Immune boosting by B.1.1.529 ( Omicron) depends on previous SARS-CoV-2 exposure

Abstract

The Omicron, or Pango lineage B.1.1.529, variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) carries multiple spike mutations with high transmissibility and partial neutralizing antibody (nAb) escape. Vaccinated individuals show protection against severe disease, often attributed to primed cellular immunity. We investigated T and B cell immunity against B.1.1.529 in triple BioNTech BNT162b2 messenger RNA-vaccinated health care workers (HCWs) with different SARS-CoV-2 infection histories. B and T cell immunity against previous variants of concern was enhanced in triple-vaccinated individuals, but the magnitude of T and B cell responses against B.1.1.529 spike protein was reduced. Immune imprinting by infection with the earlier B.1.1.7 (Alpha) variant resulted in less durable binding antibody against B.1.1.529. Previously infection-naïve HCWs who became infected during the B.1.1.529 wave showed enhanced immunity against earlier variants but reduced nAb potency and T cell responses against B.1.1.529 itself. Previous Wuhan Hu-1 infection abrogated T cell recognition and any enhanced cross-reactive neutralizing immunity on infection with B.1.1.529.

Fig. 1.. SARS-CoV-2 infection history alters Ab and B cell immunity in triple-vaccinated HCW.

(A) Graphical summary depicting the SARS-CoV-2 infection and vaccination history of HCW studied. (B) Serum Ab binding against SARS-CoV-2 N (top panel) and ancestral Wuhan Hu-1 S1 RBD (bottom panel) in infection-naïve HCW (blue, n = 11-245) and HCW with laboratory confirmed SARS-CoV-2 infection during the Wuhan Hu-1 (red, n = 20-71) or B.1.1.7 (Alpha, green, n = 12-42) waves. Data are shown pre-vaccination and at defined timepoints following first, second and third dose of BNT162b2. (C) Serum S1 RBD Ab binding and (D) nAb IC50 against ancestral Wuhan Hu-1, B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta) and B.1.1.529 (Omicron) live virus 2-3w after the third vaccine dose in infection-naïve HCW (blue, n = 25) or HCW with laboratory confirmed SARS-CoV-2 infection during the ancestral Wuhan Hu-1 (red, n = 18), B.1.1.7 (Alpha, green, n = 13) or B.1.617.2 (Delta, purple, n = 6) waves. (E) Frequency of MBC specific for ancestral Wuhan Hu-1, B.1.617.2 (Delta) and B.1.1.529 (Omicron) spike S1 protein 20-21w after the second and 2-3w after the third vaccine dose in infection-naïve (blue, n = 7-9) or HCW infected by SARS-CoV-2 during the Wuhan Hu-1 (red, n = 9-10), B.1.1.7 (Alpha, green, n = 7-9) and B.1.617.2 (Delta, purple, n = 3-6) waves. (F) MBC frequency data plotted pairwise for individual HCW at 20-21w after second dose (top panel) or 2-3w after third dose (bottom panel). (G) Correlations between S1 RBD VOC and whole spike VOC Ab binding (left-hand panel) and nAb IC50 (right-hand panel) against B.1.1.7 (Alpha) and B.1.617.2 (Delta) in infection-naïve (blue, n = 25) HCW and HCW infected during the ancestral Wuhan Hu-1 (red, n = 18), B.1.1.7 (Alpha, green, n = 13) and B.1.617.2 (Delta, purple, n = 6) waves. Statistical tests were performed using Prism 9.0. [(B) to (E)] Mann-Whitney U test, (F) Wilcoxon matched-pairs signed rank test, (G) Spearman’s rank correlation. Ab, antibody; ASC, antibody secreting cells; AU, arbitrary units; COI, cut-off index; f/u; follow-up; HCW, health care workers; N, nucleocapsid; RBD, receptor binding domain; S1, subunit 1; MBC, memory B cell; VOC, variant of concern; w, weeks.

Fig. 2.. T cell cross-recognition of B.1.1.529 (Omicron) in triple-vaccinated HCW.

(A) T cell responses against ancestral Wuhan Hu-1 spike MEP pool or ancestral Wuhan Hu-1, B.1.617.2 (Delta) and B.1.1.529 (Omicron) VOC S1 proteins in PBMC from infection-naïve HCW (blue) or HCW with laboratory confirmed SARS-CoV-2 infection during the ancestral Wuhan Hu-1 (red), B.1.1.7 (Alpha, green) and B.1.617.2 (Delta, purple) waves. PBMC were taken 2-3w after the third vaccine dose and T cell responses assessed by IFNγ ELISpot. Pie charts show the percent of responders with a detectable T cell response against each antigen. (B) Spike MEP pool and S1 protein T cell responses plotted pair-wise for each individual HCW. (C) T cell responses against peptide pools containing either the B.1.1.529 (Omicron) mutations found in SARS-CoV-2 spike or the equivalent original ancestral Wuhan Hu-1 sequences. PBMC from infection-naïve HCW (blue) or HCW infected during the ancestral Wuhan Hu-1 (red), B.1.1.7 (Alpha, green) and B.1.617.2 (Delta, purple) waves were stimulated by peptide pools containing the original Wuhan Hu-1 or B.1.1.529 sequences and plotted pair-wise. Statistical tests were performed using Prism 9.0. (A) Mann-Whitney U test, [(B) and (C)] Wilcoxon matched-pairs signed rank test. HCW, health care workers; MEP, mapped epitope peptide; PBMC, peripheral blood mononuclear cells; S1, subunit 1; SFC; spot forming cells; VOC, variant of concern; w, weeks.

Fig. 3.. B.1.1.529 (Omicron) spike mutations alter T cell recognition.

(A) HLAII transgenic mice carrying DRB1*0401 in the context of a homozygous knockout for murine H2-Aβ (7-8w) were immunized with either a B.1.1.529 (Omicron, n = 7) VOC pool of 18 peptides encompassing the Omicron sequence mutations or the ancestral Wuhan Hu-1 pool of peptides (n = 6) with the equivalent unmutated sequences. At d10 DLN cells were prepared from immunized mice and stimulated with either Wuhan Hu-1 (red) or B.1.1.529 (Omicron, black) peptide pools and T cell responses measured by IFNγ ELISpot. (B) IFNγ T cell responses were mapped against individual Wuhan Hu-1 (red) or B.1.1.529 (Omicron, black) peptides using DLN taken from Wuhan Hu-1 peptide pool (n = 7) or (C) B.1.1.529 (Omicron) peptide pool (n = 6) immunized mice. (D and E) Heatmaps showing relative gene expression of T cell activation markers in DLN cells taken from B.1.1.529 (Omicron) G142D/del143-5 peptide primed (D) (n = 6) or Wuhan Hu-1 Q493R/G496S/Q498R/N501Y/Y505H peptide primed (E) (n = 6) HLA-DRB1*04:01 transgenic mice. DLN cells were stimulated for 24h in vitro with 10 μg/ml Wuhan Hu-1 or B.1.1.529 (Omicron) variant peptide before RNA extraction. Genes shown in the heatmap are significantly up-regulated (p < 0.05) in Wuhan Hu-1 or B.1.1.529 (Omicron) variant peptide stimulated cells compared to no peptide control. Statistical tests were performed using Prism 9.0 or the Qiagen GeneGlobe data analysis tool for gene expression data. [(A) to (C)] Wilcoxon matched-pairs signed rank test, [(D) and (E)] Student’s t test. DLN, draining lymph node; SFC, spot forming cells; h, hours; VOC, variant of concern.

Fig. 4.. Ab and B cell immunity in triple-vaccinated HCW following infection during the B.1.1.529 (Omicron) wave.

(A) Graphical summary depicting the SARS-CoV-2 infection and vaccination history of HCW studied during the B.1.1.529 (Omicron wave). (B) Serum Ab binding against SARS-CoV-2 N at 14w (median 14w, IQR 3w) after third vaccine dose in infection-naïve HCW (blue, n = 11) or in HCW with laboratory confirmed SARS-CoV-2 infection during the ancestral Wuhan Hu-1 (red, n = 4), B.1.1.529 (Omicron, black, n = 11) or Wuhan Hu-1 followed by B.1.1.529 (Omicron, pink, n = 6) infection waves. (C) Serum S1 RBD (VOC) Ab binding against ancestral Wuhan Hu-1, B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta) and B.1.1.529 (Omicron) proteins in infection-naïve HCW (blue, n = 11) or HCW previously infected during the ancestral Wuhan Hu-1 (red, n = 4), B.1.1.529 (Omicron, black, n = 11) or Wuhan Hu-1 followed by B.1.1.529 (Omicron, pink, n = 6) waves. (D) Serum Ab binding against ancestral Wuhan Hu-1, B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), AY4.2 (Delta sub-variant) and B.1.1.529 (Omicron) whole spike proteins in infection-naïve HCW (blue, n = 11) or HCW previously infected during the ancestral Wuhan Hu-1 (red, n = 4), B.1.1.529 (Omicron, black, n = 11) or Wuhan Hu-1 followed by B.1.1.529 (Omicron, pink, n = 6) waves. (E) Neutralizing antibody IC50 against Wuhan Hu-1 or VOC live virus isolates in infection-naïve HCW (blue, n = 11) or HCW previously infected during the ancestral Wuhan Hu-1 (red, n = 4), B.1.1.529 (Omicron, black, n = 11) or Wuhan Hu-1 followed by B.1.1.529 (Omicron, pink, n = 6) waves. (F) Frequency of MBC specific for ancestral Wuhan Hu-1, B.1.617.2 (Delta) and B.1.1.529 (Omicron) S1 and RBD binding proteins in infection-naïve HCW (blue, n = 11) or HCW previously infected during the ancestral Wuhan Hu-1 (red, n = 4), B.1.1.529 (Omicron, black, n = 11) or Wuhan Hu-1 followed by B.1.1.529 (Omicron, pink, n = 6) waves. (G) Correlation between whole spike and S1 RBD Ab binding (left-hand panel) or nAb IC50 and S1 RBD Ab binding (right-hand panel) for B.1.1.529 (Omicron) VOC in infection-naïve (blue, n = 11) or HCW infected during the ancestral Wuhan Hu-1 (red, n = 4), B.1.1.529 (Omicron, black, n = 11) or Wuhan Hu-1 followed by B.1.1.529 (Omicron, pink, n = 6) waves. All data shown is from samples taken at 14w (median 14w, IQR 3w) after third vaccine dose. Statistical tests were performed using Prism 9.0. [(B) to (F)] Mann-Whitney U test, (G) Spearman’s rank correlation. Ab, antibody; ASC, antibody secreting cells; AU, arbitrary units; COI, cut-off index; HCW, health care workers; IQR, inter-quartile range; N, nucleocapsid; RBD, receptor binding domain; S1, subunit 1; MBC, memory B cell; VOC, variant of concern; w, weeks.

Fig. 5.. T cell responses in triple-vaccinated HCW infected during the B.1.1.529 (Omicron) wave.

(A) T cell responses against ancestral Wuhan Hu-1 spike MEP pool or Wuhan Hu-1, B.1.617.2 (Delta) and B.1.1.529 (Omicron) VOC S1 protein for PBMC taken from infection-naïve HCW (blue, n = 10) or HCW with laboratory confirmed SARS-CoV-2 infection during the Wuhan Hu-1 (red, n = 3), B.1.1.529 (Omicron, black, n = 11) or Wuhan Hu-1 followed by B.1.1.529 (Omicron, pink, n = 6) waves. PBMC were taken 14w (median 14w, IQR 3w) after the third vaccine dose and T cell responses assessed by IFNγ ELISpot. Pie charts show the percent that had a detectable T cell response against each antigen. (B) T cell responses against spike MEP pool and S1 VOC protein for previously infection naïve triple-vaccinated HCW infected during the B.1.1.529 (Omicron, black, n = 11) wave. (C) T cell responses against ancestral Wuhan Hu-1, B.1.617.2 (Delta) and B.1.1.529 (Omicron) S1 proteins plotted pair-wise for infection-naïve HCW (blue, n = 10) or HCW with laboratory confirmed SARS-CoV-2 infection during the Wuhan Hu-1 (red, n = 3), B.1.1.529 (Omicron, black, n = 11) or Wuhan Hu-1 followed by B.1.1.529 (Omicron, pink, n = 6) waves. Statistical tests were performed using Prism 9.0. (A) Mann-Whitney U test, [(B) and (C)] Wilcoxon matched-pairs signed rank test. HCW, health care workers; IQR, inter-quartile range; MEP, mapped epitope peptide; PBMC, peripheral blood mononuclear cells; S1, subunit 1; SFC; spot forming cells; VOC, variant of concern; w, weeks.

Fig. 6.. SARS-CoV-2 infection imprints differential Ab cross-reactivity to VOC.

(A) Graphical summary depicting the SARS-CoV-2 infection and vaccination history of HCW studied. Infection naïve HCW are indicated in blue. HCW infected during the different waves are indicated as follows: ancestral Wuhan Hu-1 (red), B.1.1.7 (Alpha, green) and B.1.617.2 (Delta, purple), B.1.1.529 (Omicron, black) and Wuhan Hu-1 followed by B.1.1.529 (Omicron, pink). (B and C) Serum Ab binding against ancestral Wuhan Hu-1 S1 RBD (B) and B.1.1.529 (Omicron) S1 RBD (C) in infection-naïve HCW (blue, n = 11-29) or in HCW with laboratory confirmed SARS-CoV-2 infection during the ancestral Wuhan Hu-1 (red, n = 4-27), B.1.1.7 (Alpha, green, n = 8-35), B.1.617.2 (Delta, purple, n = 6-7), B.1.1.529 (Omicron, black, n = 11) or Wuhan Hu-1 followed by B.1.1.529 (Omicron, pink, n = 6) waves. Data are shown pre-vaccination and at timepoints following first, second and third dose of vaccine. (D) Cross-reactive nAb IC50 against ancestral Wuhan Hu-1, B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta) and B.1.1.529 (Omicron) live virus 2-3w after third vaccine dose in infection-naïve HCW (blue, n = 24) or HCW with laboratory confirmed SARS-CoV-2 infection during the Wuhan Hu-1 (red, n = 18), B.1.1.7 (Alpha, green, n = 13) or B.1.617.2 (Delta, purple, n = 6) waves and at 14w (median 14w, IQR 3w) after third vaccine dose in HCW with laboratory confirmed SARS-CoV-2 during the B.1.1.529 (Omicron, black, n = 11) or Wuhan Hu-1 followed by B.1.1.529 (Omicron, pink, n = 6) waves. Data are plotted pair-wise for individual HCW. (E) Doughnuts showing the relative proportion of HCW with nAb IC50 of <50 (white), 50-199 (25% gray), 200-1,999 (50% gray), 2,000-19,999 (75% gray) and ≥ 20,000 (black) against ancestral Wuhan Hu-1, B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta) and B.1.1.529 (Omicron) live virus in infection-naïve HCW (n = 11) or HCW with laboratory confirmed infection during the B.1.1.529 (Omicron, n = 11), Wuhan Hu-1 (n = 4) or Wuhan Hu-1 followed by B.1.1.529 (Omicron, n = 6) waves at 14w (median 14w, IQR 3w) after the third vaccine dose. Statistical tests were performed using Prism 9.0. [(B) and (C)] Mann-Whitney U test. Ab, antibody; nAb neutralizing antibody; HCW, health care workers; IQR, inter-quartile range; RBD, receptor binding domain; VOC, variant of concern; w, weeks.