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Gilbert PB, Fong Y, Hejazi NS, Kenny A, Huang Y, Carone M, Benkeser D, Follmann D. Four statistical frameworks for assessing an immune correlate of protection (surrogate endpoint) from a randomized, controlled, vaccine efficacy trial. Vaccine 2024; 42:2181-2190. [PMID: 38458870 PMCID: PMC10999339 DOI: 10.1016/j.vaccine.2024.02.071] [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: 12/12/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/10/2024]
Abstract
A central goal of vaccine research is to characterize and validate immune correlates of protection (CoPs). In addition to helping elucidate immunological mechanisms, a CoP can serve as a valid surrogate endpoint for an infectious disease clinical outcome and thus qualifies as a primary endpoint for vaccine authorization or approval without requiring resource-intensive randomized, controlled phase 3 trials. Yet, it is challenging to persuasively validate a CoP, because a prognostic immune marker can fail as a reliable basis for predicting/inferring the level of vaccine efficacy against a clinical outcome, and because the statistical analysis of phase 3 trials only has limited capacity to disentangle association from cause. Moreover, the multitude of statistical methods garnered for CoP evaluation in phase 3 trials renders the comparison, interpretation, and synthesis of CoP results challenging. Toward promoting broader harmonization and standardization of CoP evaluation, this article summarizes four complementary statistical frameworks for evaluating CoPs in a phase 3 trial, focusing on the frameworks' distinct scientific objectives as measured and communicated by distinct causal vaccine efficacy parameters. Advantages and disadvantages of the frameworks are considered, dependent on phase 3 trial context, and perspectives are offered on how the frameworks can be applied and their results synthesized.
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Affiliation(s)
- Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA.
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Nima S Hejazi
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Avi Kenny
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Ying Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Marco Carone
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - David Benkeser
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Dean Follmann
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
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Qi L, Sun Y, Juraska M, Moodie Z, Magaret CA, Heng F, Carpp LN, Gilbert PB. Neutralizing antibody correlates of sequence specific dengue disease in a tetravalent dengue vaccine efficacy trial in Asia. Vaccine 2022; 40:5912-5923. [PMID: 36068106 PMCID: PMC9881745 DOI: 10.1016/j.vaccine.2022.08.055] [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: 11/11/2021] [Revised: 07/13/2022] [Accepted: 08/23/2022] [Indexed: 01/31/2023]
Abstract
In the CYD14 trial of the CYD-TDV dengue vaccine in 2-14 year-olds, neutralizing antibody (nAb) titers to the vaccine-insert dengue strains correlated inversely with symptomatic, virologically-confirmed dengue (VCD). Also, vaccine efficacy against VCD was higher against dengue prM/E amino acid sequences closer to the vaccine inserts. We integrated the nAb and sequence data types by assessing nAb titers as a correlate of sequence-specific VCD separately in the vaccine arm and in the placebo arm. In both vaccine and placebo recipients the correlation of nAb titer with sequence-specific VCD was stronger for dengue nAb contact site sequences closer to the vaccine (p = 0.005 and p = 0.012, respectively). The risk of VCD in vaccine (placebo) recipients was 6.7- (1.80)-fold lower at the 90th vs 10th percentile of nAb for viruses perfectly matched to CYD-TDV, compared to 2.1- (0.78)-fold lower at the 90th vs 10th percentile for viruses with five amino acid mismatches. The evidence for a stronger sequence-distance dependent correlate of risk for the vaccine arm indicates departure from the Prentice criteria for a valid sequence-distance specific surrogate endpoint and suggests that the nAb marker may affect dengue risk differently depending on whether nAbs arise from infection or also by vaccination. However, when restricting to baseline-seropositive 9-14 year-olds, the correlation pattern became more similar between the vaccine and placebo arms, supporting nAb titers as an approximate surrogate endpoint in this population. No sequence-specific nAb titer correlates of VCD were seen in baseline-seronegative participants. Integrated immune response/pathogen sequence data correlates analyses could help increase knowledge of correlates of risk and surrogate endpoints for other vaccines against genetically diverse pathogens. Trial registration: EU Clinical Trials Register 2014-001708-24; registration date 2014-05-26.
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Affiliation(s)
- Li Qi
- Biostatistics and Programming, Sanofi, 55 Corporate Drive, Bridgewater, NJ 08807, United States.
| | - Yanqing Sun
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, United States.
| | - Michal Juraska
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109, United States.
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109, United States.
| | - Craig A Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109, United States.
| | - Fei Heng
- Department of Mathematics and Statistics, University of North Florida, 1 UNF Drive, Jacksonville, FL 32224, United States.
| | - Lindsay N Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109, United States.
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109, United States; Department of Biostatistics, University of Washington, 3980 15th Avenue NE, Seattle, WA 98109, United States.
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Gallichotte EN, Henein S, Nivarthi U, Delacruz M, Scobey T, Bonaparte M, Moser J, Munteanu A, Baric R, de Silva AM. Vaccine-induced antibodies to contemporary strains of dengue virus type 4 show a mechanistic correlate of protective immunity. Cell Rep 2022; 39:110930. [PMID: 35675766 DOI: 10.1016/j.celrep.2022.110930] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/18/2022] [Accepted: 05/18/2022] [Indexed: 11/25/2022] Open
Abstract
The four dengue virus serotypes (DENV1-4) are mosquito-borne flaviviruses of humans. Several live-attenuated tetravalent DENV vaccines are at different stages of clinical development and approval. In children with no baseline immunity to DENVs, a leading vaccine (Dengvaxia) is efficacious against vaccine-matched DENV4 genotype II (GII) strains but not vaccine-mismatched DENV4 GI viruses. We use a panel of recombinant DENV4 viruses displaying GI or GII envelope (E) proteins to map Dengvaxia-induced neutralizing antibodies (NAbs) linked to protection. The vaccine stimulated antibodies that neutralize the DENV4 GII virus better than the GI virus. The neutralization differences map to 5 variable amino acids on the E protein located within a region targeted by DENV4 NAbs, supporting a mechanistic role for these epitope-specific NAbs in protection. In children with no baseline immunity to DENVs, levels of DENV4 serotype- and genotype-specific NAbs induced by vaccination are predictive of vaccine efficacy.
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Affiliation(s)
- Emily N Gallichotte
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Sandra Henein
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Usha Nivarthi
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Matthew Delacruz
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Trevor Scobey
- Department of Epidemiology, University of North Carolina School of Public Health, Chapel Hill, NC, USA
| | | | | | | | - Ralph Baric
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA; Department of Epidemiology, University of North Carolina School of Public Health, Chapel Hill, NC, USA.
| | - Aravinda M de Silva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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Yang T, Huang Y, Fong Y. Change Point Inference in the Presence of Missing Covariates for Principal Surrogate Evaluation in Vaccine Trials. Biometrika 2022; 108:829-843. [PMID: 35001938 DOI: 10.1093/biomet/asaa100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We consider the use of threshold-based regression models for evaluating immune response biomarkers as principal surrogate markers of a vaccine's protective effect. Threshold-based regression models, which allow the relationship between a clinical outcome and a covariate to change dramatically across a threshold value in the covariate, have been studied by various authors under fully observed data. Limited research, however, has examined these models in the presence of missing covariates, such as the counterfactual potential immune responses of a participant in the placebo arm of a standard vaccine trial had s/he been assigned to the vaccine arm instead. Based on a hinge model for a threshold effect of the principal surrogate on vaccine efficacy, we develop a regression methodology that consists of two components: (1) The estimated likelihood method is employed to handle missing potential outcomes, and (2) a penalty is imposed on the estimated likelihood to ensure satisfactory finite sample performance. We develop a method that allows joint estimation of all model parameters as well as a two-step method that separates the estimation of the threshold parameter from the rest of the parameters. Stable iterative algorithms are developed to implement the two methods and the asymptotic properties of the proposed estimators are established. In simulation studies, the proposed estimators are shown to have satisfactory finite sample performance. The proposed methods are applied to analyze a real dataset collected from dengue vaccine efficacy trials to predict how vaccine efficacy varies with an individual's potential immune response if receiving vaccine.
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Affiliation(s)
- Tao Yang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, U.S.A
| | - Ying Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, U.S.A
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, U.S.A
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Henein S, Adams C, Bonaparte M, Moser JM, Munteanu A, Baric R, de Silva AM. Dengue vaccine breakthrough infections reveal properties of neutralizing antibodies linked to protection. J Clin Invest 2021; 131:147066. [PMID: 34003796 DOI: 10.1172/jci147066] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/13/2021] [Indexed: 01/01/2023] Open
Abstract
The 4 serotypes of dengue virus (DENV1-4) are mosquito-borne flaviviruses that infect humans. Live attenuated tetravalent DENV vaccines are at different phases of clinical testing. DENV vaccine developers have relied on neutralizing antibodies (NAbs) as a correlate of protection. A leading tetravalent vaccine (Dengvaxia) stimulated NAbs to the 4 DENV serotypes, yet overall vaccine efficacy was low in children who were DENV seronegative at baseline before vaccination. We compared the properties of (a) NAbs induced by WT DENV1 or DENV3 infections, which are strongly correlated with protection from repeat infections, and (b) NAbs induced by Dengvaxia in individuals who subsequently experienced DENV1 or DENV3 breakthrough infections. WT infections induced NAbs that recognized epitopes unique (type specific) to each serotype, whereas the vaccine stimulated qualitatively different NAbs that recognized epitopes conserved (crossreactive) between serotypes. Our results indicate that, among children who were DENV-seronegative at baseline, unbalanced replication of the DENV type 4 vaccine component in the tetravalent vaccine stimulates Abs capable of crossneutralizing DENV1 and DENV3 in vitro, but not protecting in vivo. In DENV-seronegative individuals who are vaccinated, we propose that type-specific NAbs are a better correlate of protection than total levels of NAbs.
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Affiliation(s)
- Sandra Henein
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Cameron Adams
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | | | | | | | - Ralph Baric
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Aravinda M de Silva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
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Huang Y, Williamson BD, Moodie Z, Carpp LN, Chambonneau L, DiazGranados CA, Gilbert PB. Analysis of Neutralizing Antibodies as a Correlate of Instantaneous Risk of Hospitalized Dengue in Placebo Recipients of Dengue Vaccine Efficacy Trials. J Infect Dis 2021; 225:332-340. [PMID: 34174082 DOI: 10.1093/infdis/jiab342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND In the CYD14 (NCT01373281) and CYD15 (NCT01374516) dengue vaccine efficacy trials, Month 13 neutralizing antibody (nAb) titers correlated inversely with risk of symptomatic, virologically confirmed dengue (VCD) between Month 13 (one month post-final-dose) and Month 25. We assessed nAb titer as a correlate of instantaneous risk of hospitalized VCD (HVCD), for which participants were continually surveilled for 72 months. METHODS Using longitudinal nAb titers from the per-protocol immunogenicity subsets, we estimated hazard ratios (HRs) of HVCD by current nAb titer value for three correlate/endpoint pairs: average titer across all four serotypes/HVCD of any serotype (HVCD-Any), serotype-specific titer/homologous HVCD, and serotype-specific titer/heterologous HVCD. RESULTS Baseline-seropositive placebo recipients with higher average titer had lower instantaneous risk of HVCD-Any in 2-16-year-olds and in 9-16-year-olds (HR 0.26 or 0.15 per 10-fold increase in average titer by two methods, 95% CIs 0.14 to 0.45 and 0.07 to 0.34, respectively) pooled across both trials. Results were similar for homologous HVCD. There was evidence suggesting increased HVCD-Any risk in participants with low average titer (1:10 to 1:100) compared to seronegative participants (HR 1.85, 95% CI 0.93 to 3.68). CONCLUSIONS Natural infection-induced nAbs were inversely associated with hospitalized dengue, upon exceeding a relatively low threshold.
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Affiliation(s)
- Ying Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America.,Department of Biostatistics, University of Washington, Seattle, 98109, United States of America
| | - Brian D Williamson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America
| | - Lindsay N Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America
| | | | - Carlos A DiazGranados
- Clinical Sciences, Sanofi Pasteur, Swiftwater, Pennsylvania, United States of America
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America.,Department of Biostatistics, University of Washington, Seattle, 98109, United States of America
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Oishee MJ, Ali T, Jahan N, Khandker SS, Haq MA, Khondoker MU, Sil BK, Lugova H, Krishnapillai A, Abubakar AR, Kumar S, Haque M, Jamiruddin MR, Adnan N. COVID-19 Pandemic: Review of Contemporary and Forthcoming Detection Tools. Infect Drug Resist 2021; 14:1049-1082. [PMID: 33762831 PMCID: PMC7982560 DOI: 10.2147/idr.s289629] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/30/2021] [Indexed: 01/10/2023] Open
Abstract
Recent severe acute respiratory syndrome 2 (SARS-CoV-2) known as COVID-19, presents a deadly challenge to the global healthcare system of developing and developed countries, exposing the limitations of health facilities preparedness for emerging infectious disease pandemic. Opportune detection, confinement, and early treatment of infected cases present the first step in combating COVID-19. In this review, we elaborate on various COVID-19 diagnostic tools that are available or under investigation. Consequently, cell culture, followed by an indirect fluorescent antibody, is one of the most accurate methods for detecting SARS-CoV-2 infection. However, restrictions imposed by the regulatory authorities prevented its general use and implementation. Diagnosis via radiologic imaging and reverse transcriptase PCR assay is frequently employed, considered as standard procedures, whereas isothermal amplification methods are currently on the verge of clinical introduction. Notably, techniques such as CRISPR-Cas and microfluidics have added new dimensions to the SARS-CoV-2 diagnosis. Furthermore, commonly used immunoassays such as enzyme-linked immunosorbent assay (ELISA), lateral flow immunoassay (LFIA), neutralization assay, and the chemiluminescent assay can also be used for early detection and surveillance of SARS-CoV-2 infection. Finally, advancement in the next generation sequencing (NGS) and metagenomic analysis are smoothing the viral detection further in this global challenge.
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Affiliation(s)
| | - Tamanna Ali
- Gonoshasthaya-RNA Molecular Diagnostic and Research Center, Dhaka, Bangladesh
| | - Nowshin Jahan
- Gonoshasthaya-RNA Molecular Diagnostic and Research Center, Dhaka, Bangladesh
| | | | - Md Ahsanul Haq
- Gonoshasthaya-RNA Molecular Diagnostic and Research Center, Dhaka, Bangladesh
| | | | | | - Halyna Lugova
- Faculty of Medicine and Defence Health, National Defence University of Malaysia, Kuala Lumpur, Malaysia
| | - Ambigga Krishnapillai
- Faculty of Medicine and Defence Health, National Defence University of Malaysia, Kuala Lumpur, Malaysia
| | - Abdullahi Rabiu Abubakar
- Department of Pharmacology and Therapeutics, Faculty of Pharmaceutical Sciences, Bayero University, Kano, 700233, Kano, Nigeria
| | - Santosh Kumar
- Department of Periodontology and Implantology, Karnavati University, Gandhinagar, 382422, India
| | - Mainul Haque
- The Unit of Pharmacology, Faculty of Medicine and Defence Health Universiti Pertahanan, Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur, Malaysia
| | | | - Nihad Adnan
- Department of Microbiology, Jahangirnagar University, Dhaka, 1342, Bangladesh
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Bonelli F, Blocki FA, Bunnell T, Chu E, De La O A, Grenache DG, Marzucchi G, Montomoli E, Okoye L, Pallavicini L, Streva VA, Torelli A, Wagner A, Zanin D, Zierold C, Wassenberg JJ. Evaluation of the automated LIAISON ® SARS-CoV-2 TrimericS IgG assay for the detection of circulating antibodies. Clin Chem Lab Med 2021; 59:1463-1467. [PMID: 33711225 DOI: 10.1515/cclm-2021-0023] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/04/2021] [Indexed: 01/15/2023]
Abstract
OBJECTIVES COVID-19 has brought about tests from many manufacturers. While molecular and rapid antigen tests are targeted for early diagnosis, immunoassays have a larger role in epidemiological studies, understanding longitudinal immunity, and in vaccine development and response. METHODS The performance of the LIAISON® SARS-CoV-2 TrimericS IgG assay was evaluated against the Beckman ACCESS SARS-CoV-2 IgG assay in New Mexico, and against the Siemens ADVIA Centaur COV2G assay in New York. Discordant samples were parsed using a microneutralization assay. RESULTS A SARS-CoV-2 antibody positivity rate of 23.8% was observed in the samples tested in New York (September 2020), while in the same month the positivity rate was 1.5% in New Mexico. Positive and negative agreement were 67.6% (95% CI 49.5-82.6%) and 99.8% (95% CI 99.5-99.9%), respectively, with the Beckman test, and 98.0% (95% CI 95.7-99.3%) and 94.8% (95% CI 93.4-96.0%), respectively, with the Siemens test. Receiver operating characteristic analysis for the detection of SARS-CoV-2 antibodies discloses an AUC, area under the curve, of 0.996 (95% CI 0.992-0.999) for the LIAISON® SARS-CoV-2 TrimericS IgG assay. The criterion associated to the Youden Index was determined to be >12.9 kAU/L with a sensitivity of 99.44% and a specificity of 99.82%. CONCLUSIONS The LIAISON® SARS-CoV-2 TrimericS IgG assay is highly sensitive and specific. The balance of these parameters, without emphasis on high specificity alone, is particularly important when applied to high prevalence populations, where a highly sensitive assay will result in reporting a lower number of false negative subjects.
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Affiliation(s)
| | | | | | - Edward Chu
- Sherman Abrams Laboratory, Brooklyn, NY, USA
| | | | | | | | - Emanuele Montomoli
- Vismederi Srl, Siena, Italy.,Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Lilian Okoye
- TriCore Reference Laboratories, Albuquerque, NM, USA
| | | | | | | | - Aaron Wagner
- TriCore Reference Laboratories, Albuquerque, NM, USA
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