mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern

Neutralizing titers for D614G and B.1.351 declined from peak levels after the second dose to 6 months in both naïve and recovered vaccinees.

“neutralizing titers for D614G and B.1.351 declined from peak levels after the second dose to 6 months for both SARS-CoV-2–naïve and –recovered vaccinees”

Calculated decay rates for anti-spike IgG were not significantly different between SARS-CoV-2-naïve and recovered vaccinees.

“the calculated decay rates for anti-spike IgG were not significantly different between SARS-CoV-2–naïve and –recovered vaccinees”

All individuals had detectable anti-spike IgG at 6 months postvaccination.

“all individuals had detectable anti-spike IgG at 6 months”

Neutralizing titers displayed different decay kinetics with slightly longer half-lives than binding antibody responses.

“neutralizing titers displayed different decay kinetics, with slightly longer half-lives than binding antibody responses”

The decrease in anti-spike and anti-RBD IgG levels slowed from 3 to 6 months postvaccination.

“This decrease in antibody levels slowed from 3 to 6 months postvaccination”

Clones that cross-bound both WT and B.1.351 RBD trended toward higher D20 scores compared with other antigen-binding populations.

“Clones that cross-bound both WT and B.1.351 RBD trended toward higher D20 scores, suggesting greater clonal expansion and/or lower diversity compared with the other antigen-binding populations (Fig. 4C).”

In SARS-CoV-2-naïve vaccinees, IgM+ cells were most abundant at preimmune baseline and early postvaccination time points.

“IgM+ cells were most abundant at preimmune baseline and early postvaccination time points”

Significantly higher levels of SHM were observed in variant RBD cross-binding clones compared with WT RBD only clones.

“Notably, significantly higher levels of SHM were observed in variant RBD cross-binding clones compared with WT RBD only clones (Fig. 4, E and F, and fig. S5C).”

• Also stated in: § Clonal evolution of variant-specific memory B cells · plain

  “mRNA vaccine–induced memory B cells that bind variant RBDs have higher SHM compared with clones that only bind WT RBD.”

Binding antibodies remained highly correlated with neutralizing titers at 6 months postvaccination.

“binding antibodies remained highly correlated with neutralizing titers”

In the mild-infection HCW cohort, a gradual increase in the frequency of spike+ NTD+ and spike+ all variant+ memory B cells was observed from 2 weeks to 6 months after seropositive test.

“In the mild-infection HCW cohort, a gradual increase in the frequency of spike+ NTD+ and spike+ all variant+ memory B cells was observed from 2 weeks to 6 months after seropositive test”

Spike+, RBD nonbinding memory B cells had high SHM.

“Spike+, RBD nonbinding memory B cells (which include NTD- and S2-binding populations) had high SHM (Fig. 4, E and F, and fig. S5C)”

WT and cross-binding sequence variants localized on separate branches.

“Lineage analysis revealed that WT and cross-binding sequence variants localized on separate branches (representative lineages shown in Fig. 4H)”

SARS-CoV-2-specific memory B cell clones had significantly more VH nucleotide mutations compared with naïve B cell clones.

“As expected, SARS-CoV-2–specific memory B cell clones had significantly more VH nucleotide mutations compared with naïve B cell clones (Fig. 4, E and F, and fig. S5C).”

There was heterogeneity in clonal expansion across individuals.

“The clonality of antigen-binding memory B cell populations was not significantly different after vaccination on the basis of prior immunity, although there was heterogeneity in clonal expansion across individuals.”

Despite reduced neutralizing ability, 31 of 33 naïve and 9 of 9 recovered individuals still had neutralizing antibodies against B.1.351 above the limit of detection at 6 months postvaccination.

“31 of 33 SARS-CoV-2–naïve and 9 of 9 SARS-CoV-2–recovered individuals still had neutralizing antibodies against B.1.351 above the limit of detection at 6 months postvaccination”

When SARS-CoV-2-recovered subjects were immunized with mRNA vaccine, a similar immunodominance pattern was observed, with S2 specificity representing most of the total anti-spike response.

“When SARS-CoV-2–recovered subjects were immunized with mRNA vaccine, a similar immunodominance pattern was observed, with S2 specificity representing most of the total anti-spike response”

VH gene profiles were overall similar in vaccinated individuals regardless of prior SARS-CoV-2 infection status.

“Hierarchical clustering revealed that VH gene profiles were overall similar in vaccinated individuals regardless of prior SARS-CoV-2 infection status (Fig. 4D and fig. S5B)”

At 6 months postvaccination, neutralizing antibody titers to B.1.617.2 were similar to D614G.

“Neutralizing antibody titers to B.1.617.2 were similar to D614G”

In vitro anti-spike IgG production correlated with the frequency of spike+ memory B cells detected by flow cytometry.

“This in vitro anti-spike IgG production also correlated with the frequency of spike+ memory B cells detected by flow cytometry”

No changes were observed in influenza HA+ memory B cells after SARS-CoV-2 vaccination in either group.

“No changes were observed in influenza HA+ memory B cells after SARS-CoV-2 vaccination for either group”

Neutralization titers of memory B cell-derived antibodies correlated with both anti-spike IgG and RBD-ACE2 binding inhibition.

“neutralization titers correlated with both anti-spike IgG and RBD-ACE2 binding inhibition”

Between 50 and 80% of WT RBD+ cells cobound B.1.351 variant RBD.

“between 50 and 80% of WT RBD+ cells cobound B.1.351 variant RBD (Fig. 4B)”

IGHV gene usage largely clustered on the basis of antigen specificity.

“Rather, IGHV gene usage largely clustered on the basis of the antigen specificity”

At 6 months postvaccination or seropositivity, antigen-specific memory B cell frequencies were similar between all groups.

“Cross-sectional analysis at 6 months postvaccination or seropositivity revealed similar antigen-specific memory B cell frequencies between all groups”

The Beta B.1.351 variant RBD containing the K417N, E484K, and N501Y mutations resulted in the greatest loss of binding relative to WT RBD.

“Here, we focused on the Beta B.1.351 variant RBD containing the K417N, E484K, and N501Y mutations because this variant resulted in the greatest loss of binding relative to WT RBD (Fig. 3, E, G, and H).”

Boosting of infection-acquired immunity by mRNA vaccination in SARS-CoV-2-recovered donors did not produce higher SHM in RBD-binding memory B cell clones compared with vaccination alone.

“Additionally, boosting of infection-acquired immunity by mRNA vaccination in SARS-CoV-2–recovered donors did not produce higher SHM in RBD-binding memory B cell clones compared with vaccination alone (Fig. 4F).”

Among larger clones, 2.5% had sequence variants that were isolated from both WT RBD and cross-binding populations.

“Among such larger clones, 2.5% had sequence variants that were isolated from both WT RBD and cross-binding populations (Fig. 4G and fig. S5D).”

At 6 months postvaccination, neutralizing titers to B.1.351 were significantly lower than to D614G.

“neutralizing titers to B.1.351 were significantly lower than D614G”

SARS-CoV-2-recovered individuals had consistently higher frequencies of antigen-specific memory B cells up to 3 months postvaccination.

“SARS-CoV-2–recovered individuals had consistently higher frequencies of antigen-specific memory B cells up to 3 months postvaccination”

The percent of spike+ memory B cells expressing CD71 increased over the primary two-dose vaccine regimen in SARS-CoV-2-naïve individuals, peaking at 1 week after the second dose.

“The percent of spike+ memory B cells expressing CD71 increased over the course of the primary two-dose vaccine regimen in SARS-CoV-2–naïve individuals, peaking at 1 week after the second vaccine dose”

IgM+ and IgA+ memory B cells represented a minor fraction of the overall response in the blood at later time points.

“IgM+ and IgA+ memory B cells represented a minor fraction of the overall response in the blood at later time points”

There was increased usage of VH3-53 and VH3-66 in RBD cross-binding clones.

“with increased usage of VH3-53 and VH3-66 in RBD cross-binding clones (Fig. 4D and fig. S5B).”

Higher levels of SHM were observed in the variant binding sequences compared with WT only binding sequences.

“this analysis of overlapping clones revealed higher levels of SHM in the variant binding sequences compared with WT only binding sequences (Fig. 4, I and J)”

A similar decrease in CD71 expression was observed from 1 to 6 months postvaccination in SARS-CoV-2-recovered individuals.

“A similar decrease in CD71 expression was observed from 1 to 6 months postvaccination in SARS-CoV-2–recovered individuals”

B.1.351 RBD resulted in a more substantial loss of cross-binding compared with WT RBD.

“B.1.351 RBD resulted in a more-substantial loss of cross-binding”

All 6-month samples tested generated significant levels of anti-spike IgG in the in vitro stimulation assay compared with unstimulated controls.

“All 6-month samples tested generated significant levels of anti-spike IgG in this assay compared with unstimulated controls”

At 6 months postvaccination, SARS-CoV-2-naïve and recovered individuals had similar frequencies of spike+ and spike+ RBD+ memory B cells.

“both SARS-CoV-2–naïve and SARS-CoV-2–recovered individuals had similar frequencies of spike+ and spike+ RBD+ memory B cells at 6 months postvaccination”

B.1.1.7 RBD with a single N501Y mutation had relatively little change in binding compared with WT RBD.

“B.1.1.7 RBD with a single N501Y mutation had relatively little change in binding compared with WT RBD”

mRNA vaccination in SARS-CoV-2-naïve individuals induced a stronger response to B.1.351 than infection alone.

“mRNA vaccination in SARS-CoV-2–naïve individuals induced a stronger response to B.1.351 than infection alone”

Although overall frequency of NTD+ and RBD+ memory B cells increased over time, they were comparatively less immunodominant than S2 as a percentage of total spike+ memory B cells.

“Although the overall frequency of NTD+ and RBD+ memory B cells increased over time, they were comparatively less immunodominant than S2 as a percentage of total spike+ memory B cells”

Anti-spike IgG was detected in culture supernatants as early as 4 days after stimulation of memory B cells.

“Anti-spike IgG was detected in supernatants as early as 4 days after stimulation”

VOC neutralizing titers in culture supernatants correlated with the frequency of RBD-specific memory B cells by flow cytometry.

“VOC neutralizing titers in culture supernatants correlated with the frequency of RBD-specific memory B cells by flow cytometry”

In previously uninfected individuals, ~30% of spike-binding memory B cells cobound S2 at prevaccine baseline.

“In previously uninfected individuals, ~30% of spike-binding memory B cells cobound S2 at prevaccine baseline”

B.1.617.2 RBD had an intermediate effect on binding compared with WT RBD.

“B.1.617.2 RBD had an intermediate effect on binding”

The clonality of antigen-binding memory B cell populations was not significantly different after vaccination on the basis of prior immunity.

“The clonality of antigen-binding memory B cell populations was not significantly different after vaccination on the basis of prior immunity, although there was heterogeneity in clonal expansion across individuals.”

In SARS-CoV-2-naïve vaccinees, IgG+ memory B cells steadily increased over time.

“Analysis of immunoglobulin isotypes in SARS-CoV-2–naïve vaccinees revealed a steady increase in IgG+ memory B cells over time”

The percent of CD71+ antigen-specific memory B cells steadily declined by the 6-month time point in naïve individuals.

“The percent of CD71+ antigen–specific memory B cells then steadily declined by the 6-month time point”

In SARS-CoV-2-recovered individuals, vaccination resulted in a significant increase in memory B cell cross-binding to the B.1.617.2 variant.

“In SARS-CoV-2–recovered individuals, vaccination resulted in a significant increase in memory B cell cross-binding to the B.1.617.2 variant”

In convalescent individuals who recovered from mild infection, there was a gradual increase in cross-binding to variants over time.

“In convalescent individuals who recovered from a mild infection, there was a gradual increase in cross-binding to variants over time”

Antibodies produced by memory B cells upon restimulation were capable of neutralizing the B.1.351 and B.1.617.2 VOCs.

“antibodies produced by memory B cells upon restimulation were capable of neutralizing the B.1.351 and B.1.617.2 VOCs”

The D20 index ranged from <1% for naïve B cells to >20% for some antigen-binding populations.

“The D20 index ranged from <1% for naïve B cells (which is expected for a diverse, nonclonally expanded population) to >20% for some of the antigen-binding populations (Fig. 4C).”

The increase in anti-spike and anti-RBD binding antibodies was transient and returned to near baseline by 6 months postvaccination.

“The increase in anti-spike and anti-RBD binding antibodies was also transient and returned to near baseline by 6 months postvaccination (Fig. 6E).”

mRNA vaccination preferentially induced antigen-specific CD4+ circulating T follicular helper cells (cTFH cells) and T helper cells (TH1 cells) in both SARS-CoV-2-naïve and -recovered individuals, whereas TH2, TH17, and TH1/17 cells were detected at lower levels in the AIM assay.

“mRNA vaccination also preferentially induced antigen-specific CD4+ circulating T follicular helper cells (cTFH cells) and T helper cells (TH1 cells) in both SARS-CoV-2–naïve and –recovered individuals, whereas TH2, TH17, and TH1/17 cells were detected at lower levels in the AIM assay (Fig. 5I).”

Boosting of preexisting immunity with mRNA vaccine does not change the magnitude or subset composition of the CD4+ memory T cell response.

“and the boosting of preexisting immunity with mRNA vaccine does not change the magnitude or subset composition of the CD4+ memory T cell response.”

UMAP analysis revealed a continued evolution of the overall immune response in SARS-CoV-2-naïve subjects after mRNA vaccination with different time points occupying largely nonoverlapping UMAP space.

“This analysis revealed a continued evolution of the overall immune response in SARS-CoV-2–naïve subjects after mRNA vaccination with different time points occupying largely nonoverlapping UMAP space (Fig. 6A).”

Peak T cell responses after the second dose were predictive of later time points.

“Like antibodies and memory B cells, peak T cell responses after the second dose were predictive of later time points (fig. S7F).”

Primary vaccination was largely defined by rapid induction of CD4+ T cell immunity.

“Projection of individual immune components onto the UMAP space revealed that primary vaccination was largely defined by rapid induction of CD4+ T cell immunity (Fig. 6B).”

Peak antibody levels were significantly correlated with later antibody levels.

“Peak antibody levels were significantly correlated with later antibody levels (fig. S7F).”

Antibody responses after the first or second vaccine dose did not correlate with the magnitude of B cell memory at 6 months.

“Antibody responses after the first or second vaccine dose did not correlate with the magnitude of B cell memory at 6 months (Fig. 6C).”

A marked contraction phase was observed from peak responses to 3 months postvaccination, with a half-life of 47 days for CD4+ T cells and 27 days for CD8+ T cells.

“A marked contraction phase was observed from peak responses to 3 months postvaccination, with a half-life of 47 days for CD4+ T cells and 27 days for CD8+ T cells (Fig. 5, C and D).”

The frequency of SARS-CoV-2-specific memory B cells was the only feature of preexisting immunity that correlated significantly with antibody responses after vaccination.

“The frequency of SARS-CoV-2–specific memory B cells was the only feature of preexisting immunity that correlated significantly with antibody responses after vaccination (Fig. 6F)”

During contraction from peak responses, antigen-specific CCR7+ CM cells were largely lost from circulation.

“During contraction from peak responses, antigen-specific CCR7+ CM cells were largely lost from circulation”

The percentage of the peak CD4+ response that was EM1 cells was significantly associated with the durability of the overall CD4+ T cell response at 3 and 6 months postvaccination.

“Moreover, the percentage of the peak CD4+ response that was EM1 cells, but not other memory subsets, was significantly associated with the durability of the overall CD4+ T cell response at 3 and 6 months postvaccination (Fig. 5, G and H)”

Vaccination uniformly shifted SARS-CoV-2-recovered individuals at 3 months postvaccination to a region defined by high levels of all antigen-specific immune parameters analyzed.

“Vaccination uniformly shifted SARS-CoV-2–recovered individuals at 3 months postvaccination to a region defined by high levels of all antigen-specific immune parameters analyzed (Fig. 6A).”

SARS-CoV-2-recovered individuals occupied a wide range of UMAP space at baseline.

“SARS-CoV-2–recovered individuals occupied a wide range of UMAP space at baseline”

CD4+ T cell responses, especially cTFH responses, as early as 2 weeks after the first dose of mRNA vaccine were positively correlated with antibody responses up to and including 6 months postvaccination.

“CD4+ T cell responses, especially cTFH responses, as early as 2 weeks after the first dose of mRNA vaccine were positively correlated with antibody responses up to and including 6 months postvaccination (Fig. 6D and fig. S7E).”

Boosting of spike- and RBD-specific memory B cell and memory CD4+ T cell responses was transient and returned to prevaccination baseline by 3 to 6 months.

“Boosting of spike- and RBD-specific memory B cell and memory CD4+ T cell responses was transient and returned to prevaccination baseline by 3 to 6 months (Fig. 6E).”

cTFH cells declined more rapidly than TH1 cells both during the initial contraction phase and from 3 to 6 months postvaccination.

“Specifically, cTFH cells declined more rapidly than TH1 cells both during the initial contraction phase and from 3 to 6 months postvaccination (Fig. 5J)”

A majority of these memory B cells were able to cross-bind VOCs, including B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta).

“A majority of these memory B cells were able to cross-bind VOCs, including B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta)”

These distinctively high responses were transient; SARS-CoV-2-recovered individuals at 6 months postvaccination shifted toward the UMAP space occupied by memory time points in SARS-CoV-2-naïve individuals at 3 and 6 months postvaccination.

“These distinctively high responses were transient, however, as SARS-CoV-2–recovered individuals at 6 months postvaccination shifted toward the UMAP space occupied by memory time points in SARS-CoV-2–naïve individuals at 3 and 6 months postvaccination.”

SARS-CoV-2 mRNA vaccination efficiently primed antigen-specific CD4+ T cells and CD8+ T cells.

“Consistent with recent studies, SARS-CoV-2 mRNA vaccination efficiently primed antigen-specific CD4+ T cells and CD8+ T cells (Fig. 5, C and D) (20–22).”

• cites [20] V. Oberhardt, H. Luxenburger, J. Kemming, I. Schulien, K. Ciminski, S. Giese, B. Csernalabics, J. Lang-Meli, I. Janowska, J. Staniek, K. Wild, K. Basho, M. S. Marinescu, J. Fuchs, F. Topfstedt, A. Janda, O. Sogukpinar, H. Hilger, K. Stete, F. Emmerich, B. Bengsch, C. F. Waller, S. Rieg, Sagar, T., Boettler, K., Zoldan, G., Kochs, M., Schwemmle, M., Rizzi, R., Thimme, C., Neumann-Haefelin, M., Hofmann, Rapid and stable mobilization of CD8+ T cells by SARS-CoV-2 mRNA vaccine. Nature 597, 268– 273 (2021). 10.1038/s41586-021-03841-4 34320609 PMC8426185 sourceNot checked yet

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• cites [21] A. Tarke, J. Sidney, N. Methot, E. D. Yu, Y. Zhang, J. M. Dan, B. Goodwin, P. Rubiro, A. Sutherland, E. Wang, A. Frazier, S. I. Ramirez, S. A. Rawlings, D. M. Smith, R. da Silva Antunes, B. Peters, R. H. Scheuermann, D. Weiskopf, S. Crotty, A. Grifoni, A. Sette, Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals. Cell Rep. Med. 2, 100355 (2021). 10.1016/j.xcrm.2021.100355 34230917 PMC8249675 sourceNot checked yet

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• cites [22] J. Mateus, J. M. Dan, Z. Zhang, C. R. Moderbacher, M. Lammers, B. Goodwin, A. Sette, S. Crotty, D. Weiskopf, Low dose mRNA-1273 COVID-19 vaccine generates durable T cell memory and antibodies enhanced by pre-existing crossreactive T cell memory. medRxiv 2021.06.30.21259787 [Preprint] (2021). 10.1101/2021.06.30.21259787 sourceNot checked yet

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Vaccination did little to further boost prevaccination antigen-specific CD8+ T cell frequencies in SARS-CoV-2-recovered individuals.

“By contrast, vaccination did little to further boost prevaccination antigen-specific CD8+ T cell frequencies in SARS-CoV-2–recovered individuals (Fig. 5D).”

Peak CD4+ T cell responses after SARS-CoV-2 mRNA vaccination were composed predominantly of central memory (CM) and effector memory 1 (EM1) cells in both SARS-CoV-2-naïve and -recovered individuals.

“Peak CD4+ T cell responses after SARS-CoV-2 mRNA vaccination were composed of predominantly central memory [(CM); CD45RA− CD27+ CCR7+] and effector memory 1 [(EM1); CD45RA− CD27+ CCR7−] cells in both SARS-CoV-2–naïve and –recovered individuals (Fig. 5F) (19).”

• cites [19] M. M. Painter, D. Mathew, R. R. Goel, S. A. Apostolidis, A. Pattekar, O. Kuthuru, A. E. Baxter, R. S. Herati, D. A. Oldridge, S. Gouma, P. Hicks, S. Dysinger, K. A. Lundgreen, L. Kuri-Cervantes, S. Adamski, A. Hicks, S. Korte, J. R. Giles, M. E. Weirick, C. M. McAllister, J. Dougherty, S. Long, K. D’Andrea, J. T. Hamilton, M. R. Betts, P. Bates, S. E. Hensley, A. Grifoni, D. Weiskopf, A. Sette, A. R. Greenplate, E. J. Wherry, Rapid induction of antigen-specific CD4+ T cells is associated with coordinated humoral and cellular immunity to SARS-CoV-2 mRNA vaccination. Immunity 54, 2133– 2142.e3 ( sourceNot checked yet

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SARS-CoV-2-specific memory CD4+ T cells were relatively stable from 3 to 6 months after mRNA vaccination.

“In addition to durable B cell memory, SARS-CoV-2–specific memory CD4+ T cells were relatively stable from 3 to 6 months after mRNA vaccination”

All individuals in the cohort, regardless of prior infection with SARS-CoV-2, had detectable CD4+ T cell responses above their individual baseline 1 week after the second vaccine dose.

“All individuals in our cohort, regardless of prior infection with SARS-CoV-2, had detectable CD4+ T cell responses above their individual baseline 1 week after the second vaccine dose (Fig. 5C).”

Spike-specific TH1 cells did not decline in the blood from 3 to 6 months postvaccination.

“By contrast, spike-specific TH1 cells did not decline in the blood from 3 to 6 months postvaccination.”

Early CD4+ T cell responses correlated with 3- and 6-month humoral responses.

“Early CD4+ T cell responses correlated with 3- and 6-month humoral responses”

Most (36 of 41) SARS-CoV-2-naïve individuals generated detectable CD8+ T cell responses after the second dose.

“Most (36 of 41) SARS-CoV-2–naïve individuals also generated detectable CD8+ T cell responses after the second dose (Fig. 5D).”

Time since infection did not appear to fully explain the observed variability for SARS-CoV-2-recovered individuals at prevaccine baseline.

“Time since infection did not appear to fully explain the observed variability for SARS-CoV-2–recovered individuals at prevaccine baseline (fig. S7D).”

28 of 31 SARS-CoV-2-naïve individuals had vaccine-induced antigen-specific CD4+ T cell responses at 6 months postvaccination above prevaccination baseline levels.

“Overall, 28 of 31 SARS-CoV-2–naïve individuals had vaccine-induced antigen-specific CD4+ T cell responses at 6 months postvaccination above prevaccination baseline levels”

Antigen-specific CCR7- EM1 cells stabilized in frequency from 3 to 6 months postvaccination.

“whereas antigen-specific CCR7- EM1 cells stabilized in frequency from 3 to 6 months postvaccination.”

Memory B cells 6 months postvaccination were qualitatively superior at binding VOCs compared with memory B cells 6 months after recovering from mild COVID-19.

“as memory B cells 6 months postvaccination were qualitatively superior at binding VOCs compared with memory B cells 6 months after recovering from mild COVID-19.”

The vast majority of vaccinees maintained robust CD4+ T cell responses at 6 months.

“and the vast majority of vaccinees maintained robust CD4+ T cell responses at 6 months.”

There was a continued increase in SARS-CoV-2-specific memory B cells between 3 and 6 months after mRNA vaccination, even as antibody levels declined in the same individuals.

“Specifically, the continued increase in SARS-CoV-2–specific memory B cells between 3 and 6 months after mRNA vaccination, even as antibody levels declined in the same individuals”

This region was largely unoccupied by SARS-CoV-2-naïve vaccinees.

“This region was largely unoccupied by SARS-CoV-2–naïve vaccinees”

At 6 months, there was heterogeneity in the immune landscape.

“At 6 months, we observed some heterogeneity in the immune landscape.”

Memory B cell frequencies 1 week after the second dose were correlated significantly with 3- and 6-month frequencies.

“Memory B cell frequencies 1 week after the second dose were also correlated significantly with 3- and 6-month frequencies (fig. S7F).”

CD8+ T cells continued to decline from 3 to 6 months postvaccination.

“whereas CD8+ T cells continued to decline.”

13 of 31 SARS-CoV-2-naïve individuals had detectable CD8+ T cell responses above baseline at 6 months postvaccination.

“and 13 of 31 had detectable CD8+ T cell responses above baseline (Fig. 5, C and D).”

All 6-month samples clustered away from preimmune baseline samples.

“Notably, all 6-month samples clustered away from preimmune baseline samples (Fig. 6A)”

Antigen-specific memory CD4+ T cell frequencies stabilized from 3 to 6 months postvaccination with a half-life of 187 days.

“After this initial contraction, antigen-specific memory CD4+ T cell frequencies stabilized from 3 to 6 months postvaccination with a half-life of 187 days”

The decay rate of antibodies was similar between SARS-CoV-2-naïve and SARS-CoV-2-recovered vaccinees.

“Notably, the decay rate of antibodies was similar between SARS-CoV-2–naïve and SARS-CoV-2–recovered vaccinees (Fig. 6E).”

Sex did not appear to have any association with the overall antigen-specific response to mRNA vaccination.

“Sex did not appear to have any association with the overall antigen-specific response to mRNA vaccination (fig. S7C).”

The second vaccine dose induced peak antibody, CD4+ T cell, and CD8+ T cell responses.

“The second vaccine dose induced peak antibody, CD4+ T cell, and CD8+ T cell responses.”

The magnitude of CD4+ T cell responses at 6 months was correlated with antibodies at 6 months.

“Like memory B cells, the magnitude of CD4+ T cell responses at 6 months was also correlated with antibodies at 6 months (Fig. 6D)”

These data provide evidence for durable immune memory at 6 months after mRNA vaccination.

“Nevertheless, these data provide evidence for durable immune memory at 6 months after mRNA vaccination”

Boosting of preexisting immunity from prior infection with mRNA vaccination mainly resulted in a transient benefit to antibody titers with little-to-no long-term increase in cellular immune memory.

“In this setting, boosting of preexisting immunity from prior infection with mRNA vaccination mainly resulted in a transient benefit to antibody titers with little-to-no long-term increase in cellular immune memory.”

Antibody decay rates were similar in SARS-CoV-2-naive and -recovered vaccinees.

“Antibody decay rates were similar in SARS-CoV-2–naïve and –recovered vaccinees”

Cellular immunity was durable for at least 6 months after mRNA vaccination.

“the durability of cellular immunity, here demonstrated for at least 6 months”

Antibody titers decline over time after mRNA vaccination.

“Declining antibody titers over time likely reduce the potential that vaccination will completely prevent infection or provide near-sterilizing immunity.”

mRNA vaccines encoding a stabilized full-length SARS-CoV-2 spike protein have demonstrated up to 95% efficacy in preventing symptomatic COVID-19 in clinical trials.

“mRNA vaccines encoding a stabilized version of the full-length severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein have been widely administered, and clinical trial data have demonstrated up to 95% efficacy in preventing symptomatic COVID-19 (2, 3).”

• cites [2] F. P. Polack, S. J. Thomas, N. Kitchin, J. Absalon, A. Gurtman, S. Lockhart, J. L. Perez, G. Pérez Marc, E. D. Moreira, C. Zerbini, R. Bailey, K. A. Swanson, S. Roychoudhury, K. Koury, P. Li, W. V. Kalina, D. Cooper, R. W. Frenck, L. L. Hammitt, Ö. Türeci, H. Nell, A. Schaefer, S. Ünal, D. B. Tresnan, S. Mather, P. R. Dormitzer, U. Şahin, K. U. Jansen, W. C. Gruber, Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine. N. Engl. J. Med. 383, 2603– 2615 (2020). 10.1056/NEJMoa2034577 33301246 PMC7745181 sourceNot checked yet

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• cites [3] L. R. Baden, H. M. El Sahly, B. Essink, K. Kotloff, S. Frey, R. Novak, D. Diemert, S. A. Spector, N. Rouphael, C. B. Creech, J. McGettigan, S. Khetan, N. Segall, J. Solis, A. Brosz, C. Fierro, H. Schwartz, K. Neuzil, L. Corey, P. Gilbert, H. Janes, D. Follmann, M. Marovich, J. Mascola, L. Polakowski, J. Ledgerwood, B. S. Graham, H. Bennett, R. Pajon, C. Knightly, B. Leav, W. Deng, H. Zhou, S. Han, M. Ivarsson, J. Miller, T. Zaks, Efficacy and Safety of the mRNA-1273 SARS-CoV-2 Vaccine. N. Engl. J. Med. 384, 403– 416 (2021). 10.1056/NEJMoa2035389 33378609 PMC7787219 sourceNot checked yet

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mRNA vaccination generates spike-specific memory CD4+ and CD8+ T cell responses.

“mRNA vaccination has also been shown to generate spike-specific memory CD4+ and CD8+ T cell responses (19–22).”

• cites [19] M. M. Painter, D. Mathew, R. R. Goel, S. A. Apostolidis, A. Pattekar, O. Kuthuru, A. E. Baxter, R. S. Herati, D. A. Oldridge, S. Gouma, P. Hicks, S. Dysinger, K. A. Lundgreen, L. Kuri-Cervantes, S. Adamski, A. Hicks, S. Korte, J. R. Giles, M. E. Weirick, C. M. McAllister, J. Dougherty, S. Long, K. D’Andrea, J. T. Hamilton, M. R. Betts, P. Bates, S. E. Hensley, A. Grifoni, D. Weiskopf, A. Sette, A. R. Greenplate, E. J. Wherry, Rapid induction of antigen-specific CD4+ T cells is associated with coordinated humoral and cellular immunity to SARS-CoV-2 mRNA vaccination. Immunity 54, 2133– 2142.e3 ( sourceNot checked yet

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• cites [20] V. Oberhardt, H. Luxenburger, J. Kemming, I. Schulien, K. Ciminski, S. Giese, B. Csernalabics, J. Lang-Meli, I. Janowska, J. Staniek, K. Wild, K. Basho, M. S. Marinescu, J. Fuchs, F. Topfstedt, A. Janda, O. Sogukpinar, H. Hilger, K. Stete, F. Emmerich, B. Bengsch, C. F. Waller, S. Rieg, Sagar, T., Boettler, K., Zoldan, G., Kochs, M., Schwemmle, M., Rizzi, R., Thimme, C., Neumann-Haefelin, M., Hofmann, Rapid and stable mobilization of CD8+ T cells by SARS-CoV-2 mRNA vaccine. Nature 597, 268– 273 (2021). 10.1038/s41586-021-03841-4 34320609 PMC8426185 sourceNot checked yet

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• cites [21] A. Tarke, J. Sidney, N. Methot, E. D. Yu, Y. Zhang, J. M. Dan, B. Goodwin, P. Rubiro, A. Sutherland, E. Wang, A. Frazier, S. I. Ramirez, S. A. Rawlings, D. M. Smith, R. da Silva Antunes, B. Peters, R. H. Scheuermann, D. Weiskopf, S. Crotty, A. Grifoni, A. Sette, Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals. Cell Rep. Med. 2, 100355 (2021). 10.1016/j.xcrm.2021.100355 34230917 PMC8249675 sourceNot checked yet

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• cites [22] J. Mateus, J. M. Dan, Z. Zhang, C. R. Moderbacher, M. Lammers, B. Goodwin, A. Sette, S. Crotty, D. Weiskopf, Low dose mRNA-1273 COVID-19 vaccine generates durable T cell memory and antibodies enhanced by pre-existing crossreactive T cell memory. medRxiv 2021.06.30.21259787 [Preprint] (2021). 10.1101/2021.06.30.21259787 sourceNot checked yet

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Memory B and T cells can be rapidly reactivated upon exposure, resulting in enhanced control of initial viral replication and limiting viral dissemination.

“In such cases, memory B and T cells can be rapidly reactivated, resulting in the enhanced control of initial viral replication and limiting viral dissemination in the host (24, 25).”

• cites [24] M. Akkaya, K. Kwak, S. K. Pierce, B cell memory: Building two walls of protection against pathogens. Nat. Rev. Immunol. 20, 229– 238 (2020). 10.1038/s41577-019-0244-2 31836872 PMC7223087 sourceNot checked yet

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• cites [25] D. L. Farber, N. A. Yudanin, N. P. Restifo, Human memory T cells: Generation, compartmentalization and homeostasis. Nat. Rev. Immunol. 14, 24– 35 (2013). 10.1038/nri3567 24336101 PMC4032067 sourceNot checked yet

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Emergence of SARS-CoV-2 variants including Alpha, Beta, and Delta raised concerns about increased transmission and potential evasion from vaccine-induced immunity.

“The emergence of several SARS-CoV-2 variants, including B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta), has also raised concerns about increased transmission and potential evasion from vaccine-induced immunity (30–33).”

• cites [30] D. A. Collier, A. De Marco, I. A. T. M. Ferreira, B. Meng, R. P. Datir, A. C. Walls, S. A. Kemp, J. Bassi, D. Pinto, C. Silacci-Fregni, S. Bianchi, M. A. Tortorici, J. Bowen, K. Culap, S. Jaconi, E. Cameroni, G. Snell, M. S. Pizzuto, A. F. Pellanda, C. Garzoni, A. Riva, The CITIID-NIHR BioResource COVID-19 Collaboration, A. Elmer, N. Kingston, B. Graves, L. E. McCoy, K. G. C. Smith, J. R. Bradley, N. Temperton, L. Ceron-Gutierrez, G. Barcenas-Morales, The COVID-19 Genomics UK (COG-UK) Consortium, W. Harvey, H. W. Virgin, A. Lanzavecchia, L. Piccoli, R. Doffinger, M. Wills, D. Veesler, D. Corti sourceNot checked yet

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• cites [31] D. Zhou, W. Dejnirattisai, P. Supasa, C. Liu, A. J. Mentzer, H. M. Ginn, Y. Zhao, H. M. E. Duyvesteyn, A. Tuekprakhon, R. Nutalai, B. Wang, G. C. Paesen, C. Lopez-Camacho, J. Slon-Campos, B. Hallis, N. Coombes, K. Bewley, S. Charlton, T. S. Walter, D. Skelly, S. F. Lumley, C. Dold, R. Levin, T. Dong, A. J. Pollard, J. C. Knight, D. Crook, T. Lambe, E. Clutterbuck, S. Bibi, A. Flaxman, M. Bittaye, S. Belij-Rammerstorfer, S. Gilbert, W. James, M. W. Carroll, P. Klenerman, E. Barnes, S. J. Dunachie, E. E. Fry, J. Mongkolsapaya, J. Ren, D. I. Stuart, G. R. Screaton, Evidence of escape of SARS-CoV- sourceNot checked yet

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• cites [32] C. Liu, H. M. Ginn, W. Dejnirattisai, P. Supasa, B. Wang, A. Tuekprakhon, R. Nutalai, D. Zhou, A. J. Mentzer, Y. Zhao, H. M. E. Duyvesteyn, C. López-Camacho, J. Slon-Campos, T. S. Walter, D. Skelly, S. A. Johnson, T. G. Ritter, C. Mason, S. A. Costa Clemens, F. Gomes Naveca, V. Nascimento, F. Nascimento, C. Fernandes da Costa, P. C. Resende, A. Pauvolid-Correa, M. M. Siqueira, C. Dold, N. Temperton, T. Dong, A. J. Pollard, J. C. Knight, D. Crook, T. Lambe, E. Clutterbuck, S. Bibi, A. Flaxman, M. Bittaye, S. Belij-Rammerstorfer, S. C. Gilbert, T. Malik, M. W. Carroll, P. Klenerman, E. Barnes, S sourceNot checked yet

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• cites [33] W. F. Garcia-Beltran, E. C. Lam, K. St. Denis, A. D. Nitido, Z. H. Garcia, B. M. Hauser, J. Feldman, M. N. Pavlovic, D. J. Gregory, M. C. Poznansky, A. Sigal, A. G. Schmidt, A. J. Iafrate, V. Naranbhai, A. B. Balazs, Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell 184, 2372– 2383.e9 (2021). 10.1016/j.cell.2021.03.013 33743213 PMC7953441 sourceNot checked yet

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A majority of RBD epitopes in the response are shared by the WT and mutant RBDs.

“between 50 and 80% of WT RBD+ cells cobound B.1.351 variant RBD (Fig. 4B), which indicates that a majority of RBD epitopes in the response are shared by the WT and mutant RBDs.”

Spike- and RBD-specific antibody responses retain their functional characteristics and neutralizing capacity over time.

“spike- and RBD-specific antibody responses retain their functional characteristics and neutralizing capacity over time”

Robust B cell memory to multiple components of the spike protein and currently described VOCs continues to evolve and increase in frequency over time.

“Taken together, our data indicate robust B cell memory to multiple components of the spike protein as well as currently described VOCs that continues to evolve and increase in frequency over time”

Clonal evolution from WT only binding to variant RBD cobinding occurred for at least some clones.

“suggesting a clonal evolution from WT only binding to variant RBD cobinding for at least some clones.”

• Also stated in: § Concluding remarks · hedged

  “clonal relationships indicated that at least some of these cross-binding memory B cells evolved through somatic hypermutation from clones that initially lacked variant binding.”

S2-binding memory B cells detected at baseline likely reflect cross-reactivity to commonly circulating coronaviruses.

“it is likely that S2-binding memory B cells detected at baseline reflect cross-reactivity to these commonly circulating coronaviruses”

Memory B cells can act as a rapid source of secondary antibody production.

“indicating that memory B cells can act as a rapid source of secondary antibody production”

Spike+, RBD nonbinding memory B cells are consistent with germinal center-dependent responses and possible recall responses of preexisting S2 cross-reactive clones.

“consistent with germinal center–dependent responses as well as possible recall responses of preexisting S2 cross-reactive clones.”

The shift in antigen-reactivity was not a result of contamination of the sorted populations.

“indicating that the shift in antigen-reactivity was not a result of contamination of the sorted populations (in which case sequence variants localize to the same nodes).”

These cells may derive, at least partially, from different B cell clones that were independently recruited into the vaccine response.

“These differences in IGHV gene usage between WT only and variant cross-binding phenotype suggested that these cells may derive, at least partially, from different B cell clones that were independently recruited into the vaccine response.”

Ongoing evolution and selection of these clones could facilitate cross-protection against different VOCs.

“Ongoing evolution and selection of these clones could therefore facilitate cross-protection against different VOCs.”

Both vaccination and infection followed by vaccination can recruit similar clones into the response.

“indicating that both vaccination and infection followed by vaccination can recruit similar clones into the response.”

Boosting of infection-induced immunity with mRNA vaccination does not substantially enhance already durable memory B cell or memory T cell responses.

“Overall, these data suggest that boosting of infection-induced immunity with mRNA vaccination does not substantially enhance already durable memory B cell or memory T cell responses.”

Memory T cell responses have been shown to be less affected by VOCs than humoral immune responses.

“Memory T cell responses have also been shown to be less affected by VOCs than humoral immune responses (21, 50).”

• cites [21] A. Tarke, J. Sidney, N. Methot, E. D. Yu, Y. Zhang, J. M. Dan, B. Goodwin, P. Rubiro, A. Sutherland, E. Wang, A. Frazier, S. I. Ramirez, S. A. Rawlings, D. M. Smith, R. da Silva Antunes, B. Peters, R. H. Scheuermann, D. Weiskopf, S. Crotty, A. Grifoni, A. Sette, Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals. Cell Rep. Med. 2, 100355 (2021). 10.1016/j.xcrm.2021.100355 34230917 PMC8249675 sourceNot checked yet

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• cites [50] D. Geers, M. C. Shamier, S. Bogers, G. den Hartog, L. Gommers, N. N. Nieuwkoop, K. S. Schmitz, L. C. Rijsbergen, J. A. T. van Osch, E. Dijkhuizen, G. Smits, A. Comvalius, D. van Mourik, T. G. Caniels, M. J. van Gils, R. W. Sanders, B. B. O. Munnink, R. Molenkamp, H. J. de Jager, B. L. Haagmans, R. L. de Swart, M. P. G. Koopmans, R. S. van Binnendijk, R. D. de Vries, C. H. GeurtsvanKessel, SARS-CoV-2 variants of concern partially escape humoral but not T cell responses in COVID-19 convalescent donors and vaccine recipients. Sci. Immunol. 6, eabj1750 (2021). 10.1126/sciimmunol.abj1750 34035118 P sourceNot checked yet

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Recall responses to mRNA vaccination will maintain antibodies above prevaccination levels in this cohort of mostly young individuals who recovered from mild COVID-19 for ~7 to 16 months.

“We estimated from these calculations that recall responses to mRNA vaccination will maintain antibodies above prevaccination levels in this cohort of mostly young individuals who recovered from mild COVID-19 for ~7 to 16 months.”

Antibody levels may provide a useful (though incomplete) proxy for the magnitude of memory B and CD4+ T cell responses at 6 months postvaccination.

“suggesting that antibody levels may provide a useful (though incomplete) proxy for the magnitude of memory B and CD4+ T cell responses at 6 months postvaccination.”

EM1s are long-lived memory CD4+ T cells.

“which suggests that EM1s are long-lived memory CD4+ T cells”

Key temporal relationships between different branches of the human immune response are associated with long-term immune memory after mRNA vaccination.

“Taken together, these data identify key temporal relationships between different branches of the human immune response that are associated with long-term immune memory after mRNA vaccination.”

mRNA vaccination induced durable multicomponent immune memory.

“highlighting the durable multicomponent immune memory induced by mRNA vaccination.”

Rapid mobilization of CD4+ T cell responses by the first mRNA vaccine dose had a lasting effect on humoral immunity.

“This observation suggested that rapid mobilization of CD4+ T cell responses by the first mRNA vaccine dose had a lasting effect on humoral immunity.”

Memory B cells have a major role in recall responses.

“consistent with a major role for memory B cells in recall responses.”

Prolonged germinal center reactions continue to generate circulating memory B cells for at least several months after vaccination.

“suggests that prolonged germinal center reactions (14) continue to generate circulating memory B cells for at least several months after vaccination.”

• cites [14] J. S. Turner, J. A. O’Halloran, E. Kalaidina, W. Kim, A. J. Schmitz, J. Q. Zhou, T. Lei, M. Thapa, R. E. Chen, J. B. Case, F. Amanat, A. M. Rauseo, A. Haile, X. Xie, M. K. Klebert, T. Suessen, W. D. Middleton, P.-Y. Shi, F. Krammer, S. A. Teefey, M. S. Diamond, R. M. Presti, A. H. Ellebedy, SARS-CoV-2 mRNA vaccines induce persistent human germinal centre responses. Nature 596, 109– 113 (2021). 10.1038/s41586-021-03738-2 34182569 PMC8935394 sourceNot checked yet

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The durable component of the memory CD4+ T cell response at 6 months postvaccination is largely composed of TH1 cells.

“these data indicate that the durable component of the memory CD4+ T cell response at 6 months postvaccination is largely composed of TH1 cells”

Reactivating preexisting immune responses is potent.

“underscoring the potency of reactivating preexisting immune responses.”

There may be some benefit to a longer interval between initial priming and subsequent restimulation or boost of immune responses to SARS-CoV-2.

“Thus, these data suggest that there may be some benefit to a longer interval between initial priming and subsequent restimulation or boost of immune responses to SARS-CoV-2.”

The magnitude and trajectory of individual components of the immune response are patterned soon after the second vaccine dose in SARS-CoV-2-naïve individuals.

“Overall, these data suggest that the magnitude and trajectory of individual components of the immune response are patterned soon after the second vaccine dose in SARS-CoV-2–naïve individuals.”

Early skewing toward an EM1 phenotype contributes to durable CD4+ T cell memory.

“and that early skewing toward an EM1 phenotype contributes to durable CD4+ T cell memory.”

These kinetics are consistent with a typical T cell response after the effector phase.

“These kinetics are consistent with a typical T cell response after the effector phase (53).”

• cites [53] S. M. Kaech, E. J. Wherry, R. Ahmed, Effector and memory T-cell differentiation: Implications for vaccine development. Nat. Rev. Immunol. 2, 251– 262 (2002). 10.1038/nri778 12001996 sourceNot checked yet

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There is variability of infection-induced virus-specific immunity.

“highlighting the variability of infection-induced virus-specific immunity (Fig. 6A).”

Reliable subsetting of antigen-specific CD8+ T cells at memory time points was not feasible because of the low number of events.

“Although our AIM assay allows for the detection of low-frequency memory CD8+ T cell responses for overall quantification, reliable subsetting of antigen-specific CD8+ T cells at memory time points was not feasible because of the low number of events.”

The heterogeneity in the immune landscape may be partially driven by a significant negative correlation between age and anti-spike IgG.

“This heterogeneity may be partially driven by a significant negative correlation between age and anti-spike IgG (fig. S7, A and B).”

Declining antibody titers over time likely reduce the potential that vaccination will completely prevent infection or provide near-sterilizing immunity.

“Declining antibody titers over time likely reduce the potential that vaccination will completely prevent infection or provide near-sterilizing immunity.”

The cohort is skewed toward young, healthy individuals.

“our cohort is skewed toward young, healthy individuals.”

Additional vaccine doses will temporarily prolong antibody-mediated protection without fundamentally altering the underlying landscape of SARS-CoV-2 immune memory.

“which suggests that additional vaccine doses will temporarily prolong antibody-mediated protection without fundamentally altering the underlying landscape of SARS-CoV-2 immune memory.”

The results described may not fully represent the durability of vaccine-induced immunity in older individuals or in populations with chronic diseases and/or compromised immune systems.

“the results described may not fully represent the durability of vaccine-induced immunity in older individuals or in populations with chronic diseases and/or compromised immune systems”

T cell immunity has a role in shaping the overall response to vaccination.

“highlighting a role for T cell immunity in shaping the overall response to vaccination.”

• AssumptionRests on an assumption: Memory T cells can contribute to protection upon reexposure to virus.

The durability of cellular immunity may contribute to rapid recall responses that can limit initial viral replication and dissemination in the host, thereby preventing severe disease.

“However, the durability of cellular immunity, here demonstrated for at least 6 months, may contribute to rapid recall responses that can limit initial viral replication and dissemination in the host, thereby preventing severe disease.”

The overall number of subjects was limited compared with epidemiological or phase 3 clinical trials.

“the overall number of subjects, although substantial for studies with high depth of immune profiling, was still limited compared with epidemiological or phase 3 clinical trials.”

The AIM assay may not be sensitive enough to detect very low-frequency CD8+ T cells at memory time points.

“this assay may not be sensitive enough to detect very low-frequency CD8+ T cells at memory time points.”