Understanding adaptive immunity to SARS-CoV-2 is important for vaccine development, interpreting coronavirus disease 2019 (COVID-19) pathogenesis, and calibration of pandemic control measures. Using HLA class I and II predicted peptide ''megapools,'' circulating SARS-CoV-2-specific CD8 + and CD4 + T cells were identified in $70% and 100% of COVID-19 convalescent patients, respectively. CD4 + T cell responses to spike, the main target of most vaccine efforts, were robust and correlated with the magnitude of the anti-SARS-CoV-2 IgG and IgA titers. The M, spike, and N proteins each accounted for 11%-27% of the total CD4 + response, with additional responses commonly targeting nsp3, nsp4, ORF3a, and ORF8, among others. For CD8 + T cells, spike and M were recognized, with at least eight SARS-CoV-2 ORFs targeted. Importantly, we detected SARS-CoV-2-reactive CD4 + T cells in $40%-60% of unexposed individuals, suggesting crossreactive T cell recognition between circulating ''common cold'' coronaviruses and SARS-CoV-2. ll

Understanding immune memory to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for improving diagnostics and vaccines and for assessing the likely future course of the COVID-19 pandemic. We analyzed multiple compartments of circulating immune memory to SARS-CoV-2 in 254 samples from 188 COVID-19 cases, including 43 samples at ≥6 months after infection. Immunoglobulin G (IgG) to the spike protein was relatively stable over 6+ months. Spike-specific memory B cells were more abundant at 6 months than at 1 month after symptom onset. SARS-CoV-2–specific CD4+ T cells and CD8+ T cells declined with a half-life of 3 to 5 months. By studying antibody, memory B cell, CD4+ T cell, and CD8+ T cell memory to SARS-CoV-2 in an integrated manner, we observed that each component of SARS-CoV-2 immune memory exhibited distinct kinetics.

Limited knowledge is available on the relationship between antigen-specific immune responses and COVID-19 disease severity. We completed a combined examination of all three branches of adaptive immunity at the level of SARS-CoV-2-specific CD4 + and CD8 + T cell and neutralizing antibody responses in acute and convalescent subjects. SARS-CoV-2-specific CD4 + and CD8 + T cells were each associated with milder disease. Coordinated SARS-CoV-2-specific adaptive immune responses were associated with milder disease, suggesting roles for both CD4 + and CD8 + T cells in protective immunity in COVID-19. Notably, coordination of SARS-CoV-2 antigen-specific responses was disrupted in individuals > 65 years old. Scarcity of naive T cells was also associated with ageing and poor disease outcomes. A parsimonious explanation is that coordinated CD4 + T cell, CD8 + T cell, and antibody responses are protective, but uncoordinated responses frequently fail to control disease, with a connection between ageing and impaired adaptive immune responses to SARS-CoV-2.

Many unknowns exist about human immune responses to the SARS-CoV-2 virus. SARS-CoV-2 reactive CD4+ T cells have been reported in unexposed individuals, suggesting pre-existing cross-reactive T cell memory in 20-50% of people. However, the source of those T cells has been speculative. Using human blood samples derived before the SARS-CoV-2 virus was discovered in 2019, we mapped 142 T cell epitopes across the SARS-CoV-2 genome to facilitate precise interrogation of the SARS-CoV-2-specific CD4+ T cell repertoire. We demonstrate a range of pre-existing memory CD4+ T cells that are cross-reactive with comparable affinity to SARS-CoV-2 and the common cold coronaviruses HCoV-OC43, HCoV-229E, HCoV-NL63, or HCoV-HKU1. Thus, variegated T cell memory to coronaviruses that cause the common cold may underlie at least some of the extensive heterogeneity observed in COVID-19 disease.

Understanding immune memory to SARS-CoV-2 is critical for improving diagnostics and vaccines, and for assessing the likely future course of the pandemic. We analyzed multiple compartments of circulating immune memory to SARS-CoV-2 in 185 COVID-19 cases, including 41 cases at ≥6 months post-infection. Spike IgG was relatively stable over 6+ months. Spike-specific memory B cells were more abundant at 6 months than at 1 month. SARS-CoV-2-specific CD4+ T cells and CD8+ T cells declined with a half-life of 3-5 months. By studying antibody, memory B cell, CD4+ T cell, and CD8+ T cell memory to SARS-CoV-2 in an integrated manner, we observed that each component of SARS-CoV-2 immune memory exhibited distinct kinetics.

Highlights d T cell responses recognize at least 30-40 epitopes in each donor d Immunodominance is correlated with HLA binding d Immunodominant regions for CD4 + T cells have minimal overlap with antibody epitopes d CD8 + T cell responses depend on the repertoire of HLA class I alleles

Spike-specific antibody elicited by the 25-μg mRNA-1273 vaccine dose over timeAn open-label, age de-escalation phase 1 trial utilized the mRNA-1273 vaccine with 25-μg immunizations on days 1 and 29 (9,28), with blood samples collected on study day 1, 15, 43, and 209. SARS-CoV-2 spike-binding antibodies, receptorbinding domain (RBD)-binding antibodies, and SARS-CoV-2 pseudovirus (PSV) neutralization titers were determined (Fig. 1). Anti-spike and -RBD IgG were maintained at detectable levels for at least 7 months after the first vaccination, for 100% (33/33) of subjects (Fig. 1, A and B). RBD IgG was induced by one immunization in 94% (33/35) of subjects. This response rate increased to 100% (33/33) after the second immunization and was maintained for at least 6 months after the second vaccination. SARS-CoV-2 PSV neutralizing titers were detected in 29% (10/35) of subjects after one vaccination, 100% after two vaccinations (33/33), and 88% (29/33) maintained detectable neutralizing antibodies for at least 6 months after the second vaccination (Fig. 1C). All three antibody measurements demonstrated similar kinetics (Fig. 1, A to C) and were highly correlated (r = 0.89-0.90, fig. S1). Antispike IgG, anti-RBD IgG, and PSV titers at 7 months (study day 209; 181 days after the second immunization) were 6.8fold, 9.5-fold, and 9.5-fold lower than peak titers, respectively. Similar fold changes were reported for 100-μg mRNA-1273 vaccination, indicating similar memory quality and durability (40).The 25-μg mRNA-1273 vaccine-generated antibodies were comparable to antibodies from SARS-CoV-2-infected subjects collected at a similar time post-exposure (7 months post-symptom onset (PSO), 170-195 days) (Fig. 1D). Thus, significant anti-spike IgG, anti-RBD IgG, and PSV-neutralizing antibodies were induced in response to two 25-μg mRNA-1273 vaccinations. These levels were maintained in 88% to 100% of vaccinees for at least 6 months after the second immunization and were comparable to those observed after infection with SARS-CoV-2.Spike-specific CD4 + T cells elicited by the 25-μg mRNA-1273 vaccine dose over time SARS-CoV-2 spike-specific CD4 + T cell responses were first measured utilizing a flow cytometry activation-induced marker (AIM) assay (Fig. 2A and fig. S2). On day 1, before vaccination, spike-specific CD4 + T cells with a predominantly memory phenotype were detected in 49% of clinical trial subjects (17/35), demonstrating the presence of pre-existing SARS-CoV-2 spike-cross-reactive memory CD4 + T cells, as discussed in the latter part of this report. Spike-specific CD4 + T cell responses were observed after the first vaccination in 97% of subjects (34/35) (Fig. 2A). CMV-specific CD4 + T cells were unchanged, as expected, indicating no bystander influence of the mRNA-1273 vaccination (fig. S3). The SARS-CoV-2 spike-specific CD4 + T cell response rate increased to 100%

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