Modelling multiplex testing for outbreak control.

During the SARS-CoV-2 pandemic, polymerase chain reaction (PCR) and lateral flow device (LFD) tests were frequently deployed to detect the presence of SARS-CoV-2. Many of these tests were singleplex, and only tested for the presence of a single pathogen. Multiplex tests can test for the presence of several pathogens using only a single swab, which can allow for: surveillance of more pathogens, targeting of antiviral interventions, a reduced burden of testing, and lower costs. Test sensitivity, however, particularly in LFD tests, is highly conditional on the viral concentration dynamics of individuals. To inform the use of multiplex testing in outbreak detection it is therefore necessary to investigate the interactions between outbreak detection strategies and the differing viral concentration trajectories of key pathogens. Viral concentration trajectories are estimated for SARS-CoV-2 and Influenza A/B. Testing strategies for the first five symptomatic cases in an outbreak are then simulated and used to evaluate key performance indicators. Strategies that use a combination of multiplex LFD and PCR tests achieve; high levels of detection, detect outbreaks rapidly, and have the lowest burden of testing across multiple pathogens. Influenza B was estimated to have lower rates of detection due to its modelled viral concentration dynamics.

Designing cancer screening trials for reduction in late-stage cancer incidence.

Before implementing a biomarker test for early cancer detection into routine clinical care, the test must demonstrate clinical utility, that is, the test results should lead to clinical actions that positively affect patient-relevant outcomes. Unlike therapeutical trials for patients diagnosed with cancer, designing a randomized controlled trial (RCT) to demonstrate the clinical utility of an early detection biomarker with mortality and related endpoints poses unique challenges. The hurdles stem from the prolonged natural progression of the disease and the lack of information regarding the time-varying screening effect on the target asymptomatic population. To facilitate the study design of screening trials, we propose using a generic multistate disease history model and derive model-based effect sizes. The model links key performance metrics of the test, such as sensitivity, to primary endpoints like the incidence of late-stage cancer. It also incorporates the practical implementation of the biomarker-testing program in real-world scenarios. Based on the chronological time scale aligned with RCT, our method allows the assessment of study powers based on key features of the new program, including the test sensitivity, the length of follow-up, and the number and frequency of repeated tests. The calculation tool from the proposed method will enable practitioners to perform realistic and quick evaluations when strategizing screening trials for specific diseases. We use numerical examples based on the National Lung Screening Trial to demonstrate the method.

Implementation and validation of 2-D-array based tests in routine linac quality assurance.

PURPOSE: In medical linac quality assurance (QA), to replace film dosimetry with low-resolution 2-D ionization chamber array measurements, to validate the procedures, and to perform a comprehensive sensitivity analysis. METHODS: A 2-D ionization chamber array with a spatial resolution of 7.62 mm was deployed to perform the following tests: Junction tests, MLC transmission test, beam profile constancy vs. gantry angle test, beam profile constancy vs. low dose delivery test, and beam energy constancy vs. low dose delivery test. Test validation and sensitivity analyses based on short- and long-term statistics of the test results were performed. RESULTS: All selected mechanical and dosimetry tests could be successfully performed with a 2-D array. Considering the tolerance limits recommended by the AAPM Task Group 142 report (2009), sensitivities of 99.0% or better and specificities ranging from 99.5% to 99.9% could be achieved in all tests when the proper metrics were chosen. CONCLUSIONS: The results showed that a low-resolution 2-D ionization chamber array could replace film dosimetry without having to sacrifice high test sensitivity. Its implementation in the routine clinical linac QA program may involve considerable QA time savings.

Bayesian evaluation of meat juice ELISA for detecting Salmonella in slaughtered pigs without specifying a cut-off.

BACKGROUND: Consumption of pork and pork products is a major source of human infection with Salmonella. Salmonella is typically subclinical in pigs, making it difficult to identify infected pigs. Therefore, effective surveillance of Salmonella in pigs critically relies on good knowledge on how well the diagnostic tests used perform. A test that has been used in several countries for Salmonella monitoring is serological testing of meat juice using an ELISA (MJ ELISA) to detect antibodies against Salmonella. This MJ ELISA data could be used to estimate infection prevalence and trends. However, as the MJ ELISA output is a sample-to-positive (S/P) ratio, which is a continuous outcome rather than a binary (positive/negative) result, the interpretation of this data depends upon a chosen cut-off. AIM: To apply Bayesian latent class models (BLCMs) to estimate diagnostic accuracy of the MJ ELISA test values in the absence of a gold standard without needing to apply a cut-off. METHODS AND RESULTS: BLCMs were fitted to data from a UK abattoir survey carried out in 2006 in order to estimate the diagnostic accuracy of MJ ELISA with respect to the prevalence of active Salmonella infection. This survey consisted of a MJ ELISA applied in parallel with the bacteriological testing of caecal contents, carcass swabs and lymph nodes (n = 625). A BLCM was also fitted to the same data but with dichotomisation of the MJ ELISA results, in order to compare with the model using continuous outcomes. Estimates were obtained for sensitivity and specificity of the ELISA over a range of S/P values and for the bacteriological tests and were found to be similar between the models using continuous and dichotomous ELISA outcomes. CONCLUSION: The Bayesian method without specifying a cut-off does allow prevalence to be inferred without specifying a cut-off for the ELISA. The study results will be useful for estimating infection prevalence from serological surveillance data.

Study of Salmonella detection in laying hens using a Bayesian model.

As part of the measures to reduce the prevalence of Salmonella in poultry in the UK, National Control Programmes (NCPs) have been implemented. These involve regular statutory testing of poultry holdings to monitor and estimate the prevalence of Salmonella in the national flock population and to control Salmonella on holdings with positive flocks, especially those serovars most identified with human illness: Salmonella Enteritidis (SE) and S. Typhimurium (ST). It is very important to ensure that the level of testing is appropriate so that it is sufficiently effective to identify positive flocks and to monitor prevalence, but also efficient in the use of resources. The aim of this study was to estimate the sensitivity of both the Operator and Competent Authority (CA) Official sampling used to detect infected flocks, and to also estimate the true proportion of infected holdings of commercial laying flocks in GB each year of the NCP, along with the trend of any changes in prevalence for both SE/ST and non-SE/ST. A Bayesian model was developed to estimate the sensitivity of both Operator and CA Official sampling from the NCP data 2009-2018, and to estimate the true prevalence of infected holdings. The model estimate for the prevalence of infected holdings for the first complete year of the NCP was 3.9% (95% Credible Interval (CI) 2.8-6.2%) for non-SE/ST and 0.8% (95% CI: 0.4%-1.5%) for SE/ST. Prevalence had reduced to 1.6% (non-SE/ST) (95% CI 1.0%-2.5%) and 0.2% (SE/ST) (95% CI 0.1%-0.4%) in 2018. Results indicated a very low sensitivity of Operator sampling (~9%), but a much higher sensitivity of CA Official sampling (~44%). The true prevalence of Salmonella infected holdings in the UK had a mean average reduction of 10.6% (95% CI: 6.3%-15.1%) per annum (non-SE/ST) and 15.9% (95% CI: 6.0%-19.8%) annual reduction for SE/ST. This has shown the effectiveness of the NCP for Salmonella in commercial laying flocks, with reductions in Salmonella overall more or less equal to the target reduction for regulated serovars of 10% per annum. The true prevalence of SE/ST was estimated to be below the final target of less than 2% in every year and was below 0.5% at the end of the 10 year period.

High rate of missed Barrett's esophagus when screening with forceps biopsies.

BACKGROUND: Screening for Barrett's esophagus (BE) with endoscopy plus forceps biopsy (FB) has poor compliance with the recommended Seattle protocol and fails to sample large areas of mucosa. This statistical modeling study estimates, for the first time, the actual frequency of missed BE cases by FB. METHODS: Published, calibrated models in the literature were combined to calculate the age-specific prevalence of BE in white males with gastroesophageal reflux disease (GERD). We started with estimates of the prevalence of BE and GERD, and applied the relative risk for BE in patients with GERD based on the literature. This created estimates of the true prevalence of BE in white males with GERD by decade of life. The proportion of BE missed was calculated as the difference between the prevalence and the proportion with a positive screen. RESULTS: The prevalence of BE in white males with GERD was 8.9%, 12.1%, 15.3%, 18.7% and 22.0% for the third through eighth decades of life. Even after assuming no false positives, missed cases of BE were about 50% when estimated for patients of ages 50 or 60 years, and over 60% for ages of 30, 40 or 70 years. Sensitivity analysis was done for all variables in the model calculations. For ages 50 and 60 years, this resulted in values from 30.3 to 57.3% and 36.4 to 60.9%. CONCLUSION: Screening for BE with endoscopy and FB misses approximately 50% of BE cases. More sensitive methods of BE detection or better adherence to the Seattle protocol are needed.

Diagnostic accuracy of vaccine and vaccine excipient testing in the setting of allergic reactions to COVID-19 vaccines: A systematic review and meta-analysis.

For persons with immediate allergic reactions to mRNA COVID-19 vaccines, skin testing (ST) to the vaccine/excipients (polyethylene glycol[PEG] and polysorbate 80 [PS]) has been recommended, but has unknown accuracy. To assess vaccine/excipient ST accuracy in predicting all-severity immediate allergic reactions upon re-vaccination, systematic review was performed searching Medline, EMBASE, Web of Science, and the WHO global coronavirus database (inception-Oct 4, 2021) for studies addressing immediate (≤4 h post-vaccination) all-severity allergic reactions to 2nd mRNA COVID-19 vaccination in persons with 1st dose immediate allergic reactions. Cases evaluating delayed reactions, change of vaccine platform, or revaccination without vaccine/excipient ST were excluded. Meta-analysis of diagnostic testing accuracy was performed using Bayesian methods. The GRADE approach evaluated certainty of the evidence, and QUADAS-2 assessed risk of bias. Among 20 studies of mRNA COVID-19 first dose vaccine reactions, 317 individuals underwent 578 ST to any one or combination of vaccine, PEG, or PS, and were re-vaccinated with the same vaccine. Test sensitivity for either mRNA vaccine was 0.2 (95%CrI 0.01-0.52) and specificity 0.97 (95%CrI 0.9-1). PEG test sensitivity was 0.02 (95%CrI 0.00-0.07) and specificity 0.99 (95%CrI 0.96-1). PS test sensitivity was 0.03 (95%CrI 0.00-0.0.11) and specificity 0.97 (95%CrI 0.91-1). Combined for use of any of the 3 testing agents, sensitivity was 0.03 (95%CrI 0.00-0.08) and specificity was 0.98 (95%CrI 0.95-1.00). Certainty of evidence was moderate. ST has low sensitivity but high specificity in predicting all-severity repeat immediate allergic reactions to the same agent, among persons with 1st dose immediate allergic reactions to mRNA COVID-19 vaccines. mRNA COVID-19 vaccine or excipient ST has limited risk assessment utility.

Sensitivity of Reverse Transcription Polymerase Chain Reaction Tests for Severe Acute Respiratory Syndrome Coronavirus 2 Through Time.

BACKGROUND: Reverse transcription polymerase chain reaction (RT-PCR) tests are the gold standard for detecting recent infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Reverse transcription PCR sensitivity varies over the course of an individual's infection, related to changes in viral load. Differences in testing methods, and individual-level variables such as age, may also affect sensitivity. METHODS: Using data from New Zealand, we estimate the time-varying sensitivity of SARS-CoV-2 RT-PCR under varying temporal, biological, and demographic factors. RESULTS: Sensitivity peaks 4-5 days postinfection at 92.7% (91.4%-94.0%) and remains over 88% between 5 and 14 days postinfection. After the peak, sensitivity declined more rapidly in vaccinated cases compared with unvaccinated, females compared with males, those aged under 40 compared with over 40s, and Pacific peoples compared with other ethnicities. CONCLUSIONS: Reverse transcription PCR remains a sensitive technique and has been an effective tool in New Zealand's border and postborder measures to control coronavirus disease 2019. Our results inform model parameters and decisions concerning routine testing frequency.

Optimal group testing strategy for the mass screening of SARS-CoV-2.

We analyze the group testing strategy that maximizes the efficiency of the SARS-CoV-2 screening test while ensuring its effectiveness, where the effectiveness of group testing guarantees that negative results from pooled samples can be considered presumptive negative. Two aspects of test efficiency are considered, one concerning the maximization of the welfare throughput and the other concerning the maximization of the identification rate (namely, identifying as many infected individuals as possible). We show that compared with individual testing, group testing leads to a higher probability of false negative results but a lower probability of false positive results. To ensure the test effectiveness, both the group size and the prevalence of SARS-CoV-2 must be below certain respective thresholds. To achieve test efficiency that concerns either the welfare throughput maximization or the identification rate maximization, the optimal group size is jointly determined by the test accuracy parameters, the infection prevalence rate, and the relative importance of identifying infected subjects. We also show that the optimal group size that maximizes the welfare throughput is weakly smaller than the one that maximizes the identification rate.

Rapid comparative evaluation of SARS-CoV-2 rapid point-of-care antigen tests.

PURPOSE: The objective of this study was to develop a scalable approach for direct comparison of the analytical sensitivities of commercially available SARS-CoV-2 antigen point-of-care tests (AgPOCTs) to rapidly identify poor-performing products. METHODS: We present a methodology for quick assessment of the sensitivity of SARS-CoV-2 AgPOCTs suitable for quality evaluation of many different products. We established reference samples with high, medium, and low SARS-CoV-2 viral loads along with a SARS-CoV-2 negative control sample. Test samples were used to semi-quantitatively assess the analytical sensitivities of 32 different commercial AgPOCTs in a head-to-head comparison. RESULTS: Among 32 SARS-CoV-2 AgPOCTs tested, we observe sensitivity differences across a broad range of viral loads (9.8 × 108 to 1.8 × 105 SARS-CoV-2 genome copies per ml). 23 AgPOCTs detected the Ct25 test sample (1.6 × 106 copies/ml), while only five tests detected the Ct28 test sample (1.8 × 105 copies/ml). In the low-range of analytical sensitivity, we found three saliva spit tests only delivering positive results for the Ct21 sample (2.7 × 107 copies/ml). Comparison with published data supports our AgPOCT ranking. Importantly, we identified an AgPOCT widely offered, which did not reliably recognize the sample with the highest viral load (Ct16 test sample with 9.8 × 108 copies/ml) leading to serious doubts about its usefulness in SARS-CoV-2 diagnostics. CONCLUSION: The results show that the rapid sensitivity assessment procedure presented here provides useful estimations on the analytical sensitivities of 32 AgPOCTs and identified a widely-spread AgPOCT with concerningly low sensitivity.

Diurnal Variation in SARS-CoV-2 PCR Test Results: Test Accuracy May Vary by Time of Day.

False negative tests for SARS-CoV-2 are common and have important public health and medical implications. We tested the hypothesis of diurnal variation in viral shedding by assessing the proportion of positive versus negative SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) tests and cycle time (Ct) values among positive samples by the time of day. Among 86,342 clinical tests performed among symptomatic and asymptomatic patients in a regional health care network in the southeastern United States from March to August 2020, we found evidence for diurnal variation in the proportion of positive SARS-CoV-2 tests, with a peak around 1400 h and 1.7-fold variation over the day after adjustment for age, sex, race, testing location, month, and day of week and lower Ct values during the day for positive samples. These findings have important implications for public health testing and vaccination strategies.

Factors that Influence the Reported Sensitivity of Rapid Antigen Testing for SARS-CoV-2.

Tests that detect the presence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antigen in clinical specimens from the upper respiratory tract can provide a rapid means of coronavirus disease 2019 (COVID-19) diagnosis and help identify individuals who may be infectious and should isolate to prevent SARS-CoV-2 transmission. This systematic review assesses the diagnostic accuracy of SARS-CoV-2 antigen detection in COVID-19 symptomatic and asymptomatic individuals compared to quantitative reverse transcription polymerase chain reaction (RT-qPCR) and summarizes antigen test sensitivity using meta-regression. In total, 83 studies were included that compared SARS-CoV-2 rapid antigen-based lateral flow testing (RALFT) to RT-qPCR for SARS-CoV-2. Generally, the quality of the evaluated studies was inconsistent; nevertheless, the overall sensitivity for RALFT was determined to be 75.0% (95% confidence interval: 71.0-78.0). Additionally, RALFT sensitivity was found to be higher for symptomatic vs. asymptomatic individuals and was higher for a symptomatic population within 7 days from symptom onset compared to a population with extended days of symptoms. Viral load was found to be the most important factor for determining SARS-CoV-2 antigen test sensitivity. Other design factors, such as specimen storage and anatomical collection type, also affect the performance of RALFT. RALFT and RT-qPCR testing both achieve high sensitivity when compared to SARS-CoV-2 viral culture.

Systematic review and cumulative meta-analysis of the diagnostic accuracy of glial fibrillary acidic protein vs. S100 calcium binding protein B as blood biomarkers in observational studies of patients with mild or moderate acute traumatic brain injury.

Traumatic brain injuries (TBIs) and sports-related concussions (SRCs) are the leading causes of hospitalization and death in subjects <45 years old in the USA and Europe. Some biomarkers (BMs) have been used to reduce unnecessary cranial computed tomography (CCT). In recent years, the astroglial S100 calcium-binding B protein (S100B) has prevented approximately 30% of unnecessary CCTs. Glial fibrillary acidic protein (GFAP) has also been studied in direct comparison with S100B. The aim of our cumulative meta-analysis (cMA) is to compare - in the context of hospital emergency departments or SRC conditions - the differences in diagnostic accuracy (DA), sensitivity (Se) and specificity (Sp) of GFAP and S100B. The main cMA inclusion criterion was the assessment of both BMs in the included subjects since 2010, with blood samples drawn 1-30 h from the suspected TBI or SRC. The risk-of-bias (RoB) score was determined, and both the publication bias (with the Begg, Egger and Duval trim-and-fill tests) and sensitivity (with the box-and-whiskers plot) were analyzed for outliers. Seven studies with 899 subjects and nine observations (samples) were included. The diagnostic odds ratios (dORs) with their prediction intervals (PIs), Se and Sp (analyzed with a hierarchical model to respect the binomial data structure) were assessed, and a random-effects MA and a cMA of the difference in the BMs dOR natural logarithms (logOR(G-S)) between the BMs were performed. The cMA of dOR(G-S) was significant (5.78 (CI 2-16.6)) probably preventing approximately 50% of unnecessary CCTs. Further work is needed to standardize and harmonize GFAP laboratory methods.

Analysis of daily variation in the release of faecal eggs and coproantigen of Fasciola hepatica in naturally infected dairy cattle and the impact on diagnostic test sensitivity.

The liver fluke, Fasciola hepatica (F. hepatica) is a widespread parasite infection in dairy cattle in Victoria, South-eastern Australia. Robust diagnosis of fluke infection is needed in dairy cattle to identify sub-clinical infections which often go unnoticed, causing significant production losses. We tested the coproantigen ELISA (cELISA) and the FlukeFinder faecal egg count kit® on naturally infected cows in a fluke endemic region of Victoria. The aim of the study was to investigate the variation in the release of coproantigens and eggs into faeces over a 5-day period, at the morning (AM) and afternoon (PM) milkings, and to assess the impact of the timing of faecal sample collection on diagnostic test sensitivity. Ten cows were enrolled into the study based on positive F. hepatica faecal egg counts (LFEC) and faecal samples from the ten cows were collected twice daily, at the 7-9 AM and 4-6 PM milking, for five consecutive days. At the conclusion of the sampling period, the cows were euthanized and F. hepatica burden determined at necropsy. A moderate negative correlation between cow age and cELISA optical density (OD) was observed using data from all samples (R -0.63; 95 % CI -0.68 to -0.57). Over the 5-day sampling period, we observed within-animal variation between days for both the cELISA OD (2.6-8.9 fold) and LFEC (5-16 fold), with more variation in values observed in the PM samples for both tests. The correlation with total fluke burden was higher in the AM sampling using both the cELISA and LFEC (R 0.64 and 0.78, respectively). The sensitivity was 100 % for the cELISA using various cut offs from the literature (0.014 OD, 0.030 OD, and 1.3 % or 1.6 % of the positive control). The sensitivity of the FlukeFinder kit® (based on 588 faecal samples and not accounting for lack of independence in the data) was 88 % (95 % CI 85 %-90 %). Seventy one false negatives were recorded from the 588 LFEC tests all of which were observed in the cows with fluke burdens <14 flukes; 42 of the 71 false negative LFECs occurred in one individual cow which had the lowest burden of nine flukes. In dairy cows, the cut-off for production losses due to fasciolosis is estimated at> 10 fluke. Both the cELISA and the LFEC identified all cows that had burdens equal to or greater than this cut-off. Five of the ten cows also exhibited relatively high paramphistome egg counts.

Quantifying the Impact of Nasopharyngeal Specimen Quality on Severe Acute Respiratory Syndrome Coronavirus 2 Test Performance.

BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse-transcription polymerase chain reaction (RT-PCR) cycle threshold (Ct) has been used to estimate quantitative viral load, with the goal of targeting isolation precautions for individuals with coronavirus disease 2019 (COVID-19) and guiding public health interventions. However, variability in specimen quality can alter the Ct values obtained from SARS-CoV-2 clinical assays. We sought to define how variable nasopharyngeal (NP) swab quality impacts clinical SARS-CoV-2 test sensitivity. METHODS: We performed amplification of a human gene target (ß-actin) in parallel with a clinical RT-PCR targeting the SARS-CoV-2 ORF1ab gene for 1282 NP specimens collected from patients with clinical concern for COVID-19. We evaluated the relationship between NP specimen quality, characterized by late Ct values for the human gene target ß-actin Ct, and the probability of SARS-CoV-2 detection via logistic regression, as well as the linear relationship between SARS-CoV-2 and ß-actin Ct. RESULTS: Low-quality NP swabs are less likely to detect SARS-CoV-2 (odds ratio, 0.607 [95% credible interval {CrI}, .487-.753]). We observed a positive linear relationship between SARS-CoV-2 and ß-actin Ct values (slope, 0.181 [95% CrI, .097-.264]), consistent with a reduction in detection of 0.181 cycles for each additional cycle of the ß-actin target. COVID-19 disease severity was not associated with ß-actin Ct values. CONCLUSIONS: Variability in NP specimen quality significantly impacts the performance of clinical SARS-CoV-2 assays, and caution should be taken when interpreting quantitative SARS-CoV-2 Ct results. If unrecognized, low-quality NP specimens, which are characterized by a low level of amplifiable human DNA target, may limit the successful application of SARS-CoV-2 Ct values to direct infection control and public health interventions.

Longitudinal Assessment of Diagnostic Test Performance Over the Course of Acute SARS-CoV-2 Infection.

BACKGROUND: Serial screening is critical for restricting spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by facilitating timely identification of infected individuals to interrupt transmission. Variation in sensitivity of different diagnostic tests at different stages of infection has not been well documented. METHODS: In a longitudinal study of 43 adults newly infected with SARS-CoV-2, all provided daily saliva and nasal swabs for quantitative reverse transcription polymerase chain reaction (RT-qPCR), Quidel SARS Sofia antigen fluorescent immunoassay (FIA), and live virus culture. RESULTS: Both RT-qPCR and Quidel SARS Sofia antigen FIA peaked in sensitivity during the period in which live virus was detected in nasal swabs, but sensitivity of RT-qPCR tests rose more rapidly prior to this period. We also found that serial testing multiple times per week increases the sensitivity of antigen tests. CONCLUSIONS: RT-qPCR tests are more effective than antigen tests at identifying infected individuals prior to or early during the infectious period and thus for minimizing forward transmission (given timely results reporting). All tests showed >98% sensitivity for identifying infected individuals if used at least every 3 days. Daily screening using antigen tests can achieve approximately 90% sensitivity for identifying infected individuals while they are viral culture positive.

Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections.

BACKGROUND: Routine asymptomatic testing using RT-PCR of people who interact with vulnerable populations, such as medical staff in hospitals or care workers in care homes, has been employed to help prevent outbreaks among vulnerable populations. Although the peak sensitivity of RT-PCR can be high, the probability of detecting an infection will vary throughout the course of an infection. The effectiveness of routine asymptomatic testing will therefore depend on testing frequency and how PCR detection varies over time. METHODS: We fitted a Bayesian statistical model to a dataset of twice weekly PCR tests of UK healthcare workers performed by self-administered nasopharyngeal swab, regardless of symptoms. We jointly estimated times of infection and the probability of a positive PCR test over time following infection; we then compared asymptomatic testing strategies by calculating the probability that a symptomatic infection is detected before symptom onset and the probability that an asymptomatic infection is detected within 7 days of infection. RESULTS: We estimated that the probability that the PCR test detected infection peaked at 77% (54-88%) 4 days after infection, decreasing to 50% (38-65%) by 10 days after infection. Our results suggest a substantially higher probability of detecting infections 1-3 days after infection than previously published estimates. We estimated that testing every other day would detect 57% (33-76%) of symptomatic cases prior to onset and 94% (75-99%) of asymptomatic cases within 7 days if test results were returned within a day. CONCLUSIONS: Our results suggest that routine asymptomatic testing can enable detection of a high proportion of infected individuals early in their infection, provided that the testing is frequent and the time from testing to notification of results is sufficiently fast.

Interval colorectal cancers after negative faecal immunochemical test in a 13-year screening programme.

OBJECTIVE: To assess faecal immunochemical test sensitivity for cancer in a very large population-based cohort followed up for six rounds with biennial faecal immunochemical test repetition. METHODS: This study is based on interval colorectal cancers diagnosed in a cohort of subjects aged 50-69 undergoing repeated faecal immunochemical test screening (six rounds) from 2002 to 2015. Test sensitivity was calculated using both the Proportional Interval Cancer Rate and the Interval Cancer Proportion method. RESULTS: Among 441,647 faecal immunochemical tests (123,347 individuals), 150 interval colorectal cancers were detected after a negative faecal immunochemical test. Interval colorectal cancer incidence rate was 1.87 per 10,000 person-years (95%CI: 1.60-2.20), and it was higher during the second interval year (rate ratio: 1.78; 95%CI: 1.28-2.47), for proximal locations (rate ratio: 3.00; 95%CI: 1.92-4.68), and among 60-71 year old subjects (rate ratio: 2.37; 95%CI: 1.61-3.50). The Proportional Interval Cancer Rate was 13.1%, with an overall faecal immunochemical test sensitivity of 86.9% (95%CI: 84.7-89.0). Sensitivity was lowest at the first round (81.5%; 95%CI: 75.6-86.2), and increased to 91.9% (95%CI: 83.9-96.5) for subsequent rounds. Applying the Interval Cancer Proportion method, sensitivity was 83.9% (95%CI: 81.3-86.2), and it was highest at the first round (89.0%; 95%CI: 85.7-91.6), ranging between 73% and 83.1% at subsequent rounds. CONCLUSIONS: A faecal immunochemical test sensitivity for cancer higher than 80% resulted in a low incidence of interval colorectal cancers, representing an accurate estimate of one of the major limits of screening programmes. Due to intrinsic biases, the Proportional Interval Cancer Rate and the Interval Cancer Proportion methods generated different trends in faecal immunochemical test sensitivity by screening round.

Estimation of the sensitivity and specificity of four serum ELISA and one fecal PCR for diagnosis of paratuberculosis in adult dairy cattle in New Zealand using Bayesian latent class analysis.

In New Zealand, a new diagnostic approach for the control of paratuberculosis in mixed aged milking cows has been developed using a combination of ELISA and quantitative fecal PCR (f-qPCR). Our analysis was designed to evaluate performance of these individual tests in infected or infectious mixed aged cows across the prevalence of infection typically encountered on NZ dairy farms and calculate test accuracy when used as a screening test of serological ELISAs for four separate antigens read in parallel followed by a confirmatory quantitative f-qPCR test. Data from a cross-sectional study of 20 moderate prevalence herds was combined with existing data from 2 low and 20 high prevalence herds forming a dataset of 3845 paired serum and fecal samples. Incidence of clinical Johne's disease (JD) was used to classify herds into three prevalence categories. High (≥ 3% annual clinical JD for the last three years), moderate (<3 - 1%) and low (<1% incidence for at least the last five years). Positive tests were declared if> 50 ELISA units and f-qPCR at two cut-points (≥1 × 104 genomes/mL or >1 × 103 genomes/mL). Fixed Bayesian latent class models at both f-qPCR cut-points, accounted for conditional independence and paired conditional dependence. Mixed models at both f-qPCR cut-points, using a different mechanism to account for conditional dependencies between tests were also implemented. Models (24 in number) were constructed using OpenBUGS. The aim was to identify Mycobacterium avium subsp. paratuberculosis (MAP) infected cows that met at least one of two criteria: shedding sufficient MAP in feces to be detected by f-qPCR or mounting a detectable MAP antibody response. The best fit to the data was obtained by modelling pairwise dependencies between tests in a fixed model or by accounting for dependencies in a mixed model at a fecal cut-off of ≥1 × 104 genomes/mL. Test performance differed with prevalence, but models were robust to prior assumptions. For the fixed model, at a prevalence of 0.29 (95 % probability interval (PI) = 0.25-0.33), as a screening plus confirmatory f-qPCR, post-test probability for disease in a positive animal was 0.84 (95 %PI = 0.80-0.88) and 0.16 (95 %PI = 0.15-0.18) for disease in a test negative animal. In low prevalence herds (0.01(95 %PI = 0.00-0.04)) the equivalent figures were 0.84 (95 %PI = 0.08-0.92) and 0.00 (95 %PI = 0.00-0.02). These results suggest this is a useful tool to control JD on dairy farms, particularly in herds with higher levels of infection, where the sampling and testing cost per animal is defrayed across more detected animals.