key: cord-0822043-7u0rxfkk
authors: Dayam, R. M.; Law, J. C.; Goetgebuer, R. L.; Chao, G. Y.; Abe, K. T.; Sutton, M.; Finkelstein, N.; Stempak, J. M.; Pereira, D.; Croituru, D.; Acheampong, L.; Rizwan, S.; Rymaszewski, K.; Milgrom, R.; Ganatra, D.; Batista, N. V.; Girard, M.; Lau, I.; Law, R.; Cheung, M. W.; Rathod, B.; Kitaygorodsky, J.; Samson, R.; Hu, Q.; Haroon, N.; Inman, R. D.; Piguet, V.; Chandran, V.; Silverberg, M. S.; Gingras, A.-C.; Watts, T. H.
title: Antibody and T cell responses to SARS-CoV-2 mRNA vaccines during maintenance therapy for immune-mediated inflammatory diseases
date: 2022-01-28
journal: nan
DOI: 10.1101/2022.01.26.22269856
sha: ade2d26ac89c4ab2aca772aef60718ca27107f19
doc_id: 822043
cord_uid: 7u0rxfkk

Background Limited information is available on the impact of immunosuppressants on COVID-19 vaccination in patients with immune-mediated inflammatory diseases (IMID). This study investigated antibody and T cell responses to SARS-CoV-2 mRNA vaccines in IMID patients undergoing immunomodulatory maintenance therapy. Methods This observational cohort study examined the immunogenicity of SARS-CoV-2 mRNA vaccines in adult patients with inflammatory bowel disease, rheumatoid arthritis, ankylosing spondylitis or psoriatic disease, with or without maintenance immunosuppressive therapies. T cell and antibody responses to SARS-COV-2, including neutralization against SARS-CoV-2 variants were determined pre-vaccination and after 1 and 2 vaccine doses. Findings We prospectively followed 150 subjects, 26 healthy controls, 9 IMID patients on no treatment, 44 on anti-TNF, 16 on anti-TNF with methotrexate/azathioprine (MTX/AZA), 10 on anti-IL-23, 28 on anti-IL-12/23, 9 on anti-IL-17, and 8 on MTX/AZA. Most patients showed increased antibody responses from dose 1 to dose 2, with decreases apparent by 3 months post dose 2, albeit with considerable variability within groups. Overall, T cell responses were not consistently different between groups; however, antibody levels and neutralization efficacy in the anti-TNF treated group was lower than controls and waned substantially by 3 months post-dose 2. Implications These findings support the need for a third dose of mRNA vaccine and for continued monitoring of immunity over time.

Evidence before this study Based on the published literature, previous studies on immunity to SARS-CoV-2 mRNA vaccines in patients receiving glucocorticoids, methotrexate, anti-TNF, or B-cell depleting therapy have shown that these patient groups may have attenuated serological responses. A small study of 23 IMID patients showed that patients on anti-TNF agents have greater waning of humoral immunity compared to healthy controls. This was recently confirmed in a larger study still in preprint form. Data regarding the cellular immune responses to vaccination are still relatively scarce and conflicting. Several studies have shown unimpaired T cell responses to SARS-CoV-2 vaccines in immunocompromised patients compared to healthy individuals, however this has not been consistently observed.

Although IMID patients treated with biologic or anti-metabolite therapies in our cohort are not considered to be significantly immunosuppressed, there has been concern as to whether they would mount full responses to SARS-CoV-2 vaccines. Our analyses show that all the participants in our study seroconverted for spike/RBD after 2 doses of vaccine and mounted T cell responses above the limit of detection. However, there was a wide range of responses within groups, and we observed significantly reduced antibody levels and neutralization capacity of wild type and variant-specific lentiviruses in the anti-TNF treatment group, with substantial waning of these antibody responses by 3 months after second vaccine dose. T cell cytokines were not consistently different between groups, although after the first dose of vaccine some groups showed reduced IFN-g responses. T cell responses in general increased with each dose and decreased again by 3 months after the second dose, largely correlating with antibody responses.

Although most studies follow T cell responses using IFN-g or IL-2, our study monitored 9 secreted molecules and found that IL-4, an important cytokine for antibody responses and B cell memory, is substantially enhanced by two doses of vaccine. We observed higher levels of antibody and neutralizing titers as well as T cell IL-4 production in response to mRNA-1273 as compared to BTN162b vaccines in the study group overall. Our study is also of interest, as the median time interval between vaccine dose 1 and dose 2 in our cohort was 60.5 days, differing from the standard interval, consistent with Canadian vaccine policy at the time.

This study highlights the need for third doses of mRNA vaccines in patients receiving anti-TNF treatment and for continued monitoring for waning immunity. The study also suggests that a mRNA-1273 booster may be more immunogenic in this patient cohort due to its induction of higher antibody levels, higher neutralization titers and increased T cell IL-4 after 2 doses of vaccine.

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a serious health crisis. 1,2 COVID-19 infections can vary from asymptomatic or mild through to severe disease, with lethal complications such as progressive pneumonia, acute respiratory distress syndrome and organ failure driven by hyperinflammation and a cytokine storm syndrome. Patients with immune-mediated inflammatory diseases (IMID), such as inflammatory bowel disease (IBD), psoriatic disease, rheumatoid arthritis (RA) and spondyloarthritis (SpA), are frequently treated with immunosuppressants and biologics and therefore may be at increased risk for COVID- 19 . 3, 4 Age and underlying comorbidities as well as the use of some immunosuppressants have been shown to be risk factors for developing COVID-19 among IMID patients. 3, 5 Glucocorticoids and combination therapy of immunomodulators and biologics have been shown to increase the risk of severe outcomes of COVID-19. 4, 6 Although many IMID patients mount adequate serological responses to vaccination after two doses of an mRNA vaccine, a proportion of IMID patients show reduced responses compared to healthy controls, [7] [8] [9] [10] [11] [12] [13] as confirmed in recent meta-analyses. 14, 15 In particular, patients receiving glucocorticoids, methotrexate, anti-TNF and B-cell depleting therapy may have attenuated serological responses to COVID-19 vaccines. 7, 11, 13, 14, 16 A small study of 23 IMID patients showed that patients on anti-TNF therapy have greater waning of humoral immunity compared to healthy controls, 13 as confirmed in a larger study still in preprint. 17 Data regarding the cellular immune responses to vaccination are still relatively scarce and conflicting. Several studies have shown unimpaired T cell responses to SARS-CoV-2 vaccines in immunocompromised patients compared to healthy individuals, 13,18-21 though a follow-up study showed that a proportion of IMID patients on immunosuppression had reduced T cell responses to a second dose of vaccine. 22 In another study, methotrexate limited CD8 + T cell responses to vaccination in a cohort of IMID patients. 23 To gain further insight into immunity to mRNA vaccines in IMID patients on different maintenance therapies, we investigated serological and T cell responses against SARS-CoV-2 before and after one or two doses of mRNA vaccine. The results show substantial variation in responses within different treatment groups. Notably, we observed decreased serological responses in anti-TNF treated patients, including substantial waning by 3 months post second vaccine dose. While some T cell responses were near maximal by 1 dose of vaccine, T cell interleukin (IL)-4 increased substantially after 2 vaccine doses and correlated with humoral responses. These data highlight the need for third doses of SARS-CoV-2 mRNA vaccines and for continued monitoring of responses.

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted January 28, 2022. Sample and data collection: Patient information and medical history were collected at each visit. Participation was terminated when all the blood samples were collected or when a patient opted out. Clinical data included basic demographics (age, sex, weight, height), relevant past medical and surgical history, and medication use at inclusion.

Questions about prior COVID-19 diagnosis or exposure, vaccination history and side effects, changes in medical history or medication and disease activity were collected at each study visit. Blood samples were drawn from the participants at up to 4 time points: T1 = pre-vaccination, T2 = median 26 days after dose 1, T3 = median 16 days after dose 2 and T4 = median 106 days after dose 2. Peripheral blood samples were collected in BD Vacutainer ® sodium heparin tubes for plasma antibody assessment and peripheral blood mononuclear cell (PBMC) separation.

All samples were labelled with unique patient identifiers. Researchers were blinded to the identity and clinical details of the subjects. Plasma samples were stored at -80⁰C. PBMCs were isolated by density centrifugation using Ficoll-Paque PLUS (GE Healthcare). PBMCs were cryopreserved in 10% DMSO in FBS (Wisent Bioproducts) and stored in liquid nitrogen at a minimum of 2x10 6 mononuclear cells per vial.

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint

Frozen plasma was thawed and treated with 1% final Triton X-100 for one hour. Samples were analyzed by automated ELISA for IgGs to the spike trimer (spike), the spike receptor binding domain (RBD), and the nucleocapsid (NP; all antigens and secondary antibodies are produced in mammalian cells and were provided by Dr.

Yves Durocher at the National Research Council of Canada, NRC) as previously reported. 24 Luminescence values for each sample/assay were normalized to synthetic standards profiled in a 4-fold dilution series on each plate (Human anti-nucleocapsid IgG, #A02039, clone HC2003, GenScript, Piscataway, NJ, USA and humanized anti RBD/spike IgG: VHH72hFc1X7; NRC). The synthetic references, as well as a pool of positive samples from convalescent patients with high IgG level to all three antigens and negative controls (pre-COVID era samples, blank and IgG, 1 µg/ml; #I4506, Millipore-Sigma, Oakville, ON, Canada) were also added to each plate in a 4-fold dilutions series to enable quality controls across the plates and batches of samples. For each assay, log10 raw values and relative ratio of samples were compared to prior runs to confirm that the sample density distribution is within range; automated scripts, blinded to sample description and meta-data were used to extract relative ratios to the synthetic references. The assay was calibrated to the World Health Organization (WHO) reference (National Institute for Biological Standards and Control, NIBSC, Code 20/136); a table of conversion of relative ratios for each assay to Binding International Units/ml (BAU/ml) is provided (suppl. table S1). Seropositivity was defined based on both receiver operating characteristic (ROC) analysis of negative (pre-COVID era) and positive (PCR confirmed COVID-19 cases) samples (<1% false positive rate threshold) and on deviation from the log means of the negative controls (≥ 3 standard deviations). In some of the figures, the median convalescent values for serum samples from 340 PCR confirmed COVID-19 cases 21-115 days after symptom onset 24 is displayed as a reference point. Since the assays saturate in healthy controls after two doses of vaccine, all samples were processed both at the dilution used for determination of seroconversion, and a 1/16 further dilution for evaluation of the quantitative differences in antibody responses.

The lentivirus neutralization assay and the generation of spike pseudotyped lentivirus particles were performed as described previously. 25 Briefly, the lentivirus particles were generated by co-transfection in HEK293TN cells plasma was serially diluted and incubated with the lentiviral particles (1h, 37°C) prior to addition to cells (HEK293T-ACE2/TMPRSS2) for 48h; luminescence signals were detected with the Bright-Glo Luciferase assay system (Promega, E2620) on an EnVision multimode plate reader (Perkin Elmer. GraphPad Prism 9 was used to calculate 50% neutralization titer (ID50) using non-linear regression. The WHO International Standard (20/136) was evaluated in this assay, and a mean ID50 value of 5744 corresponded with 1000 IU/ml. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint

Cellular immune responses to COVID-19 vaccination were determined by measuring the release of cytokines and cytotoxic molecules in cell culture supernatants following stimulation with peptide arrays using the LEGENDplex multiplex bead assay as previously described. 26 Briefly, 1x10 6 PBMCs were seeded per well in 96-well round bottom plates with 1 µg/ml each of SARS-CoV-2 spike or Nucleoprotein (NP) peptide pools (JPT peptide technologies, GMBH, Berlin, Germany). PBMCs were cultured with anti-CD28 (clone 9.3, Bio X Cell) and anti-CD3 (clone OKT3, Bio X Cell) as a positive control, or with equimolar DMSO as a negative control. Samples with no response to positive control were not included in the analysis. After 48h incubation at 37°C, cell culture supernatants were collected and stored at -80°C. Release of cytokines and cytotoxic molecules in the supernatants were analyzed using LEGENDplex multiplex cytokine bead assay (BioLegend) as per manufacturer's instructions.

Samples were acquired on the BD LSR Fortessa flow cytometer using BD FACSDiva software. Data are reported as square root (sqrt) transformed values in pg/ml after subtracting background signal from wells containing PBMCs cultured with DMSO containing media alone, as indicated by "Δ".

T cell cytokine secretion data were analyzed using the LEGENDplex™ Data Analysis Software Suite and pandas data analysis library for Python and GraphPad Prism v9.3.1al. 27 Antibody data were analyzed with R (version 4.1.1) using package ggplot2 and custom R scripts. GraphPad Prism v 9.2.0 was used to analyze the neutralization and antibody data. Longitudinal multivariate analysis on antibody data and T cell cytokine secretion was performed using linear mixed models. Models controlled for baseline T cell/antibody data and included an interaction term between time point and the variable of interest. All multivariate analysis performed using R (version 4.1.1) and SAS 9.4.

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint

Of 177 initially recruited subjects, 150 met the inclusion criteria for this study (see methods). PBMCs and plasma were collected for T cell and antibody responses at up to 4 time points, before and after vaccination with mRNA vaccines ( figure 1A ). In our cohort, the median time between dose 1 and dose 2 of the mRNA vaccines was 60.5 days, IQR [45. . Baseline characteristics of the study subjects are shown in table I. Of note, age and BMI, but not vaccine interval, were significantly different between groups and multivariate analysis of the data took these differences into account (suppl. 

Antibody responses were measured by automated ELISA. For the entire cohort, antibody responses increased from T1 to T2 to T3, and decreased by T4 (suppl. fig. S1A ). Responses to NP were used to rule out exposure to SARS-CoV-2 (suppl. fig. S1B ). After the first dose, 97.8% and 80% of participants seroconverted to spike and RBD IgG, respectively, and the relative ratios were greater than the medians of the convalescents in 44.2% and 14.2% of the participants (figure 1B). Seroconversion increased to 100% for spike and 99.2% for RBD after the second dose and the anti-S and anti-RBD IgG levels were greater than the median levels of convalescent patients in 97% and 86.6% of participants, with a median relative ratio of 1.91 for spike and 1.55 for RBD. Analysis of antibody responses by vaccine type showed that two doses of the mRNA-1273 vaccine elicits a stronger humoral response than BNT162b, with mixed mRNA vaccines inducing significantly higher levels of anti-spike/RBD IgG than two doses of BNT162b (suppl. fig. S2A ). Although all data were included in the figures, as the majority of the cohort was vaccinated twice with BNT162b2, univariate statistical analysis between treatment groups was performed only on samples from the BNT162b/BNT162b participants. Among the BNT162b/BNT162 cohort, males had a slightly lower response to RBD than females, whereas antibody response differences by age were not significant (suppl. fig. S2B , C).

Participants undergoing anti-TNF, and anti-TNF+MTX/AZA therapies had significantly lower levels of antibodies than those in the healthy control, IMID-untreated, and anti-IL-12/23 groups after the first dose of vaccine (figure 1B and suppl. fig. S1B ). Comparison between the groups after the second dose (T3) indicates that for the BNT162b/BNT162b group, participants taking anti-TNF had significantly lower levels of anti-spike IgG than those in the healthy control, IMID-untreated, and anti-IL-12/23 groups (figure 1B). Multivariate analysis of treatment groups controlling for age/sex/BMI confirmed the deficits in anti-RBD and anti-spike in the anti-TNF group after the second dose, whether the entire cohort or only the BNT162b/BNT162b participants were evaluated (suppl . table   S2 ).

Spike and RBD antibody levels decreased by T4 (median 106 days post-dose 2), with a more rapid decline in anti-RBD levels (figure 1B). Only 66.3% and 49.4% of the participants show relative ratios greater than the medians of . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint the convalescents for spike and RBD, respectively. When data were ranked by study group, we observed that the anti-TNF, and anti-TNF+MTX/AZA therapy groups were associated with a statistically significant drop in antispike and anti-RBD IgG levels compared to the healthy control, IMID-untreated, and anti-IL-12/23 groups ( figure   1B ).

We performed at T3 spike-pseudotyped lentiviral neutralization assays using the wild-type strain and B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta) variants of concern (VOCs). Samples neutralized the wildtype more efficiently than the VOCs tested, but participants on anti-TNF and anti-TNF+MTX/AZA showed significantly lower S3B ). Overall, these data agree with the ELISA data, demonstrating that anti-TNF treated groups have weaker neutralization responses to mRNA vaccines.

To assess memory T cell responses to SARS-CoV-2, PBMCs were stimulated with spike or NP peptide pools for 48hrs. A quantitative multiplex bead-based immunoassay was used to measure the levels of 9 secreted cytokines and cytotoxic molecules in the supernatants in response to spike peptide stimulation and results are reported after subtracting the values from negative control wells. The response to NP was used as an additional control to detect memory responses to previous virus exposure. NP-specific responses pre-vaccination were minimal, consistent with study subjects being SARS-CoV-2 naïve and suggesting minimal impact of cross-reactive T cells from previous coronavirus infections (suppl. fig. S4 ). The cytokines IFN-γ, IL-2, IL-17A and IL-4 were increased over baseline (T1) after one or two doses of mRNA vaccine in all patient groups (T2 and T3), with the response predominantly of the Th1 phenotype as characterized by high levels of IFN-γ and IL-2 (figure 3, suppl. fig. S5 ). Molecules associated with cytotoxicity such as granzyme (Gzm) A, GzmB, perforin and sFasL were also increased over baseline following one dose of vaccine and did not consistently increase with the second dose (figure 4, suppl. fig. S5 ). TNF was not detected over baseline (data not shown). Most study groups showed a wide range of responses to spike peptide pools after first or second vaccine doses (figures 3, 4, suppl. fig.S5 ) When multivariate analysis was performed either on the entire cohort or the BNT162b/BNT162b group only, after controlling for age/sex/BMI, we observed deficits in IFN-g production in IMID untreated, anti-TNF, MTX/AZA, anti-IL-12/23 and anti-IL-23 groups relative to healthy controls after dose one, which largely recovered by dose two (suppl. table S2). When results from all subjects were pooled, there was a trend towards increased responses from first to second dose, with IL-2 showing significant increases, and IL-4 decreased by T4 (suppl. fig. S6AB ). We also noted higher IL-4 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint responses following vaccination with mRNA-1273 compared to BNT162b or mixed doses (suppl. fig. S7A ).

Although T cell responses overall were similar based on age or sex (suppl. fig. S7B ,C), multivariate analysis revealed lower IL-4 and IFN-g responses in the over 60 group (suppl. table S3).

Levels of secreted IL-2 were positively correlated with plasma IgG against RBD (r=0.50) and whole spike trimer (r=0.51). Similarly, there was a positive correlation between IL-4 and plasma IgG against RBD (r=0.58) and whole spike trimer (r=0.59), and between IFN-γ and RBD IgG (r=0.36) and whole spike trimer IgG (r=0.36) ( figure 5 ).

Here we studied a cohort of patients with inflammatory bowel disease, rheumatoid arthritis, ankylosing spondylitis or psoriatic disease, treated with biologics (anti-TNF, anti-IL-12/23, anti-IL-23, anti-IL-17) or antimetabolites to assess their response to COVID-19 mRNA vaccines. Although this group is not considered to be significantly immunosuppressed, there has been concern as to how their treatments could impact the response to the vaccines.

Although there was considerable variability within groups, 100% of participants seroconverted for spike after 2 doses of vaccine. There was also a clear indication of higher responses to mRNA-1273 vaccine compared to BNT162b vaccine with respect to antibody levels and neutralization titers, as well as T cell IL-4 production. Of concern, antibody levels and neutralization activity were lower in the anti-TNF treated study subjects even after two doses of vaccine. Moreover, the response to two doses of mRNA vaccine in anti-TNF treated patients showed substantial waning by 3 months after dose two. These findings are in agreement with a recent small study from Geissen et al. 13 who showed decreased responses and waning immunity with anti-TNF agents in 23 IMID patients at 6 months post dose 2, and also confirmed with a larger cohort in a recent pre-print. 17 In our study, the vaccine dose interval was a median of 60.5 days rather than the standard 21 or 28 days used in the other studies, which could impact the results. Some limitations of our study are the small numbers of study subjects in some of the groups and grouping together of drugs by class.

T cell responses, including IL-4, IL-2 and IFN-g production, showed a significant correlation with RBD and spikespecific antibody responses. There was substantial induction of T cell cytokines and release of cytotoxic molecules following spike peptide pool stimulation of PBMCs collected following one dose of vaccine. Some subgroups and parameters showed increases in T cell cytokines with two doses. Multivariate analysis of the data showed that several groups had decreased IFN-g after dose 1 of vaccine, but these deficits were largely corrected following the second vaccine dose. When data were pooled for all subjects, it was apparent that the IL-4 response was particularly dependent on 2 doses of vaccine and showed a waning trend 3 months later. As IL-4 is an important mediator of B cell proliferation, which in turn impacts antibody levels and B cell memory, 28 the lower IL-4 response after 1 dose as compared to 2 doses of vaccine highlights the need for second doses to maximize B cell responses.

Taken together, our study shows generally robust T cell responses in most patient groups treated with immunosuppressants or biologics after 1 or 2 doses of mRNA vaccine, improving somewhat with a second dose but . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint with some attenuation by 3 months after the second dose. We observed some deficits in antibody responses even after two doses of vaccine, particularly in the anti-TNF treated groups, with waning immunity by three months after dose two. These findings highlight the need for a third vaccine dose, particularly in patients undergoing treatment with TNF inhibitors. As there is limited information available about the duration of immune memory induced by mRNA vaccines, it will also be important to follow these responses for longer time periods and to evaluate the impact of additional vaccine doses in this cohort as well as the possible contribution of natural infection to persistence of immune response.

MSS and THW conceived the study and obtained funding.

ACG and THW supervised the laboratory assays, analyzed data, acquired funding, and wrote the manuscript. BR was responsible for sample intake and ELISA assays.

RS and QH generated and titrated the lentiviral stocks and optimized the neutralization assays for VOCs.

KTA and JK wrote scripts for data analysis of the antibody data and generated figures.

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. JS, DP, LA, SR, RM, KR, DG contributed to study coordination, and patient recruitment.

Dr Inman has served as consultant for Abbvie, Janssen, Lilly, Novartis and has received research funding support from Abbvie and Novartis. Dr. Chandran has received research grants from AbbVie, Amgen and Eli-Lilly and has received honoraria for advisory board member roles from AbbVie, Amgen, BMS, Eli Lilly, Janssen, Novartis, Pfizer and UCB. His spouse is an employee of AstraZeneca.

Dr Silverberg has received research support, consulting fees and speaker honoraria from Abbvie, Janssen, Takeda, Pfizer, Gilead and Amgen.

All other authors have no conflicts to declare.

De-identified data will be made available by the authors upon request.

We thank Juan and Stefania Speck for their generous donation to the University of Toronto for this study. We thank Drs. Jesse Bloom and Katharine Crawford for the initial spike lentiviral construct, and Dr. W Rod Hardy from CoVaRR-Net for the variant lentiviral constructs. All antigens and protein reagents for the automated ELISAs were a kind gift from Dr. Yves Durocher at the National Research Council of Canada (NRC) generated within the NRC's Pandemic Response Challenge Program. We thank all members of the serology team at the Network Biology Collaborative Centre for help with ELISA assay development and automated ELISA processing, and in particular . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. (pre-vaccination); n=102, T2; n=117, T3; n=126, and T4; n= 88, with timepoints defined in figure 1A . Colored dots represent the type of vaccine (defined in figure 1B) . The gray line indicates the median. Values are reported in pg/ml after subtracting background signal from wells containing PBMCs cultured with DMSO alone, as indicated by "Δ".

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint Ctrl = Healthy controls, inh = inhibitor, MTX = methotrexate, AZA = thiopurines. Comparisons between groups in entire cohort were made by Dunn's multiple comparisons test. *p≤0.05, **p≤0.01.

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint Healthy controls, inh = inhibitor, MTX = methotrexate, AZA = thiopurines. Comparisons on entire cohort were made by Dunn's multiple comparisons test. *p≤0.05.

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint black line is the linear regression and gray shading indicates the 95% confidence interval. P-values and Spearman's rho coefficients are indicated in each graph for the entire cohort.

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint Figure S4 . Cellular immune responses in IMID patients to NP before or after first and second doses of mRNA vaccine. The release of cytokines and cytotoxic molecules in cell culture supernatants were analyzed by multiplex bead array following 48h stimulation with SARS-CoV-2 NP peptide pools. Violin plots show (A) release of cytokines IFN-γ, IL-2, IL-17A and IL-4 and (B) release of cytotoxic molecules GzmA, GzmB, perforin and sFasL at T1, n=102; T2, n=117; T3, n=126; and T4, n= 88, with T1 to T4 defined in figure 1A . The grey line indicates the median. Values are reported in pg/ml after subtracting background signal from wells containing PBMCs cultured with DMSO alone, as indicated by "Δ". Ctrl = Healthy controls, inh = inhibitor, MTX = methotrexate, AZA = azathioprine.

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint Figure S5 . Cytokine and cytotoxic responses in IMID patients to spike peptide pools over time. The release of cytokines and cytotoxic molecules in cell culture supernatants was analyzed by multiplex bead array following 48h stimulation with SARS-CoV-2 S peptide pools. Violin plots show release of (A) cytokines IFN-γ, IL-2, IL-17A and IL-4 and (B) cytotoxic molecules GzmA, GzmB, Perforin and sFasL at timepoints T1-T4 (see figure 1A ) within each study group. The median value is indicated by the black line. Pairwise comparisons were made by mixedeffects ANOVA with the Geisser-Greenhouse correction. *p≤0.05, **p≤0.01, ***p≤0.001, ****p≤0.0001 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted January 28, 2022. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted January 28, 2022. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted January 28, 2022. ; https://doi.org/10.1101/2022.01.26.22269856 doi: medRxiv preprint

Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study

A Novel Coronavirus from Patients with Pneumonia in China

But Not TNF Antagonists, Are Associated With Adverse COVID-19 Outcomes in Patients With Inflammatory Bowel Diseases: Results From an International Registry

Prevalence and clinical outcomes of COVID-19 in patients with autoimmune diseases: a systematic review and meta-analysis

Characteristics associated with hospitalisation for COVID-19 in people with rheumatic disease: data from the COVID-19 Global Rheumatology Alliance physician-reported registry

IBD in the COVID-19 era: the value of international collaboration

Immunogenicity and safety of the BNT162b2 mRNA COVID-19 vaccine in adult patients with autoimmune inflammatory rheumatic diseases and in the general population: a multicentre study

Humoral Immune Response to Messenger RNA COVID-19 Vaccines Among Patients With Inflammatory Bowel Disease

Anti-SARS-CoV-2 mRNA vaccine in patients with rheumatoid arthritis

Examining the Immunological Effects of COVID-19 Vaccination in Patients with Conditions Potentially Leading to Diminished Immune Response Capacity -The OCTAVE Trial

Infliximab is associated with attenuated immunogenicity to BNT162b2 and ChAdOx1 nCoV-19 SARS-CoV-2 vaccines in patients with IBD

Immunogenicity and safety of anti-SARS-CoV-2 mRNA vaccines in patients with chronic inflammatory conditions and immunosuppressive therapy in a monocentric cohort

Humoral protection to SARS-CoV2 declines faster in patients on TNF alpha blocking therapies

Serologic Response to Coronavirus Disease 2019 (COVID-19) Vaccination in Patients With Immune-Mediated Inflammatory Diseases: A Systematic Review and Meta-analysis

Response to SARS-CoV-2 vaccination in immune mediated inflammatory diseases: Systematic review and meta-analysis

Glucocorticoids and B Cell Depleting Agents Substantially Impair Immunogenicity of mRNA Vaccines to SARS-CoV-2. medRxiv

The effect of methotrexate and targeted immunosuppression on humoral and cellular immune responses to the COVID-19 vaccine BNT162b2: a cohort study

T cell response after SARS-CoV-2 vaccination in immunocompromised patients with inflammatory bowel disease

Humoral and T-cell responses to SARS-CoV-2 vaccination in patients receiving immunosuppression

* *** ** **