Bayesian Analysis of Tests with Unknown Specificity and Sensitivity.

When testing for a rare disease, prevalence estimates can be highly sensitive to uncertainty in the specificity and sensitivity of the test. Bayesian inference is a natural way to propagate these uncertainties, with hierarchical modelling capturing variation in these parameters across experiments. Another concern is the people in the sample not being representative of the general population. Statistical adjustment cannot without strong assumptions correct for selection bias in an opt-in sample, but multilevel regression and post-stratification can at least adjust for known differences between the sample and the population. We demonstrate hierarchical regression and post-stratification models with code in Stan and discuss their application to a controversial recent study of SARS-CoV-2 antibodies in a sample of people from the Stanford University area. Wide posterior intervals make it impossible to evaluate the quantitative claims of that study regarding the number of unreported infections. For future studies, the methods described here should facilitate more accurate estimates of disease prevalence from imperfect tests performed on non-representative samples.

Advancements in COVID- 19 Testing: An in-depth overview.

COVID-19 rapidly evolved as a pandemic, killing and hospitalising millions of people, creating unprecedented hurdles for communities and health care systems worldwide. The rapidly evolving pandemic prompted the head of the World Health Organisation to deliver a critical message: "test, test, test." The response from the diagnostic industry and researchers worldwide was overwhelming, resulting in more than a thousand commercial tests available in the market worldwide. Several sampling approaches and diagnostic techniques have been employed from the early stages of the pandemic, such as SARS-CoV-2 detection by targeting the viral RNA or protein, indirectly via antibody testing, biochemical estimation, and various imaging techniques, and many are still in the various stages of development and yet to be marketed. Accurate testing techniques and appropriate sampling are the need of the hour to manage, diagnose and treat the pandemic, especially in the current crisis, where SARS-CoV-2 undergoes constant mutation, evolving into various strains, which are pretty challenging. The article discusses various testing techniques as well as screening methods for detection, treatment, and management of COVID-19 transmission, such as NAAT, PCR, isothermal detection including RT-LAMP, RPA, NASBA, RCA, SDA, NEAR, and TMA, CRISPR strategy, nanotechnology approach, metagenomic profiling, point of care tests, virus neutralization test, ELISA, biomarker estimation, utilization of imaging techniques such as CT, ultrasonography, brain MRI in COVID-19 complications, and other novel strategies including microarray methods, microfluidic methods and artificial intelligence with an emphasis on advancements in the testing strategies for the diagnosis, management, and prevention of COVID-19.

Collaboration-competition dilemma in flattening the COVID-19 curve.

Testing for COVID-19 is a key intervention that supports tracking and isolation to prevent further infections. However, diagnostic tests are a scarce and finite resource, so abundance in one country can quickly lead to shortages in others, creating a competitive landscape. Countries experience peaks in infections at different times, meaning that the need for diagnostic tests also peaks at different moments. This phase lag implies opportunities for a more collaborative approach, although countries might also worry about the risks of future shortages if they help others by reallocating their excess inventory of diagnostic tests. This article features a simulation model that connects three subsystems: COVID-19 transmission, the diagnostic test supply chain, and public policy interventions aimed at flattening the infection curve. This integrated system approach clarifies that, for public policies, there is a time to be risk-averse and a time for risk-taking, reflecting the different phases of the pandemic (contagion vs. recovery) and the dominant dynamic behavior that occurs in these phases (reinforcing vs. balancing). In the contagion phase, policymakers cannot afford to reject extra diagnostic tests and should take what they can get, in line with a competitive mindset. In the recovery phase, policymakers can afford to give away excess inventory to other countries in need (one-sided collaboration). When a country switches between taking and giving, in a form of two-sided collaboration, it can flatten the curve, not only for itself but also for others.

An Old Acquaintance: Could Adenoviruses Be Our Next Pandemic Threat?

Human adenoviruses (HAdV) are one of the most important pathogens detected in acute respiratory diseases in pediatrics and immunocompromised patients. In 1953, Wallace Rowe described it for the first time in oropharyngeal lymphatic tissue. To date, more than 110 types of HAdV have been described, with different cellular tropisms. They can cause respiratory and gastrointestinal symptoms, even urinary tract inflammation, although most infections are asymptomatic. However, there is a population at risk that can develop serious and even lethal conditions. These viruses have a double-stranded DNA genome, 25-48 kbp, 90 nm in diameter, without a mantle, are stable in the environment, and resistant to fat-soluble detergents. Currently the diagnosis is made with lateral flow immunochromatography or molecular biology through a polymerase chain reaction. This review aimed to highlight the HAdV variability and the pandemic potential that a HAdV3 and 7 recombinant could have considering the aggressive outbreaks produced in health facilities. Herein, we described the characteristics of HAdV, from the infection to treatment, vaccine development, and the evaluation of the social determinants of health associated with HAdV, suggesting the necessary measures for future sanitary control to prevent disasters such as the SARS-CoV-2 pandemic, with an emphasis on the use of recombinant AdV vaccines to control other potential pandemics.

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

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

Evolution of SARS-CoV-2 Variants: Implications on Immune Escape, Vaccination, Therapeutic and Diagnostic Strategies.

The COVID-19 pandemic caused by SARS-CoV-2 is associated with a lower fatality rate than its SARS and MERS counterparts. However, the rapid evolution of SARS-CoV-2 has given rise to multiple variants with varying pathogenicity and transmissibility, such as the Delta and Omicron variants. Individuals with advanced age or underlying comorbidities, including hypertension, diabetes and cardiovascular diseases, are at a higher risk of increased disease severity. Hence, this has resulted in an urgent need for the development of better therapeutic and preventive approaches. This review describes the origin and evolution of human coronaviruses, particularly SARS-CoV-2 and its variants as well as sub-variants. Risk factors that contribute to disease severity and the implications of co-infections are also considered. In addition, various antiviral strategies against COVID-19, including novel and repurposed antiviral drugs targeting viral and host proteins, as well as immunotherapeutic strategies, are discussed. We critically evaluate strategies of current and emerging vaccines against SARS-CoV-2 and their efficacy, including immune evasion by new variants and sub-variants. The impact of SARS-CoV-2 evolution on COVID-19 diagnostic testing is also examined. Collectively, global research and public health authorities, along with all sectors of society, need to better prepare against upcoming variants and future coronavirus outbreaks.

Intelligent Information System for Detection of COVID-19 Based on AI

The pandemic is changing the clinical needs and potential for AI-driven computer-assisted diagnoses (CDS). Since the beginning, rapid identification of COVID-19 patients has been a significant difficulty, especially in areas with limited diagnostic testing capacity. Intelligent Information System (IIS) represents the knowledge progression of available data. It has been directed by recent technological integration, data processing, and distribution in multiple computational environments. Intelligent Information Systems are aimed to work like an advanced human brain, where, as per the requirement of changing circumstances, the optimal decision can be evolved. IIS tools are expected to be adaptive, which may vary according to their processing data. As a result, the goal of this study was to provide a complete analysis of various technologies for combating COVID-19, with a focus on their features, problems, and domiciliation nation. Our findings demonstrate the performance of developing technologies. © 2023, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

A comprehensive review and clinical guide to molecular and serological diagnostic tests and future development: In vitro diagnostic testing for COVID-19

COVID-19 is a contagious syndrome caused by SARS Coronavirus 2 (SARS-CoV-2) that requires rapid diagnostic testing to identify and manage in the affected persons, characterize epidemiology, and promptly make public health decisions and manage the virus present in the affected person and promptly make public health decisions by characterizing the epidemiology. Technical problems, especially contamination occurring during manual real-time polymerase chain reaction (RT-PCR), can result in false-positive NAAT results. In some cases, RNA detection technology and antigen testing are alternatives to RT-PCR. Sequencing is vital for tracking the SARS-CoV-2 genome's evolution, while antibody testing is beneficial for epidemiology. SARS-CoV-2 testing can be made safer, faster, and easier without losing accuracy. Continued technological advancements, including smartphone integration, will help in the current epidemic and prepare for the next. Nanotechnology-enabled progress in the health sector has aided disease and pandemic management at an early stage. These nanotechnology-based analytical tools can be used to quickly diagnose COVID-19. The SPOT system is used to diagnose the coronavirus quickly, sensibly, accurately, and with portability. The SPOT assay consists of RT-LAMP, followed by pfAgo-based target sequence detection. In addition, SPOT system was used to detect both positive and negative SARS-CoV-2 samples. This combination of speed, precision, sensitivity, and mobility will allow for cost-effective and high-volume COVID-19 testing. © 2023 the author(s), published by De Gruyter.

COVID-19: Test, Test and Test.

A new virus was identified in late December 2019 when China reported the first cases of pneumonia in Wuhan, and a global COVID-19 pandemic followed. The world was not late to respond, with a number of sweeping measures ranging from social distancing protocols, stringent hygienic practices, and nation-wide lockdowns, as well as COVID-19 testing campaigns in an attempt to prevent the transmission of the disease and contain the pandemic. Currently, different types of diagnostic testing have been adopted globally, such as nucleic acid detection tests, immunological tests and imaging approaches; however, real-time reverse transcriptase-polymerase chain reaction (RT-PCR) remains the "gold standard" for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pre-analytical factors, such as specimen selection and collection, are crucial for RT-PCR, and any suboptimal collection may contribute to false-negative results. Herein, we address some of the specimen types that have been used in molecular detection methods for COVID-19. However, the pandemic is still evolving, and information might change as more studies are conducted.

SARS-CoV-2 Seroprevalence Compared with Confirmed COVID-19 Cases among Children, Colorado, USA, May-July 2021.

To compare SARS-CoV-2 antibody seroprevalence among children with seropositive confirmed COVID-19 case counts (case ascertainment by molecular amplification) in Colorado, USA, we conducted a cross-sectional serosurvey during May-July 2021. For a convenience sample of 829 Colorado children, SARS-CoV-2 seroprevalence was 36.7%, compared with prevalence of 6.5% according to individually matched COVID-19 test results reported to public health. Compared with non-Hispanic White children, seroprevalence was higher among Hispanic, non-Hispanic Black, and non-Hispanic other race children, and case ascertainment was significantly lower among Hispanic and non-Hispanic Black children. This serosurvey accurately estimated SARS-CoV-2 prevalence among children compared with confirmed COVID-19 case counts and revealed substantial racial/ethnic disparities in infections and case ascertainment. Continued efforts to address racial and ethnic differences in disease burden and to overcome potential barriers to case ascertainment, including access to testing, may help mitigate these ongoing disparities.

The Usability of Homelab, a Digital Self-service at a Dutch General Practice, for Diagnostic Tests: Pilot Study With a Questionnaire.

BACKGROUND: eHealth potentially can make health care more accessible and efficient and help reduce the workload in primary health care. Homelab is an eHealth tool implemented in a general practice environment, and it offers relatively simple laboratory diagnostic tests without the referral of the general practitioner. After logging in this eHealth tool, patients select and order a diagnostic test based on their symptoms. The test results are presented online to the general practitioner and the patient. OBJECTIVE: This study aims to evaluate the use, usability, and user characteristics of Homelab. Further, it aims to evaluate whether Homelab replaces an appointment with the general practitioner. METHODS: Homelab has been implemented since May 2021 as a pilot in a Dutch general practice. The number of requests and the ordered diagnostic packages are monitored. After using Homelab, patients are invited to complete a short questionnaire. The questionnaire contains demographic questions and assesses usability using the System Usability Scale (10 items). In addition, questions about requesting an appointment with the general practitioner without Homelab are included. All data were anonymous. RESULTS: The questionnaire was filled by 74 individual patients. The mean age of the patients was 40.33 (SD 12.11) years, and half of them were females (39/74, 53%). The majority of the patients were highly educated (56/74, 76%) and employed (53/74, 72%). Approximately 81% (60/74) of the patients reported that they would use Homelab again in the future and 66% (49/74) reported that they would have gone to the general practitioner if they had not used Homelab. The usability of Homelab was perceived higher by the younger age group (mean 73.96, SD 14.74) than by the older age group (mean 61.59, SD 14.37). In total, 106 test packages were ordered over 1 year, and the most requested diagnostic package was "Am I still healthy? I want to do my annual health checkup." Homelab was used the most during the months of the COVID-19 lockdown. CONCLUSIONS: The use of Homelab, a digital self-service for ordering diagnostic tests, was monitored in this study, and its usability was perceived as above average. Our findings showed that patients are willing to use Homelab in the future and they would use it most of the time as a replacement for regular consultations. Homelab offers opportunities for more accessible and efficient health care for both the patient and the general practitioner.

Agile design and development of a high throughput cobas SARS-CoV-2 RT-PCR diagnostic test.

Diagnostic testing is essential for management of the COVID-19 pandemic. An agile assay design methodology, optimized for the cobas® 6800/8800 system, was used to develop a dual-target, qualitative SARS-CoV-2 RT-PCR test using commercially available reagents and existing sample processing and thermocycling profiles. The limit of detection was 30-52 copies/mL for USA-WA1/2020. Assay sensitivity was confirmed for SARS-CoV-2 variants Alpha, Beta, Gamma, Delta and Kappa. The coefficients of variation of the cycle threshold number (Ct) were between 1.1 and 2.2%. There was no difference in Ct using nasopharyngeal compared to oropharyngeal swabs in universal transport medium (UTM). A small increase in Ct was observed with specimens collected in cobas PCR medium compared to UTM. In silico analysis indicated that the dual-target test is capable of detecting all >1,800,000 SARS-CoV-2 sequences in the GISAID database. Our agile assay design approach facilitated rapid development and deployment of this SARS-CoV-2 RT-PCR test.

Strategies for using antigen rapid diagnostic tests to reduce transmission of SARS-CoV-2 in low- and middle-income countries: a mathematical modelling study applied to Zambia.

BACKGROUND: Increasing the availability of antigen rapid diagnostic tests (Ag-RDTs) in low- and middle-income countries (LMICs) is key to alleviating global SARS-CoV-2 testing inequity (median testing rate in December 2021-March 2022 when the Omicron variant was spreading in multiple countries; high-income countries = 600 tests/100,000 people/day; LMICs = 14 tests/100,000 people/day). However, target testing levels and effectiveness of asymptomatic community screening to impact SARS-CoV-2 transmission in LMICs are unclear. METHODS: We used PATAT, an LMIC-focused agent-based model to simulate COVID-19 epidemics, varying the amount of Ag-RDTs available for symptomatic testing at healthcare facilities and asymptomatic community testing in different social settings. We assumed that testing was a function of access to healthcare facilities and availability of Ag-RDTs. We explicitly modelled symptomatic testing demand from non-SARS-CoV-2 infected individuals and measured impact based on the number of infections averted due to test-and-isolate. RESULTS: Testing symptomatic individuals yields greater benefits than any asymptomatic community testing strategy until most symptomatic individuals who sought testing have been tested. Meeting symptomatic testing demand likely requires at least 200-400 tests/100,000 people/day on average as symptomatic testing demand is highly influenced by non-SARS-CoV-2 infected individuals. After symptomatic testing demand is satisfied, excess tests to proactively screen for asymptomatic infections among household members yields the largest additional infections averted. CONCLUSIONS: Testing strategies aimed at reducing transmission should prioritize symptomatic testing and incentivizing test-positive individuals to adhere to isolation to maximize effectiveness.

The Role of a Tertiary Level Safety Net Hospital in New York City's 2022 Mpox Outbreak.

Similar to the early phases of the COVID-19 pandemic, New York City was the national epicenter of the ongoing 2022 mpox (formerly monkeypox) outbreak. Cases quickly began to rise in July 2022, primarily in gay, bisexual, or other men who have sex with men. Tools in the form of a reliable diagnostic test, an effective vaccine, and a viable treatment option have been available from the onset, although logistically complex to roll out. The special pathogens program at NYC Health + Hospitals/Bellevue, the flagship facility for the largest public hospital system in the United States, collaborated with multiple departments within Bellevue, the hospital system, and the NYC Department of Health and Mental Hygiene, to swiftly establish ambulatory testing, immunizations, patient-centered inpatient care, and outpatient therapeutics. With the ongoing mpox outbreak, hospitals and local health departments must prepare a systemwide response to identify and isolate patients and provide high-quality care. Findings from our experience can help guide institutions in developing a multipronged, comprehensive response to the ongoing mpox outbreak.

Evaluation of RT-LAMP Assay for Rapid Detection of SARS-CoV-2.

OBJECTIVE: To evaluate the accuracy of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in community or primary-care settings. METHOD: We systematically searched the Web of Science, Embase, PubMed, and Cochrane Library databases. We conducted quality evaluation using ReviewManager software (version 5.0). We then used MetaDisc software (version 1.4) and Stata software (version 12.0) to build forest plots, along with a Deeks funnel plot and a bivariate boxplot for analysis. RESULT: Overall, the sensitivity, specificity, and diagnostic odds ratio were 0.79, 0.97, and 328.18, respectively. The sensitivity for the subgroup with RNA extraction appeared to be higher, at 0.88 (0.86-0.90), compared to the subgroup without RNA extraction, at 0.50 (0.45-0.55), with no significant difference in specificity. CONCLUSION: RT-LAMP assay exhibited high specificity regarding current SARS-CoV-2 infection. However, its overall sensitivity was relatively moderate. Extracting RNA was found to be beneficial in improving sensitivity.

The dynamic relationship between COVID-19 cases and SARS-CoV-2 wastewater concentrations across time and space: Considerations for model training data sets.

During the COVID-19 pandemic, wastewater-based surveillance has been used alongside diagnostic testing to monitor infection rates. With the decline in cases reported to public health departments due to at-home testing, wastewater data may serve as the primary input for epidemiological models, but training these models is not straightforward. We explored factors affecting noise and bias in the ratio between wastewater and case data collected in 26 sewersheds in California from October 2020 to March 2022. The strength of the relationship between wastewater and case data appeared dependent on sampling frequency and population size, but was not increased by wastewater normalization to flow rate or case count normalization to testing rates. Additionally, the lead and lag times between wastewater and case data varied over time and space, and the ratio of log-transformed individual cases to wastewater concentrations changed over time. This ratio decreased between the Epsilon/Alpha and Delta variant surges of COVID-19 and increased during the Omicron BA.1 variant surge, and was also related to the diagnostic testing rate. Based on this analysis, we present a framework of scenarios describing the dynamics of the case to wastewater ratio to aid in data handling decisions for ongoing modeling efforts.

Limitations introduced by a low participation rate of SARS-CoV-2 seroprevalence data.

BACKGROUND: There has been a large influx of COVID-19 seroprevalence studies, but comparability between the seroprevalence estimates has been an issue because of heterogeneities in testing platforms and study methodology. One potential source of heterogeneity is the response or participation rate. METHODS: We conducted a review of participation rates (PR) in SARS-CoV-2 seroprevalence studies collected by SeroTracker and examined their effect on the validity of study conclusions. PR was calculated as the count of participants for whom the investigators had collected a valid sample, divided by the number of people invited to participate in the study. A multivariable beta generalized linear model with logit link was fitted to determine if the PR of international household and community-based seroprevalence studies was associated with the factors of interest, from 1 December 2019 to 10 March 2021. RESULTS: We identified 90 papers based on screening and were able to calculate the PR for 35 out of 90 papers (39%), with a median PR of 70% and an interquartile range of 40.92; 61% of the studies did not report PR. CONCLUSIONS: Many SARS-CoV-2 seroprevalence studies do not report PR. It is unclear what the median PR rate would be had a larger portion not had limitations in reporting. Low participation rates indicate limited representativeness of results. Non-probabilistic sampling frames were associated with higher participation rates but may be less representative. Standardized definitions of participation rate and data reporting necessary for the PR calculations are essential for understanding the representativeness of seroprevalence estimates in the population of interest.

Evaluation of STANDARD TM M10 SARS-CoV-2, a Novel Cartridge-Based Real-Time PCR Assay for the Rapid Identification of Severe Acute Respiratory Syndrome Coronavirus 2

Since the beginning of the pandemic, SARS-CoV-2 has caused problems for all of world's population, not only in terms of deaths but also in terms of overloading healthcare facilities in all countries. Diagnosis is one of the key aspects of controlling the spread of SARS-CoV-2, and among the current molecular techniques, real-time PCR is considered as the gold standard. The availability of tests that allow for the rapid and accurate identification of SARS-CoV-2 is therefore of considerable importance. Moreover, if these tests allow for even minimal intervention by the operator, any risk of contamination is reduced. In this study, the performances of the new STANDARDTM M10 SARS-CoV-2 (SD Biosensor Inc., Suwon, Korea) rapid molecular test, which incorporates the above-mentioned features, were characterized. The clinical and analytical performances measured by testing different variants circulating in Italy of STANDARDTM M10 SARS-CoV-2 were compared to the test already on the market and recognized as the gold standard: Xpert Xpress SARS-CoV-2 (Cepheid, Sunnyvale, CA, USA). The results obtained between the two tests are largely comparable, suggesting that STANDARDTM M10 SARS-CoV-2 can be used with excellent results in the fight against the global spread of SARS-CoV-2. [ FROM AUTHOR]

Development and design of a diagnostic report to support communication in dementia: Co-creation with patients and care partners.

Introduction: Clear communication of diagnostic test results and dementia diagnosis is challenging yet important to empower patients and care partners. A personalized diagnostic report could support the communication of dementia diagnostics and aid patients' understanding of diagnosis. In this study, we aimed to design a diagnostic report in co-creation with patients and care partners. Methods: We used a mixed-methods approach, combining surveys with focus groups in iteration. Phase 1 consisted of an international survey assessing needs among patients (n = 50) and care partners (n = 46), and phase 2 consisted of focus group meetings (n = 3) to co-create the content and to hands-on co-design the layout of the diagnostic report with patients (n = 7) and care partners (n = 7). Phase 3 validated results from phase 2 in a survey among patients (n = 28) and care partners (n = 12), and phase 4 comprised final feedback by dementia (care) experts (n = 5). Descriptive statistics were used to report quantitative results and directed content analysis was used to analyze qualitative data. Results: Most patients (39/50, 78%) and care partners (38/46, 83%) positively valued a diagnostic report to summarize test results. The report should be brief, straightforward, and comprise results of the diagnostic tests, including brain imaging and information on future expectations. Despite a clear preference for visual display of test results, several visualization options were deemed best and were equally comprehended. Discussion: In this study, we developed a prototype of a personalized patient report through an iterative design process and learned that co-creation is highly valuable to meet the specific needs of end-users.