Testing at scale during the COVID-19 pandemic

Seroprevalence of antibodies against SARS-Cov-2 in the high impacted sub-district in Jakarta, Indonesia

Background

Understanding the actual prevalence of COVID-19 transmission in the community is vital for strategic responses to the pandemic. This study aims to estimate the actual infection of COVID-19 through a seroprevalence survey and to predict infection fatality rate (IFR) in Tanjung Priok, the hardest-hit sub-district by the COVID-19 in Jakarta, Indonesia.

Methods

We conducted a venous blood sampling (phlebotomy) to 3,196 individuals in Tanjung Priok between Nov 23, 2020, and Feb 19, 2021 to detect their antibodies against SARS-CoV-2. Using an enumerator-administered questionnaire, we collected data on the respondents’ demographic characteristics, COVID-19 test history, COVID-19 symptoms in the last 14 days, comorbidities, and protective behaviours during the last month. We employed descriptive analysis to estimate the seroprevalence and IFR.

Findings

The prevalence of Antibody against SARS-CoV-2 was 28.52% (95% CI 25.44–31.81%), with the result being higher in females than males (OR 1.20; 95% CI 1.02–1.42). By the end of the data collection (February 9, 2021), the cumulative cases of COVID-19 in Tanjung Priok were reported to be experienced by 9,861 people (2.4%). Those aged 45–65 were more likely to be seropositive than 15–19 years old (OR 1.42; 95% CI 1.05–1.92). Nearly one third (31%) of the subjects who developed at least one COVID-19 symptom in the last 14 days of the data collection were seropositive. The estimated IFR was 0.08% (95% CI 0.07–0.09), with a higher figure recorded in males (0.09; 95% CI 0.08–0.10) than females (0.07; 95% CI 0.06–0.08), and oldest age group (45–65) (0.21; 95% CI 0.18–0.23) than other younger groups.

Conclusion

An under-reporting issue was found between the estimated COVID-19 seroprevalence and the reported cumulative cases in Tanjung Priok. More efforts are required to amplify epidemiological surveillance by the provincial and local governments.

Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach

The coronavirus disease 2019 (COVID-19) pandemic has sparked the rapid development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics. However, emerging variants pose the risk for target dropout and false-negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY® SARS-CoV-2 Panel combines reverse-transcription polymerase chain reaction and matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses. Herein, we utilize a deidentified data set of 1262 SARS-CoV-2-positive specimens from Mount Sinai Health System (New York City) from December 2020 to April 2021 to evaluate target results and corresponding sequencing data. Overall, the level of PBS mismatches was greater in specimens with target dropout. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly specific for the Alpha (B.1.1.7) variant of concern. These data highlight the benefit of redundancy in target design and the potential for target performance to illuminate the dynamics of circulating SARS-CoV-2 variants.

Adherence and sustainability of interventions informing optimal control against the COVID-19 pandemic

Background

After one year of stop-and-go COVID-19 mitigation, in the spring of 2021 European countries still experienced sustained viral circulation due to the Alpha variant. As the prospect of entering a new pandemic phase through vaccination was drawing closer, a key challenge remained on how to balance the efficacy of long-lasting interventions and their impact on the quality of life.

Methods

Focusing on the third wave in France during spring 2021, we simulate intervention scenarios of varying intensity and duration, with potential waning of adherence over time, based on past mobility data and modeling estimates. We identify optimal strategies by balancing efficacy of interventions with a data-driven "distress" index, integrating intensity and duration of social distancing.

Results

We show that moderate interventions would require a much longer time to achieve the same result as high intensity lockdowns, with the additional risk of deteriorating control as adherence wanes. Shorter strict lockdowns are largely more effective than longer moderate lockdowns, for similar intermediate distress and infringement on individual freedom.

Conclusions

Our study shows that favoring milder interventions over more stringent short approaches on the basis of perceived acceptability could be detrimental in the long term, especially with waning adherence.

The Role of SARS-CoV-2 Testing on Hospitalizations in California

The rapid spread of the new SARS-CoV-2 virus triggered a global health crisis, disproportionately impacting people with pre-existing health conditions and particular demographic and socioeconomic characteristics. One of the main concerns of governments has been to avoid health systems becoming overwhelmed. For this reason, they have implemented a series of non-pharmaceutical measures to control the spread of the virus, with mass tests being one of the most effective controls. To date, public health officials continue to promote some of these measures, mainly due to delays in mass vaccination and the emergence of new virus strains. In this research, we studied the association between COVID-19 positivity rate and hospitalization rates at the county level in California using a mixed linear model. The analysis was performed in the three waves of confirmed COVID-19 cases registered in the state to September 2021. Our findings suggest that test positivity rate is consistently associated with hospitalization rates at the county level for all study waves. Demographic factors that seem to be related to higher hospitalization rates changed over time, as the profile of the pandemic impacted different fractions of the population in counties across California.

Early warning signal reliability varies with COVID-19 waves

Early warning signals (EWSs) aim to predict changes in complex systems from phenomenological signals in time series data. These signals have recently been shown to precede the emergence of disease outbreaks, offering hope that policymakers can make predictive rather than reactive management decisions. Here, using a novel, sequential analysis in combination with daily COVID-19 case data across 24 countries, we suggest that composite EWSs consisting of variance, autocorrelation and skewness can predict nonlinear case increases, but that the predictive ability of these tools varies between waves based upon the degree of critical slowing down present. Our work suggests that in highly monitored disease time series such as COVID-19, EWSs offer the opportunity for policymakers to improve the accuracy of urgent intervention decisions but best characterize hypothesized critical transitions.

SARS-CoV-2 virulence evolution: Avirulence theory, immunity and trade-offs

The COVID-19 pandemic has led to a resurgence of the debate on whether host-parasite interactions should evolve towards avirulence. In this review, we first show that SARS-CoV-2 virulence is evolving, before explaining why some expect the mortality caused by the epidemic to converge towards that of human seasonal alphacoronaviruses. Leaning on existing theory, we then include viral evolution into the picture and discuss hypotheses explaining why the virulence has increased since the beginning of the pandemic. Finally, we mention some potential scenarios for the future.

COVID-19 challenges: From SARS-CoV-2 infection to effective point-of-care diagnosis by electrochemical biosensing platforms

In January 2020, the World Health Organization (WHO) identified a new zoonotic virus, SARS-CoV-2, responsible for causing the COVID-19 (coronavirus disease 2019). Since then, there has been a collaborative trend between the scientific community and industry. Multidisciplinary research networks try to understand the whole SARS-CoV-2 pathophysiology and its relationship with the different grades of severity presented by COVID-19. The scientific community has gathered all the data in the quickly developed vaccines that offer a protective effect for all variants of the virus and promote new diagnostic alternatives able to have a high standard of efficiency, added to shorter response analysis time and portability. The industry enters in the context of accelerating the path taken by science until obtaining the final product. In this review, we show the principal diagnostic methods developed during the COVID-19 pandemic. However, when we observe the diagnostic tools section of an efficient infection outbreak containment report and the features required for such tools, we could observe a highlight of electrochemical biosensing platforms. Such devices present a high standard of analytical performance, are low-cost tools, easy to handle and interpret, and can be used in the most remote and low-resource regions. Therefore, probably, they are the ideal point-of-care diagnostic tools for pandemic scenarios.

AI-aided on-chip nucleic acid assay for smart diagnosis of infectious disease

Global pandemics such as COVID-19 have resulted in significant global social and economic disruption. Although polymerase chain reaction (PCR) is recommended as the standard test for identifying the SARS-CoV-2, conventional assays are time-consuming. In parallel, although artificial intelligence (AI) has been employed to contain the disease, the implementation of AI in PCR analytics, which may enhance the cognition of diagnostics, is quite rare. The information that the amplification curve reveals can reflect the dynamics of reactions. Here, we present a novel AI-aided on-chip approach by integrating deep learning with microfluidic paper-based analytical devices (µPADs) to detect synthetic RNA templates of the SARS-CoV-2 ORF1ab gene. The µPADs feature a multilayer structure by which the devices are compatible with conventional PCR instruments. During analysis, real-time PCR data were synchronously fed to three unsupervised learning models with deep neural networks, including RNN, LSTM, and GRU. Of these, the GRU is found to be most effective and accurate. Based on the experimentally obtained datasets, qualitative forecasting can be made as early as 13 cycles, which significantly enhances the efficiency of the PCR tests by 67.5% (∼40 min). Also, an accurate prediction of the end-point value of PCR curves can be obtained by GRU around 20 cycles. To further improve PCR testing efficiency, we also propose AI-aided dynamic evaluation criteria for determining critical cycle numbers, which enables real-time quantitative analysis of PCR tests. The presented approach is the first to integrate AI for on-chip PCR data analysis. It is capable of forecasting the final output and the trend of qPCR in addition to the conventional end-point Cq calculation. It is also capable of fully exploring the dynamics and intrinsic features of each reaction. This work leverages methodologies from diverse disciplines to provide perspectives and insights beyond the scope of a single scientific field. It is universally applicable and can be extended to multiple areas of fundamental research.

Evaluation of the Practicability of Biosynex Antigen Self-Test COVID-19 AG+ for the Detection of SARS-CoV-2 Nucleocapsid Protein from Self-Collected Nasal Mid-Turbinate Secretions in the General Public in France

Due to their ease-of-use, lateral flow assay SARS-CoV-2 antigen-detecting rapid diagnostic tests could be suitable candidates for antigen-detecting rapid diagnostic self-test (Ag-RDST). We evaluated the practicability of the Ag-RDST BIOSYNEX Antigen Self-Test COVID-19 Ag+ (Biosynex Swiss SA, Freiburg, Switzerland), using self-collected nasal secretions from the turbinate medium (NMT), in 106 prospectively included adult volunteers living in Paris, France. The majority of the participants correctly understood the instructions for use (94.4%; 95% confidence interval (CI): 88.3-97.4), showing a great ability to perform the entire self-test procedure to obtain a valid and interpretable result (100%; 95% CI: 96.5-100), and demonstrated the ability to correctly interpret test results (96.2%; 95% CI: 94.2-97.5) with a high level of general satisfaction. About one in eight participants (# 15%) needed verbal help to perform or interpret the test, and only 3.8% of test results were misinterpreted. By reference to multiplex real-time RT-PCR, the Ag-RDST showed 90.9% and 100% sensitivity and specificity, respectively, and high agreement (98.1%), reliability (0.94), and accuracy (90.9%) to detect SARS-CoV-2 antigen. Taken together, our study demonstrates the high usability and accuracy of BIOSYNEX Antigen Self-Test COVID-19 Ag+ for supervised self-collected NMT sampling in an unselected adult population living in France.

Assessing Values and Preferences Toward SARS-CoV-2 Self-testing Among the General Population and Their Representatives, Health Care Personnel, and Decision-Makers: Protocol for a Multicountry Mixed Methods Study

BACKGROUND

Accessible, safe, and client-centered SARS-CoV-2 testing services are an effective way to halt its transmission. Testing enables infected individuals to isolate or quarantine to prevent further transmission. In countries with limited health systems and laboratory capacity, it can be challenging to provide accessible and safe screening for COVID-19. Self-testing provides a convenient, private, and safe testing option; however, it also raises important concerns about lack of counseling and ensuring timely reporting of self-test results to national surveillance systems. Investigating community members' views and perceptions regarding SARS-CoV-2 self-testing is crucial to inform the most effective and safe strategies for implementing said testing.

OBJECTIVE

We aimed to determine whether SARS-CoV-2 self-testing was useful to diagnose and prevent the spread of SARS-CoV-2 for populations in low-resource settings and under which circumstances it would be acceptable.

METHODS

This multisite, mixed methods, observational study will be conducted in 9 countries-Brazil, India, Indonesia, Kenya, Malawi, Nigeria, Peru, the Philippines, and South Africa-and will consists of 2 components: cross-sectional surveys and interviews (semistructured and group) among 4 respondent groupings: the general population, general population representatives, health care workers, and decision-makers. General population and health care worker survey responses will be analyzed separately from each other, using bivariate and multivariate inferential analysis and descriptive statistics. Semistructured interviews and group interviews will be audiorecorded, transcribed, and coded for thematic comparative analysis.

RESULTS

As of November 19, 2021, participant enrollment is ongoing; 4364 participants have been enrolled in the general population survey, and 2233 participants have been enrolled in the health care workers survey. In the qualitative inquiry, 298 participants have been enrolled. We plan to complete data collection by December 31, 2021 and publish results in 2022 via publications, presentations at conferences, and dissemination events specifically targeted at local decision-makers, civil society, and patient groups.

CONCLUSIONS

The views and perceptions of local populations are crucial in the discussion of the safest strategies for implementing SARS-CoV-2 self-testing. We intend to identify sociocultural specificities that may hinder or accelerate the widespread utilization of SARS-CoV-2 self-testing.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

DERR1-10.2196/33088.

Point-of-care diagnostics: recent developments in a pandemic age

In this review, we provide an overview of developments in point-of-care (POC) diagnostics during the COVID-19 pandemic. We review these advances within the framework of a holistic POC ecosystem, focusing on points of interest - both technological and non-technological - to POC researchers and test developers. Technologically, we review design choices in assay chemistry, microfluidics, and instrumentation towards nucleic acid and protein detection for severe acute respiratory coronavirus 2 (SARS-CoV-2), and away from the lab bench, developments that supported the unprecedented rapid development, scale up, and deployment of POC devices. We describe common features in the POC technologies that obtained Emergency Use Authorization (EUA) for nucleic acid, antigen, and antibody tests, and how these tests fit into four distinct POC use cases. We conclude with implications for future pandemics, infectious disease monitoring, and digital health.

Nanodiagnostics to Face SARS-CoV-2 and Future Pandemics: From an Idea to the Market and Beyond

The COVID-19 pandemic made clear how our society requires quickly available tools to address emerging healthcare issues. Diagnostic assays and devices are used every day to screen for COVID-19 positive patients, with the aim to decide the appropriate treatment and containment measures. In this context, we would have expected to see the use of the most recent diagnostic technologies worldwide, including the advanced ones such as nano-biosensors capable to provide faster, more sensitive, cheaper, and high-throughput results than the standard polymerase chain reaction and lateral flow assays. Here we discuss why that has not been the case and why all the exciting diagnostic strategies published on a daily basis in peer-reviewed journals are not yet successful in reaching the market and being implemented in the clinical practice.

Effect of delayed awareness and fatigue on the efficacy of self-isolation in epidemic control

The isolation of infectious individuals is a key measure of public health for the control of communicable diseases. However, involving a strong perturbation of daily life, it often causes psychosocial distress, and severe financial and social costs. These may act as mechanisms limiting the adoption of the measure in the first place or the adherence throughout its full duration. In addition, difficulty of recognizing mild symptoms or lack of symptoms may impact awareness of the infection and further limit adoption. Here we study an epidemic model on a network of contacts accounting for limited adherence and delayed awareness to self-isolation, along with fatigue causing overhasty termination. The model allows us to estimate the role of each ingredient and analyze the tradeoff between adherence and duration of self-isolation. We find that the epidemic threshold is very sensitive to an effective compliance that combines the effects of imperfect adherence, delayed awareness and fatigue. If adherence improves for shorter quarantine periods, there exists an optimal duration of isolation, shorter than the infectious period. However, heterogeneities in the connectivity pattern, coupled to a reduced compliance for highly active individuals, may almost completely offset the effectiveness of self-isolation measures on the control of the epidemic.

A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue

Efforts to control SARS-CoV-2 have been challenged by the emergence of variant strains that have important implications for clinical and epidemiological decision making. Four variants of concern (VOCs) have been designated by the Centers for Disease Control and Prevention (CDC), namely, B.1.617.2 (delta), B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma), although the last three have been downgraded to variants being monitored (VBMs). VOCs and VBMs have shown increased transmissibility and/or disease severity, resistance to convalescent SARS-CoV-2 immunity and antibody therapeutics, and the potential to evade diagnostic detection. Methods are needed for point-of-care (POC) testing to rapidly identify these variants, protect vulnerable populations, and improve surveillance. Antigen-detection rapid diagnostic tests (Ag-RDTs) are ideal for POC use, but Ag-RDTs that recognize specific variants have not yet been implemented. Here, we describe a mAb (2E8) that is specific for the SARS-CoV-2 spike protein N501 residue. The 2E8 mAb can distinguish the delta VOC from variants with the N501Y meta-signature, which is characterized by convergent mutations that contribute to increased virulence and evasion of host immunity. Among the N501Y-containing mutants formerly designated as VOCs (alpha, beta, and gamma), a previously described mAb, CB6, can distinguish beta from alpha and gamma. When used in a sandwich ELISA, these mAbs sort these important SARS-CoV-2 variants into three diagnostic categories, namely, (1) delta, (2) alpha or gamma, and (3) beta. As delta is currently the predominant variant globally, they will be useful for POC testing to identify N501Y meta-signature variants, protect individuals in high-risk settings, and help detect epidemiological shifts among SARS-CoV-2 variants.

Assessment of the National Test Strategy on the Development of the COVID-19 Pandemic in Denmark

During the COVID-19 pandemic, Denmark has pursued a mass testing strategy culminating in the testing of 12.167 individuals per 100,000 inhabitants per day during the spring of 2021. The strategy included free access to COVID-19 testing, and since 2021, compulsory documentation for negative tests or vaccination has been required for access to workplace, educational institutions, restaurants, and many other places. Testing and subsequent isolation if testing was positive were voluntary. The present study provides an analysis of whether testing frequency in Denmark showed any correlation to hospitalizations throughout the relevant stages of the pandemic. Mass testing was found not to correlate significantly with the number of hospitalizations during the pandemic. Interestingly, during the highest level of testing in spring 2021 the fraction of positive tests increased slightly; thus, the Danish mass testing strategy, at its best, failed to reduce the prevalence of COVID-19. Furthermore, the relationship between positives in antigen testing and in rt-PCR testing indicated that many patients were not tested early in their infection when the risk of transmission was at the highest. In conclusion, the Danish mass testing strategy for COVID-19 does not appear to have a detectable correlation to the number of hospitalizations due to COVID-19.

Optimizing and evaluating PCR-based pooled screening during COVID-19 pandemics

Population screening played a substantial role in safely reopening the economy and avoiding new outbreaks of COVID-19. PCR-based pooled screening makes it possible to test the population with limited resources by pooling multiple individual samples. Our study compared different population-wide screening methods as transmission-mitigating interventions, including pooled PCR, individual PCR, and antigen screening. Incorporating testing-isolation process and individual-level viral load trajectories into an epidemic model, we further studied the impacts of testing-isolation on test sensitivities. Results show that the testing-isolation process could maintain a stable test sensitivity during the outbreak by removing most infected individuals, especially during the epidemic decline. Moreover, we compared the efficiency, accuracy, and cost of different screening methods during the pandemic. Our results show that PCR-based pooled screening is cost-effective in reversing the pandemic at low prevalence. When the prevalence is high, PCR-based pooled screening may not stop the outbreak. In contrast, antigen screening with sufficient frequency could reverse the epidemic, despite the high cost and the large numbers of false positives in the screening process.

Portable Tools for COVID-19 Point-of-Care Detection: A Review

Recently, several methods for SARS-CoV-2 detection have been developed to obtain rapid, portable, cheap, and easy-to-use diagnostic tools. This review paper summarizes and discusses studies on the development of point-of-care devices for SARS-CoV-2 diagnosis with comparisons between them from several aspects. Various detection methods of the recently developed portable COVID-19 biosensor will be presented in this review. The discussion is divided into four major classifications based on the target biomarkers of SARS-CoV-2, such as antibodies, nucleic acids, antigens, and metabolic products. An overview of the potential development for future study is also provided. Moreover, basic knowledge of biosensors is also explained for tutoring the implementation of theory into the research of COVID-19 biosensors. This review paper is aimed to provide a tutorial by collecting the information on the development of a point-of-care device for SARS-CoV-2 detection to provide information for further research and propose the new COVID-19 portable diagnostic tool.

Diagnostic Accuracy of SARS-CoV-2 Antigen Tests for Community Transmission Screening: A Systematic Review and Meta-Analysis

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) caused the global pandemic of coronavirus disease 2019 (COVID-19). Rapid identification and isolation of infectious patients are critical methods to block COVID-19 transmission. Antigen tests can contribute to prompt identification of infectious individuals. This meta-analysis aims to evaluate the diagnostic accuracy of antigen tests for SARS-CoV-2. We conducted a literature search in PubMed, Embase, the Cochrane Library, and Biomed Central databases. Studies evaluating the diagnostic accuracy of antigen tests for SARS-CoV-2 in community participants were included. Only English-language articles were reviewed. We included eligible studies that provided available data to construct a 2 × 2 table on a per-patient basis. Overall sensitivity and specificity for antigen tests were generated using a bivariate random-effects model. Eighteen studies with 34,865 participants were retrieved. The meta-analysis for SARS-CoV-2 antigen tests generated a pooled sensitivity of 0.82 and a pooled specificity of 1.00. A subgroup analysis of ten studies that reported outcomes for 5629 symptomatic participants generated a pooled sensitivity of 0.87 and a pooled specificity of 1.00. Antigen tests might have higher sensitivity in detecting SARS-CoV-2 in symptomatic patients in the community and may be an effective tool to identify patients to be quarantined to prevent further SARS-CoV-2 transmission.

Does the data tell the true story? A modelling assessment of early COVID-19 pandemic suppression and mitigation strategies in Ghana

This paper uses publicly available data and various statistical models to estimate the basic reproduction number (R0) and other disease parameters for Ghana's early COVID-19 pandemic outbreak. We also test the effectiveness of government imposition of public health measures to reduce the risk of transmission and impact of the pandemic, especially in the early phase. R0 is estimated from the statistical model as 3.21 using a 0.147 estimated growth rate [95% C.I.: 0.137-0.157] and a 15-day time to recovery after COVID-19 infection. This estimate of the initial R0 is consistent with others reported in the literature from other parts of Africa, China and Europe. Our results also indicate that COVID-19 transmission reduced consistently in Ghana after the imposition of public health interventions-such as border restrictions, intra-city movement, quarantine and isolation-during the first phase of the pandemic from March to May 2020. However, the time-dependent reproduction number (Rt) beyond mid-May 2020 does not represent the true situation, given that there was not a consistent testing regime in place. This is also confirmed by our Jack-knife bootstrap estimates which show that the positivity rate over-estimates the true incidence rate from mid-May 2020. Given concerns about virus mutations, delays in vaccination and a possible new wave of the pandemic, there is a need for systematic testing of a representative sample of the population to monitor the reproduction number. There is also an urgent need to increase the availability of testing for the general population to enable early detection, isolation and treatment of infected individuals to reduce progression to severe disease and mortality.

High-Throughput CRISPR-Cas13 SARS-CoV-2 Test

BACKGROUND

The ability to control the spread of COVID-19 continues to be hampered by a lack of rapid, scalable, and easily deployable diagnostic solutions.

METHODS

: We developed a diagnostic method based on CRISPR that can deliver sensitive, specific, and high-throughput detection of Sudden Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). The assay utilizes SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) for the qualitative detection of SARS-CoV-2 RNA and may be performed directly on a swab or saliva sample without nucleic acid extraction. The assay uses a 384-well format and provides results in less than one hour.

RESULTS

Assay performance was evaluated with 105 (55 negative, 50 positive) remnant SARS-CoV-2 specimens previously identified as positive using Food and Drug Administration emergency use authorized assays and re-tested with a modified version of the Centers for Disease Control and Prevention (CDC) RT-qPCR assay. When combined with magnetic bead-based extraction, the high throughput SHERLOCK SARS-CoV-2 assay was 100% concordant (n = 60) with the CDC RT-qPCR. When used with direct sample addition the high throughput assay was also 100% concordant with the CDC RT-qPCR direct method (n = 45). With direct saliva sample addition, the negative and positive percent agreements were 100% (15/15, 95% CI : 81.8-100%) and 88% (15/17, 95% CI : 63.6-98.5%), respectively, compared with results from a collaborating clinical laboratory.

CONCLUSIONS

This high throughput assay identifies SARS-CoV-2 from patient samples with or without nucleic acid extraction with high concordance to RT-qPCR methods. This test enables high complexity laboratories to rapidly increase their testing capacities with simple equipment.

Valid and Reliable Assessment of Upper Respiratory Tract Specimen Collection Skills during the COVID-19 Pandemic

Proper specimen collection is the most important step to ensure accurate testing for the coronavirus disease 2019 (COVID-19) and other infectious diseases. Assessment of healthcare workers' upper respiratory tract specimen collection skills is needed to ensure samples of high-quality clinical specimens for COVID-19 testing. This study explored the validity evidence for a theoretical MCQ-test and checklists developed for nasopharyngeal (NPS) and oropharyngeal (OPS) specimen collection skills assessment. We found good inter-item reliability (Cronbach's alpha = 0.76) for the items of the MCQ-test and high inter-rater reliability using the checklist for the assessment of OPS and NPS skills on 0.86 and 0.87, respectively. The MCQ scores were significantly different between experts (mean 98%) and novices (mean 66%), p < 0.001, and a pass/fail score of 91% was established. We found a significant discrimination between checklist scores of experts (mean 95% score for OPS and 89% for NPS) and novices (mean 50% score for OPS and 36% for NPS), p < 0.001, and a pass/fail score was established of 76% for OPS and 61% for NPS. Further, the results also demonstrated that a group of non-healthcare educated workers can perform upper respiratory tract specimen collection comparably to experts after a short and focused simulation-based training session. This study, therefore, provides validity evidence for the use of a theoretical and practical test for upper respiratory specimens' collection skills that can be used for competency-based training of the workers in the COVID-19 test centers.

Results of an early second PCR test performed on SARS-CoV-2 positive patients may support risk assessment for severe COVID-19

Identifying patients at increased risk for severe COVID-19 is of high priority during the pandemic as it could affect clinical management and shape public health guidelines. In this study we assessed whether a second PCR test conducted 2–7 days after a SARS-CoV-2 positive test could identify patients at risk for severe illness. Analysis of a nationwide electronic health records data of 1683 SARS-CoV-2 positive individuals indicated that a second negative PCR test result was associated with lower risk for severe illness compared to a positive result. This association was seen across different age groups and clinical settings. More importantly, it was not limited to recovering patients but also observed in patients who still had evidence of COVID-19 as determined by a subsequent positive PCR test. Our study suggests that an early second PCR test may be used as a supportive risk-assessment tool to improve disease management and patient care.

A novel benchmark for COVID-19 pandemic testing effectiveness enables the accurate prediction of new Intensive Care Unit admissions

The positivity rate of testing is currently used both as a benchmark of testing adequacy and for assessing the evolution of the COVID-19 pandemic. However, since the former is a prerequisite for the latter, its interpretation is often conflicting. We propose as a benchmark for COVID-19 testing effectiveness a new metric, termed 'Severity Detection Rate' (SDR), that represents the daily needs for new Intensive Care Unit (ICU) admissions, per 100 cases detected (t - i) days ago, per 10,000 tests performed (t - i) days ago. Based on the announced COVID-19 monitoring data in Greece from May 2020 until August 2021, we show that beyond a certain threshold of daily tests, SDR reaches a plateau of very low variability that begins to reflect testing adequacy. Due to the stabilization of SDR, it was possible to predict with great accuracy the daily needs for new ICU admissions, 12 days ahead of each testing data point, over a period of 10 months, with Pearson r = 0.98 (p = 10^-197), RMSE = 7.16. We strongly believe that this metric will help guide the timely decisions of both scientists and government officials to tackle pandemic spread and prevent ICU overload by setting effective testing requirements for accurate pandemic monitoring. We propose further study of this novel metric with data from more countries to confirm the validity of the current findings.

Impact of COVID-19 on materials science research innovation and related pandemic response

ABSTRACT

The scope of impact that the coronavirus SARS-CoV-2 has had and continues to have on life, society, and the world as we know it will be debated for years to come. One thing is for certain, scientists, engineers, clinicians, and researchers around the globe rallied to heed the call for innovation, particularly in the field of materials science. In this special issue of MRS Bulletin, we feature six articles, two of which showcase primary consumable materials research and development, along with four review articles highlighting materials innovation over the last 18 months in diagnostics, prevention, and treatment of SARS-CoV-2 infection.

GRAPHIC ABSTRACT

COVID-19 Testing and Diagnostics: A Review of Commercialized Technologies for Cost, Convenience and Quality of Tests

Population-scale and rapid testing for SARS-CoV-2 continues to be a priority for several parts of the world. We revisit the in vitro technology platforms for COVID-19 testing and diagnostics-molecular tests and rapid antigen tests, serology or antibody tests, and tests for the management of COVID-19 patients. Within each category of tests, we review the commercialized testing platforms, their analyzing systems, specimen collection protocols, testing methodologies, supply chain logistics, and related attributes. Our discussion is essentially focused on test products that have been granted emergency use authorization by the FDA to detect and diagnose COVID-19 infections. Different strategies for scaled-up and faster screening are covered here, such as pooled testing, screening programs, and surveillance testing. The near-term challenges lie in detecting subtle infectivity profiles, mapping the transmission dynamics of new variants, lowering the cost for testing, training a large healthcare workforce, and providing test kits for the masses. Through this review, we try to understand the feasibility of universal access to COVID-19 testing and diagnostics in the near future while being cognizant of the implicit tradeoffs during the development and distribution cycles of new testing platforms.

Evaluation of the Advanta Dx SARS-CoV-2 RT-PCR Assay, a High-Throughput Extraction-Free Diagnostic Test for the Detection of SARS-CoV-2 in Saliva: A Diagnostic Accuracy Study

Nasopharyngeal swab specimen (NPS) molecular testing is considered the gold standard for SARS-CoV-2 detection. However, saliva is an attractive, noninvasive specimen alternative. The aim of the study was to evaluate the diagnostic accuracy of Advanta Dx SARS-CoV-2 RT-PCR saliva-based assay against paired NPS tested with either NeumoDxTM SARS-CoV-2 assay or Abbott Real Time SARS-CoV-2 assay as the reference method. We prospectively evaluated the method in two settings: a diagnostic outpatient and a healthcare worker screening convenience sample, collected in November-December 2020. SARS-CoV-2 was detected in 27.7% (61/220) of diagnostic samples and in 5% (10/200) of screening samples. Overall, saliva test in diagnostic samples had a sensitivity of 88.5% (77.8-95.3%) and specificity of 98.1% (94.6-99.6%); in screening samples, the sensitivity was 90% (55.5-99.7%) and specificity 100% (98.1-100%). Our data suggests that the Fluidigm Advanta Dx RT-PCR saliva-based assay may be a reliable diagnostic tool for COVID-19 diagnosis in symptomatic individuals and screening asymptomatic healthcare workers.

Large-Scale Screening of Asymptomatic Persons for SARS-CoV-2 Variants of Concern and Gamma Takeover, Brazil

We performed a large-scale severe acute respiratory syndrome coronavirus 2 screening campaign using 2 PCR-based approaches, coupled with variant genotyping, aiming to provide a safer environment for employees of Federal University in Curitiba, Brazil. We observed the rapid spread of the Gamma variant of concern, which replaced other variants in <3 months.

On timeline of enhancing testing-capacity of COVID-19: A case study via an optimal replacement model

Process of enhancing testing-capacity regarding COVID-19 is a topic of interest. This task of enhancing is constrained by socio-economic background of a country either in favorable or unfavorable ways. In this paper, we investigate timing of enhancing testing-capacity as an optimal problem, where the enhancement is quantified via number of tests as an instant measure and recovered portion as a long-term measure. The proposed work is structured analogous to an optimal machine replacement model based on a non-linear integral equation. Overall model is partially identifiable and compatible parameter estimations are carried out for a specific case study covering an early stage scenario. In addition, scenario development criteria on demand and effort for enhancing testing-capacity are introduced for predictions. In one numerical experiment, it is observed that frequency of enhancing testing-capacity starts decreasing after two increments indicating a favorable direction amidst effort constraints.

Automated processing of thermal imaging to detect COVID-19

Rapid and sensitive screening tools for SARS-CoV-2 infection are essential to limit the spread of COVID-19 and to properly allocate national resources. Here, we developed a new point-of-care, non-contact thermal imaging tool to detect COVID-19, based on advanced image processing algorithms. We captured thermal images of the backs of individuals with and without COVID-19 using a portable thermal camera that connects directly to smartphones. Our novel image processing algorithms automatically extracted multiple texture and shape features of the thermal images and achieved an area under the curve (AUC) of 0.85 in COVID-19 detection with up to 92% sensitivity. Thermal imaging scores were inversely correlated with clinical variables associated with COVID-19 disease progression. In summary, we show, for the first time, that a hand-held thermal imaging device can be used to detect COVID-19. Non-invasive thermal imaging could be used to screen for COVID-19 in out-of-hospital settings, especially in low-income regions with limited imaging resources.

Spatial scales, patterns, and positivity trends of SARS-CoV-2 pandemics in mass rapid antigen testing in Slovakia

We study geographical epidemic scales and patterns and positivity trends of SARS-CoV-2 pandemics in mass antigen testing in Slovakia in 2020. The observed test positivity was exponentially distributed with a long scale exponential spatial trend, and its characteristic correlation length was approximately 10 km. Spatial scales also play an important role in test positivity reduction between two consecutive testing rounds. While test positivity decreased in all counties, it increased in individual municipalities with low test positivity in the earlier testing round in a way statistically different from a mean-reversion process. Also, non-residents testing influences the mass testing results as test positivity of non-residents was higher than of residents when testing was offered only in municipalities with the highest positivity in previous rounds. Our results provide direct guidance for pandemic geographical data surveillance and epidemic response management.

Detection of SARS-CoV-2 in Wastewater Northeast of Mexico City: Strategy for Monitoring and Prevalence of COVID-19

A month-long wastewater sampling project was conducted along the northeast periphery of Mexico City, specifically in the state of Hidalgo, to assess the presence of SARS-CoV-2. To determine the prevalence of infection and obtain a range of COVID-19 cases in the main metropolitan zones. Viral RNA residues (0-197,655 copies/L) were measured in wastewater from the five central municipalities in the state. By recording the number of RNA viral copies per liter, micro-basins delimitation, demographic and physiological data, an interval of infected people and virus prevalence was estimated using a Monte Carlo model (with 90% confidence) in the micro-basin of five municipalities with metropolitan influence or industrial activity. Our procedure determined that the percentage of the infected population ranges from 1.4% to 41.7%, while the official data reports 0.1-0.3%. This model is proposed as a helpful method of regional epidemiological monitoring through the analysis of viral prevalence.

A plug-and-play platform of ratiometric bioluminescent sensors for homogeneous immunoassays

Heterogeneous immunoassays such as ELISA have become indispensable in modern bioanalysis, yet translation into point-of-care assays is hindered by their dependence on external calibration and multiple washing and incubation steps. Here, we introduce RAPPID (Ratiometric Plug-and-Play Immunodiagnostics), a mix-and-measure homogeneous immunoassay platform that combines highly specific antibody-based detection with a ratiometric bioluminescent readout. The concept entails analyte-induced complementation of split NanoLuc luciferase fragments, photoconjugated to an antibody sandwich pair via protein G adapters. Introduction of a calibrator luciferase provides a robust ratiometric signal that allows direct in-sample calibration and quantitative measurements in complex media such as blood plasma. We developed RAPPID sensors that allow low-picomolar detection of several protein biomarkers, anti-drug antibodies, therapeutic antibodies, and both SARS-CoV-2 spike protein and anti-SARS-CoV-2 antibodies. With its easy-to-implement standardized workflow, RAPPID provides an attractive, fast, and low-cost alternative to traditional immunoassays, in an academic setting, in clinical laboratories, and for point-of-care applications.

Many current immunoassays require multiple washing, incubation and optimization steps. Here the authors present Ratiometric Plug-and-Play Immunodiagnostics (RAPPID), a generic assay platform that uses ratiometric bioluminescent detection to allow sandwich immunoassays to be performed directly in solution.

Retrospective SARS-CoV-2 IgG screening during the first wave (March-June 2020) of the COVID-19 pandemic in the United Kingdom

During the “first wave” of the coronavirus disease 2019 (COVID‐19) pandemic in the United Kingdom (March–June 2020), the city of Leicester was particularly hard hit, resulting in reimposed lockdown measures. Although initial polymerase chain reaction testing for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) was attempted within the community, testing was soon abandoned due to an inability to keep up with demand by local laboratories. It is therefore feasible that undiagnosed transmission of COVID‐19 in the community by asymptomatic individuals was a real possibility. Therefore, retrospective SARS‐CoV‐2 immunoglobulin G (IgG) testing of archived sera from out‐patients visiting University Hospitals of Leicester NHS Trust service was performed to investigate the transmission of SARS‐CoV‐2 in the community. A total of 1779 sera samples were tested from samples collected between 16th March and 3rd June 2020, of which 202 (11.35%) were SARS‐CoV‐2 IgG positive. Positivity was lowest in March (2.54%) at the beginning of the pandemic before peaking in April (17.16%) before a decline in May and June (11.16% and 12.68%, respectively). This retrospective screening offers some insight into the early patterns of SARS‐CoV‐2 transmission within a sampled community population during the first wave of the COVID‐19 pandemic; supporting the argument for more community screening during high incidences of pandemics.

Investigation into the transmission of SARS‐CoV‐2 through retrospectively screening community serum samples.

Growing evidence that improved community testing is required to reduce the rates of SARS‐CoV‐2 tranmission in the community.

Thoracic Surgery in the COVID-19 Pandemic: A Novel Approach to Reach Guideline Consensus

The COVID-19 pandemic challenges international and national healthcare systems. In the field of thoracic surgery, procedures may be deferred due to mandatory constraints of the access to diagnostics, staff and follow-up facilities. There is a lack of prospective data on the management of benign and malignant thoracic conditions in the pandemic. Therefore, we derived recommendations from 14 thoracic societies to address key questions on the topic of COVID-19 in the field of thoracic surgery. Respective recommendations were extracted and the degree of consensus among different organizations was calculated. A high degree of consensus was found to temporarily suspend non-critical elective procedures or procedures for benign conditions and to prioritize patients with symptomatic or advanced cancer. Prior to hospitalization, patients should be screened for respiratory symptoms indicating possible COVID-19 infection and most societies recommended to screen all patients for COVID-19 prior to admission. There was a weak consensus on the usage of serology tests and CT scans for COVID-19 diagnostics. Nearly all societies suggested to postpone elective procedures in patients with suspected or confirmed COVID-19 and recommended constant reevaluation of these patients. Additionally, we summarized recommendations focusing on precautions in the theater and the management of chest drains. This study provides a novel approach to informed guidance for thoracic surgeons during the COVID-19 pandemic in the absence of scientific evidence-based data.