Early Release Estimates for SARS-CoV-2 Prevalence and Antibody Response: Interim Weighting for Probability-Based Sample Surveys (Preprint)

2020 ◽  
Author(s):  
Heather Bradley ◽  
Mansour Fahimi ◽  
Travis Sanchez ◽  
Ben Lopman ◽  
Martin Frankel ◽  
...  
Keyword(s):  
Antibody Response ◽  
Selection Bias ◽  
Burden Of Disease ◽  
Clinical Characteristics ◽  
Diagnostic Testing ◽  
Sample Surveys ◽  
Early Release ◽  
Testing Data ◽  
Selection Probabilities ◽  
National Prevalence

UNSTRUCTURED Many months into the SARS-CoV-2 pandemic, basic epidemiologic parameters describing burden of disease are lacking. To reduce selection bias in current burden of disease estimates derived from diagnostic testing data or serologic testing in convenience samples, we are conducting a national probability-based sample SARS-CoV-2 serosurvey. Sampling from a national address-based frame and using mailed recruitment materials and test kits will allow us to estimate national prevalence of SARS-CoV-2 infection and antibodies, overall and by demographic, behavioral, and clinical characteristics. Data will be weighted for unequal selection probabilities and non-response and will be adjusted to population benchmarks. Due to the urgent need for these estimates, expedited interim weighting of serosurvey responses will be undertaken to produce early release estimates, which will be published on the study website, COVIDVu.org. Here, we describe a process for computing interim survey weights and guidelines for release of interim estimates.

scholarly journals Early Release Estimates for SARS-CoV-2 Prevalence and Antibody Response Interim Weighting for Probability-Based Sample Surveys

2020 ◽  
Author(s):  
Heather Bradley ◽  
Mansour Fahimi ◽  
Travis Sanchez ◽  
Ben Lopman ◽  
Martin Frankel ◽  
...  
Keyword(s):  
Antibody Response ◽  
Sample Surveys ◽  
Early Release

The authors have withdrawn this manuscript because analytic strategies for this project have changed. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

scholarly journals Interpreting HIV Diagnostic Histories into Infection Time Estimates: Analytical Framework and Online Tool

2018 ◽  
Author(s):  
Eduard Grebe ◽  
Shelley N. Facente ◽  
Jeremy Bingham ◽  
Christopher D. Pilcher ◽  
Andrew Powrie ◽  
...  
Keyword(s):  
Hiv Infection ◽  
Diagnostic Testing ◽  
Diagnostic Delay ◽  
Analytical Framework ◽  
Online Tool ◽  
Infection Time ◽  
Test Sensitivity ◽  
Time Estimates ◽  
Hiv Test ◽  
Testing Data

AbstractBackgroundIt is frequently of epidemiological and/or clinical interest to estimate the date of HIV infection or time-since-infection of individuals. Yet, for over 15 years, the only widely-referenced infection dating algorithm that utilises diagnostic testing data to estimate time-since-infection has been the ‘Fiebig staging’ system. This defines a number of stages of early HIV infection through various standard combinations of contemporaneous discordant diagnostic results, using tests of different sensitivity.ObjectiveTo develop a new, more nuanced infection dating algorithm, we generalised the Fiebig approach to accommodate positive and negative diagnostic results generated on the same or different dates, and arbitrary current or future tests – as long as the test sensitivity is known. For this purpose, test sensitivity is conceptualised as the probability that a specimen will produce a positive result, expressed as a function of time since infection. This can be summarised as a median ‘diagnostic delay’ parameter, together with a measure of inter-subject variability.MethodsThe present work outlines the analytical framework for infection date estimation using subject-level diagnostic testing histories, and data on test sensitivity. We introduce a publicly-available online HIV infection dating tool that implements this estimation method, bringing together 1) curatorship of HIV test performance data, and 2) infection date estimation functionality, to calculate plausible intervals within which infection likely became detectable for each individual. The midpoints of these intervals are interpreted as infection time ‘point estimates’ and referred to as Estimated Dates of Detectable Infection (EDDIs).ResultsIn many settings, including most research studies, detailed diagnostic testing data are routinely recorded, and can provide reasonably precise estimates of the timing of HIV infection. We present a simple logic to the interpretation of ‘diagnostic testing histories’ into ‘infection time estimates’, either as a point estimate (EDDI) or an interval (earliest plausible to latest plausible dates of detectable infection), along with a publicly-accessible online tool that supports wide application of this logic.ConclusionsThis tool, available at https://tools.incidence-estimation.org/idt/, is readily updatable as test technology evolves, given the simple architecture of the system and its nature as an open source project.

scholarly journals Clinical characteristics and antibody response to SARS-CoV-2 spike 1 protein using VITROS Anti-SARS-CoV-2 antibody tests in COVID-19 patients in Japan

2021 ◽  
Vol 70 (4) ◽  
Author(s):  
Mayu Nagura-Ikeda ◽  
Kazuo Imai ◽  
Katsumi Kubota ◽  
Sakiko Noguchi ◽  
Yutaro Kitagawa ◽  
...  
Keyword(s):  
Antibody Response ◽  
Disease Severity ◽  
Clinical Utility ◽  
Clinical Characteristics ◽  
Igg Antibody ◽  
Laboratory Findings ◽  
Disease Prognosis ◽  
Antibody Assays ◽  
Clinical Records ◽  
Antibody Tests

Introduction. Serological tests for COVID-19 are important in providing results for surveillance and supporting diagnosis. Investigating the serological response in COVID-19 patients with different disease severity is important for assessing the clinical utility of serological assays. Gap Statement. However, few studies have investigated the clinical utility of antibody assays for COVID-19 or differences in antibody response in association with disease severity. Aim. The study aimed to evaluate the clinical characteristics and clinical utility of VITROS SARS-CoV-2 antibody tests according to COVID-19 severity in patients in Japan. Methodology. We analysed 255 serum specimens from 130 COVID-19 patients and examined clinical records and laboratory data. Presence of total (IgA, IgM, and IgG) and specific IgG antibody for the spike 1 antigen of SARS-CoV-2 was determined using VITROS Anti-SARS-CoV-2 antibody tests. Results. Overall, 98 (75.4 %) and 32 (24.6 %) patients had mild and severe COVID-19, respectively. On admission, 76 (58.5 %) and 45 (34.6 %) patients were positive for total and IgG antibody assays. Among 91 patients at discharge, 90 (98.9 %) and 81 (89.0 %) were positive for total and IgG antibody, respectively. Clinical background and laboratory findings on admission, but not the prevalence or concentration of total or IgG antibody, were associated with disease prognosis. Total and IgG antibody intensities were significantly higher in severe cases than in mild cases in serum collected >11 days after onset, but not within 10 days. Conclusion. VITROS Anti-SARS-CoV-2 total and IgG assays will be useful as supporting diagnostic and surveillance tools and for evaluation of humoral immune response to COVID-19. Optimal prediction of disease prognosis is made from considering both clinical history and laboratory findings.

Tracking the uptake of outcomes of hepatitis B virus testing using laboratory data in Victoria, 2011–16: a population-level cohort study

Sexual Health ◽  
2019 ◽  
Vol 16 (4) ◽  
pp. 358
Author(s):  
Caroline van Gemert ◽  
Wayne Dimech ◽  
Mark Stoove ◽  
Rebecca Guy ◽  
Jess Howell ◽  
...  
Keyword(s):  
Hepatitis B ◽  
Hepatitis B Surface Antigen ◽  
National Laboratory ◽  
Diagnostic Testing ◽  
Laboratory Data ◽  
Population Level ◽  
Sentinel Surveillance ◽  
Sexually Transmissible Infections ◽  
Testing Data ◽  
Hepatitis B Testing

Background A priority area in the 2016 Victorian Hepatitis B Strategy is to increase diagnostic testing. This study describes hepatitis B testing and positivity trends in Victoria between 2011 and 2016 using data from a national laboratory sentinel surveillance system. Methods: Line-listed diagnostic and monitoring hepatitis B testing data among Victorian individuals were collated from six laboratories participating in the Australian Collaboration for Coordinated Enhanced Sentinel Surveillance (ACCESS) of sexually transmissible infections and blood-borne viruses. Diagnostic tests included hepatitis B surface antigen (HBsAg)-only tests and guideline-based hepatitis B tests (defined as a single test event for HBsAg, hepatitis B surface antibody and hepatitis B core antibody). Using available data, the outcomes of testing and/or infection were further classified. Measures reported include the total number of HBsAg and guideline-based tests conducted and the proportion positive, classified as either HBsAg positive or chronic hepatitis B infection. Results: The number of HBsAg tests decreased slightly each year between 2011 and 2016 (from 91043 in 2011 to 79664 in 2016; P < 0.001), whereas the number of guideline-based hepatitis B tests increased (from 8732 in 2011 to 16085 in 2016; P <0.001). The proportion of individuals classified as having chronic infection decreased from 25% in 2011 to 7% in 2016, whereas the proportion classified as susceptible and immune due to vaccination increased (from 29% to 39%, and from 27% to 34%, respectively; P < 0.001). Conclusions: The study findings indicate an increased uptake of guideline-based hepatitis B testing. The ongoing collection of testing data can help monitor progress towards implementation of the Victorian Hepatitis B Strategy.

scholarly journals Humoral Immune Response Associated with Lyme Borreliosis in Nonhuman Primates: Analysis by Immunoblotting and Enzyme-Linked Immunosorbent Assay with Sonicates or Recombinant Proteins

2002 ◽  
Vol 9 (6) ◽  
pp. 1348-1355 ◽  
Author(s):  
A. R. Pachner ◽  
D. Dail ◽  
L. Li ◽  
L. Gurey ◽  
S. Feng ◽  
...  
Keyword(s):  
Immune Response ◽  
Antibody Response ◽  
Lyme Borreliosis ◽  
Recombinant Proteins ◽  
Diagnostic Testing ◽  
Sensu Stricto ◽  
Immunoglobulin M ◽  
Enzyme Linked Immunosorbent Assay ◽  
Igg Antibody ◽  
Humoral Immune

ABSTRACT The immune response to Borrelia burgdorferi, the causative agent of Lyme disease, is complex. We studied the immunoglobulin M (IgM) and IgG antibody response to N40Br, a sensu stricto strain, in the rhesus macaque(nonhuman primate [NHP]) model of infection to identify the spirochetal protein targets of specific antibody. Antigens used in enzyme-linked immunosorbent assays were whole-cell sonicates of the spirochete and recombinant proteins of B. burgdorferi. Immunoblotting with a commercially available strip and subsequent quantitative densitometry of the bands were also used. Sera from four different groups of NHPs were used: immunocompetent, transiently immunosuppressed, extended immunosuppressed, and uninfected. In immunocompetent and transiently immunosuppressed NHPs, there was a strong IgM and IgG response. Major proteins for the early IgM response were P39 and P41 and recombinant BmpA and OspC. Major proteins for the later IgG response were P39, P41, P18, P60, P66, and recombinant BmpA and DbpA. There was no significant response in the NHPs to recombinant OspA or to Arp, a 37-kDa protein that elicits an antibody response during infection in mice. Most antibody responses, except for that to DbpA, were markedly diminished by prolonged dexamethasone treatment. This study supports the hypothesis that recombinant proteins may provide a useful adjunct to current diagnostic testing for Lyme borreliosis.

scholarly journals Interpreting HIV Diagnostic Histories into Infection Time Estimates: Analytical Framework and Online Tool

2019 ◽  
Author(s):  
Eduard Grebe ◽  
Shelley N. Facente ◽  
Jeremy Bingham ◽  
Christopher D. Pilcher ◽  
Andrew Powrie ◽  
...  
Keyword(s):  
Hiv Infection ◽  
Diagnostic Testing ◽  
Diagnostic Delay ◽  
Analytical Framework ◽  
Online Tool ◽  
Infection Time ◽  
Test Sensitivity ◽  
Time Estimates ◽  
Hiv Test ◽  
Testing Data

Abstract Background It is frequently of epidemiological and/or clinical interest to estimate the date of HIV infection or time-since-infection of individuals. Yet, for over 15 years, the only widely-referenced infection dating algorithm that utilises diagnostic testing data to estimate time-since-infection has been the ‘Fiebig staging’ system. This defines a number of stages of early HIV infection through various standard combinations of contemporaneous discordant diagnostic results, using tests of different sensitivity. Objective To develop a new, more nuanced infection dating algorithm, we generalised the Fiebig approach to accommodate positive and negative diagnostic results generated on the same or different dates, and arbitrary current or future tests – as long as the test sensitivity is known. For this purpose, test sensitivity is conceptualised as the probability that a specimen will produce a positive result, expressed as a function of time since infection. This can be summarised as a median ‘diagnostic delay’ parameter, together with a measure of inter-subject variability. Methods The present work outlines the analytical framework for infection date estimation using subject-level diagnostic testing histories, and data on test sensitivity. We introduce a publicly-available online HIV infection dating tool that implements this estimation method, bringing together 1) curatorship of HIV test performance data, and 2) infection date estimation functionality, to calculate plausible intervals within which infection likely became detectable for each individual. The midpoints of these intervals are interpreted as infection time ‘point estimates’ and referred to as Estimated Dates of Detectable Infection (EDDIs). Results In many settings, including most research studies, detailed diagnostic testing data are routinely recorded, and can provide reasonably precise estimates of the timing of HIV infection. We present a simple logic to the interpretation of ‘diagnostic testing histories’ into ‘infection time estimates’, either as a point estimate (EDDI) or an interval (earliest plausible to latest plausible dates of detectable infection), along with a publicly-accessible online tool that supports wide application of this logic. Conclusions This tool, available at https://tools.incidence-estimation.org/idt/, is readily updatable as test technology evolves, given the simple architecture of the system and its nature as an open source project.

scholarly journals Clinical Characteristics of an Internet-Based Cohort of Patient-Reported Diagnosis of Granulomatosis With Polyangiitis and Microscopic Polyangiitis: Observational Study

10.2196/17231 ◽  
2020 ◽  
Vol 22 (7) ◽  
pp. e17231
Author(s):  
Jason Michael Springer ◽  
Tanaz A Kermani ◽  
Antoine Sreih ◽  
Dianne G Shaw ◽  
Kalen Young ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Clinical Characteristics ◽  
Granulomatosis With Polyangiitis ◽  
Microscopic Polyangiitis ◽  
Renal Involvement ◽  
Diagnostic Testing ◽  
Research Network ◽  
Joint Involvement ◽  
Patient Reported ◽  
Prospective Longitudinal

Background Utilizing the traditional centers of excellence approach to conduct clinical trials involving rare diseases remains challenging. Patient-based registries have been shown to be both feasible and valid in several other diseases. Objective This report outlines the clinical characteristics of a large internet registry cohort of participants with a self-reported diagnosis of granulomatosis with polyangiitis or microscopic polyangiitis. Methods Patients with a self-reported diagnosis of granulomatosis with polyangiitis or microscopic polyangiitis in an internet-based prospective longitudinal cohort (from the Vasculitis Patient-Powered Research Network) were included. Data on symptoms, diagnostic testing, and treatment were collected using standardized questionnaires. Results The study compared patients with granulomatosis with polyangiitis (n=762) and patients with microscopic polyangiitis (n=164). Of the cohort, 97.7% (904/925) reported the diagnosis had been confirmed by a physician. Compared to microscopic polyangiitis, patients with granulomatosis with polyangiitis reported significantly more ear, nose, and throat manifestations (granulomatosis with polyangiitis: 641/723, 88.7%; microscopic polyangiitis: 89/164, 54.3%; z=10.42, P<.001), fevers (granulomatosis with polyangiitis: 325/588, 55.3%; microscopic polyangiitis: 64/139, 46.0%; z=1.96, P=.05), joint involvement (granulomatosis with polyangiitis: 549/688, 79.8%; microscopic polyangiitis: 106/154, 68.8%; z=2.96, P=.003), and pulmonary involvement (granulomatosis with polyangiitis: 523/734, 71.3%; microscopic polyangiitis: 90/154, 58.4%; z=3.13, P=.002). Compared to microscopic polyangiitis, patients with granulomatosis with polyangiitis reported significantly less renal involvement (granulomatosis with polyangiitis: 457/743, 61.5%; microscopic polyangiitis: 135/163, 82.8%; z=–5.18, P<.001) and renal transplantation (granulomatosis with polyangiitis: 10/721, 1.4%; microscopic polyangiitis: 7/164, 4.3%; z=–2.43, P=.02). Antineutrophil cytoplasmic antibody positivity was reported in 94.2% (652/692) of patients with granulomatosis with polyangiitis and 96.1% (147/153) of patients with microscopic polyangiitis. A biopsy showing vasculitis was reported in 77.0% (562/730) of patients with granulomatosis with polyangiitis and 81.9% (131/160) of patients with microscopic polyangiitis. Conclusions In this large, internet-based cohort of patients with a self-reported diagnosis of granulomatosis with polyangiitis or microscopic polyangiitis, disease manifestations were consistent with expectations for each type of vasculitis. Given the rarity of these and other vasculitides, conducting some types of research through internet-based registries may provide an efficient alternative to inperson, center-of-excellence clinical trials.

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