Probabilistic classification of anti-SARS-CoV-2 antibody responses improves seroprevalence estimates.

Objectives: Population-level measures of seropositivity are critical for understanding the epidemiology of an emerging pathogen, yet most antibody tests apply a strict cutoff for seropositivity that is not learnt in a data-driven manner, leading to uncertainty when classifying low-titer responses. To improve upon this, we evaluated cutoff-independent methods for their ability to assign likelihood of SARS-CoV-2 seropositivity to individual samples.
Methods: Using robust ELISAs based on SARS-CoV-2 spike (S) and the receptor-binding domain (RBD), we profiled antibody responses in a group of SARS-CoV-2 PCR+ individuals ( n  = 138). Using these data, we trained probabilistic learners to assign likelihood of seropositivity to test samples of unknown serostatus ( n  = 5100), identifying a support vector machines-linear discriminant analysis learner (SVM-LDA) suited for this purpose.
Results: In the training data from confirmed ancestral SARS-CoV-2 infections, 99% of participants had detectable anti-S and -RBD IgG in the circulation, with titers differing > 1000-fold between persons. In data of otherwise healthy individuals, 7.2% ( n =  367) of samples were of uncertain serostatus, with values in the range of 3-6SD from the mean of pre-pandemic negative controls ( n  = 595). In contrast, SVM-LDA classified 6.4% ( n  = 328) of test samples as having a high likelihood (> 99% chance) of past infection, 4.5% ( n  = 230) to have a 50-99% likelihood, and 4.0% ( n  = 203) to have a 10-49% likelihood. As different probabilistic approaches were more consistent with each other than conventional SD-based methods, such tools allow for more statistically-sound seropositivity estimates in large cohorts.
Conclusion: Probabilistic antibody testing frameworks can improve seropositivity estimates in populations with large titer variability.
Competing Interests: The study authors declare no competing financial interests that could compromise the study. CW also receives funding from GlaxoSmithKline and Merck Sharp & Dohme; these funders had no role in the design, analysis or interpretation of this study. The views expressed are those of the authors.
(© 2022 The Authors. Clinical & Translational Immunology published by John Wiley & Sons Australia, Ltd on behalf of Australian and New Zealand Society for Immunology, Inc.)