Multiplex assays for the identification of serological signatures of SARS-CoV-2 infection: an antibody-based diagnostic and machine learning study

Abstract

Background Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces an antibody response targeting multiple antigens that changes over time. This study aims to take advantage of this complexity to develop more accurate serological diagnostics. MethodsA multiplex serological assay was developed to measure IgG and IgM antibody responses to seven SARS-CoV-2 spike or nucleoprotein antigens, two antigens for the nucleoproteins of the 229E and NL63 seasonal coronaviruses, and three non-coronavirus antigens. Antibodies were measured in serum samples collected up to 39 days after symptom onset from 215 adults in four French hospitals (53 patients and 162 health-care workers) with quantitative RT-PCR-confirmed SARS-CoV-2 infection, and negative control serum samples collected from healthy adult blood donors before the start of the SARS-CoV-2 epidemic (335 samples from France, Thailand, and Peru). Machine learning classifiers were trained with the multiplex data to classify individuals with previous SARS-CoV-2 infection, with the best classification performance displayed by a random forests algorithm. A Bayesian mathematical model of antibody kinetics informed by prior information from other coronaviruses was used to estimate timevarying antibody responses and assess the sensitivity and classification performance of serological diagnostics during the first year following symptom onset. A statistical estimator is presented that can provide estimates of seroprevalence in very low-transmission settings. Findings IgG antibody responses to trimeric spike protein (S tri ) identified individuals with previous SARS-CoV-2 infection with 91•6% (95% CI 87•5-94•5) sensitivity and 99•1% (97•4-99•7) specificity. Using a serological signature of IgG and IgM to multiple antigens, it was possible to identify infected individuals with 98•8% (96•5-99•6) sensitivity and 99•3% (97•6-99•8) specificity.Informed by existing data from other coronaviruses, we estimate that 1 year after infection, a monoplex assay with optimal anti-S tri IgG cutoff has 88•7% (95% credible interval 63•4-97•4) sensitivity and that a four-antigen multiplex assay can increase sensitivity to 96•4% (80•9-100•0). When applied to populationlevel serological surveys, statistical analysis of multiplex data allows estimation of seroprevalence levels less than 2%, below the false-positivity rate of many other assays.Interpretation Serological signatures based on antibody responses to multiple antigens can provide accurate and robust serological classification of individuals with previous SARS-CoV-2 infection. This provides potential solutions to two pressing challenges for SARS-CoV-2 serological surveillance: classifying individuals who were infected more than 6 months ago and measuring seroprevalence in serological surveys in very low-transmission settings.

Dynamics of SARS-CoV-2 with waning immunity in the UK population

“…Plausible estimates on which to base expectations for the duration of immunity are sparse in the current literature. Rosado et al [ 39 ] estimated that antibodies could wane in 50% of recovered individuals after 1 year, which is similar to the estimated duration of immunity against seasonal circulating coronaviruses [ 13 , 29 ]. Even with this consideration, there are many probability distributions that can be used to capture a median duration of immunity, and our selection of an Erlang distribution with a shape parameter of two is somewhat arbitrary.…”

SARS-CoV-2 Serum Neutralization Assay: A Traditional Tool for a Brand-New Virus

“…To date, a number of assays have been developed and evaluated to replace the traditional live-virus-based neutralization test [3] with the aim of avoiding the requirement for a BSL-3 facility and to speed up the laboratory turnaround time (e.g., anti-RBD Ig immunoassays, ACE2-RBD competitive tests, high-throughput serologic platforms, and multiplex assays) [29][30][31][32][33]. However, as we also observed, these tests show a variable correlation to neutralization assays.…”

Humoral immunity to SARS-CoV-2 and seasonal coronaviruses in children and adults in north-eastern France

“…In this study, comprising a large number of serum samples from children and adults hospitalized for other reasons than COVID-19 , we aimed to measure exposure to seasonal coronaviruses and to SARS-CoV-2 using three different immunoassays, a bead-based multiplex serological [26] assay, a Luciferase-Linked ImmunoSorbent Assay (LuLISA, [27,28] and a pseudo neutralisation assay [27,28].…”