Effective screening strategies for safe opening of universities under Omicron and Delta variants of COVID-19.

As new COVID-19 variants emerge, and disease and population characteristics change, screening strategies may also need to change. We develop a decision-making model that can assist a college to determine an optimal screening strategy based on their characteristics and resources, considering COVID-19 infections/hospitalizations/deaths; peak daily hospitalizations; and the tests required. We also use this tool to generate screening guidelines for the safe opening of college campuses. Our compartmental model simulates disease spread on a hypothetical college campus under co-circulating variants with different disease dynamics, considering: (i) the heterogeneity in disease transmission and outcomes for faculty/staff and students based on vaccination status and level of natural immunity; and (ii) variant- and dose-dependent vaccine efficacy. Using the Spring 2022 academic semester as a case study, we study routine screening strategies, and find that screening the faculty/staff less frequently than the students, and/or the boosted and vaccinated less frequently than the unvaccinated, may avert a higher number of infections per test, compared to universal screening of the entire population at a common frequency. We also discuss key policy issues, including the need to revisit the mitigation objective over time, effective strategies that are informed by booster coverage, and if and when screening alone can compensate for low booster coverage.

Benefits of integrated screening and vaccination for infection control.

IMPORTANCE: Screening and vaccination are essential in the fight against infectious diseases, but need to be integrated and customized based on community and disease characteristics. OBJECTIVE: To develop effective screening and vaccination strategies, customized for a college campus, to reduce COVID-19 infections, hospitalizations, deaths, and peak hospitalizations. DESIGN, SETTING, AND PARTICIPANTS: We construct a compartmental model of disease spread under vaccination and routine screening, and study the efficacy of four mitigation strategies (routine screening only, vaccination only, vaccination with partial or full routine screening), and a no-intervention strategy. The study setting is a hypothetical college campus of 5,000 students and 455 faculty members during the Fall 2021 academic semester, when the Delta variant was the predominant strain. For sensitivity analysis, we vary the screening frequency, daily vaccination rate, initial vaccine coverage, and screening and vaccination compliance; and consider scenarios that represent low/medium/high transmission and test efficacy. Model parameters come from publicly available or published sources. RESULTS: With low initial vaccine coverage (30% in our study), even aggressive vaccination and screening result in a high number of infections: 1,020 to 2,040 (1,530 to 2,480) with routine daily (every other day) screening of the unvaccinated; 280 to 900 with daily screening extended to the newly vaccinated in base- and worst-case scenarios, which respectively consider reproduction numbers of 4.75 and 6.75 for the Delta variant. CONCLUSION: Integrated vaccination and routine screening can allow for a safe opening of a college when both the vaccine effectiveness and the initial vaccine coverage are sufficiently high. The interventions need to be customized considering the initial vaccine coverage, estimated compliance, screening and vaccination capacity, disease transmission and adverse outcome rates, and the number of infections/peak hospitalizations the college is willing to tolerate.

Screening multi-dimensional heterogeneous populations for infectious diseases under scarce testing resources, with application to COVID-19.

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.

A robust pooled testing approach to expand COVID-19 screening capacity.

Limited testing capacity for COVID-19 has hampered the pandemic response. Pooling is a testing method wherein samples from specimens (e.g., swabs) from multiple subjects are combined into a pool and screened with a single test. If the pool tests positive, then new samples from the collected specimens are individually tested, while if the pool tests negative, the subjects are classified as negative for the disease. Pooling can substantially expand COVID-19 testing capacity and throughput, without requiring additional resources. We develop a mathematical model to determine the best pool size for different risk groups, based on each group's estimated COVID-19 prevalence. Our approach takes into consideration the sensitivity and specificity of the test, and a dynamic and uncertain prevalence, and provides a robust pool size for each group. For practical relevance, we also develop a companion COVID-19 pooling design tool (through a spread sheet). To demonstrate the potential value of pooling, we study COVID-19 screening using testing data from Iceland for the period, February-28-2020 to June-14-2020, for subjects stratified into high- and low-risk groups. We implement the robust pooling strategy within a sequential framework, which updates pool sizes each week, for each risk group, based on prior week's testing data. Robust pooling reduces the number of tests, over individual testing, by 88.5% to 90.2%, and 54.2% to 61.9%, respectively, for the low-risk and high-risk groups (based on test sensitivity values in the range [0.71, 0.98] as reported in the literature). This results in much shorter times, on average, to get the test results compared to individual testing (due to the higher testing throughput), and also allows for expanded screening to cover more individuals. Thus, robust pooling can potentially be a valuable strategy for COVID-19 screening.

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

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.

Sequential prevalence estimation with pooling and continuous test outcomes.

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.

Proactive Risk Assessment of Surgical Site Infections in Ambulatory Surgery Centers.

BACKGROUND: The Socio-Technical Probabilistic Risk Assessment, a proactive risk assessment tool imported from high-risk industries, was used to identify risks for surgical site infections (SSIs) associated with the ambulatory surgery center setting and to guide improvement efforts. OBJECTIVES: This study had 2 primary objectives: (1) to identify the critical risk factors associated with SSIs resulting from procedures performed at ambulatory surgery centers and (2) to design an intervention to mitigate the probability of SSI for the highest risk factors identified. METHODS: Inputs included quantitative and qualitative data sources from the evidence-based literature and from health care providers. The Socio-Technical Probabilistic Risk Assessment ranked the failure points (events) on the basis of their contribution to an SSI. The event, entitled "Failure to protect the patient effectively," which included several failure points, was the most critical unique event with the highest contribution to SSI risk. RESULTS: A total of 51.87% of SSIs in this setting were caused by this failure. Consequently, we proposed an intervention aimed at all 5 major components of this failure. CONCLUSIONS: The intervention targets improvements in skin preparation; proper administration of antibiotics; staff training in infection control principles, including practices for the prevention of glove punctures; and procedures to ensure the removal of watches, jewelry, and artificial nails.

Residual risk and waste in donated blood with pooled nucleic acid testing.

An accurate estimation of the residual risk of transfusion-transmittable infections (TTIs), which includes the human immunodeficiency virus (HIV), hepatitis B and C viruses (HBV, HCV), among others, is essential, as it provides the basis for blood screening assay selection. While the highly sensitive nucleic acid testing (NAT) technology has recently become available, it is highly costly. As a result, in most countries, including the United States, the current practice for human immunodeficiency virus, hepatitis B virus, hepatitis C virus screening in donated blood is to use pooled NAT. Pooling substantially reduces the number of tests required, especially for TTIs with low prevalence rates. However, pooling also reduces the test's sensitivity, because the viral load of an infected sample might be diluted by the other samples in the pool to the point that it is not detectable by NAT, leading to potential TTIs. Infection-free blood may also be falsely discarded, resulting in wasted blood. We derive expressions for the residual risk, expected number of tests, and expected amount of blood wasted for various two-stage pooled testing schemes, including Dorfman-type and array-based testing, considering infection progression, infectivity of the blood unit, and imperfect tests under the dilution effect and measurement errors. We then calibrate our model using published data and perform a case study. Our study offers key insights on how pooled NAT, used within different testing schemes, contributes to the safety and cost of blood. Copyright © 2016 John Wiley & Sons, Ltd.

Cost-effectiveness of Babesia microti antibody and nucleic acid blood donation screening using results from prospective investigational studies.

BACKGROUND: Babesia microti causes transfusion-transmitted babesiosis (TTB); currently, blood donor screening assays are unlicensed but used investigationally. STUDY DESIGN AND METHODS: We developed a decision tree model assessing the comparative- and cost-effectiveness of B. microti blood donation screening strategies in endemic areas compared to the status quo (question regarding a history of babesiosis), including testing by: (1) universal antibody (Ab), (2) universal polymerase chain reaction (PCR), (3) universal Ab/PCR, and (4) recipient risk-targeted Ab/PCR. The model predicted the number of TTB cases, complicated TTB cases, cases averted, and quality-adjusted life years (QALYs). Economic outcomes included each strategy's per-donation cost, waste (number of infection-free units incorrectly discarded), and waste index (number wasted units/number true positives). Sensitivity analyses examined uncertainty in transmission probabilities, prevalence rates, and other key model inputs. RESULTS: Universal PCR in four endemic states would prevent 24 to 31 TTB cases/100,000 units transfused (pht) at an incremental cost-effectiveness ratio (ICER) of $26,000 to $44,000/QALY (transmission probability dependent) and waste index of zero. Universal Ab/PCR would prevent 33 to 42 TTB cases pht at an ICER of $54,000 to $83,000/QALY and waste index of 0.05. The questionnaire is most wasteful (99.62 units wasted pht; 208.62 waste index), followed by the risk-targeted strategy (76.27 units wasted pht; 0.68 waste index). The model predicted zero cases of TTB or complicated TTB with universal Ab/PCR (versus [33, 42] and [13, 18] pht, respectively [no screening]). Results are highly sensitive to transmission probabilities. CONCLUSIONS: Universal PCR in endemic states is an effective blood donation screening strategy at a threshold of $50,000/QALY. Using a higher cost-effectiveness ratio, universal Ab/PCR is the most effective strategy.

A socio-technical, probabilistic risk assessment model for surgical site infections in ambulatory surgery centers.

BACKGROUND: To understand how structural and process elements may affect the risk for surgical site infections (SSIs) in the ambulatory surgery center (ASC) environment, the researchers employed a tool known as socio-technical probabilistic risk assessment (ST-PRA). ST-PRA is particularly helpful for estimating risks in outcomes that are very rare, such as the risk of SSI in ASCs. OBJECTIVE: Study objectives were to (1) identify the risk factors associated with SSIs resulting from procedures performed at ASCs and (2) design an intervention to mitigate the likelihood of SSIs for the most common risk factors that were identified by the ST-PRA for a particular surgical procedure. METHODS: ST-PRA was used to study the SSI risk in the ASC setting. Both quantitative and qualitative data sources were utilized, and sensitivity analysis was performed to ensure the robustness of the results. RESULTS: The event entitled "fail to protect the patient effectively" accounted for 51.9% of SSIs in the ambulatory care setting. Critical components of this event included several failure risk points related to skin preparation, antibiotic administration, staff training, proper response to glove punctures during surgery, and adherence to surgical preparation rules related to the wearing of jewelry, watches, and artificial nails. Assuming a 75% reduction in noncompliance on any combination of 2 of these 5 components, the risk for an SSI decreased from 0.0044 to between 0.0027 and 0.0035. CONCLUSION: An intervention that targeted the 5 major components of the major risk point was proposed, and its implications were discussed.

A probabilistic method for the estimation of residual risk in donated blood.

The residual risk (RR) of transfusion-transmitted infections, including the human immunodeficiency virus and hepatitis B and C viruses, is typically estimated by the incidence[Formula: see text]window period model, which relies on the following restrictive assumptions: Each screening test, with probability 1, (1) detects an infected unit outside of the test's window period; (2) fails to detect an infected unit within the window period; and (3) correctly identifies an infection-free unit. These assumptions need not hold in practice due to random or systemic errors and individual variations in the window period. We develop a probability model that accurately estimates the RR by relaxing these assumptions, and quantify their impact using a published cost-effectiveness study and also within an optimization model. These assumptions lead to inaccurate estimates in cost-effectiveness studies and to sub-optimal solutions in the optimization model. The testing solution generated by the optimization model translates into fewer expected infections without an increase in the testing cost.