Ensuring accuracy in the development and application of nucleic acid amplification tests (NAATs) for infectious disease.

Diagnostic tests were heralded as crucial during the Coronavirus disease (COVID-19) pandemic with most of the key methods using bioanalytical approaches that detected larger molecules (RNA, protein antigens or antibodies) rather than conventional clinical biochemical techniques. Nucleic Acid Amplification Tests (NAATs), like the Polymerase Chain Reaction (PCR), and other molecular methods, like sequencing (that often work in combination with NAATs), were essential to the diagnosis and management during COVID-19. This was exemplified both early in the pandemic but also later on, following the emergence of new genetic SARS-CoV-2 variants. The 100 day mission to respond to future pandemic threats highlights the need for effective diagnostics, therapeutics and vaccines. Of the three, diagnostics represents the first opportunity to manage infectious diseases while also being the most poorly supported in terms of the infrastructure needed to demonstrate effectiveness. Where performance targets exist, they are not well served by consensus on how to demonstrate they are being met; this includes analytical factors such as limit of detection (LOD) false positive results as well as how to approach clinical evaluation. The selection of gold standards or use of epidemiological factors such as predictive value, reference ranges or clinical thresholds are seldom correctly considered. The attention placed on molecular diagnostic tests during COVID-19 illustrates important considerations and assumptions on the use of these methods for infectious disease diagnosis and beyond. In this manuscript, we discuss state-of-the-art approaches to diagnostic evaluation and explore how they may be better tailored to diagnostic techniques like NAATs to maximise the impact of these highly versatile bioanalytical tools, both generally and during future outbreaks.

Patient Self-Testing of Kidney Function at Home, a Prospective Clinical Feasibility Study in Kidney Transplant Recipients.

Introduction: People with long-term health conditions often attend clinics for kidney function tests. The Self-Testing Own Kidneys (STOK) study assessed feasibility of kidney transplant recipients using hand-held devices to self-test kidney function at home and investigated agreement between home self-test and standard clinic test results. Methods: A prospective, observational, single-center, clinical feasibility study (TRN: ISRCTN68116915), with N = 15 stable kidney transplant recipients, investigated blood potassium and creatinine results agreement between index self-tests at home (patient self-testing of capillary blood, using Abbott i-STAT Alinity analyzers [i-STAT]) and reference tests in clinic (staff sampled venous blood, analyzed with laboratory Siemens Advia Chemistry XPT analyzer) using Bland-Altman and error grid analysis. Results: The mean within-patient difference between index and reference test in creatinine was 2.25 µmol/l (95% confidence interval [CI]: -12.13, 16.81 µmol/l) and in potassium was 0.66 mmol/l (95% CI: -1.47, 2.79 mmol/l). All creatinine pairs and 27 of 40 (67.5%) potassium pairs were judged clinically equivalent. Planned follow-up analysis suggests that biochemical variables associated with potassium measurement in capillary blood were predominant sources of paired test result differences. Paired patient and nurse i-STAT capillary blood test potassium results were not statistically significantly different. Conclusions: This small feasibility study observed that training selected patients to competently use hand-held devices to self-test kidney function at home is possible. Self-test creatinine results showed good analytical and clinical agreement with standard clinic test results. Self-test potassium results showed poorer agreement with standard clinic test results; however, patient self-use of i-STATs at home was not a statistically significant source of difference between paired potassium test results.

Perceived feasibility, facilitators and barriers to incorporating point-of-care testing for SARS-CoV-2 into emergency medical services by ambulance service staff: a survey-based approach.

OBJECTIVES: This body of work aimed to elicit ambulance service staff's perceptions on the barriers and facilitators to adoption, and clinical utility of incorporating rapid SARS-CoV-2 testing during ambulance assessments. DESIGN: A mixed-methods survey-based project using a framework analysis method to organise qualitative data. SETTING: Emergency and non-emergency care ambulatory services in the UK were approached to take part. PARTICIPANTS: Current, practising members of the UK ambulance service (paramedics, technicians, assistants and other staff) were included in this body of work. RESULTS: Survey 1: 226 responses were collected between 3 December 2020 and 11 January 2021, 179 (79.2%) of which were completed in full. While the majority of respondents indicated that an ambulance-based testing strategy was feasible in concept (143/190, 75.3%), major barriers to adoption were noted. Many open-ended responses cited concerns regarding misuse of the service by the general public and other healthcare services, timing and conveyance issues, and increased workloads, alongside training and safety concerns. Survey 2: 26 responses were received between 8 February 2021 and 22 February 2021 to this follow-up survey. Survey 2 revealed conveyance decision-making, and risk stratification to be the most frequently prioritised use cases among ambulance service staff. Optimal test characteristics for clinical adoption according to respondents were; accuracy (above 90% sensitivity and specificity), rapidity (<30 min time to results) and ease of sample acquisition. CONCLUSIONS: The majority of commercially available lateral flow devices are unlikely to be supported by paramedics as their duty of care requires both rapid and accurate results that can inform clinical decision making in an emergency situation. Further investigation is needed to define acceptable test characteristics and criteria required for ambulance service staff to be confident and supportive of deployment of a SARS-CoV-2 test in an emergency care setting.

Systematic review of studies investigating ventilator associated pneumonia diagnostics in intensive care.

BACKGROUND: Ventilator-associated pneumonia (VAP) is an important diagnosis in critical care. VAP research is complicated by the lack of agreed diagnostic criteria and reference standard test criteria. Our aim was to review which reference standard tests are used to evaluate novel index tests for suspected VAP. METHODS: We conducted a comprehensive search using electronic databases and hand reference checks. The Cochrane Library, MEDLINE, CINHAL, EMBASE, and web of science were searched from 2008 until November 2018. All terms related to VAP diagnostics in the intensive treatment unit were used to conduct the search. We adopted a checklist from the critical appraisal skills programme checklist for diagnostic studies to assess the quality of the included studies. RESULTS: We identified 2441 records, of which 178 were selected for full-text review. Following methodological examination and quality assessment, 44 studies were included in narrative data synthesis. Thirty-two (72.7%) studies utilised a sole microbiological reference standard; the remaining 12 studies utilised a composite reference standard, nine of which included a mandatory microbiological criterion. Histopathological criteria were optional in four studies but mandatory in none. CONCLUSIONS: Nearly all reference standards for VAP used in diagnostic test research required some microbiological confirmation of infection, with BAL culture being the most common reference standard used.

Care pathway and prioritization of rapid testing for COVID-19 in UK hospitals: a qualitative evaluation.

OBJECTIVES: The second wave of the coronavirus pandemic is now established, occurring at a time of winter pressure on acute care in the NHS. This is likely to be more challenging then the first wave for the diagnosis of COVID-19 because of the similar symptomology with other respiratory conditions highly prevalent in winter. This study sought to understand the care pathways in place in UK NHS hospitals during the first wave (March-July 2020) for identification of patients with COVID-19 and to learn lessons to inform optimal testing strategies within the COVID-19 National Diagnostic Research and Evaluation Platform (CONDOR). DESIGN, SETTING & PARTICIPANTS: Sixteen hospital-based clinicians from 12 UK NHS Trusts covering 10 different specialties were interviewed following a semi-structured topic guide. Data were coded soon after the interviews and analysed thematically. RESULTS: We developed a diagrammatic, high-level visualisation of the care pathway describing the main clinical decisions associated with the diagnosis and management of patients with suspected COVID-19. COVID-19 testing influenced infection control considerations more so than treatment decisions. Two main features of service provision influenced the patient management significantly: access to rapid laboratory testing and the number of single occupancy rooms. If time to return of result was greater than 24 h, patients with a presumptive diagnosis would often be cohorted based on clinical suspicion alone. Undetected COVID-19 during this time could therefore lead to an increased risk of viral transmission. CONCLUSIONS: During the winter months, priority for provision of rapid testing at admission should be given to hospitals with limited access to laboratory services and single room availability. Access to rapid testing is essential for urgent decisions related to emergency surgery, maternity services and organ transplant. The pathway and prioritization of need will inform the economic modelling, clinical evaluations, and implementation of new clinical tests in UK.

Utility of Routine Laboratory Biomarkers to Detect COVID-19: A Systematic Review and Meta-Analysis.

No routine laboratory biomarkers perform well enough in diagnosing COVID-19 in isolation for them to be used as a standalone diagnostic test or to help clinicians prioritize patients for treatment. Instead, other diagnostic tests are needed. The aim of this work was to statistically summarise routine laboratory biomarker measurements in COVID-19-positive and -negative patients to inform future work. A systematic literature review and meta-analysis were performed. The search included names of commonly used, routine laboratory tests in the UK NHS, and focused on research papers reporting laboratory results of patients diagnosed with COVID-19. A random effects meta-analysis of the standardized mean difference between COVID-19-positive and -negative groups was conducted for each biomarker. When comparing reported laboratory biomarker results, we identified decreased white blood cell, neutrophil, lymphocyte, eosinophil, and platelet counts; while lactate dehydrogenase, aspartate aminotransferase, and alanine aminotransferase were elevated in COVID-19-positive compared to COVID-19-negative patients. Differences were identified across a number of routine laboratory biomarkers between COVID-19-positive and -negative patients. Further research is required to identify whether routine laboratory biomarkers can be used in the development of a clinical scoring system to aid with triage of patients.

Unmet clinical needs for COVID-19 tests in UK health and social care settings.

There is an urgent requirement to identify which clinical settings are in most need of COVID-19 tests and the priority role(s) for tests in these settings to accelerate the development of tests fit for purpose in health and social care across the UK. This study sought to identify and prioritize unmet clinical needs for COVID-19 tests across different settings within the UK health and social care sector via an online survey of health and social care professionals and policymakers. Four hundred and forty-seven responses were received between 22nd May and 15th June 2020. Hospitals and care homes were recognized as the settings with the greatest unmet clinical need for COVID-19 diagnostics, despite reporting more access to laboratory molecular testing than other settings. Hospital staff identified a need for diagnostic tests for symptomatic workers and patients. In contrast, care home staff expressed an urgency for screening at the front door to protect high-risk residents and limit transmission. The length of time to test result was considered a widespread problem with current testing across all settings. Rapid tests for staff were regarded as an area of need across general practice and dental settings alongside tests to limit antibiotics use.

At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR-based tests? A systematic review of individual participant data.

BACKGROUND: Tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA) using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity. METHODS: We conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. We searched PubMed, LitCOVID, medRxiv, and COVID-19 Living Evidence databases. We assessed risk of bias using a QUADAS-2 adaptation. Outcomes were the percentage of positive test results by time and the duration of detectable virus, by anatomical sampling sites. RESULTS: Of 5078 studies screened, we included 32 studies with 1023 SARS-CoV-2 infected participants and 1619 test results, from - 6 to 66 days post-symptom onset and hospitalisation. The highest percentage virus detection was from nasopharyngeal sampling between 0 and 4 days post-symptom onset at 89% (95% confidence interval (CI) 83 to 93) dropping to 54% (95% CI 47 to 61) after 10 to 14 days. On average, duration of detectable virus was longer with lower respiratory tract (LRT) sampling than upper respiratory tract (URT). Duration of faecal and respiratory tract virus detection varied greatly within individual participants. In some participants, virus was still detectable at 46 days post-symptom onset. CONCLUSIONS: RT-PCR misses detection of people with SARS-CoV-2 infection; early sampling minimises false negative diagnoses. Beyond 10 days post-symptom onset, lower RT or faecal testing may be preferred sampling sites. The included studies are open to substantial risk of bias, so the positivity rates are probably overestimated.

The Clinical Need for New Diagnostics in the Identification and Management of Patients with Suspected Sepsis in UK NHS Hospitals: A Survey of Healthcare Professionals.

Development of a new diagnostic is ideally driven by an understanding of the clinical need that the test addresses and the optimal role the test will have within a care pathway. This survey aimed to understand the clinical need for new sepsis diagnostics and to identify specific clinical scenarios that could be improved by testing. An electronic, cross-sectional survey was circulated to UK National Health Service (NHS) doctors and nurses who care for patients with suspected sepsis in hospitals. Two hundred and sixty-five participants completed the survey, representing 64 NHS Trusts in England. Sixty-seven percent of respondents suggested that the major cause of delay was during the initial identification of sepsis and the subsequent recognition of patients who were deteriorating. Existing blood tests did not enhance the confidence of consultants making their diagnoses. Those surveyed identified a role for a near-patient test to "rule out" suspected sepsis and, thereby, stop or postpone use of antibiotics. Current diagnostic tests are slow, non-specific, and do not reliably identify patients with a high suspicion of sepsis. As a result, they have a limited use in patient management and antibiotic stewardship. Future development of sepsis diagnostics should focus on overcoming these limitations.

High Variability in Sepsis Guidelines in UK: Why Does It Matter?

It is recommended that developers of Point Of Care Tests (POCTs) assess the care pathway of the patient population of interest in order to understand if the POCT fits within the pathway and has the potential to improve it. If the variation of the pathway across potential hospitals is large, then it is likely that the evaluation of effectiveness is harder and the route towards large-scale takes adoption longer. Evaluating care pathways can be a time-consuming activity when conducted through clinical audits or interviews with healthcare professionals. We have developed a more rapid methodology which extrapolates the care pathway from local hospital guidelines and assesses their variation. Sepsis kills 46,000 people per year in the UK with societal costs of up to £10 billion. Therefore, there is a clinical need for an optimized pathway. By applying our method in this field, we were able to assess the variation in current hospital guidelines for sepsis and infer the potential impact this may have on the evidence development on innovations in this applications. We obtained 15 local sepsis guidelines. Two independent reviewers extracted: use of the national early warning score (NEWS), signs and risk factors informing the decision to prescribe antibiotics, and the number of decisional steps up to this point. Considerable variation was observed in all the variables, which is likely to have an impact on future clinical and economic evaluations and adoption of POCT for the identification of patients with sepsis.

How to Ease the Pain of Taking a Diagnostic Point of Care Test to the Market: A Framework for Evidence Development.

Bringing a diagnostic point of care test (POCT) to a healthcare market can be a painful experience as it requires the manufacturer to meet considerable technical, financial, managerial, and regulatory challenges. In this opinion article we propose a framework for developing the evidence needed to support product development, marketing, and adoption. We discuss each step in the evidence development pathway from the invention phase to the implementation of a new POCT in the healthcare system. We highlight the importance of articulating the value propositions and documenting the care pathway. We provide guidance on how to conduct care pathway analysis as little has been published on this. We summarize the clinical, economic and qualitative studies to be considered for developing evidence, and provide useful links to relevant software, on-line applications, websites, and give practical advice. We also provide advice on patient and public involvement and engagement (PPIE), and on product management. Our aim is to help device manufacturers to understand the concepts and terminology used in evaluation of in vitro diagnostics (IVDs) so that they can communicate effectively with evaluation methodologists, statisticians, and health economists. Manufacturers of medical tests and devices can use the proposed framework to plan their evidence development strategy in alignment with device development, applications for regulatory approval, and publication.

Executive function late effects in survivors of pediatric brain tumors and acute lymphoblastic leukemia.

BACKGROUND: Survivors of pediatric brain tumors (BT) and acute lymphoblastic leukemia (ALL) are at risk for neurocognitive late effects related to executive function. PROCEDURE: Survivors of BT (48) and ALL (50) completed neurocognitive assessment. Executive function was compared to estimated IQ and population norms by diagnostic group. RESULTS: Both BT and ALL demonstrated relative executive function weaknesses. As a group, BT survivors demonstrated weaker executive functioning than expected for age. Those BT survivors with deficits exhibited a profile suggestive of global executive dysfunction, while affected ALL survivors tended to demonstrate specific rapid naming deficits. CONCLUSION: Findings suggest that pediatric BT and ALL survivors may exhibit different profiles of executive function late effects, which may necessitate distinct intervention plans.