scholarly journals Missing two key parameters in the pooled testing strategy

2021 ◽  
Author(s):  
Xuhua Xia
Keyword(s):  
Maximum Likelihood ◽  
Maximum Likelihood Estimators ◽  
Infection Prevalence ◽  
Testing Strategy ◽  
Significant Saving ◽  
Pooled Testing ◽  
Testing Strategies ◽  
Testing Data ◽  
Pooled Samples ◽  
Time Resource

Abstract The pooled testing strategy [1] misses two key parameters, the infection prevalence p and its variance mentioned many times in the paper as the key determinants of any pooled testing strategy. For illustrating their methods, the authors used p from other studies that employed individual tests. It turned that that no statistical estimators for p and its variance have ever been derived for testing data of pooled samples since the first formulation of testing strategies based on pooled sampled in 1943 [2]. Here I derive the maximum likelihood estimators for p and its variance based on tests of pooled samples. This should result in significant saving in time, resource, and costs.

scholarly journals Pooled Sputum for Xpert MTB/RIF Testing: A Cost Effectiveness Diagnostic Tool in Mwanza, Tanzania

2021 ◽  
Author(s):  
Shimba Henerico ◽  
Richard V. Makapa ◽  
Bernard C. Okamo ◽  
Benson R. Kidenya ◽  
Geoffrey Japhet ◽  
...  
Keyword(s):  
Cost Effectiveness ◽  
Low Income ◽  
Public Health Problem ◽  
Positive Sample ◽  
Low Income Countries ◽  
Global Public Health ◽  
Testing Strategy ◽  
Pooled Testing ◽  
The Individual ◽  
Pooled Samples

Abstract Background: Tuberculosis (TB) is a global public health problem, with the highest burden occurring in low-income countries, wherein the use of more sensitive diagnostics, such as Xpert MTB/RIF (GeneXpert), is still limited by costs. Testing of pooled samples from various individuals has been thought and thus investigated as a cost saving strategy to diagnose some diseases including TB. Then in cases where a pool is positive, retesting of the individual samples in that pool is done to identify the positive sample. We assessed the utility of a pooled testing strategy to optimize the affordability of GeneXpert for the diagnosis of TB Mwanza Tanzania. Methods: Remainder of samples from presumptive TB patients submitted for routine TB diagnosis were used for pooled samples (5 per pool) testing. The agreement of the results between individual sample testing against pooled samples testing and cost-effectiveness were assessed.Results: A total of 250 individual routinely submitted samples for TB diagnosis were tested using the established protocols. The median age of study participants was 35 [IQR 27 – 40] years and 143 (57.2%) were males. Of the 250 samples, 28 (11.2%) were detected to have MTB whereas 222 (88.8%) samples, were negative. Of the 50 sputum pools made, MTB were detected in 17 (34.0%) pools. Following retesting of these 17 positive pools, all 28 (100%) individual MTB samples were detected with the overall agreement being 100% (With the sensitivity of 100% and specificity of 100%). The number of individual MTB positive ranged from 1 to 3 per pool. Using pooling of sputum samples, the technique saved 115 (46.0%) of the cartridges in running 250 samples. This is equivalent to saving US$ 1147.7. Conclusion: The pooled sputum testing strategy reduced cartridge costs by 46.0%. The use of the pooled testing strategy reduces costs and has the potential to increase the affordability of GeneXpert testing in countries with limited resources. Pooled sputum for Xpert MTB/RIF can be used as an affordable diagnostic and/or screening tool in resource limited settings, such as Tanzania.

scholarly journals Estimating Viral Prevalence with Data Integration for Adaptive Two-Phase Pooled Sampling

2021 ◽  
Author(s):  
Andrew Hoegh ◽  
Alison Peel ◽  
Wyatt Madden ◽  
Manuel Ruiz-Aravena ◽  
Aaron Morris ◽  
...  
Keyword(s):  
Data Integration ◽  
Reservoir Host ◽  
Efficient Estimation ◽  
Second Phase ◽  
Infection Prevalence ◽  
Pooled Testing ◽  
Population Prevalence ◽  
Pathogen Prevalence ◽  
Reservoir Hosts ◽  
Pooled Samples

1. The COVID-19 pandemic has highlighted the importance of efficient sampling strategies and statistical methods for monitoring infection prevalence, both in humans and reservoir hosts. Pooled testing can be an efficient tool for learning pathogen prevalence in a population. Typically pooled testing requires a second phase follow up procedure to identify infected individuals, but when the goal is solely to learn prevalence in a population, such as a reservoir host, there are more efficient methods for allocating the second phase samples. 2. To estimate pathogen prevalence in a population, this manuscript presents an approach for data integration with two-phased testing of pooled samples that allows more efficient estimation of prevalence with less samples than traditional methods. The first phase uses pooled samples to estimate the population prevalence and inform efficient strategies for the second phase. To combine information from both phases, we introduce a Bayesian data integration procedure that combines pooled samples with individual samples for joint inferences about the population prevalence. 3. Data integration procedures result in more efficient estimation of prevalence than traditional procedures that only use individual samples or a single phase of pooled sampling. 4. The manuscript presents guidance on implementing the first phase and second phase sampling plans using data integration. Such methods can be used to assess the risk of pathogen spillover from reservoir hosts to humans, or to track pathogens such as SARS-CoV-2 in populations.

scholarly journals Pooled Testing and Its Applications in the COVID-19 Pandemic

2021 ◽  
pp. 217-249
Author(s):  
Matthew Aldridge ◽  
David Ellis
Keyword(s):  
Standard Method ◽  
Group Testing ◽  
Two Stage ◽  
Pooled Testing ◽  
Testing Strategies ◽  
Pooling Strategies ◽  
Pooled Samples

AbstractWhen testing for a disease such as COVID-19, the standard method is individual testing: we take a sample from each individual and test these samples separately. An alternative is pooled testing (or ‘group testing’), where samples are mixed together in different pools, and those pooled samples are tested. When the prevalence of the disease is low and the accuracy of the test is fairly high, pooled testing strategies can be more efficient than individual testing. In this chapter, we discuss the mathematics of pooled testing and its uses during pandemics, in particular the COVID-19 pandemic. We analyse some one- and two-stage pooling strategies under perfect and imperfect tests, and consider the practical issues in the application of such protocols.

scholarly journals Testing Pooled Sputum with Xpert MTB/RIF for Diagnosis of Pulmonary Tuberculosis To Increase Affordability in Low-Income Countries

2015 ◽  
Vol 53 (8) ◽  
pp. 2502-2508 ◽  
Author(s):  
Saddiq T. Abdurrahman ◽  
Omezikam Mbanaso ◽  
Lovett Lawson ◽  
Olanrewaju Oladimeji ◽  
Matthew Blakiston ◽  
...  
Keyword(s):  
Low Income ◽  
Public Health Problem ◽  
Low Income Countries ◽  
Global Public Health ◽  
Testing Strategy ◽  
Content Type ◽  
Pooled Testing ◽  
Negative Results ◽  
The Individual ◽  
Pooled Samples

Tuberculosis (TB) is a global public health problem, with the highest burden occurring in low-income countries. In these countries, the use of more sensitive diagnostics, such as Xpert MTB/RIF (Xpert), is still limited by costs. A cost-saving strategy to diagnose other diseases is to pool samples from various individuals and test them with single tests. The samples in positive pool samples are then retested individually to identify the patients with the disease. We assessed a pooled testing strategy to optimize the affordability of Xpert for the diagnosis of TB. Adults with presumptive TB attending hospitals or identified by canvassing of households in Abuja, Nigeria, were asked to provide sputum for individual and pooled (4 per pool) testing. The agreement of the results of testing of individual and pooled samples and costs were assessed. A total of 738 individuals submitted samples, with 115 (16%) beingMycobacterium tuberculosispositive. Valid Xpert results for individual and pooled samples were available for 718 specimens. Of these, testing of pooled samples detected 109 (96%) of 114 individualM. tuberculosis-positive samples, with the overall agreement being 99%. Xpert semiquantitativeM. tuberculosislevels had a positive correlation with the smear grades, and the individual sample-positive/pooled sample-negative results were likely due to theM. tuberculosisconcentration being below the detection limit. The strategy reduced cartridge costs by 31%. Savings were higher with samples from individuals recruited in the community, where the proportion of positive specimens was low. The results of testing of pooled samples had a high level of agreement with the results of testing of individual samples, and use of the pooled testing strategy reduced costs and has the potential to increase the affordability of Xpert in countries with limited resources.

scholarly journals Evaluation of Group Testing for SARS-CoV-2 RNA

2020 ◽  
Author(s):  
Nasa Sinnott-Armstrong ◽  
Daniel L. Klein ◽  
Brendan Hickey
Keyword(s):  
Rna Extraction ◽  
Group Testing ◽  
Disease Status ◽  
Behavioral Changes ◽  
Limiting Factor ◽  
Testing Strategy ◽  
Pooled Testing ◽  
Testing Strategies ◽  
Test Kit ◽  
Testing Protocols

AbstractDuring the current COVID-19 pandemic, testing kit and RNA extraction kit availability has become a major limiting factor in the ability to determine patient disease status and accurately quantify prevalence. Current testing strategies rely on individual tests of cases matching restrictive diagnostic criteria to detect SARS-CoV-2 RNA, limiting testing of asymptomatic and mild cases. Testing these individuals is one effective way to understand and reduce the spread of COVID-19.Here, we develop a pooled testing strategy to identify these low-risk individuals. Drawing on the well-studied group testing literature, modeling suggests practical changes to testing protocols which can reduce test costs and stretch a limited test kit supply. When most tests are negative, pooling reduces the total number of tests up to four-fold at 2% prevalence and eight-fold at 0.5% prevalence. At current SARS-CoV-2 prevalence, randomized group testing optimized per country could double the number of tested individuals from 1.85M to 3.7M using only 671k more tests.This strategy is well-suited to supplement testing for asymptomatic and mild cases who would otherwise go untested, and enable them to adopt behavioral changes to slow the spread of COVID-19.

Using Approximation Non-Bayesian Computation with Fuzzy Data to Estimation Inverse Weibull Parameters and Reliability Function

2018 ◽  
pp. 397
Author(s):  
Nadia Hashim Al-Noor ◽  
Shurooq A.K. Al-Sultany
Keyword(s):  
Maximum Likelihood ◽  
Expectation Maximization ◽  
Mean Squared Error ◽  
Maximum Likelihood Estimators ◽  
Reliability Function ◽  
Fuzzy Data ◽  
Monte Carlo Simulation Study ◽  
Weibull Parameters ◽  
Squared Error ◽  
Newton Raphson

        In real situations all observations and measurements are not exact numbers but more or less non-exact, also called fuzzy. So, in this paper, we use approximate non-Bayesian computational methods to estimate inverse Weibull parameters and reliability function with fuzzy data. The maximum likelihood and moment estimations are obtained as non-Bayesian estimation. The maximum likelihood estimators have been derived numerically based on two iterative techniques namely “Newton-Raphson” and the “Expectation-Maximization” techniques. In addition, we provide compared numerically through Monte-Carlo simulation study to obtained estimates of the parameters and reliability function in terms of their mean squared error values and integrated mean squared error values respectively.

scholarly journals Pooled testing with replication as a mass testing strategy for the COVID-19 pandemics

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Julius Žilinskas ◽  
Algirdas Lančinskas ◽  
Mario R. Guarracino
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Group Testing ◽  
Testing Strategy ◽  
Testing Technique ◽  
Testing Procedures ◽  
Pooled Testing ◽  
Replication Scheme ◽  
Speed Up ◽  
Multiple Patients

AbstractDuring the COVID-19 pandemic it is essential to test as many people as possible, in order to detect early outbreaks of the infection. Present testing solutions are based on the extraction of RNA from patients using oropharyngeal and nasopharyngeal swabs, and then testing with real-time PCR for the presence of specific RNA filaments identifying the virus. This approach is limited by the availability of reactants, trained technicians and laboratories. One of the ways to speed up the testing procedures is a group testing, where the swabs of multiple patients are grouped together and tested. In this paper we propose to use the group testing technique in conjunction with an advanced replication scheme in which each patient is allocated in two or more groups to reduce the total numbers of tests and to allow testing of even larger numbers of people. Under mild assumptions, a 13 ×  average reduction of tests can be achieved compared to individual testing without delay in time.

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