Infection and Vaccine Induced Spike Antibody Responses Against SARS-CoV-2 Variants of Concern in COVID-19-Naïve Children and Adults

Abstract

Although a more efficient adaptive humoral immune response has been proposed to underlie the usually favorable outcome of pediatric COVID-19, the breadth of viral and vaccine cross-reactivity toward the ever-mutating Spike protein among variants of concern (VOCs) has not yet been compared between children and adults. We assessed antibodies to conformational Spike in COVID-19-naïve children and adults vaccinated by BNT162b2 and ChAdOx1, and naturally infected with SARS-CoV-2 Early Clade, Delta, and Omicron. Sera were analyzed against Spike including naturally occurring VOCs Alpha, Beta, Gamma, Delta, and Omicron BA.1, BA.2, BA.5, BQ.1.1, BA2.75.2, and XBB.1, and variants of interest Epsilon, Kappa, Eta, D.2, and artificial mutant Spikes. There was no notable difference between breadth and longevity of antibody against VOCs in children and adults. Vaccinated individuals displayed similar immunoreactivity profiles across variants compared with naturally infected individuals. Delta-infected patients had an enhanced cross-reactivity toward Delta and earlier VOCs compared to patients infected by Early Clade SARS-CoV-2. Although Omicron BA.1, BA.2, BA.5, BQ.1.1, BA2.75.2, and XBB.1 antibody titers were generated after Omicron infection, cross-reactive binding against Omicron subvariants was reduced across all infection, immunization, and age groups. Some mutations, such as 498R and 501Y, epistatically combined to enhance cross-reactive binding, but could not fully compensate for antibody-evasive mutations within the Omicron subvariants tested. Our results reveal important molecular features central to the generation of high antibody titers and broad immunoreactivity that should be considered in future vaccine design and global serosurveillance in the context of limited vaccine boosters available to the pediatric population.

Keywords: Pediatric COVID-19; SARS-CoV-2; Spike antibody; adult COVID-19; cross-reactivity; epistasis; vaccine; variant of concern.

Fig. 1

Persistence of sera Spike antibodies against natural variants in children and adults. a Schematic showing timeline of different waves of infections in Australia. Convalescent patient sera from individuals naturally infected with Early Clade, Delta, or Omicron Spike or vaccinated individuals were examined for SARS-CoV-2 antibodies in a total of 47 children and 40 adults. In each cohort, the dots indicate the beginning and end of the sample collection timeframe. b IgG, IgM, and IgA responses against Spike over time in Early Clade–infected children (ages 0–18 years old, peach) and adults (>18 years old, gray) shown since viral exposure. c COVID-19 severity caused by the Early Clade SARS-CoV-2 was mostly mild or asymptomatic in children, whereas “close contact” inter-related adults presented more often with a moderate disease which was associated with higher Spike IgG levels. d Schematic indicating primary mutations in VOCs within the Spike protein. e Peak IgG responses generated against Early clade, Delta, BA.1, BA.2, BA.5, BQ.1.1, BA2.75.2, and XBB.1 Spike VOCs in naturally infected individuals. f Peak IgG responses generated against Early Clade, Delta, BA.1, BA.2, BA.5, BQ.1.1, BA2.75.2, and XBB.1 Spike VOCs in vaccinated individuals. All points shown were reported seropositive against a control cohort and calculated positive threshold. ∆MFI, delta median fluorescence intensity; Ab, antibody; VOIs, variants of interest; VOCs, variants of concern. p values were determined by comparing VOC Spikes vs Early Clade Spike. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001

Fig. 2

Spike IgG immunoreactivity against VOCs in naturally infected and vaccinated children and adults. a Schematic showing mutations within VOCs along SARS-CoV-2 Spike protein. b WHO International NIBSC SARS-CoV-2 standard (20/136) tested against VOCs and titer of IgG against VOCs. c WHO International NIBSC SARS-CoV-2 standard (21/234) tested against VOCs and cross-reactive binding compared to Early Clade Spike (percentage). Evaluation of Spike VOCs cross-reactive binding in comparison to Early Clade Spike in sera samples from d naturally Early Clade–infected children (n=14) and adults (n=5), e naturally Delta-infected children (n=9) and adults (n=9), f naturally Omicron-infected children (n=6) and adults (n=3), and g vaccinated children (n=8), adults who received BNT162b2 vaccine (n=8), and adults who received ChAdOx1 vaccine (n=8). Summarized comparison of immunoreactivity across VOCs in different cohorts of h children and i adults. All points shown were collected at the peak of the immune response (Table 1) and were seropositive against a control cohort and calculated positive threshold. The dotted line shows the reference binding on Early Clade Spike. p values were determined by comparing VOC Spikes vs Early Clade Spike. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001. ∆MFI, delta median fluorescence intensity; Ab, antibody; VOCs, variants of concern

Fig. 3

Additive effects of mutations within SARS-CoV-2 Spike RBD. a Schematic showing mutations in different VOCs at specific positions within the SARS-CoV-2 Spike protein. b WHO International NIBSC SARS-CoV-2 standard tested on variants Delta, Kappa, and Epsilon, titer of Ab binding to variants (left) and cross-reactive binding compared to Early Clade Spike (percentage) (right). Proportion of Spike VOC cross-reactive binding compared to Early Clade Spike in sera samples from c Early Clade–infected individuals, d Delta-infected individuals, e Omicron-infected individuals, and f vaccinated individuals. g Summarized comparison of immunoreactivity toward Kappa and Delta Spike variants across different cohorts. h Mutations within SARS-CoV-2 Spike variants within the RBD. i WHO International NIBSC SARS-CoV-2 standard tested on Eta and Early Clade Spike variants, titers of Ab binding to variants (left) and cross-reactive binding compared to Early Clade Spike (right). Cross-reactive binding compared to Early Clade Spike VOC against Eta, Beta, Gamma, and Alpha Spike variants in j Early Clade–infected individuals, k Delta-infected individuals, l Omicron-infected individuals, and m vaccinated individuals. n Summarized comparison of cross-reactive binding toward Eta, Beta, Gamma, and Alpha Spike variants across different cohorts. All points shown were collected at the peak of the immune response (Table 1) and were seropositive against a control cohort and calculated positive threshold. The dotted line shows the reference binding on Early Clade Spike. p values were determined by comparing VOC Spikes vs Early Clade Spike. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001. ∆MFI, delta median fluorescence intensity; Ab, antibody; VOCs, variants of concern.

Fig. 4

Epistatic effect of mutations within the Spike RBD. a Schematic of mutation within the RBD for AM1 Spike, D.2 Spike, AM2 Spike, and Omicron subvariants. b Cross-reactive binding against AM1, D.2, AM2, BA.1, BA.2, BA.5, BQ.1.1, BA2.75.2, and XBB.1 Spikes in sera from Early Clade–infected individuals, c Delta-infected individuals, d Omicron-infected individuals, and e vaccinated individuals. f Summarized comparison of cross-reactive binding toward AM1 Spike, D.2 Spike, and AM2 Spike across different cohorts. All points shown were collected at the peak of the immune response (Table 1) and were seropositive against a control cohort and calculated positive threshold. The dotted line shows the reference binding on Early Clade Spike. p values were determined by comparing VOC Spikes vs Early Clade Spike. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001. ∆MFI, delta median fluorescence intensity; Ab, antibody; VOCs, variants of concern