Neutralising reactivity against SARS-CoV-2 Delta and Omicron variants by vaccination and infection history

Abstract

Background: The continuous emergence of SARS-CoV-2 variants of concern (VOC) with immune escape properties, such as Delta (B.1.617.2) and Omicron (B.1.1.529), questions the extent of the antibody-mediated protection against the virus. Here we investigated the long-term antibody persistence in previously infected subjects and the extent of the antibody-mediated protection against B.1, B.1.617.2 and BA.1 variants in unvaccinated subjects previously infected, vaccinated naïve and vaccinated previously infected subjects.

Methods: Blood samples collected 15 months post-infection from unvaccinated (n=35) and vaccinated (n=41) previously infected subjects (Vo' cohort) were tested for the presence of antibodies against the SARS-CoV-2 spike (S) and nucleocapsid (N) antigens using the Abbott, DiaSorin, and Roche immunoassays. The serum neutralising reactivity was assessed against B.1, B.1.617.2 (Delta), and BA.1 (Omicron) SARS-CoV-2 strains through micro-neutralisation. The antibody titres were compared to those from previous timepoints, performed at 2- and 9-months post-infection on the same individuals. Two groups of naïve subjects were used as controls, one from the same cohort (unvaccinated n=29 and vaccinated n=20) and a group of vaccinated naïve healthcare workers (n=61).

Results: We report on the results of the third serosurvey run in the Vo' cohort. With respect to the 9-month time point, antibodies against the S antigen significantly decreased (P=0.0063) among unvaccinated subjects and increased (P<0.0001) in vaccinated individuals, whereas those against the N antigen decreased in the whole cohort. When compared with control groups (naïve Vo' inhabitants and naïve healthcare workers), vaccinated subjects that were previously infected had higher antibody levels (P<0.0001) than vaccinated naïve subjects. Two doses of vaccine elicited stronger anti-S antibody response than natural infection (P<0.0001). Finally, the neutralising reactivity of sera against B.1.617.2 and BA.1 was 4-fold and 16-fold lower than the reactivity observed against the original B.1 strain.

Conclusions: These results confirm that vaccination induces strong antibody response in most individuals, and even stronger in previously infected subjects. Neutralising reactivity elicited by natural infection followed by vaccination is increasingly weakened by the recent emergence of VOCs. While immunity is not completely compromised, a change in vaccine development may be required going forward, to generate cross-protective pan-coronavirus immunity in the global population.

Keywords: Antibody persistence; COVID-19; Delta variant; Neutralising antibodies; Omicron variant; SARS-CoV-2; Vaccination.

Fig. 1

Study description. a Timeline of the surveys conducted in the study area since the start of the SARS-CoV-2 epidemic in Vo’. b Flow chart illustrating the study design, which focuses on the subjects who were found to be positive early in the pandemic (from February 2020 to May 2020, according to the ground truth definition). The serosurveys were conducted in Vo’ on three time points, 1st–3rd May 2020, 28th–29th November 2020, and 5th June 2021

Fig. 2

Anti-S antibody titres and dynamics in vaccinated and unvaccinated subjects previously infected by SARS-CoV-2. a–d Observed antibody titres in unvaccinated and vaccinated subjects infected by SARS-CoV-2 and tested in May 2020, November 2020 and June 2021 by DiaSorin (vaccinated n=38, P < 0.0001 from November 2020 to June 2021; unvaccinated n=33, P = 0.0063 from November 2020 to June 2021) and micro-neutralisation assays (vaccinated n=38, P < 0.0001 from November 2020 to June 2021; unvaccinated n=32, P = 0.0053 from November 2020 to June 2021). The horizontal line represents the median, the vertical line represents the 95% confidence intervals. e–h Observed individual-level paired antibody titres in subjects infected by SARS-CoV-2 and tested in May 2020, November 2020 and June 2021. In June 2021, 59.4% (19 out of 32 unvaccinated subjects, 95% CI 40.6–76.3%) and 6.3% (2 out of 32 unvaccinated individuals, 95% CI 0.8–20.8%) had antibodies more than 15 months post infection according to DiaSorin and micro-neutralisation, respectively. Subjects with increasing titres are coloured in green, while subjects with a negative result in June 2021 are presented in red. i, j Estimated antibody decay rate distributions calculated among the unvaccinated subjects infected by SARS-CoV-2 in February/March 2020, tested in May 2020, November 2020 and June 2021. Each bar represents the frequency of each slope (in units of days), calculated on the logarithm of individual-level sequential titres. We estimated a median half-life of 214 (95% CI 168–288) days and 174 (95% CI 146–202) days for the antibodies detected by the DiaSorin and micro-neutralisation assays, respectively. To estimate the median half-life, only subjects with no doubling antibodies from May 2020 were considered. Asterisks indicate *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. Statistical significance of antibody levels was evaluated by Friedman test followed by Dunn’s multiple comparisons test

Fig. 3

Anti-N antibody titres and dynamics in subjects previously infected by SARS-CoV-2. a-b) Observed antibody titres in subjects infected by SARS-CoV-2 and tested in May 2020, November 2020 and June 2021 with Abbott (n=65, P < 0.0001 from November 2020 to June 2021) and Roche assays (n=65, P < 0.0001 from November 2020 to June 2021). The horizontal line represents the median, the vertical line represents the 95% confidence intervals. c, d Observed individual-level paired antibody titres in subjects infected by SARS-CoV-2 and tested in May 2020, November 2020 and June 2021. In June 2021, 13.8% (9 out of 65 subjects, 95% CI 6.5–24.7%) and 95.4% (62 out of 65 subjects, 95% CI 87.1–99.0) resulted positive to Abbott and Roche assays respectively, more than 15 months post infection. Subjects with increasing titres are coloured in green, and subjects with a negative result in June 2021 are presented in red. e, f Estimated antibody decay rate distribution calculated among subjects infected by SARS-CoV-2 in February/March 2020 and tested in May 2020, November 2020, and June 2021. Each bar represents the frequency of each slope (in units of days), calculated on the logarithm of individual-level sequential titres. We estimated a median half-life of 115 (95% CI 105–126) days and 179 (95% CI 153–255) days for the antibodies detected by the Abbott and Roche assays, respectively. To estimate the median half-life, only subjects with no doubling antibodies from May 2020 were considered. Asterisks indicate *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. Statistical significance of antibody levels was evaluated by Friedman test followed by Dunn’s multiple comparisons test

Fig. 4

Antibody levels in vaccinated naïve and vaccinated previously infected individuals according to DiaSorin and micro-neutralisation assays. a, b Observed antibody levels measured by DiaSorin assays in vaccinated naïve and previously infected individuals with at least one dose of vaccine (Mann-Whitney test, P < 0.0001) and with one or two doses of vaccine (Kruskal-Wallis test followed by Dunn’s multiple comparisons test, vaccinated naïve versus previously infected subjects after one vaccine dose, P < 0.0001; after two vaccine doses, P = 0.01; vaccinated naïve HCW versus previously infected subjects after two vaccine doses, P < 0.0001). c, d Observed neutralising antibody titres measured by a micro-neutralisation assay in vaccinated naïve and previously infected individuals with at least one dose of vaccine (Mann-Whitney test, P < 0.0001) and with one or two doses of vaccine (Kruskal-Wallis test followed by Dunn’s multiple comparisons test, vaccinated naïve versus previously infected subjects after one or two vaccine doses, P < 0.0001; vaccinated naïve HCW versus previously infected subjects after two vaccine doses, P < 0.0001). Asterisks indicate *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. HCW: healthcare workers. Previous infection is defined according to the ground truth definition provided in the text

Fig. 5

Anti-S antibody levels and neutralisation titres induced by vaccination and natural infection. Observed antibody levels in Vo’ unvaccinated individuals previously infected with SARS-CoV-2, Vo’ subjects and HCW subjects vaccinated when naïve, according to a DiaSorin S1/S2 (Kruskal-Wallis test followed by Dunn’s multiple comparisons test, unvaccinated previously infected versus vaccinated when naïve after one dose of vaccine, P = 1, or two doses of vaccine, P < 0.0001), b DiaSorin TrimericS (Mann-Whitney test, unvaccinated previously infected versus HCW subjects vaccinated when naïve, P < 0.0001) (c, d) and micro-neutralisation (Kruskal-Wallis test followed by Dunn’s multiple comparisons test, unvaccinated previously infected versus vaccinated when naïve after one dose of vaccine, P = 0.001, or two doses of vaccine, P = 1; Mann-Whitney test, unvaccinated previously infected versus HCW subjects vaccinated when naïve, P < 0.001) assays. Asterisks indicate *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. HCW: healthcare workers. Previous infection is defined according to the ground truth definition provided in the text

Fig. 6

Neutralisation titres against the B.1, B.1.617.2 and BA.1 SARS-CoV-2 variants in naïve and previously infected subjects according to vaccination. a Neutralising antibody titres against B.1, B.1.617.2 and BA.1 SARS-CoV-2 variants in (left) previously infected (Friedman test followed by Dunn’s multiple comparisons test, serum of previously infected subjects with one vaccine dose against B.1 versus B.1.617.2 and BA.1, P = 0.004 and P < 0.0001 respectively; serum of previously infected subjects with two vaccine doses against B.1 versus B.1.617.2 and BA.1, P = 0.02 and P < 0.0001, respectively) and (right) naïve subjects (Friedman test followed by Dunn’s multiple comparisons test, serum of naïve subjects with two doses of vaccine against B.1 versus B.1.617.2 and BA.1, P = 0.03 and P <0.0001, respectively). Asterisks indicate *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. b, c Fold changes in serum neutralisation titres of previously infected subjects with b one dose of vaccine and c two doses of vaccine tested for B.1.617.2 and BA.1 variants compared to B.1 (fold change of 4× and 16× for both one or two doses of vaccine for B.1.617.2 and BA.1, respectively). Previous infection is defined according to the ground truth definition given in the text