scholarly journals Application of pooled testing in estimating the prevalence of COVID-19

2021 ◽  
Author(s):  
Pritha Guha ◽  
Apratim Guha ◽  
Tathagata Bandyopadhyay
Keyword(s):  
Pooled Testing

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 Prediction‐driven pooled testing methods: Application to HIV treatment monitoring in Rakai, Uganda

2021 ◽  
Author(s):  
Adam Brand ◽  
Susanne May ◽  
James P. Hughes ◽  
Gertrude Nakigozi ◽  
Steven J. Reynolds ◽  
...  
Keyword(s):  
Treatment Monitoring ◽  
Hiv Treatment ◽  
Testing Methods ◽  
Pooled Testing

scholarly journals Performance of Unobserved Self-Collected Nasal Swabs for Detection of SARS-CoV-2 by RT-PCR Utilizing a Remote Specimen Collection Strategy

2021 ◽  
Author(s):  
Ron M Kagan ◽  
Amy A Rogers ◽  
Gwynngelle A Borillo ◽  
Nigel J Clarke ◽  
Elizabeth M Marlowe
Keyword(s):  
Return To Work ◽  
Screening Program ◽  
False Negative ◽  
N Gene ◽  
Rt Pcr ◽  
Pooled Testing ◽  
Specimen Collection ◽  
Asymptomatic Patients ◽  
Nasal Swabs ◽  
The Impact

Abstract Background The use of a remote specimen collection strategy employing a kit designed for unobserved self-collection for SARS-CoV-2 RT-PCR can decrease the use of PPE and exposure risk. To assess the impact of unobserved specimen self-collection on test performance, we examined results from a SARS-CoV-2 qualitative RT-PCR test for self-collected specimens from participants in a return-to-work screening program and assessed the impact of a pooled testing strategy in this cohort. Methods Self-collected anterior nasal swabs from employee return to work programs were tested using the Quest Diagnostics SARS-CoV-2 RT-PCR EUA. The Ct values for the N1 and N3 N-gene targets and a human RNase P (RP) gene control target were tabulated. For comparison, we utilized Ct values from a cohort of HCP-collected specimens from patients with and without COVID-19 symptoms. Results Among 47,923 participants, 1.8% were positive. RP failed to amplify for 13/115,435 (0.011%) specimens. The median (IQR) Cts were 32.7 (25.0-35.7) for N1 and 31.3 (23.8-34.2) for N3. Median Ct values in the self-collected cohort were significantly higher than those of symptomatic, but not asymptomatic patients. Based on Ct values, pooled testing with 4 specimens would have yielded inconclusive results in 67/1,268 (5.2%) specimens but only a single false-negative result. Conclusions Unobserved self-collection of nasal swabs provides adequate sampling for SARS-CoV-2 RT-PCR testing. These findings alleviate concerns of increased false negatives in this context. Specimen pooling could be used for this population as the likelihood of false negative results is very low due when using a sensitive, dual-target methodology.

scholarly journals Pooling of Upper Respiratory Specimens Using a SARS-CoV-2 Real-time RT-PCR Assay Authorized for Emergency Use in Low-Prevalence Populations for High-Throughput Testing

2020 ◽  
Vol 7 (11) ◽  
Author(s):  
Gwynngelle A Borillo ◽  
Ron M Kagan ◽  
Russell E Baumann ◽  
Boris M Fainstein ◽  
Lamela Umaru ◽  
...  
Keyword(s):  
Real Time ◽  
False Negative ◽  
False Negative Rate ◽  
Nucleic Acid Amplification ◽  
Rt Pcr ◽  
Pooled Testing ◽  
Negative Results ◽  
Single Positive ◽  
Upper Respiratory ◽  
Respiratory Specimens

Abstract Background Nucleic acid amplification testing is a critical tool for addressing the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Specimen pooling can increase throughput and conserve testing resources but requires validation to ensure that reduced sensitivity does not increase the false-negative rate. We evaluated the performance of a real-time reverse transcription polymerase chain reaction (RT-PCR) test authorized by the US Food and Drug Administration (FDA) for emergency use for pooled testing of upper respiratory specimens. Methods Positive specimens were selected from 3 prevalence groups, 1%–3%, >3%–6%, and >6%–10%. Positive percent agreement (PPA) was assessed by pooling single-positive specimens with 3 negative specimens; performance was assessed using Passing-Bablok regression. Additionally, we assessed the distributions of RT-PCR cycle threshold (Ct) values for 3091 positive specimens. Results PPA was 100% for the 101 pooled specimens. There was a linear relationship between Ct values for pooled and single-tested specimens (r = 0.96–0.99; slope ≈ 1). The mean pooled Ct shifts at 40 cycles were 2.38 and 1.90, respectively, for the N1 and N3 targets. The median Cts for 3091 positive specimens were 25.9 (N1) and 24.7 (N3). The percentage of positive specimens with Cts between 40 and the shifted Ct was 1.42% (N1) and 0.0% (N3). Conclusions Pooled and individual testing of specimens positive for SARS-CoV-2 demonstrated 100% agreement, which demonstrates the viability of pooled specimens for SARS-COV-2 testing using a dual-target RT-PCR system. Pooled specimen testing can help increase testing capacity for SARS-CoV-2 with a low risk of false-negative results.

scholarly journals A methodology for deriving the sensitivity of pooled testing, based on viral load progression and pooling dilution

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Ngoc T. Nguyen ◽  
Hrayer Aprahamian ◽  
Ebru K. Bish ◽  
Douglas R. Bish
Keyword(s):  
Viral Load ◽  
Pooled Testing

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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