported by the Centers for Disease Control and Prevention (CDC) were the most important predictors, and vaccination status was a useful predictor as well. Whether or not a patient lives in a nursing home was an effective predictor before vaccination, but became less predictive after vaccination.

Conclusion

As found in our study, the dynamics of the prediction model are frequently changing as the pandemic evolves. County-level infection information and vaccination information are crucial for the success of early COVID-19 prediction models. Our results show that the proposed model can effectively identify SARS-CoV-2 infections during the incubation period. Prospective studies are warranted to explore the application of such prediction models in daily clinical practice.

Epidemiologic, clinical, and serum markers may improve discrimination between bacterial and viral etiologies of childhood pneumonia

Background

Discrimination of bacterial and viral etiologies of childhood community-acquired pneumonia (CAP) is often challenging. Unnecessary antibiotic administration exposes patients to undue risks and may engender antimicrobial resistance. This study aimed to develop a prediction model using epidemiological, clinical and laboratory data to differentiate between bacterial and viral CAP.

Methods

Data from 155 children with confirmed bacterial or mixed bacterial and viral infection (N = 124) and viral infection (N = 31) were derived from a comprehensive assessment of causative pathogens [Partnerships for Enhanced Engagement in Research-Pneumonia in Pediatrics (PEER-PePPeS)] conducted in Indonesia. Epidemiologic, clinical and biomarker profiles (hematology and inflammatory markers) were compared between groups. The area under the receiver operating characteristic curve (AUROC) for varying biomarker levels was used to characterize performance and determine cut-off values for discrimination of bacterial and mixed CAP versus viral CAP. Diagnostic predictors of bacterial and mixed CAP were assessed by multivariate logistic regression.

Results

Diarrhea was more frequently reported in bacterial and mixed CAP, while viral infections more frequently occurred during Indonesia's rainy season. White blood cell counts (WBC), absolute neutrophil counts (ANC), neutrophil-lymphocyte ratio (NLR), C-reactive protein (CRP), and procalcitonin (PCT) were significantly higher in bacterial and mixed cases. After adjusting for covariates, the following were the most important predictors of bacterial or mixed CAP: rainy season (aOR 0.26; 95% CI 0.08-0.90; p = 0.033), CRP ≥5.70 mg/L (aOR 4.71; 95% CI 1.18-18.74; p = 0.028), and presence of fever (aOR 5.26; 95% CI 1.07-25.91; p = 0.041). The model assessed had a low R-squared (Nagelkerke R² = 0.490) but good calibration (p = 0.610 for Hosmer Lemeshow test). The combination of CRP and fever had moderate predictive value with sensitivity and specificity of 62.28 and 65.52%, respectively.

Conclusion

Combining clinical and laboratory profiles is potentially valuable for discriminating bacterial and mixed from viral pediatric CAP and may guide antibiotic use. Further studies with a larger sample size should be performed to validate this model.

VLP-ELISA for the Detection of IgG Antibodies against Spike, Envelope, and Membrane Antigens of SARS-CoV-2 in Indian Population

Background: Serological methods to conduct epidemiological survey are often directed only against the spike protein. To overcome this limitation, we have designed PRAK-03202, a virus-like particle (VLP), by inserting three antigens (Spike, envelope and membrane) of SARS-CoV-2 into a highly characterized S. cerevisiae-based D-Crypt™ platform. Methods: Dot blot analysis was performed to confirm the presence of S, E, and M proteins in PRAK-03202. The number of particles in PRAK-03202 was measured using nanoparticle tracking analysis (NTA). The sensitivity of VLP-ELISA was evaluated in 100 COVID positive. PRAK-03202 was produced at a 5 L scale using fed-batch fermentation. Results: Dot blot confirmed the presence of S, E, and M proteins in PRAK-03202. The number of particles in PRAK-03202 was 1.21 × 109 mL−1. In samples collected >14 days after symptom onset, the sensitivity, specificity, and accuracy of VLP-ELISA were 96%. We did not observe any significant differences in sensitivity, specificity, and accuracy when post-COVID-19 samples were used as negative controls compared to pre-COVID-samples. At a scale of 5 L, the total yield of PRAK-03202 was 100–120 mg/L. Conclusion: In conclusion, we have successfully developed an in-house VLP-ELISA to detect IgG antibodies against three antigens of SARS-CoV-2 as a simple and affordable alternative test.

Global SARS-CoV-2 genomic surveillance: What we have learned (so far)

The COVID-19 pandemic has brought significant challenges for genomic surveillance strategies in public health systems worldwide. During the past thirty-four months, many countries faced several epidemic waves of SARS-CoV-2 infections, driven mainly by the emergence and spread of novel variants. In that line, genomic surveillance has been a crucial toolkit to study the real-time SARS-CoV-2 evolution, for the assessment and optimization of novel diagnostic assays, and to improve the efficacy of existing vaccines. During the pandemic, the identification of emerging lineages carrying lineage-specific mutations (particularly those in the Receptor Binding domain) showed how these mutations might significantly impact viral transmissibility, protection from reinfection and vaccination. So far, an unprecedented number of SARS-CoV-2 viral genomes has been released in public databases (i.e., GISAID, and NCBI), achieving 14 million genome sequences available as of early-November 2022. In the present review, we summarise the global landscape of SARS-CoV-2 during the first thirty-four months of viral circulation and evolution. It demonstrates the urgency and importance of sustained investment in genomic surveillance strategies to timely identify the emergence of any potential viral pathogen or associated variants, which in turn is key to epidemic and pandemic preparedness.

SARS-CoV-2 molecular diagnostic point-of-care testing based on loop-mediated isothermal amplification: A prospective, single-center validation study

Objectives

Rapid and accurate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic tests are crucial for controlling the spread of infections in emergency settings. This study evaluated the diagnostic accuracy of a point-of-care (POC) test based on loop-mediated isothermal amplification (LAMP) that produces rapid results within 30 min.

Methods

We prospectively included adult patients (age >19 years) who were diagnosed with SARS-CoV-2 infection within the last 3 days and symptomatic patients who had visited the emergency room. Posterior nasopharyngeal (PNP) swabs and throat swabs collected by physicians were used to test the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy, and Cohen's Kappa coefficient (k) of the POC index and reference reverse transcription quantitative polymerase chain reaction (RT-qPCR) test devices.

Results

Of the 352 participants, 102 (29.0%) tested positive via the RT-PCR-based reference test device; the RT-LAMP-based POC test had a sensitivity of 70.6% and specificity of 98.0%, with 93.5% PPV, 89.1% NPV, 35.5% PLR, and 3.4% NLR. Cohen's k correlation of results from the two devices was 0.74. The cycle threshold value between the positive and negative POC test results differed (17.6 vs. 24.6, p < 0.001).

Conclusions

The RT-LAMP POC test in the emergency medical setting has a fair predictive value in high viral load cases in terms of infectivity.

Expression, purification, and study on the efficiency of a new potent recombinant scFv antibody against the SARS-CoV-2 spike RBD in E. coli BL21

Many efforts have been made around the world to combat SARS-CoV-2. Among these are recombinant antibodies considered to be suitable as an alternative for some diagnostics/therapeutics. Based on their importance, this study aimed to investigate the expression, purification, and efficiency of a new potent recombinant scFv in the E. coli BL21 (DE3) system. The expression studies were performed after confirming the scFv cloning into the pET28a vector using specific PCRs. After comprehensive expression studies, a suitable strategy was adopted to extract and purify periplasmic proteins using Ni²⁺-NTA resin. Besides the purified scFv, the crude bacterial lysate was also used to develop a sandwich ELISA (S-ELISA) for the detection of SARS-CoV-2. The use of PCR, E. coli expression system, western blotting (WB), and S-ELISA confirmed the functionality of this potent scFv. Moreover, the crude bacterial lysate also showed good potential for detecting SARS-CoV-2. This could be decreasing the costs and ease its utilization for large-scale applications. The production of high-quality recombinant proteins is essential for humankind. Moreover, with attention to the more aggressive nature of SARS-CoV-2 than other coronaviruses, the development of an effective detection method is urgent. Based on our knowledge, this study is one of the limited investigations in two fields: (1) The production of anti-SARS-CoV-2 scFv using E. coli [as a cheap heterologous host] in relatively high amounts and with good stability, and (2) Designing a sensitive S-ELISA for its detection. It may also be utilized as potent therapeutics after further investigations.

Analysis of Bacteriophage Behavior of a Human RNA Virus, SARS-CoV-2, through the Integrated Approach of Immunofluorescence Microscopy, Proteomics and D-Amino Acid Quantification

SARS-CoV-2, one of the human RNA viruses, is widely studied around the world. Significant efforts have been made to understand its molecular mechanisms of action and how it interacts with epithelial cells and the human microbiome since it has also been observed in gut microbiome bacteria. Many studies emphasize the importance of surface immunity and also that the mucosal system is critical in the interaction of the pathogen with the cells of the oral, nasal, pharyngeal, and intestinal epithelium. Recent studies have shown how bacteria in the human gut microbiome produce toxins capable of altering the classical mechanisms of interaction of viruses with surface cells. This paper presents a simple approach to highlight the initial behavior of a novel pathogen, SARS-CoV-2, on the human microbiome. The immunofluorescence microscopy technique can be combined with spectral counting performed at mass spectrometry of viral peptides in bacterial cultures, along with identification of the presence of D-amino acids within viral peptides in bacterial cultures and in patients' blood. This approach makes it possible to establish the possible expression or increase of viral RNA viruses in general and SARS-CoV-2, as discussed in this study, and to determine whether or not the microbiome is involved in the pathogenetic mechanisms of the viruses. This novel combined approach can provide information more rapidly, avoiding the biases of virological diagnosis and identifying whether a virus can interact with, bind to, and infect bacteria and epithelial cells. Understanding whether some viruses have bacteriophagic behavior allows vaccine therapies to be focused either toward certain toxins produced by bacteria in the microbiome or toward finding inert or symbiotic viral mutations with the human microbiome. This new knowledge opens a scenario on a possible future vaccine: the probiotics vaccine, engineered with the right resistance to viruses that attach to both the epithelium human surface and gut microbiome bacteria.

Smart healthcare: A prospective future medical approach for COVID-19

COVID-19 has greatly affected human life for over 3 years. In this review, we focus on smart healthcare solutions that address major requirements for coping with the COVID-19 pandemic, including (1) the continuous monitoring of severe acute respiratory syndrome coronavirus 2, (2) patient stratification with distinct short-term outcomes (eg, mild or severe diseases) and long-term outcomes (eg, long COVID), and (3) adherence to medication and treatments for patients with COVID-19. Smart healthcare often utilizes medical artificial intelligence (AI) and cloud computing and integrates cutting-edge biological and optoelectronic techniques. These are valuable technologies for addressing the unmet needs in the management of COVID. By leveraging deep learning/machine learning capabilities and big data, medical AI can perform precise prognosis predictions and provide reliable suggestions for physicians' decision-making. Through the assistance of the Internet of Medical Things, which encompasses wearable devices, smartphone apps, internet-based drug delivery systems, and telemedicine technologies, the status of mild cases can be continuously monitored and medications provided at home without the need for hospital care. In cases that develop into severe cases, emergency feedback can be provided through the hospital for rapid treatment. Smart healthcare can possibly prevent the development of severe COVID-19 cases and therefore lower the burden on intensive care units.

Model training periods impact estimation of COVID-19 incidence from wastewater viral loads

Wastewater-based epidemiology (WBE) has been deployed broadly as an early warning tool for emerging COVID-19 outbreaks. WBE can inform targeted interventions and identify communities with high transmission, enabling quick and effective responses. As the wastewater (WW) becomes an increasingly important indicator for COVID-19 transmission, more robust methods and metrics are needed to guide public health decision-making. This research aimed to develop and implement a mathematical framework to infer incident cases of COVID-19 from SARS-CoV-2 levels measured in WW. We propose a classification scheme to assess the adequacy of model training periods based on clinical testing rates and assess the sensitivity of model predictions to training periods. A testing period is classified as adequate when the rate of change in testing is greater than the rate of change in cases. We present a Bayesian deconvolution and linear regression model to estimate COVID-19 cases from WW data. The effective reproductive number is estimated from reconstructed cases using WW. The proposed modeling framework was applied to three Northern California communities served by distinct WW treatment plants. The results showed that training periods with adequate testing are essential to provide accurate projections of COVID-19 incidence.

Outcome of Newborns with Confirmed or Possible SARS-CoV-2 Vertical Infection-A Scoping Review

Severe acute respiratory syndrome virus 2 (SARS-CoV-2), the virus that causes 2019 coronavirus disease (COVID-19), has been isolated from various tissues and body fluids, including the placenta, amniotic fluid, and umbilical cord of newborns. In the last few years, much scientific effort has been directed toward studying SARS-CoV-2, focusing on the different features of the virus, such as its structure and mechanisms of action. Moreover, much focus has been on developing accurate diagnostic tools and various drugs or vaccines to treat COVID-19. However, the available evidence is still scarce and consistent criteria should be used for diagnosing vertical transmission. Applying the PRISMA ScR guidelines, we conducted a scoping review with the primary objective of identifying the types, and examining the range, of available evidence of vertical transmission of SARS-CoV-2 from mother to newborn. We also aimed to clarify the key concepts and criteria for diagnosis of SARS-CoV-2 vertical infection in neonates and summarize the existing evidence and advance the awareness of SARS-CoV-2 vertical infection in pregnancy. Most studies we identified were case reports or case series (about 30% of poor quality and inconsistent reporting of the findings). Summarizing the existing classification criteria, we propose an algorithm for consistent diagnosis. Registration: INPLASY2022120093.

Performance and correlation of ten commercial immunoassays for the detection of SARS-CoV-2 antibodies

Accurate immunoassays with a good correlation to neutralizing antibodies are required to support SARS-CoV-2 diagnosis, management, vaccine deployment, and epidemiological investigation. We conducted a study to evaluate the performance and correlation of the surrogate virus neutralization test (sVNT) and other commercial immunoassays. We tested 107 sera of COVID-19 confirmed cases from three different time points, 58 confirmed non-COVID-19 sera, and 52 sera collected before the pandemic with two sVNTs, seven chemiluminescent assays, and one fluorescein assay. All assays achieved excellent sensitivity (95%-100%, ≥15 days after onset of illness), specificity (95.5%-100%), and showed moderate to high correlation with GenScript sVNT (r = 0.58 to r = 0.98), except Roche total antibodies (r = 0.48). Vazyme sVNT and Siemens total antibodies showed the highest correlation with GenScript sVNT (r = 0.98 and 0.88, respectively). Median indexes that may be used to estimate sera with the highest ability to inhibit SARS-CoV-2 and ACE-2 receptor attachment (GenScript sVNT inhibition 90%-100%) were 6.9 S/C (Abbott IgG), 161.9 COI (FREND™ IgG), 16.8 AU/ml (Snibe IgG), 40.1 S/CO (Beckman IgG), 281.9 U/ml (Mindray IgG), 712.2 U/ml (Mindray total antibodies), >10 index (Siemens total antibodies), and 95.3% inhibition (Vazyme sVNT). All ten commercial COVID-19 serology assays, with different targeting antigens, demonstrated a reliable performance, supporting the utility of those assays in clinical and research settings. However, further studies using more samples are needed to refine the results of evaluating the performances of these marketed serological assays. Reliable serological assays would be useful for clinicians, researchers and epidemiologists in confirming SARS-CoV-2 infections, observing SARS-CoV-2 transmission, and immune response post infection and vaccination, leading to better management and control of the disease.

A Survey of Public Health Failures During COVID-19

The prolonged coronavirus disease 2019 (COVID-19) pandemic has raised concerns about the failures in the public health measures used to manage the spread of this deadly virus. This review focuses its attention on research papers that at their core highlight the individual public health measures instituted by organizations, institutions, and the government of the United States (US) since the start of the COVID-19 pandemic and that were published in 2019 to 2022. Together, these sources help paint a well-rounded view of the US management of this pandemic so that conclusions may be drawn from mistakes that were made and this country may respond better in the future to such situations. This paper is unique because it highlights the areas where improvement is needed, whereas other published work describes the measures taken and how they were carried out, not the failures, which leaves a gap in the literature that this paper hopes to fill. Through a deep dive into public health measures, seven areas in which improvements could be made were pinpointed by the authors. Such measures included mask mandates, social distancing, lockdown/quarantine, hand hygiene, COVID-19 testing, travel screening, and vaccine hesitancy. In exploring each measure, a discussion was carried out about its benefits and shortcomings in alleviating the ramifications of a global pandemic. In addition to the poor supply chain for critical products like personal protective equipment (PPE), the miscommunication between states and federal policies did not allow for the entirety of the US to respond cohesively in the face of the COVID-19 pandemic. This general review is crucial to know what is working and what needs to be changed to increase the benefits provided to the population.

Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the associated coronavirus disease 2019 (COVID-19), which severely affect the respiratory system and several organs and tissues, and may lead to death, have shown how science can respond when challenged by a global emergency, offering as a response a myriad of rapid technological developments. Development of vaccines at lightning speed is one of them. SARS-CoV-2 outbreaks have stressed healthcare systems, questioning patients care by using standard non-adapted therapies and diagnostic tools. In this scenario, nanotechnology has offered new tools, techniques and opportunities for prevention, for rapid, accurate and sensitive diagnosis and treatment of COVID-19. In this review, we focus on the nanotechnological applications and nano-based materials (i.e., personal protective equipment) to combat SARS-CoV-2 transmission, infection, organ damage and for the development of new tools for virosurveillance, diagnose and immune protection by mRNA and other nano-based vaccines. All the nano-based developed tools have allowed a historical, unprecedented, real time epidemiological surveillance and diagnosis of SARS-CoV-2 infection, at community and international levels. The nano-based technology has help to predict and detect how this Sarbecovirus is mutating and the severity of the associated COVID-19 disease, thereby assisting the administration and public health services to make decisions and measures for preparedness against the emerging variants of SARS-CoV-2 and severe or lethal COVID-19.

Evaluation of Various Alternative Economical and High Throughput SARS-CoV-2 Testing Methods within Resource-Limited Settings

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak posed a challenge for diagnostic laboratories worldwide, with low-middle income countries (LMICs) being the most affected. The polymerase chain reaction (PCR) is the gold standard method for detecting SARS-CoV-2 infection. However, the challenge with this method is that it is expensive, which has resulted in under-testing for SARS-CoV-2 infection in many LMICs. Hence, this study aimed to compare and evaluate alternative methods for the mass testing of SARS-CoV-2 infection in laboratories with limited resources to identify cost-effective, faster, and accurate alternatives to the internationally approved kits. A total of 50 residual nasopharyngeal swab samples were used for evaluation and comparison between internationally approved kits (Thermo Fisher PureLink™ RNA Isolation Kit and Thermo Fisher TaqPath™ COVID-19 Assay Kit) and alternative methods (three RNA extraction and four commercial SARS-CoV-2 RT-PCR assay kits) in terms of the cost analysis, diagnostic accuracy, and turnaround time. In terms of performance, all of the alternative RNA extraction methods evaluated were comparable to the internationally approved kits but were more cost-effective (Lucigen QuickExtract™ RNA Extraction Kit, Bosphore EX-Tract Dry Swab RNA Solution and Sonicator method) and four commercial SARS-CoV-2 RT-PCR assay kits (Nucleic Acid COVID-19 Test Kit (SARS-CoV-2), abTESTM COVID-19 qPCR I Kit, PCL COVID19 Speedy RT-PCR Kit, and PCLMD nCoV One-Step RT-PCR Kit) with a sensitivity range of 76-100% and specificity of 96-100%. The cost per sample was reduced by more than 50% when compared to internationally approved kits. When compared to the Thermo Fisher PureLink™ Kit and Thermo Fisher TaqPath™ COVID-19 Assay Kit, the alternative methods had a faster turnaround time, indicating that laboratories with limited resources may be able to process more samples in a day. The above-mentioned cost-effective, fast, and accurate evaluated alternative methods can be used in routine diagnostic laboratories with limited resources for mass testing for SARS-CoV-2 because these were comparable to the internationally approved kits, Thermo Fisher PureLink™ Kit and Thermo Fisher TaqPath™ COVID-19 Assay Kit. The implementation of alternative methods will be the most cost-effective option for testing SARS-CoV-2 infection in LMICs.

A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2

Background

Since inception of the COVID-19 pandemic, early detection and isolation of positive cases is one of the key strategies to restrict disease transmission. Real time reverse transcription polymerase chain reaction (qRTPCR) has been the mainstay of diagnosis. Most of the qRTPCR kits were designed against the target genes of original strain of SARS-CoV-2. However, with the emergence of variant strains of SARS-CoV-2, sensitivity of the qRTPCR assays has reportedly reduced. In view of this, it is critical to continuously monitor the performance of the qRTPCR kits in the backdrop of variant strains of SARS-CoV-2. Real world monitoring of assay performance is challenging. Therefore, we developed a two-step in-silico screening process for evaluating the performance of various qRTPCR kits used in India.

Results

We analysed 73 qRT-PCR kits marketed in India, against the two SARS-CoV-2 VoCs. Sequences of both Delta (B.1.617.2) and Omicron (B.1.1.529) VoCs submitted to GISAID within a specific timeframe were downloaded, clustered to identify unique sequences and aligned with primer and probe sequences. Results were analysed following a two-step screening process. Out of 73 kits analysed, seven were unsatisfactory for detection of both Delta and Omicron VoCs, 10 were unsatisfactory for Delta VoC whereas 2 were unsatisfactory for only Omicron VoC.

Conclusion

Overall, we have developed a useful screening process for evaluating the performance of qRTPCR assays against Delta and Omicron VoCs of SARS-CoV-2 which can be used for detecting SARS-CoV-2 VoCs that may emerge in future and can also be redeployed for other evolving pathogens of public health importance.

Wastewater surveillance allows early detection of SARS-CoV-2 omicron in North Rhine-Westphalia, Germany

Wastewater-based epidemiology (WBE) has demonstrated its importance to support SARS-CoV-2 epidemiology complementing individual testing strategies. Due to their immune-evasive potential and the resulting significance for public health, close monitoring of SARS-CoV-2 variants of concern (VoC) is required to evaluate the regulation of early local countermeasures. In this study, we demonstrate a rapid workflow for wastewater-based early detection and monitoring of the newly emerging SARS-CoV-2 VoCs Omicron in the end of 2021 at the municipal wastewater treatment plant (WWTP) Emschermuendung (KLEM) in the Federal State of North-Rhine-Westphalia (NRW, Germany). Initially, available primers detecting Omicron-related mutations were rapidly validated in a central laboratory. Subsequently, RT-qPCR analysis of purified SARS-CoV-2 RNA was performed in a decentral PCR laboratory in close proximity to KLEM. This decentralized approach enabled the early detection of K417N present in Omicron in samples collected on 8th December 2021 and the detection of further mutations (N501Y, Δ69/70) in subsequent biweekly sampling campaigns. The presence of Omicron in wastewater was confirmed by next generation sequencing (NGS) in a central laboratory with samples obtained on 14th December 2021. Moreover, the relative increase of the mutant fraction of Omicron was quantitatively monitored over time by dPCR in a central PCR laboratory starting on 12th December 2021 confirming Omicron as the dominant variant by the end of 2021. In conclusions, WBE plays a crucial role in surveillance of SARS-CoV-2 variants and is suitable as an early warning system to identify variant emergence. In particular, the successive workflow using RT-qPCR, RT-dPCR and NGS demonstrates the strength of WBE as a versatile tool to monitor variant spreading.

Ferrobotic swarms enable accessible and adaptable automated viral testing

Expanding our global testing capacity is critical to preventing and containing pandemics^1–9. Accordingly, accessible and adaptable automated platforms that in decentralized settings perform nucleic acid amplification tests resource-efficiently are required^10–14. Pooled testing can be extremely efficient if the pooling strategy is based on local viral prevalence^15–20; however, it requires automation, small sample volume handling and feedback not available in current bulky, capital-intensive liquid handling technologies^21–29. Here we use a swarm of millimetre-sized magnets as mobile robotic agents (‘ferrobots’) for precise and robust handling of magnetized sample droplets and high-fidelity delivery of flexible workflows based on nucleic acid amplification tests to overcome these limitations. Within a palm-sized printed circuit board-based programmable platform, we demonstrated the myriad of laboratory-equivalent operations involved in pooled testing. These operations were guided by an introduced square matrix pooled testing algorithm to identify the samples from infected patients, while maximizing the testing efficiency. We applied this automated technology for the loop-mediated isothermal amplification and detection of the SARS-CoV-2 virus in clinical samples, in which the test results completely matched those obtained off-chip. This technology is easily manufacturable and distributable, and its adoption for viral testing could lead to a 10–300-fold reduction in reagent costs (depending on the viral prevalence) and three orders of magnitude reduction in instrumentation cost. Therefore, it is a promising solution to expand our testing capacity for pandemic preparedness and to reimagine the automated clinical laboratory of the future.

A handheld printed circuit board-based programmable platform using ferrobots can perform the complex, laboratory-equivalent procedures involved in multiplexed and pooled nucleic acid amplification testing, allowing for the decentralization of viral diagnostics.

A comparison of conventional and advanced electroanalytical methods to detect SARS-CoV-2 virus: A concise review

Respiratory viruses are a serious threat to human wellbeing that can cause pandemic disease. As a result, it is critical to identify virus in a timely, sensitive, and precise manner. The present novel coronavirus-2019 (COVID-19) disease outbreak has increased these concerns. The research of developing various methods for COVID-19 virus identification is one of the most rapidly growing research areas. This review article compares and addresses recent improvements in conventional and advanced electroanalytical approaches for detecting COVID-19 virus. The popular conventional methods such as polymerase chain reaction (PCR), loop mediated isothermal amplification (LAMP), serology test, and computed tomography (CT) scan with artificial intelligence require specialized equipment, hours of processing, and specially trained staff. Many researchers, on the other hand, focused on the invention and expansion of electrochemical and/or bio sensors to detect SARS-CoV-2, demonstrating that they could show a significant role in COVID-19 disease control. We attempted to meticulously summarize recent advancements, compare conventional and electroanalytical approaches, and ultimately discuss future prospective in the field. We hope that this review will be helpful to researchers who are interested in this interdisciplinary field and desire to develop more innovative virus detection methods.

An opinion on Wastewater-Based Epidemiological Monitoring (WBEM) with Clinical Diagnostic Test (CDT) for detecting high-prevalence areas of community COVID-19 Infections

Wastewater-Based Epidemiological Monitoring (WBEM) is an efficient surveillance tool during the COVID-19 pandemic as it meets all requirements of a complete monitoring system including early warning, tracking the current trend, prevalence of the disease, detection of genetic diversity as well asthe up-surging SARS-CoV-2 new variants with mutations from the wastewater samples. Subsequently, Clinical Diagnostic Test is widely acknowledged as the global gold standard method for disease monitoring, despite several drawbacks such as high diagnosis cost, reporting bias, and the difficulty of tracking asymptomatic patients (silent spreaders of the COVID-19 infection who manifest nosymptoms of the disease). In this current reviewand opinion-based study, we first propose a combined approach) for detecting COVID-19 infection in communities using wastewater and clinical sample testing, which may be feasible and effective as an emerging public health tool for the long-term nationwide surveillance system. The viral concentrations in wastewater samples can be used as indicatorsto monitor ongoing SARS-CoV-2 trends, predict asymptomatic carriers, and detect COVID-19 hotspot areas, while clinical sampleshelp in detecting mostlysymptomaticindividuals for isolating positive cases in communities and validate WBEM protocol for mass vaccination including booster doses for COVID-19.

Development of a high-sensitivity and short-duration fluorescence in situ hybridization method for viral mRNA detection in HEK 293T cells

Coronavirus disease 2019 (COVID-19) is an extremely contagious illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Early disease recognition of COVID-19 is crucial not only for prompt diagnosis and treatment of the patients, but also for effective public health surveillance and response. The reverse transcription-polymerase chain reaction (RT-PCR) is the most common method for the detection of SARS-CoV-2 viral mRNA and is regarded as the gold standard test for COVID-19. However, this test and those for antibodies (IgM and IgG) and antigens have certain limitations (e.g., by yielding false-negative and false-positive results). We have developed an RNA fluorescence in situ hybridization (FISH) method for high-sensitivity detection of SARS-CoV-2 mRNAs in HEK 293T cell cultures as a model. After transfection of HEK 293T cells with plasmids, Spike (S)/envelope (E) proteins and their mRNAs were clearly detected inside the cells. In addition, hybridization time could be reduced to 2 hours for faster detection when probe concentration was increased. Our approach might thus significantly improve the sensitivity and specificity of SARS-CoV-2 detection and be widely applied for the high-sensitivity single-molecular detection of other RNA viruses (e.g., Middle East respiratory syndrome coronavirus (MERS-CoV), Hepatitis A virus, all influenza viruses, and human immunodeficiency virus (HIV)) in various types of samples including tissue, body fluid, blood, and water. RNA FISH can also be utilized for the detection of DNA viruses (e.g., Monkeypox virus, human papillomavirus (HPV), and cytomegalovirus (CMV)) by detection of their mRNAs inside cells or body fluid.

Clinical evaluation of an automated, rapid mariPOC antigen test in screening of symptomatics and asymptomatics for SARS-CoV-2 infection

A novel automated mariPOC SARS-CoV-2 antigen test was evaluated in a Health Care Center Laboratory among symptomatic and asymptomatic individuals seeking SARS-CoV-2 testing. According to the national testing strategy, reverse transcription polymerase chain reaction (RT-PCR) was used as a reference method. A total of 962 subjects were included in this study, 4.8% (46/962) of their samples were SARS-CoV-2 RT-PCR-positive, and 87% (40/46) of these were from symptomatics. Among the symptomatics, the overall sensitivity of the mariPOC SARS-CoV-2 test was 82.5% (33/40), though the sensitivity increased to 97.1% (33/34) in samples with a C_t  < 30. The mariPOC SARS-CoV-2 test detected two of six PCR-positive samples among the asymptomatics, four cases that remained antigen test negative had C_t values between 28 and 36. The specificity of the mariPOC SARS-CoV-2 test was 100% (916/916). The evaluation showed that the mariPOC SARS-CoV-2 rapid antigen test is very sensitive and specific for the detection of individuals who most probably are contagious.

Evaluating the role of SARS-CoV-2 target genes based on two nucleic acid assay kits

Background

Effective isolation and early treatment of coronavirus disease 2019 (COVID-19) relies on rapid, accurate, and straightforward diagnostic tools. In response to the rapidly increasing number of cases, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays for multiple target genes have become widely available in the market.

Methods

In total, 236 COVID-19 patients with positive results in both RT-qPCR and rapid antigen diagnosis (Ag-RDT) were enrolled in the study. The cycle threshold (Ct) was compared with different onset times and target genes. Comparison between groups was evaluated with the Kruskal-Wallis test and Dunn test. The correlation between target genes was analyzed by Spearman.

Results

In samples of Ct ≤ 21, Ct was different for the nucleocapsid (N), open reading frame 1ab (ORF1ab), and envelope (E) genes (P < 0.05). Mild COVID-19 patients within 7 days of onset accounted for 67.80% of all enrolled patients. At the above stage, all target genes reached the trough of Ct, and N genes showed lower values than the other target genes. The Ct of the ORF1ab and N gene in asymptomatic patients differed from those of mild patients within 7 days and more than 14 days of onset. The kits used in the study showed strong consistency among target genes, with all correlation coefficients >0.870.

Conclusion

RT-qPCR confirmed that the N gene performed well in Ct ≤ 21 and samples within 7 days of onset. Ag-RDT was discriminatory for patients within 7 days of onset. This study facilitated early identification and control of COVID-19 prevalence among patients.

Development and Validation of Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) as a Simple and Rapid Diagnostic Tool for SARS-CoV-2 Detection

Since the COVID-19 pandemic outbreak in the world, many countries have searched for quick diagnostic tools to detect the virus. There are many ways to design diagnostic assays; however, each may have its limitations. A quick, sensitive, specific, and simple approach is essential for highly rapidly transmitted infections, such as SARS-CoV-2. This study aimed to develop a rapid and cost-effective diagnostic tool using a one-step Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) approach. The results were observed using the naked eye within 30–60 min using turbidity or colorimetric analysis. The sensitivity, specificity, and lowest limit of detection (LoD) for SARS-CoV-2 RNA against the RT-LAMP assay were assessed. This assay was also verified and validated against commercial quantitative RT-PCR used by health authorities in Saudi Arabia. Furthermore, a quick and direct sampling from the saliva, or buccal cavity, was applied after simple modification, using proteinase K and heating at 98 °C for 5 min to avoid routine RNA extraction. This rapid single-tube diagnostic tool detected COVID-19 with an accuracy rate of 95% for both genes (ORF1a and N) and an LoD for the ORF1a and N genes as 39 and 25 copies/reaction, respectively. It can be potentially used as a high-throughput national screening for different respiratory-based infections within the Middle East region, such as the MERS virus or major zoonotic pathogens such as Mycobacterium paratuberculosis and Brucella spp., particularly in remote and rural areas where lab equipment is limited.