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Santos APA, Rios DRA, Trindade CLC, Oliveira FEG, Oliveira MB, de Melo SN, Belo VS. Prevalence, incidence, risk factors and residual risk associated with viral infections among eligible Brazilian blood donors. Transfus Med 2024; 34:46-53. [PMID: 38165014 DOI: 10.1111/tme.13022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 10/27/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Knowledge regarding the profile of eligible blood donors presenting positive results in laboratory screening is essential for reducing transfusion-transmitted human immunodeficiency virus (HIV), hepatitis B virus (HBV) and hepatitis C virus (HCV). Our study aimed to evaluate the prevalence, incidence, predictor variables and residual risk (RR) of HIV/HBV/HCV in blood bags donated in Minas Gerais, Brazil. This study analysed data retrieved from the records of a large blood bank relating to donations collected at multiple centres within the period 2012-2018, during which 1 991 120 blood bags were screened using immunoassays and nucleic acid tests (NATs). Multilevel modelling was used to investigate the association between sex, civil status and age group with HIV/HBV/HCV. RR was estimated from the incidence values (restricted to negative and positive tests within the study period) and window periods for infections. The prevalence in first time donors, incidence and RR of HCV (223.73 cases per 100 000; 54.84 per 100 000 persons-year and 1.6527 per 100 000, respectively) were higher than those of HIV (172.65 cases per 100 000; 28.25 per 100 000 persons-year and 0.8514 per 100 000) and HBV (168.17 cases per 100 000; 18.54 per 100 000 persons-year and 0.5588 per 100 000). The odds of acquiring infection were greater in male, single and older donors. Sixteen donors were identified as seronegative and NATs+ during the 7-year span of the study. Our study has clarified some spatiotemporal trends regarding HIV/HBV/HCV infections in donated blood in Brazil. The results will contribute to the formulation of directives addressed to high-risk donors.
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Affiliation(s)
- Ana Paula Alves Santos
- Universidade Federal de São João Del Rei, Campus Centro-Oeste Dona Lindu, Divinópolis, MG, Brazil
| | | | | | | | | | - Saulo Nascimento de Melo
- Universidade Federal de São João Del Rei, Campus Centro-Oeste Dona Lindu, Divinópolis, MG, Brazil
| | - Vinícius Silva Belo
- Universidade Federal de São João Del Rei, Campus Centro-Oeste Dona Lindu, Divinópolis, MG, Brazil
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2
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Bobkova N, Chen Y, Eraslan H. Optimal group testing with heterogeneous risks. ECONOMIC THEORY 2023:1-32. [PMID: 37360771 PMCID: PMC10243685 DOI: 10.1007/s00199-023-01502-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 05/08/2023] [Indexed: 06/28/2023]
Abstract
We consider optimal group testing of individuals with heterogeneous risks for an infectious disease. Our algorithm significantly reduces the number of tests needed compared to Dorfman (Ann Math Stat 14(4):436-440, 1943). When both low-risk and high-risk samples have sufficiently low infection probabilities, it is optimal to form heterogeneous groups with exactly one high-risk sample per group. Otherwise, it is not optimal to form heterogeneous groups, but homogeneous group testing may still be optimal. For a range of parameters including the U.S. Covid-19 positivity rate for many weeks during the pandemic, the optimal size of a group test is four. We discuss the implications of our results for team design and task assignment.
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Affiliation(s)
- Nina Bobkova
- Department of Economics, Rice University and CEPR, Houston, USA
| | - Ying Chen
- Department of Economics, Johns Hopkins University, Baltimore, USA
| | - Hülya Eraslan
- Department of Economics, Rice University and NBER, Houston, USA
- Institute of Social and Economics Research, Osaka University, Osaka, Japan
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El Hajj H, Bish DR, Bish EK, Aprahamian H. Screening multi-dimensional heterogeneous populations for infectious diseases under scarce testing resources, with application to COVID-19. NAVAL RESEARCH LOGISTICS 2022; 69:3-20. [PMID: 38607835 PMCID: PMC8251476 DOI: 10.1002/nav.21985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 05/12/2023]
Abstract
Testing provides essential information for managing infectious disease outbreaks, such as the COVID-19 pandemic. When testing resources are scarce, an important managerial decision is who to test. This decision is compounded by the fact that potential testing subjects are heterogeneous in multiple dimensions that are important to consider, including their likelihood of being disease-positive, and how much potential harm would be averted through testing and the subsequent interventions. To increase testing coverage, pooled testing can be utilized, but this comes at a cost of increased false-negatives when the test is imperfect. Then, the decision problem is to partition the heterogeneous testing population into three mutually exclusive sets: those to be individually tested, those to be pool tested, and those not to be tested. Additionally, the subjects to be pool tested must be further partitioned into testing pools, potentially containing different numbers of subjects. The objectives include the minimization of harm (through detection and mitigation) or maximization of testing coverage. We develop data-driven optimization models and algorithms to design pooled testing strategies, and show, via a COVID-19 contact tracing case study, that the proposed testing strategies can substantially outperform the current practice used for COVID-19 contact tracing (individually testing those contacts with symptoms). Our results demonstrate the substantial benefits of optimizing the testing design, while considering the multiple dimensions of population heterogeneity and the limited testing capacity.
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Affiliation(s)
- Hussein El Hajj
- Department of Industrial and Systems EngineeringVirginia TechBlacksburgVirginiaUSA
| | - Douglas R. Bish
- Department of Information Systems, Statistics, and Management ScienceUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Ebru K. Bish
- Department of Information Systems, Statistics, and Management ScienceUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Hrayer Aprahamian
- Department of Industrial and Systems EngineeringTexas A&MCollege StationTexasUSA
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Abid S, Ferjani S, El Moussi A, Ferjani A, Nasr M, Landolsi I, Saidi K, Gharbi H, Letaief H, Hechaichi A, Safer M, Ben Alaya NBE, Boubaker IBB. Assessment of sample pooling for SARS-CoV-2 molecular testing for screening of asymptomatic persons in Tunisia. Diagn Microbiol Infect Dis 2020; 98:115125. [PMID: 32768876 PMCID: PMC7335417 DOI: 10.1016/j.diagmicrobio.2020.115125] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/03/2022]
Abstract
The aim of this study is to test a pooling approach for the RT-PCR test to detect low viral loads of SARS-CoV-2. We found that a single positive specimen can still be detected in pools of up to 10. Each laboratory should conduct its own evaluation and validation of pooling protocols according to its specific context.
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Affiliation(s)
- Salma Abid
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
| | - Sana Ferjani
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia.
| | - Awatef El Moussi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
| | - Asma Ferjani
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
| | - Mejda Nasr
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Ichrak Landolsi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Karima Saidi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Hanène Gharbi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Hajer Letaief
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006, Tunis, Tunisia
| | - Aicha Hechaichi
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006, Tunis, Tunisia
| | - Mouna Safer
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006, Tunis, Tunisia
| | | | - Ilhem Boutiba-Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
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Implementation of Antibody Rapid Diagnostic Testing versus Real-Time Reverse Transcription-PCR Sample Pooling in the Screening of COVID-19: a Case of Different Testing Strategies in Africa. mSphere 2020; 5:5/4/e00524-20. [PMID: 32727861 PMCID: PMC7392544 DOI: 10.1128/msphere.00524-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has wreaked havoc across the globe; although the number of cases in Africa remains lower than in other regions, it is on a gradual upward trajectory. To date, COVID-19 cases have been reported in 54 out of 55 African countries. However, due to limited severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time reverse transcription-PCR (rRT-PCR) testing capacity and scarcity of testing reagents, it is probable that the total number of cases could far exceed published statistics. In this viewpoint, using Ghana, Malawi, South Africa, and Zimbabwe as examples of countries that have implemented different testing strategies, we argue that the implementation of sample pooling for rRT-PCR over antibody rapid diagnostic testing could have a greater impact in assessing disease burden. Sample pooling offers huge advantages compared to single test rRT-PCR, as it reduces diagnostic costs, personnel time, burnout, and analytical run times. Africa is already strained in terms of testing resources for COVID-19; hence, cheaper alternative ways need to be implemented to conserve resources, maximize mass testing, and reduce transmission in the wider population.
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Bukhari SUK, Khalid SS, Syed A, Shah SSH. Smart Pooled Sample Testing for COVID-19: A Possible Solution For Sparcity of Test Kits (Preprint). J Med Internet Res 2020. [DOI: 10.2196/20831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Nguyen NT, Aprahamian H, Bish EK, Bish DR. A methodology for deriving the sensitivity of pooled testing, based on viral load progression and pooling dilution. J Transl Med 2019; 17:252. [PMID: 31387586 PMCID: PMC6683472 DOI: 10.1186/s12967-019-1992-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pooled testing, in which biological specimens from multiple subjects are combined into a testing pool and tested via a single test, is a common testing method for both surveillance and screening activities. The sensitivity of pooled testing for various pool sizes is an essential input for surveillance and screening optimization, including testing pool design. However, clinical data on test sensitivity values for different pool sizes are limited, and do not provide a functional relationship between test sensitivity and pool size. We develop a novel methodology to accurately compute the sensitivity of pooled testing, while accounting for viral load progression and pooling dilution. We demonstrate our methodology on the nucleic acid amplification testing (NAT) technology for the human immunodeficiency virus (HIV). METHODS Our methodology integrates mathematical models of viral load progression and pooling dilution to derive test sensitivity values for various pool sizes. This methodology derives the conditional test sensitivity, conditioned on the number of infected specimens in a pool, and uses the law of total probability, along with higher dimensional integrals, to derive pooled test sensitivity values. We also develop a highly accurate and easy-to-compute approximation function for pooled test sensitivity of the HIV ULTRIO Plus NAT Assay. We calibrate model parameters using published efficacy data for the HIV ULTRIO Plus NAT Assay, and clinical data on viral RNA load progression in HIV-infected patients, and use this methodology to derive and validate the sensitivity of the HIV ULTRIO Plus Assay for various pool sizes. RESULTS We demonstrate the value of this methodology through optimal testing pool design for HIV prevalence estimation in Sub-Saharan Africa. This case study indicates that the optimal testing pool design is highly efficient, and outperforms a benchmark pool design. CONCLUSIONS The proposed methodology accounts for both viral load progression and pooling dilution, and is computationally tractable. We calibrate this model for the HIV ULTRIO Plus NAT Assay, show that it provides highly accurate sensitivity estimates for various pool sizes, and, thus, yields efficient testing pool design for HIV prevalence estimation. Our model is generic, and can be calibrated for other infections.
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Affiliation(s)
- Ngoc T Nguyen
- Grado Department of Industrial and Systems Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Hrayer Aprahamian
- Department of Industrial and Systems Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Ebru K Bish
- Grado Department of Industrial and Systems Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Douglas R Bish
- Grado Department of Industrial and Systems Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
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McCullough J, Alter HJ, Ness PM. Interpretation of pathogen load in relationship to infectivity and pathogen reduction efficacy. Transfusion 2018; 59:1132-1146. [PMID: 30592305 DOI: 10.1111/trf.15103] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 01/12/2023]
Affiliation(s)
| | - Harvey J Alter
- Department of Transfusion Medicine, NIH Clinical Center, Bethesda, Maryland
| | - Paul M Ness
- Departments of Pathology and Medicine, Johns Hopkins University, Baltimore, Maryland
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Nguyen NT, Bish EK, Aprahamian H. Sequential prevalence estimation with pooling and continuous test outcomes. Stat Med 2018; 37:2391-2426. [PMID: 29687473 DOI: 10.1002/sim.7657] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 01/17/2018] [Accepted: 02/15/2018] [Indexed: 01/02/2023]
Abstract
Prevalence estimation is crucial for controlling the spread of infections and diseases and for planning of health care services. Prevalence estimation is typically conducted via pooled, or group, testing due to limited testing budgets. We study a sequential estimation procedure that uses continuous pool readings and considers the dilution effect of pooling so as to efficiently estimate an unknown prevalence rate. Embedded into the sequential estimation procedure is an optimization model that determines the optimal pooling design (number of pools and pool sizes) under a limited testing budget, considering the trade-off between testing cost and estimation accuracy. Our numerical study indicates that the proposed sequential estimation procedure outperforms single-stage procedures, or procedures that use binary test outcomes. Further, the sequential procedure provides robust prevalence estimates in cases where the initial estimate of the unknown prevalence rate is poor, or the assumed distribution of the biomarker load in infected subjects is inaccurate. Thus, when limited and unreliable information is available about the current status of, or biomarker dynamics related to, an infection, the sequential procedure becomes an attractive estimation strategy, due to its ability to mitigate the initial bias.
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Affiliation(s)
- Ngoc T Nguyen
- Grado Department of Industrial and Systems Engineering, Virginia Tech, Blacksburg, Virginia, 24061, USA
| | - Ebru K Bish
- Grado Department of Industrial and Systems Engineering, Virginia Tech, Blacksburg, Virginia, 24061, USA
| | - Hrayer Aprahamian
- Grado Department of Industrial and Systems Engineering, Virginia Tech, Blacksburg, Virginia, 24061, USA
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10
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Practical Guidelines for Evaluating Transfusion Needs. Tech Orthop 2017. [DOI: 10.1097/bto.0000000000000204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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