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Pugh S, Fosdick BK, Nehring M, Gallichotte EN, VandeWoude S, Wilson A. Estimating cutoff values for diagnostic tests to achieve target specificity using extreme value theory. BMC Med Res Methodol 2024; 24:30. [PMID: 38331732 PMCID: PMC10851584 DOI: 10.1186/s12874-023-02139-5] [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: 09/11/2023] [Accepted: 12/28/2023] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Rapidly developing tests for emerging diseases is critical for early disease monitoring. In the early stages of an epidemic, when low prevalences are expected, high specificity tests are desired to avoid numerous false positives. Selecting a cutoff to classify positive and negative test results that has the desired operating characteristics, such as specificity, is challenging for new tests because of limited validation data with known disease status. While there is ample statistical literature on estimating quantiles of a distribution, there is limited evidence on estimating extreme quantiles from limited validation data and the resulting test characteristics in the disease testing context. METHODS We propose using extreme value theory to select a cutoff with predetermined specificity by fitting a Pareto distribution to the upper tail of the negative controls. We compared this method to five previously proposed cutoff selection methods in a data analysis and simulation study. We analyzed COVID-19 enzyme linked immunosorbent assay antibody test results from long-term care facilities and skilled nursing staff in Colorado between May and December of 2020. RESULTS We found the extreme value approach had minimal bias when targeting a specificity of 0.995. Using the empirical quantile of the negative controls performed well when targeting a specificity of 0.95. The higher target specificity is preferred for overall test accuracy when prevalence is low, whereas the lower target specificity is preferred when prevalence is higher and resulted in less variable prevalence estimation. DISCUSSION While commonly used, the normal based methods showed considerable bias compared to the empirical and extreme value theory-based methods. CONCLUSIONS When determining disease testing cutoffs from small training data samples, we recommend using the extreme value based-methods when targeting a high specificity and the empirical quantile when targeting a lower specificity.
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Affiliation(s)
- Sierra Pugh
- Department of Statistics, Colorado State University, 102 Statistics Building, Fort Collins, 80523, Colorado, USA
| | - Bailey K Fosdick
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - Mary Nehring
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Emily N Gallichotte
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Ander Wilson
- Department of Statistics, Colorado State University, 102 Statistics Building, Fort Collins, 80523, Colorado, USA.
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Sexton NR, Cline PJ, Gallichotte EN, Fitzmeyer E, Young MC, Janich AJ, Pabilonia KL, Ehrhart N, Ebel GD. SARS-CoV-2 entry into and evolution within a skilled nursing facility. Sci Rep 2023; 13:11657. [PMID: 37468595 DOI: 10.1038/s41598-023-38544-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
SARS-CoV-2 belongs to the family Coronaviridae which includes multiple human pathogens that have an outsized impact on aging populations. As a novel human pathogen, SARS-CoV-2 is undergoing continuous adaptation to this new host species and there is evidence of this throughout the scientific and public literature. However, most investigations of SARS-CoV-2 evolution have focused on large-scale collections of data across diverse populations and/or living environments. Here we investigate SARS-CoV-2 evolution in epidemiologically linked individuals within a single outbreak at a skilled nursing facility beginning with initial introduction of the pathogen. The data demonstrate that SARS-CoV-2 was introduced to the facility multiple times without establishing an interfacility transmission chain, followed by a single introduction that infected many individuals within a week. This large-scale introduction by a single genotype then persisted in the facility. SARS-CoV-2 sequences were investigated at both the consensus and intra-host variation levels. Understanding the variability in SARS-CoV-2 during transmission chains will assist in understanding the spread of this disease and can ultimately inform best practices for mitigation strategies.
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Affiliation(s)
- Nicole R Sexton
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68504, USA
| | - Parker J Cline
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Emily N Gallichotte
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Emily Fitzmeyer
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Michael C Young
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Ashley J Janich
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Kristy L Pabilonia
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Nicole Ehrhart
- Columbine Health Systems Center for Healthy Aging and Department of Clinical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
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Liang C, Wagstaff J, Aharony N, Schmit V, Manheim D. Managing the Transition to Widespread Metagenomic Monitoring: Policy Considerations for Future Biosurveillance. Health Secur 2023; 21:34-45. [PMID: 36629860 PMCID: PMC9940815 DOI: 10.1089/hs.2022.0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The technological possibilities and future public health importance of metagenomic sequencing have received extensive attention, but there has been little discussion about the policy and regulatory issues that need to be addressed if metagenomic sequencing is adopted as a key technology for biosurveillance. In this article, we introduce metagenomic monitoring as a possible path to eventually replacing current infectious disease monitoring models. Many key enablers are technological, whereas others are not. We therefore highlight key policy challenges and implementation questions that need to be addressed for "widespread metagenomic monitoring" to be possible. Policymakers must address pitfalls like fragmentation of the technological base, private capture of benefits, privacy concerns, the usefulness of the system during nonpandemic times, and how the future systems will enable better response. If these challenges are addressed, the technological and public health promise of metagenomic sequencing can be realized.
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Affiliation(s)
- Chelsea Liang
- Chelsea Liang is an Independent Researcher, University of New South Wales, School of Biotechnology and Biomolecular Sciences, Sydney, Australia
| | - James Wagstaff
- James Wagstaff, PhD, is a Research Fellow, Future of Humanity Institute, University of Oxford, Oxford, UK
| | - Noga Aharony
- Noga Aharony, MS, is a PhD Student, Department of Systems Biology, Columbia University, New York, NY
| | - Virginia Schmit
- Virginia Schmit, PhD, is Director of Research, 1DatSooner, DE, and a Policy Specialist, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - David Manheim
- David Manheim, PhD, is Head of Policy and Research, ALTER, Rehovot, Israel; Lead Researcher, 1DaySooner, Claymont, DE,Visiting Researcher, Humanities and Arts Department, Technion – Israel Institute of Technology, Haifa, Israel.,Address correspondence to: David B. Manheim, 8734 First Avenue, Silver Spring, MD 20910
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Neutralizing Antibody Responses Among Residents and Staff of Long-Term Care Facilities in the State of New Jersey During the First Wave of the COVID-19 Pandemic. J Community Health 2023; 48:50-58. [PMID: 36197535 PMCID: PMC9532818 DOI: 10.1007/s10900-022-01142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2022] [Indexed: 10/24/2022]
Abstract
Expanding a previous study of the immune response to SARS-CoV-2 in 10 New Jersey long-term care facilities (LTCFs) during the first wave of the pandemic, this study characterized the neutralizing antibody (NAb) response to infection and vaccination among residents and staff. Sera from the original study were tested using the semi-quantitative enzyme-linked immunosorbent cPass neutralization-antibody detection assay. Almost all residents (97.8%) and staff (98.1%) who were positive for IgG S antibody to the spike protein were positive for NAb. In non-vaccinated subjects with a history of infection (positive polymerase chain reaction (PCR) or antigen test), the distribution of mean intervals from infection to serology date was not significantly different for S antibody positives versus negatives. More than 80% of both were positive at 10 months. Similarly, the mean NAb titer for residents and staff was not associated with interval from PCR/antigen positive to serology date, F = 0.1.01, Pr > F = 0.4269 and F = 0.77, Pr > F = 0.6548 respectively. Titers remained high as the interval reached 10 months. In vaccinees who had no history of infection, the NAb titer was near the test maximum when the serum was drawn seven or more days after the second vaccine dose. In staff the mean NAb titer increased significantly as the vaccine number increased from one to two doses, F = 11.69, Pr > F < 0.0001. NAb titers to SARS-CoV-2 in residents and staff of LTCFs were consistently high 10 months after infection and after two doses of vaccine. Ongoing study is needed to determine whether this antibody provides protection as the virus continues to mutate.
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Nehring M, Pugh S, Dihle T, Gallichotte E, Nett T, Weber E, Mayo C, Lynn L, Ebel G, Fosdick BK, VandeWoude S. Laboratory-Based SARS-CoV-2 Receptor Binding Domain Serologic Assays Perform with Equivalent Sensitivity and Specificity to Commercial FDA-EUA Approved Tests. Viruses 2022; 15:106. [PMID: 36680146 PMCID: PMC9860642 DOI: 10.3390/v15010106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023] Open
Abstract
During early phases of the SARS-CoV-2 epidemic, many research laboratories repurposed their efforts towards developing diagnostic testing that could aid public health surveillance while commercial and public diagnostic laboratories developed capacity and validated large scale testing methods. Simultaneously, the rush to produce point-of-care and diagnostic facility testing resulted in FDA Emergency Use Authorization with scarce and poorly validated clinical samples. Here, we review serologic test results from 186 serum samples collected in early phases of the pandemic (May 2020) from skilled nursing facilities tested with six laboratory-based and two commercially available assays. Serum neutralization titers were used to set cut-off values using positive to negative ratio (P/N) analysis to account for batch effects. We found that laboratory-based receptor binding domain (RBD) binding assays had equivalent or superior sensitivity and specificity compared to commercially available tests. We also determined seroconversion rate and compared with qPCR outcomes. Our work suggests that research laboratory assays can contribute reliable surveillance information and should be considered important adjuncts to commercial laboratory testing facilities during early phases of disease outbreaks.
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Affiliation(s)
- Mary Nehring
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Sierra Pugh
- Department of Statistics, Colorado State University, Fort Collins, CO 80523, USA
| | - Tina Dihle
- Health and Medical Center Laboratory, Colorado State University, Fort Collins, CO 80523, USA
| | - Emily Gallichotte
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Terry Nett
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Eric Weber
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Christie Mayo
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Lori Lynn
- Health and Medical Center Laboratory, Colorado State University, Fort Collins, CO 80523, USA
| | - Greg Ebel
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Bailey K. Fosdick
- Department of Biostatistics and Informatics, Colorado School of Public Health, Denver, CO 80206, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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Impact of Prior Infection on SARS-CoV-2 Antibody Responses in Vaccinated Long-Term Care Facility Staff. mSphere 2022; 7:e0016922. [PMID: 35862798 PMCID: PMC9429942 DOI: 10.1128/msphere.00169-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 and has resulted in millions of deaths worldwide. Certain populations are at higher risk for infection, especially staff and residents at long-term care facilities (LTCF), due to the congregant living setting and high proportions of residents with many comorbidities. Prior to vaccine availability, these populations represented large fractions of total coronavirus disease 2019 (COVID-19) cases and deaths in the United States. Due to the high-risk setting and outbreak potential, staff and residents were among the first groups to be vaccinated. To define the impact of prior infection on the response to vaccination, we measured antibody responses in a cohort of staff members at an LTCF, many of whom were previously infected by SARS-CoV-2. We found that neutralizing, receptor-binding domain (RBD)-binding, and nucleoprotein (NP)-binding antibody levels were significantly higher after the full vaccination course in individuals that were previously infected and that NP antibody levels could discriminate individuals with prior infection from vaccinated individuals. While an anticipated antibody titer increase was observed after a vaccine booster dose in naive individuals, a boost response was not observed in individuals with previous COVID-19 infection. We observed a strong relationship between neutralizing antibodies and RBD-binding antibodies postvaccination across all groups, whereas no relationship was observed between NP-binding and neutralizing antibodies. One individual with high levels of neutralizing and binding antibodies experienced a breakthrough infection (prior to the introduction of Omicron), demonstrating that the presence of antibodies is not always sufficient for complete protection against infection. These results highlight that a history of COVID-19 exposure significantly increases SARS-CoV-2 antibody responses following vaccination. IMPORTANCE Long-term care facilities (LTCFs) have been disproportionately impacted by COVID-19, due to their communal nature, the high-risk profile of residents, and the vulnerability of residents to respiratory pathogens. In this study, we analyzed the role of prior natural immunity to SARS-CoV-2 in postvaccination antibody responses. The LTCF in our cohort experienced a large outbreak, with almost 40% of staff members becoming infected. We found that individuals that were infected prior to vaccination had higher levels of neutralizing and binding antibodies postvaccination. Importantly, the second vaccine dose significantly boosted antibody levels in those that were immunologically naive prior to vaccination, but not in those that had prior immunity. Regardless of the prevaccination immune status, the levels of binding and neutralizing antibodies were highly correlated. The presence of NP-binding antibodies could be used to identify individuals that were previously infected when prevaccination immune status was not known. Our results reveal that vaccination antibody responses differ depending on prior natural immunity.
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