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 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 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.

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.

scholarly journals Optimal sample sizes for group testing in two-stage sampling

2014 ◽  
Vol 25 (01) ◽  
pp. 12-28 ◽  
Author(s):  
Osval Antonio Montesinos-López ◽  
Kent Eskridge ◽  
Abelardo Montesinos-López ◽  
José Crossa
Keyword(s):  
Group Testing ◽  
Sample Sizes ◽  
Two Stage ◽  
Optimal Sample

Bounds on the Efficiency of Two-Stage Group Testing

1998 ◽  
pp. 213-232 ◽  
Author(s):  
Toby Berger ◽  
James W. Mandell
Keyword(s):  
Group Testing ◽  
Two Stage

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.

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