Differentiation marker-negative CD4+T cells persist after yellow fever virus vaccination and contribute to durable memory

Factors that contribute to durable immunological memory remain incompletely understood. In our longitudinal analyses of CD4+ T cell responses to the yellow fever virus (YFV) vaccine by peptide-MHC tetramers, we unexpectedly found naïve phenotype virus-specific CD4+ T cells that persisted months to years after immunization. These Marker negative T cells (TMN) lacked CD95, CXCR3, CD11a, and CD49d surface protein expression, distinguishing them from previously discovered stem-cell memory T cells. Functionally, they resembled genuine naïve T cells upon in vitro stimulation. Single-cell TCR sequencing detected expanded clonotypes within the TMN subset and identified a shared repertoire with memory and effector T cells. T cells expressing TMN-associated TCRs were rare before vaccination, suggesting their expansion following vaccination. Longitudinal tracking of YFV-specific responses over the subsequent years revealed superior stability of the TMN subset and their association with the longevity of the overall population. The identification of these long-lived, antigen-experienced T cells may inform the design of durable T cell-based vaccines and engineered T cell therapies.

Functional immunological memory underlies the protective efficacy of vaccines against subsequent infections (1, 2). However, why protection from some vaccines last decades while others wane after a few months remains unknown. A crucial aspect of immune memory involves T cells (3). CD8+ T cells produce anti-viral cytokines and eliminate infected cells, while CD4+ T cells provide key signals for B cell maturation and high- affinity antibody production (4). CD4+ T cells are also needed to support the expansion and maintenance of functional CD8+ T cells and can directly contribute to anti-viral effects (4-6). Past studies in mice and humans have identified naïve-like antigen-experienced T cells with superior longevity and plasticity as a source of durable memory (7-9). Broadly categorized as stem cell-like memory T cells (TSCM), these cells phenotypically resemble naïve T cells by positive CCR7 and CD45RA or negative CD45RO expression, yet they display differentiation markers such as CD95, CXCR3, and CD49d (9, 10). In people immunized with the highly efficacious and durable Yellow Fever Virus (YFV) vaccine, class I tetramer analyses identified TSCM as the predominant phenotype of virus-specific CD8+ T cells greater than 8 years after vaccination (10, 11). The durability of CD4+ T cell memory is less understood. Although capable of differentiating into TSCM cells (12- 15), CD4+ T cells are generally less responsive to homeostatic cytokines IL-7 and IL-15 (16-18), which augment TSCM differentiation in cultured CD8+ T cells (19). Here, we examined virus-specific CD4+ T cells after YFV vaccination to delineate key features of durable CD4+ T cell responses. YFV-specific CD4+ T cells were .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint identified and tracked longitudinally by direct ex vivo class II peptide-MHC (pMHC) tetramers staining. YFV- specific CD4+ T cells existed in various memory states, including a TSCM subset. Unexpectedly, some tetramer- labeled T cells remained negative for all measured differentiation markers several months after vaccination. Focused analyses of these marker-negative T cells (TMN) showed that they responded to cognate peptide stimulation in vitro and had likely undergone proliferation in vivo by clonal expansion. Further, their T cell receptor (TCR) sequences overlapped with that of classically defined memory T cells of the same specificity, implicating a shared clonal origin. TMN cells functionally resembled genuine naïve T cells, exhibited superior stability over other memory subsets, and were associated with the long-term persistence of the overall population years after vaccination. Our findings expand the current definition of antigen-experienced T cells to include those that retain an undifferentiated phenotype. These cells opened new avenues for understanding the durability of immune responses and developing strategies to enhance long-lasting immunologic memory.

Detection of naïve-like CD4+ T cells after YFV vaccination We had previously performed a longitudinal study of YFV-specific CD4+ T cells to evaluate the impact of pre- existing repertoire on T cell responses to primary immunization with the YFV vaccine (20). Starting with this dataset, we examined the features of memory T cells that developed at least 7 months after vaccination. This showed that approximately half of the YFV-specific memory pool consisted of central memory T cells (TCM), with about 21% of tetramer+ cells retaining a naïve-like CD45RO-CCR7+ phenotype (Fig. 1A-B). Proportionally, the abundance of CD45RO-CCR7+ subset was highest before vaccination, decreased initially post-vaccination, then reaccumulated several months later (Fig. 1C). By frequency, CD45RO-CCR7+ tetramer+ cells increased steadily after vaccination (Fig. 1D). The frequency of CD45RO-CCR7+ T cell subset did not differ by donor age but was instead associated with the robustness of the response (Fig. S1A-C). CD45RO-CCR7+ YFV-specific T cells were more abundant in populations that reached a higher frequency and positively correlated with the fold-change between the peak and the pre-vaccine baseline (Fig S1B-C). At a later memory time point, the frequencies of CD45RO-CCR7+ YFV-specific T cells were higher within larger populations that were recruited into the memory pool (Fig. 1E-F). These data suggest that CD45RO-CCR7+CD4+ T cells is a feature of an effective T cell response. Post-immune T cells are heterogeneous and include a differentiation marker negative subset We hypothesized that the post-vaccine CD45RO-CCR7+ subset largely consisted of TSCM cells as in CD8+ T cells (10, 11). To test this, we performed tetramer staining on 28 YFV-specific CD4+ populations from 7 individuals, recognizing 16 unique epitopes with antibodies against TSCM-associated markers, CXCR3, CD95, CD11a, and CD49d (Tables S1 and S2). Staining with this broader antibody panel on blood collected 7 to 48 months after vaccination indeed identified CD45RO-CCR7+ tetramer+ T cells that expressed one or more TSCM markers. However, we noted that a portion of CD45RO-CCR7+ CD4+ T cells remained negative for CXCR3, CD95, CD11a, and CD49d expression (Fig. 2A, S2A-B). To gain further insights into the heterogeneity within the CD45RO-CCR7+ subset, we combined 1465 YFV-specific CD4+ T cells from one donor and visualized combinatorial antibody staining on UMAP using the Spectre pipeline (21). This identified regions with low CD45RO and high CCR7 signals, which encompassed a CXCR3+ (cluster 0) and a TSCM marker negative population (cluster 4) (Fig. 2B-D). We defined CD45RO-CCR7+ cells lacking any measured differentiation markers as marker-negative T cells (TMN) and classified those expressing at least one of CXCR3, CD95, CD11a, or CD49d as TSCM cells (Table S3). On average, a quarter of the CD45RO-CCR7+ subset consisted of TMN cells (Fig. 2E). Among TSCM cells, the majority expressed CXCR3 alone or in combination with other differentiation markers (Fig. 2E-F, S2C). Finding antigen-specific T cells that do not express known memory or TSCM markers after a clear prior exposure was unexpected. To test if TMN cells functionally behave like antigen- experienced T cells despite lacking surface markers of differentiation, we treated post-vaccine PBMCs with PMA and ionomycin for 4 to 5 hours. Antigen-specific T cells were captured by tetramers, divided into distinct phenotypic subsets, and analyzed for TNF-a and IFN-g production. This showed that post-immune TMN subset produced significantly less cytokines compared to memory T cells within the same tetramer+ population (Fig. 2G-H). Thus, YFV vaccination induced a diverse post-immune repertoire that included CD4+ TSCM cells and a naïve-like TMN population that lacked phenotypic and functional features of antigen experience. Virus-specific TMN cells respond to antigens We were intrigued by the existence of virus-specific T cells that retained a naïve functional phenotype after vaccination. Past studies have identified non-stimulatory TCR interactions that decoupled T cell activation from .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint ligand binding (22). The impaired ability to respond productively to antigens may be one reason why some tetramer-labeled T cells retained a naïve phenotype. To investigate this possibility, we quantified TMN, TSCM, and TCM cells for differences in their functional avidity by peptide stimulation. YFV-specific T cell clones were generated using samples from two donors obtained 7 to 8 months after YFV vaccination. Among the 48 clones that grew, 40 clones (90%) had the correct specificity by tetramer re-staining and/or response to peptides (Fig. 3A-B, S3A). We did not identify peptide-nonresponsive T cells as all clones that were stained with tetramers responded to peptide stimulation. To determine if TMN cells might be harder to activate due to a lower functional avidity, we divided the clones according to their direct ex vivo phenotype and selected 5 clones each from TCM, TSCM, TMN groups for further analyses. YFV-specific clones were stimulated with decreasing concentrations of the cognate peptide and analyzed for response by cytokine production (Fig. S3B). TMN-derived clones responded similarly to peptides by TNF-a production, with no significant differences in maximal effective peptide concentration (EC50) values between groups (Fig. 3C-D). T cell clones, regardless of their ex vivo phenotypes, also produced similar levels of IFN-g, IL-2, and had comparable TNF-a+IFN-g+IL-2+ co-expression (Fig. 3E). In addition, we evaluated the proliferative capacity of TMN, TSCM, and TCM-derived clones by CellTrace Violet (CTV) dilution and observed no significant differences in the proliferative response to peptide stimulation (Fig. 3F-G, Fig. S3C). Thus, TCR-ligand engagement is likely intact for vaccine-specific T cells that retained a naïve phenotype after vaccination. TMN cells are clonally related to memory and effector T cells While TMN cells respond well to antigens in vitro, it remains possible for them to be less competitive in resource-limiting environments. To investigate this, we reason that we can use TCR sequences to infer stimulation and proliferative response in vivo. Because T cell progenies originating from a T cell express identical TCR sequences, we can further leverage these sequences as molecular barcodes to investigate the clonal relationship between distinct phenotypic subsets. However, capturing sufficient numbers of TMN cells was challenging due to their limited number within the available blood samples. To overcome this problem, we generated new tetramers using affinity-matured DR monomers containing mutations that enhanced CD4 binding to improve the overall capture efficiency (23). When compared to the wild-type (wt) DR, these tetramers stained a larger population of T cells without significantly skewing the phenotypic proportions (Fig. S4A-C). In total, we sorted single cells from 5 tetramer-labeled populations and obtained TCR sequences from 607 YFV-specific CD4+ T cells after amplification and sequencing (Fig. 4A, Table S4). Consistent with clonal expansion after vaccination, over 70% of the sequences were identified in more than one tetramer-labeled T cell. Among expanded sequences, 25 to 52% were abundant and found in at least 10 individual T cells (Fig. 4B). Most T cells displayed a TCM or TEM phenotype based on antibody staining at the time of sorting. TMN phenotype was infrequent, expressed by 3 to 4% of sequenced T cells and confined to the two most extensively sequenced populations recognizing YF45. Consistent with in vivo expansion, TMN cells did not preferentially express unique TCRs, but rather, they were distributed across various clone sizes (Fig. 4C). We focused the subsequent analyses on YF45-specific T cells that included the TMN subset. Early post-vaccine measurements of YF45-specific T cells from HD2 and HD3 showed that both populations had generated robust responses to the YFV vaccine (Fig. 4D) (20). In agreement with an antigen-driven response, TMN cells contained expanded clonotypes and shared overlapping sequences with various memory subsets (Fig. 4E-F, S4E). In separately generated T cell clones from the same individuals, TMN-derived clones expressed TCRs that matched the sequences from ex vivo sorted T cells of diverse clone sizes and phenotypes (Fig. S4F). The presence of shared TCR sequences with memory T cells, together with clonal expansion, suggest that TMN cells had encountered and responded to antigens. Alternatively, there could be numerous naïve T cells in the precursor repertoire, some of which could retain a naïve phenotype if only a subset was recruited into the vaccine response. To investigate this possibility, we examined the pre-vaccination repertoire of YF45-specific T cells in these individuals to determine if TMN-associated TCRs were abundant before vaccination (20). The changes in clonal dynamics were assessed by tetramer staining, sorting, and sequencing the TCRs of YF45- specific T cells from blood collected 14 days after vaccination. In total, we examined TCR sequences from 129 precursor T cells and 238 effector T cells (Fig. 5A, Table S5). Before vaccination, no pre-vaccine TCRs matched TMN-derived TCRs from HD2 and only one sequence was identified in HD3. This shared TCR mapped to a unique sequence and not to the expanded pre-existing clonotypes in this individual. By contrast, 7% (HD2, 5 cells) and 23% (HD3, 38 cells) of TCRs in day 14 blood samples expressed a TMN-associated TCR (Fig. 5B). Matched T cells in the day 14 sample expressed a variety of differentiation phenotypes and included expanded .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint clonotypes (Fig. 5C). Together, these data indicate that TMN precursors were rare in the pre-immune repertoire and underwent expansion in response to antigen stimulation after vaccination. TMN cells contribute to durable memory While memory T cells are essential for generating rapid recall responses, naïve T cells are known for their persistence (24, 25). We hypothesize that this unique naïve-appearing antigen-experienced subset would retain this key property and contribute to durable immune responses. To test this idea, we analyzed additional time points from five donors who had longitudinal PBMCs collections up to 6.7 years after YFV vaccination (Fig. 6A, Fig. S5A). Past modeling of cellular turnover suggests that different phenotypic subpopulations undergo separate and distinct in vivo dynamics (26, 27). To evaluate the stability of individual phenotypic subsets, we subdivided 19 YFV-specific populations according to TMN, TSCM, TCM, TEM, and TEMRA phenotypes based on CD45RO, CCR7, CD95, CXCR3, CD11a, and CD49d expression. Their time-dependent change was quantified as a fitted slope using a mixed-effects exponential decay model. This revealed different rates of decay between cells in distinct differentiation states. CD4+ TEM cells had the largest negative slope, indicating the greatest decrease over time. In contrast, TMN cells exhibited remarkable stability, with no discernible decline observed during the follow-up period. The stability of the TMN subset significantly surpassed that of other phenotypic subsets, including TSCM and TCM cells, which are typically considered to be long-lived (Fig.6B). Next, we examined the decay kinetics of the overall YFV-specific CD4+ T cell responses. Because some data were generated before switching to modified DR, paired analyses by wildtype and modified tetramers on the same blood sample were used to generate an equation for normalizing the frequencies across experiments (Fig. S4D). Among the five donors followed longitudinally, two received one YFV dose as typical for the YFV vaccine, while three had been revaccinated 7 months to a year after the initial dose (Table S6). We grouped the donors based on vaccine dosing to model the frequency of each tetramer+ population over time. This revealed a highly durable CD4+ T cell memory response after a single dose that becomes further stabilized after re-vaccination (Fig. S5B). Consistent with the longevity of YFV vaccine-mediated protection, YFV-specific CD4+ T cells displayed an average half-life (t1/2) of close to 4 years after one YFV immunization (Fig. 6C). We observed more TMN cells in the two-dose group, although the difference was not statistically significant (Fig. S5C). Considering the heterogeneity at the population level, we analyzed the tetramer+ populations by TMN frequency and divided them into top and bottom halves (Fig. 6D). This showed that populations with more TMN cells were more stable compared to populations in the bottom TMN group (Fig. 6E). The TMN frequency within a given virus-specific population also demonstrated a positive correlation with the stability of the overall population (Fig. 6F). By contrast, we did not find significant differences between high and low groups based on TSCM, TCM, TEM, and TEMRA frequencies (Fig. S5D). On the phenotypic level, all tetramer+ populations contained various memory subsets, but the top TMN group was more phenotypically diverse. We divided populations based on the first TMN frequency obtained within the 1-2 years after YFV vaccination and showed that those having more TMN cells exhibited a higher diversity of differentiation states over time as measured by the Shannon diversity index (Fig. 6G-H). Collectively, these data highlight the stability of the TMN subset and uncover their association with durable and diverse T cell memory after YFV vaccination.

We examined CD4+ T cell memory to YFV vaccination to define key features of durable memory by direct ex vivo class II tetramer staining and enrichment. This showed a diverse memory pool comprised of various differentiation states after YFV vaccination. A portion of YFV-specific CD4+ T cells acquired TSCM phenotype after vaccination as in CD8+ T cells. Unexpectedly, we also uncovered antigen-experienced T cells that lacked typical markers of TSCM and other memory cells, including CD95, CD11a, CD49d, and CXCR3. Similar to genuine naïve T cells, TMN cells expressed the lymphoid homing chemokine receptor, CCR7 (28), and functionally resembled naïve T cells after polyclonal stimulation by PMN and ionomycin. Despite their naïve appearance, TMN cells are antigen-experienced. TMN cells engaged with and responded to antigens in vitro. TMN responses to the YFV vaccine in vivo were supported by single-cell TCR sequencing, which revealed clonal expansion and a shared repertoire with memory T cells. Longitudinal clonal tracking further identified an expansion of TMN-associated TCRs during effector response. Thus, our analyses of CD4+ T cell responses to the highly durable and efficacious YFV vaccine revealed that some human CD4+ T cells can appear indistinguishable from genuine naïve T cells despite prior antigen experience and expansion. .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint A T cell is typically referred to as naïve if it has not yet encountered its specific cognate antigen(s). Because a clear antigenic history is often not available, especially in human studies, specific surface markers are commonly used to infer antigen experience (29, 30). However, with the advances in single-cell technologies, there is increasing appreciation for the complexity within the naïve compartment. A recent multi-omic analysis discovered age-related epigenetic and transcriptional changes in naïve CD4+ and CD8+ T cells (31). Naïve T cells were defined by CD45RA, CCR7, and CD27 expression using multiple sequencing modalities. Even when naive T cells were further characterized by the lack of CD49d, CD95, and IFN-g expression, these cells showed distinct chromatin accessibility and transcription factor expression between children and older adults (31). The TCR repertoire also undergoes age-related changes and displays a decrease in repertoire diversity in the elderly (32). Generally, these changes are thought to have occurred by homeostatic mechanisms that maintain the peripheral naïve repertoire (33, 34). While we did not investigate how cytokines impact TMN differentiation, cells uniquely driven by a cytokine-mediated bystander response would not be expected to have a similar TCR repertoire as memory and effector T cells. Partial recruitment of precursor T cells remains formally possible, although TMN precursors were not numerous and past studies in mice suggest a highly efficient recruitment process (35, 36). For CD8+ T cells expressing OT-1 transgenic TCR, even the weakest altered peptide ligands, about 700-fold less potent than the wt sequence, induced effector response and generated memory T cells (36). Regardless of the mechanism of TMN differentiation, our data indicate that some cells considered naïve by phenotypic criteria have actually encountered and responded to foreign antigens. Over a lifetime, these cells may accumulate and add to non-antigen experienced T cells as a part of the naïve repertoire, thereby changing naïve T cell composition over time. Only a few select vaccines are capable of mediating life-long protection. How durable immunological memory is maintained remains a key unresolved question. While Memory T cells are the cornerstone of protective immunity by virtue of their ability to rapidly initiate a functional response to pathogen rechallenge, naïve T cells possess superior self-renewal capacity and differentiation plasticity (3, 24, 37). Considering the phenotypic and functional similarities between TMN and naïve T cells, we asked if TMN cells contribute to the longevity of T cell response after YFV vaccination. Our findings revealed remarkable stability of TMN cells, exhibiting minimal decay for nearly 7 years. Their ability to persist suggests that TMN cells could potentially support the longevity of the overall immune response, extending it beyond the lifespan of individual memory T cells. Consistent with this model, TMN cells are more abundant in durable CD4+ populations that are stable over time. Based on the diverse memory phenotypes in TMN-enriched populations, we further speculate that TMN cells have the potential to differentiate into multiple states, thereby contributing to the phenotypic diversity of T cell memory. In summary, our analyses of durable CD4+ T cell responses uncovered virus-specific CD4+ T cells that retain a naïve functional phenotype after vaccination. TMN cells differ from TSCM and other memory subsets by the lack of differentiation marker expression, yet they are antigen-experienced by TCR lineage analyses. The TMN subset displays superior stability over time and is linked to durable and diverse T cell memory after vaccination. Understanding the generation, maintenance, and protective potential of TMN cells could aid the future development of improved vaccine strategies for a broad range of pathogens.

of Study Our memory and naïve subsets are defined using phenotypic markers, without having examined their transcriptional or epigenetic states. While we have ruled out non-productive TCR engagement as a cause, how naïve phenotype is retained within a responding population remains unknown. Future studies will be needed to determine the differentiation trajectory toward TMN state and if similar signals that drive TSCM differentiation also promote TMN development. As our analyses are focused on CD4+ T cell responses to YFV in healthy individuals, broader studies on CD8+ and CD4+ T cell responses to other pathogens would be needed to understand the prevalence of antigen-experienced TMN cells and how they change with advanced age and disease. Notably, our data supporting TMN in long-lived responses are correlational due to the nature of observational studies. Future investigations will be necessary to establish if TMN cells directly contribute to durable immunologic memory, generate protective responses upon recall, and how they might be targeted to enhance the longevity of protective memory.

.CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Study Design This study uses cryopreserved cells stored in fetal bovine serum (FBS) with 10% DMSO from an ongoing vaccine study at the University of Pennsylvania (20). This study includes 7 healthy adult participants with no prior YFV exposure who received one or two doses of the 17D live-attenuated YFV vaccine (YF-VAX®, Sanofi Pasteur). Five participants were followed longitudinally for 2 to 6.7 years after vaccination. All samples were de-identified and obtained with IRB regulatory approval from the University of Pennsylvania. Subject characteristics are shown in Table S1. Cell lines Hi5 cells (ThermoFisher) were maintained by insect cell culture medium (ESF921, Expression Systems) supplemented with 0.02% gentamicin at 28℃. Protein expression and tetramer production HIS-tagged HLA-DRA/B1*0301, 0401, 0407, and 1501 protein monomers of wild type (wt) sequence or with L112W, S118H, V143M, T157I mutations (23) were produced by Hi5 insect cells and extracted from culture supernatant using Ni-NTA (Qiagen). HLA-DR monomers were biotinylated overnight at 4oC using BirA biotin ligase (Avidity) and purified by size exclusion chromatography using Superdex 200 size exclusion column (AKTA, GE Healthcare). Biotinylation was confirmed by gel-shift assay. Peptide exchange and tetramerization for wildtype and modified affinity-matured DR were performed using standard protocols as previously described (38, 39). In brief, HLA-DR proteins were incubated with thrombin (Millipore) at room temperature for 3 - 4 hours and exchanged with peptides of interest in 50-fold excess at 37oC for 16 hours. Peptide-loaded HLA-DR monomers were incubated with fluorochrome-conjugated streptavidin at 4 - 5: 1 ratio for 2 min at room temperature, followed by a 15 min incubation with an equal volume of biotin-agarose slurry (Millipore). Tetramers were buffered exchanged into PBS, concentrated using Amicon ULTRA 0.5ml 100KDa (Millipore), and kept at 4 oC for no more than 2 weeks prior to use. Ex vivo T cell analyses and cell sorting Phenotypic analyses and frequency quantification: Tetramer staining was performed on at least 10 million PBMCs with 5 ug of tetramers in 100 µl reaction for 1 hour at room temperature as previously described (20, 39, 40). Tetramer-tagged cells were enriched by adding anti-fluorochrome and anti-HIS MicroBeads (MiltenyiBiotec). The mixture was passed through LS columns (MiltenyiBiotec). Column-bound cells were washed and eluted according to manufacturer protocol. For antibody staining, the enriched samples were stained with viability dyes, exclusion markers (anti-CD19 and anti-CD11b, BioLegend), and surface markers (anti-CD3, anti-CD4, anti-CD45RO, anti-CCR7, anti-CD11a, anti-CD95, anti-CD49d, anti-CXCR3) in 50 to 100ul of FACS buffer (PBS plus 2% FCS, 2.5mM EDTA, 0.025% Sodium Azide) for 30 minutes at 4oC. Samples were fixed with 2% paraformaldehyde and acquired by flow cytometry using LSRII (BD). Data analyses were performed by FlowJo (BD). Frequency calculation was obtained by mixing 1/10th of samples with 200,000 fluorescent beads (Spherotech) for normalization. For longitudinal experiments involving both wt and modified DR, paired data from wt and mutant DR, with a minimum of two data points per time point for each specificity, were used to derive the equation for normalization: log2(Freqmodified)=3.72+0.35 * log2(Freqwt) (Fig. S4D). Frequencies generated by wt tetramers that were below the normalized values were adjusted. Mixed effects exponential decay models were used to analyze longitudinal changes in antigen-specific T cell populations and estimate the corresponding slopes. These models were implemented in MonolixSuite 2021R1 (Lixoft) and fitted to data after vaccination. Initial T cell specificity values were lognormally distributed, exponential decay rates were normally distributed, and lognormal multiplicative error was used. The estimation of the population parameters was performed using the Stochastic Approximation Expectation-Maximization (SAEM) algorithm. Half-lives were calculated as ln(2)/k, where the corresponding k values represented the estimated exponential decay rate constants. Estimated decay rates were converted into slopes as -k. For multi-dimensional analyses, a total of 1465 manually gated tetramer+ cells were exported from FlowJo, read into R by flowCore, and combined into one single dataset for subsequent data processing and analyses using the Spectre package in R (21). Staining intensities were converted using Arcsinh transformation with a cofactor of 200. Batch alignment was performed using the CytoNorm (41). Clustering was performed using .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Phenograph with nearest neighbors set to 55 (k = 55) (42). UMAP was used for dimensional reduction and visualization (43). Function response: T cells were rested overnight, followed by 4 - 5 hours of stimulation by phorbol myristate acetate (PMA, 5 ng/ml, Sigma) and ionomycin (500 ng/ml, Sigma) in the presence of monensin (2 uM, Sigma) and Brefeldin A (5 ug/ml, Sigma). Tetramer and surface antibody staining were performed as above. Intracellular staining with antibodies to TNF-a, IFN-g, IL-2, CD3 and CD4 (Biolegend) was performed following BD Cytofix/Cytoperm Fixation/Permeabilization Kit according to manufacturer protocol (BD). Cell sorting: Cell numbers were increased to around 60 million CD3+ or CD4+ T cells, stained in up to 10 ug of each tetramer in a 100 ul reaction. Antibody staining was performed as above without fixation. Individual tetramer-labeled cells were isolated for TCR sequencing or T cell cloning by index sorting using the purity mode on FACS Aria (BD). Generation and stimulation of T cell clones Clone generation: Cells were stained with tetramers and enriched with magnetic beads as described above. Single tetramer-stained CD4+ T cells were sorted into individual wells in a round bottom 96-well plate containing 105 irradiated PBMCs, 104 JY cell line (ThermoFisher), PHA (1:100, ThermoFisher), IL-7 (25 ng/ml, PeproTech), and IL-15 (25 ng/ml, PeproTech). IL-2 (50 IU/ml, PeproTech) was added on day 5 and replenished every 3-5 days. Cells were resupplied with fresh medium with IL-2 (50 IU/ml), PHA (1:100), and 105 irradiated PBMCs every two weeks. DCs generation: Monocytes from HLA-DR allele-matched donors were isolated using negative enrichment kits (RosetteSep Human Monocyte Enrichment Cocktail, StemCell). 10 million cryopreserved monocytes were cultured in 15 ml DC media (RPMI 1640 plus Glutamine,10% FCS, 1X Pen/Strep, 10 mM HEPES) in the presence of 100 ng/ml GM-CSF and 500 U/ml IL-4. Three days later, half the culture media was replaced with fresh DC media with 100 ng/ml GM-CSF, 500 U/ml IL-4, and 0.05 mM 2-mercaptoethanol. Cells in suspension were harvested at 5 to 6 days and added to a flat-bottom 96-well plate at 25,000 DCs per well. DCs were treated with 100 ng LPS and peptides (0.00001 ug/ml to 10ug/ml) for 16 hours and replenished with fresh media before co-culturing with T cells. Stimulation of T cell clones: T cell clones were rested overnight in fresh media without IL-2 and added to wells containing matured DCs at 1:1 ratio in the presence of monensin (2 uM, Sigma) and Brefeldin A (5 ug/ml, Sigma). After 5 hours, cells were transferred into a new 96-well round bottom plate, washed once with FACS buffer, and stained with viability dyes, exclusion markers (anti-CD19 and anti-CD11b, BioLegend) for 30 minutes at 4°C. Intracellular staining with antibodies to TNF-a, IFN-g, IL-2, CD3 and CD4 (Biolegend) was performed following BD Cytofix/Cytoperm Fixation/Permeabilization Kit according to manufacturer protocol (BD). Half maximal effective concentration (EC50) was determined using the percentage of T cell clones that produced TNF-a in response to decreasing peptide concentrations (10, 1, 0.1, 0.01, 0.001, 0.0001, and 0.00001 ug/ml). A non-linear fit without constraint was applied to log-transformed concentration using the equation Y=Bottom + (Top-Bottom)/(1+10^((LogEC50-X)*HillSlope)) in Prism (GraphPad). For proliferation assay, T cell clones were labeled with 1:1000 diluted CellTrace Violet (CTV, ThermoFisher Scientific) following manufacturer protocol. The CTV-stained cells were rested in fresh media without IL-2 for 16 hours. 25,000 rested T cells were co-cultured with DC pulsed with 10 ug/ml cognate peptides or treated with PHA as a positive control (1:100, ThermoFisher). After 5 days, cells were harvested and stained with viability dyes and surface antibodies (anti-CD19, anti-CD11b, anti-CD3, and anti-CD4, BioLegend) for 30 minutes at 4°C followed by fixation with 2% paraformaldehyde. Samples were acquired by flow cytometry using LSRII (BD) and analyzed by FlowJo (BD). Single-cell TCR sequencing and analyses Single-cell TCR Sequencing by nested PCRs was performed using the primer sets and the protocol as previously described (20, 44). In brief, reverse transcription was performed with CellsDirect One-Step qRT- PCR kit according to the manufacturer’s instructions (CellsDirect, Invitrogen) using a pool of 5’ TRVB-region specific primers and 3’ C-region primers. The cDNA library was amplified using a second set of multiple internally nested V-region and C-region primers with HotStarTaq DNA polymerase kit (Qiagen). The final PCR reaction was performed on an aliquot of the second reaction using a primer containing common base .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint sequence and a third internally nested Cb primer. PCR products were gel purified (Qiagen) and sequenced on Novaseq 6000 platform (Illumina). TCR sequences were pre-processed as previously described (20). In brief, forward and reverse reads were converted into one paired end read using pandaseq (45). Data were demultiplexed by the unique combination of plate, row, and column barcodes. Consensus TCRβ sequences were identified using the V(D)J alignment software MiXCR (46). A threshold of a read count of 200 reads per sequence was applied to the consensus sequences. If more than one TCRa or TCRb chain passes this criterion we retain the dominant TCRb and the two TCRa chains with the highest read count. For data obtained from cells several months after vaccination, we additionally require phenotypic annotation based on antibody staining from index sort data. Data were excluded if phenotypic information was not retained or ambiguous. For downstream analyses, data wrangling was performed using the tidyverse package. TCRs were matched by TCRb if only the beta chain was available, or by TCRb plus at least one TCRa if alpha chain(s) were called. Circos plots were made using the circlize package of R software (47). Statistical Methods Normality was assessed using D’Agostino-Pearson test. Spearman was used if either of the two variables being correlated was non-normal. Otherwise, Pearson was used to measure the degree of association. Least squares linear regression was used to calculate the best-fitting line. Statistical comparisons were performed using two-tailed Student’s t-test, paired t-test, Welch’s one-way ANOVA, repeated measures one-way ANOVA, two-way ANOVA, or mixed effects model. A p-values of <0.05 was used as the significance level and adjusted if multiple comparisons were performed. Statistical analyses were performed using GraphPad Prism. Lines and bars represent the mean and variability is represented by the standard error of the mean (SEM). * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001. Supplementary Materials Figure S1: CD45RO-CCR7+ YFV-specific CD4+ T cells by age and their relationship to the effector response. Figure S2: YFV tetramer+ CD45RO-CCR7+ T cells contain various phenotypic subsets Figure S3: Tetramer staining and peptide responses of YFV-specific T cell clones. Figure S4: T MN cells are antigen-experienced. Figure S5: Longitudinal dynamics of YFV-specific populations. Table S1: Donor characteristics. Table S2: List of YFV peptides. Table S3: phenotypic markers. Table S4: YFV-specific CD4+ T cells 7months or longer after vaccination. Table S5: YF45 tetramer+ T cells before and 14 days after YFV vaccination. Table S6: Longitudinal follow-up visits.

1. A. F. Kathryn, M. S. Jason, C. J. Stephen, V. Vaiva, M. David, Preexisting high frequencies of memory CD8+ T cells favor rapid memory differentiation and preservation of proliferative potential upon boosting. Immunity 39, 171-183 (2013). 2. J. R. Martin, C. N. Jeffrey, T. H. John, Pathogen-Specific Inflammatory Milieux Tune the Antigen Sensitivity of CD8(+) T Cells by Enhancing T Cell Receptor Signaling. Immunity, (2012). 3. E. J. Wherry, D. H. Barouch, T cell immunity to COVID-19 vaccines. Science 377, 821-822 (2022). 4. S. Crotty, T follicular helper cell differentiation, function, and roles in disease. Immunity 41, 529-542 (2014). 5. B. J. Laidlaw, J. E. Craft, S. M. Kaech, The multifaceted role of CD4(+) T cells in CD8(+) T cell memory. Nat Rev Immunol 16, 102-111 (2016). 6. S. L. Swain, K. K. McKinstry, T. M. Strutt, Expanding roles for CD4(+) T cells in immunity to viruses. Nat Rev Immunol 12, 136-148 (2012). 7. L. Gattinoni et al., A human memory T cell subset with stem cell-like properties. Nat Med 17, 1290-1297 (2011). 8. Y. Zhang, G. Joe, E. Hexner, J. Zhu, S. G. Emerson, Host-reactive CD8+ memory stem cells in graft- versus-host disease. Nat Med 11, 1299-1305 (2005). .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint 9. V. Pulko et al., Human memory T cells with a naive phenotype accumulate with aging and respond to persistent viruses. Nat Immunol 17, 966-975 (2016). 10. S. A. Fuertes Marraco et al., Long-lasting stem cell-like memory CD8+ T cells with a naive-like profile upon yellow fever vaccination. Science translational medicine 7, 282ra248 (2015). 11. R. S. Akondy et al., Origin and differentiation of human memory CD8 T cells after vaccination. Nature 552, 362-367 (2017). 12. H. M. Long et al., MHC II tetramers visualize human CD4+ T cell responses to Epstein-Barr virus infection and demonstrate atypical kinetics of the nuclear antigen EBNA1 response. J Exp Med 210, 933-949 (2013). 13. M. J. Buzon et al., HIV-1 persistence in CD4+ T cells with stem cell-like properties. Nat Med 20, 139- 142 (2014). 14. C. A. M. Mpande et al., Functional, Antigen-Specific Stem Cell Memory (T(SCM)) CD4(+) T Cells Are Induced by Human Mycobacterium tuberculosis Infection. Frontiers in immunology 9, 324 (2018). 15. M. Pawel et al., Th17 cells are long lived and retain a stem cell-like molecular signature. Immunity 35, 972-985 (2011). 16. J. T. Tan et al., Interleukin (IL)-15 and IL-7 jointly regulate homeostatic proliferation of memory phenotype CD8+ cells but are not required for memory phenotype CD4+ cells. J Exp Med 195, 1523- 1532 (2002). 17. J. H. Cho, H. O. Kim, C. D. Surh, J. Sprent, T cell receptor-dependent regulation of lipid rafts controls naive CD8+ T cell homeostasis. Immunity 32, 214-226 (2010). 18. M. Guimond et al., Interleukin 7 signaling in dendritic cells regulates the homeostatic proliferation and niche size of CD4+ T cells. Nat Immunol 10, 149-157 (2009). 19. N. Cieri et al., IL-7 and IL-15 instruct the generation of human memory stem T cells from naive precursors. Blood 121, 573-584 (2013). 20. Y. G. Pan et al., Vaccination reshapes the virus-specific T cell repertoire in unexposed adults. Immunity, (2021). 21. T. M. Ashhurst et al., Integration, exploration, and analysis of high-dimensional single-cell cytometry data using Spectre. Cytometry A 101, 237-253 (2022). 22. L. V. Sibener et al., Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding. Cell 174, 672-687 e627 (2018). 23. K. Sugata et al., Affinity-matured HLA class II dimers for robust staining of antigen-specific CD4(+) T cells. Nat Biotechnol 39, 958-967 (2021). 24. L. Gattinoni, D. E. Speiser, M. Lichterfeld, C. Bonini, T memory stem cells in health and disease. Nat Med 23, 18-27 (2017). 25. T. van den Broek, J. A. M. Borghans, F. van Wijk, The full spectrum of human naive T cells. Nat Rev Immunol 18, 363-373 (2018). 26. B. Asquith, C. Debacq, D. C. Macallan, L. Willems, C. R. Bangham, Lymphocyte kinetics: the interpretation of labelling data. Trends Immunol 23, 596-601 (2002). 27. G. Gossel, T. Hogan, D. Cownden, B. Seddon, A. J. Yates, Memory CD4 T cell subsets are kinetically heterogeneous and replenished from naive T cells at high levels. eLife 6, (2017). 28. R. Forster et al., CCR7 coordinates the primary immune response by establishing functional microenvironments in secondary lymphoid organs. Cell 99, 23-33 (1999). 29. Y. D. Mahnke, T. M. Brodie, F. Sallusto, M. Roederer, E. Lugli, The who's who of T-cell differentiation: human memory T-cell subsets. Eur J Immunol 43, 2797-2809 (2013). 30. N. Caccamo, S. A. Joosten, T. H. M. Ottenhoff, F. Dieli, Atypical Human Effector/Memory CD4(+) T Cells With a Naive-Like Phenotype. Frontiers in immunology 9, 2832 (2018). 31. Z. Thomson et al., Trimodal single-cell profiling reveals a novel pediatric CD8alphaalpha(+) T cell subset and broad age-related molecular reprogramming across the T cell compartment. Nat Immunol 24, 1947-1959 (2023). 32. Q. Qi et al., Diversity and clonal selection in the human T-cell repertoire. Proc Natl Acad Sci U S A 111, 13139-13144 (2014). 33. I. den Braber et al., Maintenance of peripheral naive T cells is sustained by thymus output in mice but not humans. Immunity 36, 288-297 (2012). 34. J. J. Goronzy, F. Fang, M. M. Cavanagh, Q. Qi, C. M. Weyand, Naive T cell maintenance and function in human aging. J Immunol 194, 4073-4080 (2015). .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint 35. J. W. van Heijst et al., Recruitment of antigen-specific CD8+ T cells in response to infection is markedly efficient. Science 325, 1265-1269 (2009). 36. D. Zehn, S. Y. Lee, M. J. Bevan, Complete but curtailed T-cell response to very low-affinity antigen. Nature 458, 211-214 (2009). 37. M. Kunzli, D. Masopust, CD4(+) T cell memory. Nat Immunol 24, 903-914 (2023). 38. C. L. Day et al., Ex vivo analysis of human memory CD4 T cells specific for hepatitis C virus using MHC class II tetramers. J Clin Invest 112, 831-842 (2003). 39. L. F. Su, B. A. Kidd, A. Han, J. J. Kotzin, M. M. Davis, Virus-Specific CD4(+) Memory-Phenotype T Cells Are Abundant in Unexposed Adults. Immunity 38, 373-383 (2013). 40. L. Bartolo et al., SARS-CoV-2-specific T cells in unexposed adults display broad trafficking potential and cross-react with commensal antigens. Sci Immunol, eabn3127 (2022). 41. S. Van Gassen, B. Gaudilliere, M. S. Angst, Y. Saeys, N. Aghaeepour, CytoNorm: A Normalization Algorithm for Cytometry Data. Cytometry A 97, 268-278 (2020). 42. J. H. Levine et al., Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell 162, 184-197 (2015). 43. E. Becht et al., Dimensionality reduction for visualizing single-cell data using UMAP. Nat Biotechnol, (2018). 44. A. Han, J. Glanville, L. Hansmann, M. M. Davis, Linking T-cell receptor sequence to functional phenotype at the single-cell level. Nat Biotechnol 32, 684-692 (2014). 45. A. P. Masella, A. K. Bartram, J. M. Truszkowski, D. G. Brown, J. D. Neufeld, PANDAseq: paired-end assembler for illumina sequences. BMC bioinformatics 13, 31 (2012). 46. D. A. Bolotin et al., MiXCR: software for comprehensive adaptive immunity profiling. Nat Methods 12, 380-381 (2015). 47. Z. Gu, L. Gu, R. Eils, M. Schlesner, B. Brors, circlize Implements and enhances circular visualization in R. Bioinformatics 30, 2811-2812 (2014). Acknowledgments: We thank our study subjects for their participation. Funding: NIH R01AI134879 (L.F.S), NIH R01AI66358 (L.F.S), VA Merit Award I01CX001460(L.F.S), VA COVID Award I01BX005422 (L.F.S). Author contributions: Conceptualization, L.F.S.; Experimentation, Y.P.; Sequence analyses, L.B.; High- dimensional phenotypic analyses, R. X.; Study recruitment, B.P; Modeling and statistical support, V.Z.; Supervision, L.F.S.; Manuscript preparation, L.F.S., L.B., Y.P, and V. Z. Competing interests: The authors declare no competing interests. Data and material availability: All data needed to evaluate the conclusions in the paper are present in the paper or the supplementary materials. .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Main Figures Figure 1: Identification of a CD45RO-CCR7+ subset of virus-specific CD4+ T cells after YFV vaccination. (A) Direct ex vivo tetramer and antibody staining of a representative YFV tetramer+ population using blood collected about 7 months after YFV vaccination. (B) The percentage of YFV tetramer+ T cells with the indicated combination of CD45RO and CCR7 expression. Plot summarizes data from 36 specificities 7 to 34 months after YFV vaccination from 7 donors. (C-D) The abundance of CD45RO-CCR7+ YFV tetramer+ CD4+ T cells in 7 healthy subjects was quantified as a percentage of tetramer+ cells (C) or by frequency (D). Each symbol represents data from a distinct YFV-specific population. Experiments were repeated an average of 3.3 times. (E-F) Correlation between the frequency of CD45RO-CCR7+ subset with the corresponding overall frequency (E) and the fold change between memory frequency and the pre-vaccine baseline (F) (n = 36). RM one-way ANOVA (B) or Mixed-effect analysis (C and D) was performed and corrected with Tukey’s multiple comparisons test. For E and F, Pearson correlation was computed. .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Figure 2: Post-vaccine CD4+ T cells are heterogeneous and include naïve-like subsets. (A) FACS plots show the expression of the indicated marker on a representative YFV-specific population. The tetramer+ population is overlaid onto tetramer- bulk CD4+ T cells. (B) UMAP displays Phenograph-defined clusters. Data combine 1465 CD4+ cells labeled by 7 YFV tetramers from HD3. (C-D) The staining intensity of individual markers is shown on a heatmap for each cluster (C) or displayed on the UMAP. (E-F) The relative abundance of CD45RO-CCR7+ YFV-specific T cells by the indicated numbers of markers (E) or the type of markers (F). Frequency in F combines all cells positive for a particular marker within the CD45RO-CCR7+ subset. Each symbol represents a tetramer+ population (n = 28). Experiments were repeated an average of 2.5 times. (G) PBMCs were stimulated for 4 - 5 hours by PMA and ionomycin and assayed for cytokine production by intracellular cytokine staining. The plot shows representative TNF-a and IFN-g expression by TMN cells and non-CD45RO-CD28+ (memory) T cells from the same tetramer-labeled population. (H) T cell responses by TNF-a and IFN-g production for the indicated phenotypic subset. Each population was identified with a pool of 5-7 tetramers of the same DR allele, using cells from 3 donors. For E and F, RM one-way ANOVA was performed and corrected with Tukey’s multiple comparison test. For H, the Friedman test was performed and corrected using Dunn’s multiple comparison test. .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Figure 3: TMN-derived T cell clones respond to antigen stimulation. (A) Schematics of single-cell T cell cloning. Post-vaccine T cells from HD2 and HD3 were stained with 1501-YF45 tetramers, sorted based on TMN, TSCM, or TCM phenotypes, and expanded for 2 to 3 weeks in culture. (B) In vitro expanded T cell clones were restained with tetramers and cultured with vehicle or peptide-treated monocyte-derived dendritic cells. Representative plots show tetramer staining and cytokine production by intracellular cytokine staining. (C-D) T cell clones were stimulated with decreasing concentrations of YFV peptide. The response was measured by TNF-a production (C) and quantified by EC50 values after subtracting the background signal from vehicle- treated control (D). (E) Peptide dose response of T cell clones by IFN-g, IL-2, and IL2+TNF-a+IFN- g + production. (F) Representative histograms show CTV dilution in response to 10ug/ml of peptide stimulation. (G) Plot summarizes the frequency of CTVlow population after a 5-day culture for clones in each phenotypic group. All experiments were repeated at least twice with n= 5 in each group. For (C) and (E), RM two-way ANOVA was performed and corrected with Tukey’s multiple comparison test. For (D) and (G), Kruskal-Wallis test and Dunn’s multiple comparison test were used. .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Figure 4: TMN cells are clonally related to memory T cells. (A) The plot summarizes the number of cells sequenced from indicated specificity and donor collected 242 (HD2) and 210 (HD3) days after primary YFV vaccination. (B) Clone size and phenotypic distribution of YFV tetramer+ populations in A. Phenotypic information were obtained by index sorting. TMN (CD45RO-CCR7+CXCR3-CD95-CD11a-CD49d-), TSCM (CD45RO-CCR7+ and positive for at least one of CXCR3, CD95, CD11a, or CD49d), TCM (CD45RO+CCR7+), TEM (CD45RO+CCR7-), TEMRA (CD45RO-CCR7-). Cells with ambiguous phenotypes were excluded. (C) Distribution of phenotypes in B by clonotype frequency, ranked from largest to unique clonotypes. (D) Pre- vaccine frequency and early post-vaccine dynamics of YF45-specific T cells preceding the memory time point. (E) Each circus plot represents TCRs from YF45 tetramer+ cells obtained 242 (HD2) or 210 (HD3) days after vaccination, separated by the associated indexed phenotypes. Cells are ordered by frequency within each arc. Gray marks cells expressing unique TCRs, other colors represent expanded or shared sequences. Shared TCRb or TCRa/b, when a TCRa is available, is connected by a line across distinct phenotypic subsets. Blue lines highlight TCRs from TMN cells that are shared with cells expressing other phenotypes. (F) The percentage of TCRs in each memory subset that matched TMN-derived sequences. .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Figure 5: TMN cells are clonally related to effector T cells. (A) The number of TCRs from YF45 tetramer+ T cells from the indicated donors, before vaccination and 14 days after YFV vaccination. (B) Lines link TMN- derived TCRs in the day 210-242 post-vaccine samples with matched TCRs expressed by T cells in a previous time point from each donor. Shared TCRs are matched by TCRb or TCRa/b when a TCRa is available. (C) The CDR3 sequences and the phenotypes of T cells in the d14 sample that matched a TMN-derived clonotype in the memory time point. .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Figure 6: TMN cells are stable and associated with durable T cell memory. (A) Representative plots show YFV-specific CD4+ T cells over the indicated time points from HD2. (B) Each tetramer+ population of a given specificity was subdivided according to phenotypes. The change over time for each phenotypic subset was quantified by the estimated slope using a mixed effects exponential decay model (n = 19 tetramer+ populations from 5 donors). (C) A mixed effects exponential decay model fitted to the dynamics of YFV-specific CD4+ T cells after a single YFV vaccination (n = 8 populations, combined from donors 4 and 5). The estimated decay (blue line) was used for calculating the half-life (t1/2). (D) Ranking of tetramer+ populations by the averaged frequency of TMN T cells within each population across all time points. (E) Plot summarizes the estimated slopes of individual tetramer+ populations, divided into top and bottom halves by TMN frequency in D. (F) The correlation between slopes characterizing the change over time for the overall tetramer+ populations and their corresponding averaged TMN frequencies. (G) Pie-charts show the distribution of memory subsets. Populations were divided into top and bottom groups by the first measured TMN frequency obtained within 1-2 years after YFV vaccination. (H) Phenotypic diversity of each tetramer+ population was quantified using Shannon Diversity Index, categorized into top or bottom groups based on TMN frequency as in G. Each symbol represents one tetramer+ population. Experiments were repeated an average of 2.3 times. Data are represented as mean ± SEM. For (B), RM one-way ANOVA was performed and corrected with Tukey’s multiple comparisons test. Welch’s t-test was performed for (E) and (H). For (F), Spearman correlation was performed. .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Supplementary Material Figure S1: CD45RO-CCR7+ YFV-specific CD4+ T cells by age and their relationship to the effector response. (A) The frequency of post-immune CD45RO-CCR7+ YFV tetramer+ CD4+ T cells in relationship to donor age. Distinct tetramer+ populations from the same donor are combined and represented as an average (n = 7). (B) The correlation between the frequency of CD45RO-CCR7+ YFV tetramer+ cells measured at least 7 months after vaccination and the highest total tetramer+ frequency from a previous time point measured within the first month after vaccination (n = 36). (C) The correlation between CD45RO-CCR7+ YFV tetramer+ T cell frequency at least 7 months after vaccination and the fold-change between peak frequency and the pre- vaccine baseline. Pearson correlation was computed. .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Figure S2: YFV tetramer+ CD45RO-CCR7+ T cells contain various phenotypic subsets. (A) Representative plots show the gating strategy used to identify tetramer+ cells. (B) FACS plots show the phenotype of YF45- specific T cells by the indicated antibody staining. (C) Boolean gates for CD11a, CD49d, CD95, and CXCR3 were applied onto manually gated CD45RO-CCR7+ YFV tetramer+ T cells. The plot shows various phenotypic combinations. Each symbol represents a tetramer+ population (n = 28). One-way ANOVA was performed and corrected with Tukey’s multiple comparison test. .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Figure S3: Tetramer staining and peptide responses of YFV-specific T cell clones. (A) Representative tetramer staining of TMN, TSCM, and TCM-derived YFV-specific T clones. (B) Plots show cytokine response by a TMN clone to decreasing concentrations of the cognate YF45 peptide after a 5-hour co-culture with peptide- loaded DCs. (C) Representative plots show CTV staining of a CTV-labeled T cell clone after a 5-day culture with vehicle-treated or peptide-loaded DCs. .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Figure S4: T MN cells are antigen-experienced. (A) Representative plots show the identification of YFV- specific T cells using tetramers generated from wt or modified DR (L112W, S118H, V143M, T157I). (B) CD45RO and CCR7 expression of YF57-specific T cells stained by wt or modified DR. (C) Quantification of TMN fraction within tetramer+ populations identified by wt or modified tetramers using the same sample. (D) The plot displays paired data from wt and modified DR, with a minimum of two data points per time point for each specificity, which were used to derive the equation for normalization (top). (E) Pie-charts show the distribution of unique versus expanded clonotypes within TMN subset of YF45-specific T cells obtained 210-242 days after YFV vaccination. The sequences of the expanded clonotype from each donor are as indicated. (F) TMN-derived T cell clones were re-stained with tetramers and sorted for TCR sequencing. Clone-derived TCRs were compared with sequences from directly sorted T cells. The graph shows clones with matched TCRs and indicates the number of matched cells and their associated ex vivo phenotypes. For (C), Wilcoxon matched- pairs signed rank test was performed. .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Figure S5: Longitudinal dynamics of YFV-specific populations. (A) The frequency of tetramer+ populations by donor. Filled circles represent individual tetramer+ populations. A line connects T cells labeled by the same tetramer across time points. Mixed effects exponential decay models were fitted to the longitudinal frequencies of individual tetramer-labeled populations for each donor. Blue lines represent the estimated decay. (B) Longitudinal dynamics of tetramer+ populations were combined for donors who received one YFV dose (donors 4 and 5) and two doses (donors 1, 2, 3). A mixed-effects exponential decay model was employed to estimate the corresponding population slopes for the two groups. (C) The plot summarizes TMN frequency in donors who received one (donors 4, 5) or two doses (donors 1, 2, 3) of the YFV vaccine. (D) Plots summarize the estimated slopes of individual tetramer+ populations, divided into top and bottom halves by the averaged frequency of cells expressing the indicated phenotypes. (B) Wald test was used. (C) Mann-Whitney test was used. (D) Welch’s t-test was used. .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Table S1: Donor characteristics ID Sex Age at the time of YFV vaccination Vaccine dates Sample collection dates HD1 M 37 8/25/16 8/28/17 HD2 F 32 9/12/16 5/12/17 HD3 M 64 1/4/17 8/2/17 HD4 M 25 5/22/17 4/23/18 HD5 F 50 4/21/17 2/7/19 HD6 M 53 3/6/17 10/24/19 HD7 M 27 3/6/17 2/23/21 Table S2: List of YFV peptides Peptide YFV Protein Sequence YF108 NS5 VIKILTYPWDRIEEVTR YF23 NS3 ESATILMTATPPGTS YF25 NS3 KGPLRISASSAAQRR YF38 RNA Polymerase EEFIAKVRSHAAIGA YF42 RNA Polymerase ACLSKAYANMWSLMY YF44 NS5 IHLVIHRIRTLIGQE YF45 NS3 GEVIGLYGNGILVGD YF50 Protein E TIRVLALGNQEGSLKTA YF51 Protein E TDKMFFVKNPTDTGHGT YF53 NS3 GLYGNGILVGDNSFVSA YF54 NS3 LPSIRAANVMAASLRKA YF57 NS5 TLGEVWKRELNLLDKRQ YF69 NS3 WILADKRPTAWFLPSIR YF80 Protein E TGHGTVVMQVKVSKGAP YF91 NS5 PPAGTRKIMKVVNRWLF YF93 Protein E MGAVLIWVGINTRNMTM Table S3: phenotypic markers Phenotype CD45RO and CCR7 staining CD95, CXCR3, CD49d, CD11a staining Naive CD45RO-CCR7+ not available TCM CD45RO+CCR7+ TEM CD45RO+CCR7- TEMRA CD45RO-CCR7- TSCM CD45RO-CCR7+ positive for one of the following: CD95, CXCR3, CD49d, CD11a TMN CD45RO-CCR7+ negative for all of the following: CD95, CXCR3, CD49d, CD11a .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Table S4: YFV-specific CD4+ T cells 7months or longer after vaccination Donor specificity Phenotype TCRb TCRa-TCRb clone size HD3 1501-YF91 TCM CASASVAGGTYEQYF CALSEGDQGGKLIF-CASASVAGGTYEQYF 6 HD3 1501-YF91 TCM CASASVAGGTYEQYF CALSEGDQGGKLIF-CASASVAGGTYEQYF 6 HD3 1501-YF91 TCM CASASVAGGTYEQYF CALSEGDQGGKLIF-CASASVAGGTYEQYF 6 HD3 1501-YF91 TCM CASASVAGGTYEQYF CALSEGDQGGKLIF-CASASVAGGTYEQYF 6 HD2 0407-YF80 TCM CASEGGGSGANVLTF CASEGGGSGANVLTF 3 HD2 0407-YF80 TCM CASGTGSSGANVLTF CASGTGSSGANVLTF 9 HD2 0407-YF80 TCM CASGTGSSGANVLTF CASGTGSSGANVLTF 9 HD2 0407-YF80 TCM CASGTGSSGANVLTF CASGTGSSGANVLTF 9 HD2 1501-YF45 TCM CASHEGWTVGNTIYF CIVRENSGNTGKLIF-CASHEGWTVGNTIYF 1 HD2 0407-YF80 TCM CASIEGGEGDTQYF CASIEGGEGDTQYF 1 HD2 0407-YF80 TCM CASIGGGEGNEQFF CASIGGGEGNEQFF 5 HD2 0407-YF80 TCM CASIGGGEGNEQFF CASIGGGEGNEQFF 5 HD2 0407-YF80 TCM CASIGGGEGNEQFF CASIGGGEGNEQFF 5 HD2 0407-YF80 TCM CASIGGGEGNEQFF CASIGGGEGNEQFF 5 HD2 1501-YF45 TCM CASIKIGVLGYGYTF CVVSFLW_GYNKLIF-CASIKIGVLGYGYTF 12 HD2 1501-YF45 TCM CASIKIGVLGYGYTF CVVSFLW_GYNKLIF-CASIKIGVLGYGYTF 12 HD3 1501-YF91 TCM CASKHRPDSYEQYF CASKHRPDSYEQYF 2 HD2 0407-YF80 TCM CASLTSGEGATEAFF CASLTSGEGATEAFF 1 HD2 0407-YF80 TCM CASPKSSGSTDTQYF CVVSSRHTDKLIF-CASPKSSGSTDTQYF 14 HD2 0407-YF80 TCM CASPKSSGSTDTQYF CASPKSSGSTDTQYF 14 HD2 0407-YF80 TCM CASPKSSGSTDTQYF CASPKSSGSTDTQYF 14 HD2 1501-YF45 TCM CASQTGASVTYEQYF CIVRVAAGNTGKLIF-CASQTGASVTYEQYF 9 HD2 1501-YF45 TCM CASQTGASVTYEQYF CIVRVAAGNTGKLIF-CASQTGASVTYEQYF 9 HD2 1501-YF45 TCM CASQTGASVTYEQYF CIVRVAAGNTGKLIF-CASQTGASVTYEQYF 9 HD3 1501-YF45 TCM CASRDLYGYTF CIVRVAAEAAGNKLTF-CASRDLYGYTF 3 HD3 1501-YF45 TCM CASRDLYGYTF CIVRVAAEAAGNKLTF-CASRDLYGYTF 3 HD2 0407-YF80 TCM CASRVTDNEQFF CVVSSRHTDKLIF-CASRVTDNEQFF 1 HD2 0407-YF80 TCM CASRWDGNSPLHF CASRWDGNSPLHF 6 HD2 0407-YF80 TCM CASRWDGNSPLHF CASRWDGNSPLHF 6 HD2 0407-YF80 TCM CASRWDGNSPLHF CALITQGGSEKLVF- CASRWDGNSPLHF;CVVSSRHTDKLIF - CASRWDGNSPLHF 6 HD2 0407-YF80 TCM CASRWDGNSPLHF CASRWDGNSPLHF 6 HD3 1501-YF91 TCM CASSEDSWRGGSTDTQYF CVVSEVQGYGGSQGNLIF- CASSEDSWRGGSTDTQYF 1 HD2 1501-YF45 TCM CASSEGHIPMNTEAFF CIVRVAAGQSGYALNF-CASSEGHIPMNTEAFF 5 HD3 1501-YF45 TCM CASSFGTVVDTEAFF CIVRVAADYKLSF-CASSFGTVVDTEAFF 1 HD3 1501-YF45 TCM CASSFPRGQNINQPQHF CIVRVGAQGAQKLVF-CASSFPRGQNINQPQHF 1 HD3 1501-YF91 TCM CASSFQTGGIVTDTQYF CIVRVRGGNNDMRF-CASSFQTGGIVTDTQYF 1 HD2 1501-YF45 TCM CASSGKMTSFSYEQYF CIVRVTNQAGTALIF-CASSGKMTSFSYEQYF 1 HD3 1501-YF91 TCM CASSGSIELSGYTF CAVPRVEWYGGATNKLIF-CASSGSIELSGYTF 1 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD2 1501-YF45 TCM CASSKTSGLQSYNEQFF CILRPNYGGSQGNLIF- CASSKTSGLQSYNEQFF;CILRPNYGGSQGNLIF - CASSKTSGLQSYNEQFF 2 HD2 1501-YF45 TCM CASSLAGVGPGGYEQFF CARMSGGFKTIF-CASSLAGVGPGGYEQFF 2 HD2 1501-YF45 TCM CASSLAVTVRSSNYGYTF CIVRVQTGANNLFF-CASSLAVTVRSSNYGYTF 3 HD3 1501-YF45 TCM CASSLEAGLSTDTQYF CVVIPNW_ANNLFF-CASSLEAGLSTDTQYF 4 HD3 1501-YF45 TCM CASSLEAGLSTDTQYF CASSLEAGLSTDTQYF 4 HD3 1501-YF45 TCM CASSLGASGGAAGEQFF CALSDRDTGNQFYF-CASSLGASGGAAGEQFF 1 HD3 1501-YF45 TCM CASSLGDQVSNQPQHF CAAGT**_AGNMLTF-CASSLGDQVSNQPQHF 1 HD2 1501-YF45 TCM CASSLGFSMTDRGYTF CIVRPSAGNTGKLIF-CASSLGFSMTDRGYTF 3 HD2 1501-YF45 TCM CASSLGLSVANEQFF CAFMRGAGANNLFF-CASSLGLSVANEQFF 1 HD2 0407-YF80 TCM CASSLGSAGANVLTF CASSLGSAGANVLTF 3 HD2 1501-YF45 TCM CASSLGSLAGSYNEQFF CIVRVRAGNTPLVF-CASSLGSLAGSYNEQFF 4 HD3 1501-YF45 TCM CASSLQGPLSYEQYF CIVRVVTDYKLSF-CASSLQGPLSYEQYF 1 HD3 1501-YF45 TCM CASSMTVQGAIGANVLTF CAGAGGTSYGKLTF-CASSMTVQGAIGANVLTF 5 HD2 1501-YF45 TCM CASSPGGLSTEAFF CASSPGGLSTEAFF 4 HD2 1501-YF45 TCM CASSPGGLSTEAFF CAVGAQGRGFQKLVF-CASSPGGLSTEAFF 4 HD2 1501-YF45 TCM CASSPGQTLVTEAFF CIVRALSGNTGKLIF-CASSPGQTLVTEAFF 1 HD3 0407-YF54 TCM CASSPGTGDGYTF CAGEKL_GNKLTF-CASSPGTGDGYTF 1 HD3 1501-YF45 TCM CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 14 HD3 1501-YF45 TCM CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 14 HD3 1501-YF45 TCM CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 14 HD3 1501-YF45 TCM CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 14 HD3 1501-YF45 TCM CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 14 HD3 1501-YF45 TCM CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 14 HD3 1501-YF45 TCM CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 14 HD3 1501-YF45 TCM CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 14 HD3 1501-YF45 TCM CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 14 HD3 0407-YF54 TCM CASSPQGQRPYEQYV CASSPQGQRPYEQYV 1 HD2 1501-YF45 TCM CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 15 HD2 1501-YF45 TCM CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 15 HD2 1501-YF45 TCM CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 15 HD2 1501-YF45 TCM CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 15 HD2 1501-YF45 TCM CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 15 HD2 1501-YF45 TCM CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 15 HD3 0407-YF54 TCM CASSPTSGRGYEQYF CALIGDDMRF-CASSPTSGRGYEQYF 2 HD3 1501-YF91 TCM CASSQDLAGGSYNSPLHF CALSEGDQGGKLIF-CASSQDLAGGSYNSPLHF 1 HD3 1501-YF91 TCM CASSQDLGFENSPLHF CAVGAR_TYKYIF-CASSQDLGFENSPLHF 4 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD3 1501-YF91 TCM CASSQDLGFENSPLHF CAVGAR_TYKYIF-CASSQDLGFENSPLHF 4 HD3 1501-YF91 TCM CASSQDLGFENSPLHF CASSQDLGFENSPLHF 4 HD3 1501-YF91 TCM CASSQDVGGEIGNSPLHF CAGVGMNRDDKIIF-CASSQDVGGEIGNSPLHF 4 HD3 1501-YF91 TCM CASSQDVGGEIGNSPLHF CAGVGMNRDDKIIF-CASSQDVGGEIGNSPLHF 4 HD3 1501-YF45 TCM CASSQGGLNTEAFF CASSQGGLNTEAFF 1 HD3 0407-YF54 TCM CASSQIGTSGSFSYNEQFF CAVNDRDDKIIF-CASSQIGTSGSFSYNEQFF 1 HD2 1501-YF45 TCM CASSQQQGLNTEAFF CALGGFKTIF-CASSQQQGLNTEAFF 7 HD3 1501-YF45 TCM CASSRDRGPYEQYF CAENTNTGGFKTIF-CASSRDRGPYEQYF 1 HD3 1501-YF45 TCM CASSRNGGPFSEQYF CASSRNGGPFSEQYF 1 HD2 1501-YF45 TCM CASSSGASTPGYEQYF CIVRSAGNMLTF-CASSSGASTPGYEQYF 5 HD2 1501-YF45 TCM CASSSGASTPGYEQYF CIVRSAGNMLTF- CASSSGASTPGYEQYF;CIVRSAGNMLTF - CASSSGASTPGYEQYF 5 HD2 1501-YF45 TCM CASSSGEVLGEQYF CIVRPSAGGGNKLTF-CASSSGEVLGEQYF 1 HD2 1501-YF45 TCM CASSSGGLNTEAFF CASSSGGLNTEAFF 2 HD3 1501-YF45 TCM CASSSGLAIEQYF CIVRVGNYGQNFVF-CASSSGLAIEQYF 3 HD2 1501-YF45 TCM CASSSGSNTVNTEAFF CIVRYSGGSNYKLTF-CASSSGSNTVNTEAFF 1 HD2 1501-YF45 TCM CASSSMGLAGGLTGELFF CAGRTNTGNQFYF-CASSSMGLAGGLTGELFF 12 HD2 1501-YF45 TCM CASSSMGLAGGLTGELFF CAGRTNTGNQFYF-CASSSMGLAGGLTGELFF 12 HD2 1501-YF45 TCM CASSSMGLAGGLTGELFF CAGRTNTGNQFYF-CASSSMGLAGGLTGELFF 12 HD2 1501-YF45 TCM CASSSMGLAGGLTGELFF CAGRTNTGNQFYF-CASSSMGLAGGLTGELFF 12 HD2 1501-YF45 TCM CASSSMGLAGGLTGELFF CAGRTNTGNQFYF-CASSSMGLAGGLTGELFF 12 HD2 1501-YF45 TCM CASSSMGLAGGLTGELFF CAGRTNTGNQFYF- CASSSMGLAGGLTGELFF;CALVNRDNARLMF - CASSSMGLAGGLTGELFF 12 HD3 1501-YF45 TCM CASSSPGLNTEAFF CALCTGGGNKLTF-CASSSPGLNTEAFF 2 HD3 1501-YF45 TCM CASSSPGLNTEAFF CALCTGGGNKLTF-CASSSPGLNTEAFF 2 HD3 1501-YF45 TCM CASSSSGGIYNEQFF CIVKVQTGANNLFF-CASSSSGGIYNEQFF 4 HD3 1501-YF45 TCM CASSSSGGIYNEQFF CIVKVQTGANNLFF-CASSSSGGIYNEQFF 4 HD3 1501-YF45 TCM CASSSSGGIYNEQFF CASSSSGGIYNEQFF 4 HD3 1501-YF91 TCM CASSSSTYEQYF CAGTDRGSTLGRLYF- CASSSSTYEQYF;CAGAPGGR _GADGLTF- CASSSSTYEQYF 1 HD2 1501-YF45 TCM CASSSTTDGYTF CASSSTTDGYTF 7 HD2 1501-YF45 TCM CASSSTTDGYTF CASSSTTDGYTF 7 HD2 1501-YF45 TCM CASSSTTDGYTF CASSSTTDGYTF 7 HD2 1501-YF45 TCM CASSSTTDGYTF CAVGAQGGFGNVLHC-CASSSTTDGYTF 7 HD2 1501-YF45 TCM CASSTGGLTTEAFF CASSTGGLTTEAFF 3 HD2 1501-YF45 TCM CASSTGGLTTEAFF CASSTGGLTTEAFF 3 HD3 1501-YF45 TCM CASSTQGLITEAFF CASSTQGLITEAFF 8 HD3 1501-YF45 TCM CASSTQGLITEAFF CAENNNNARLMF-CASSTQGLITEAFF 8 HD3 1501-YF45 TCM CASSTQGLITEAFF CASSTQGLITEAFF 8 HD3 1501-YF45 TCM CASSTQGLITEAFF CASSTQGLITEAFF 8 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD2 1501-YF45 TCM CASSVGMGSTDTQYF CAVQAWDKIIF-CASSVGMGSTDTQYF 7 HD3 1501-YF91 TCM CASSVIDNEQFF CLVGDIDNAGNMLTF-CASSVIDNEQFF 1 HD2 1501-YF45 TCM CASSWTGALGEQYF CIVRPLSGNTPLVF-CASSWTGALGEQYF 1 HD3 1501-YF91 TCM CASSYEAGSSSGANVLTF CAVRVTGGFKTIF-CASSYEAGSSSGANVLTF 1 HD3 1501-YF45 TCM CASSYPGTANTEAFF CIAKATGTASKLTF-CASSYPGTANTEAFF 1 HD2 0407-YF80 TCM CASSYRDRAFSRRGTEAFF CASSYRDRAFSRRGTEAFF 1 HD3 1501-YF91 TCM CASSYRPDTEAFF CIPTL_YALNF-CASSYRPDTEAFF 1 HD3 1501-YF45 TCM CASTKSGGVYNEQFF CIVRVQTGANNLFF-CASTKSGGVYNEQFF 2 HD2 1501-YF45 TCM CASTLSGGVYNEQFF CIVRVASAGNNRKLIW-CASTLSGGVYNEQFF 1 HD2 1501-YF45 TCM CASTSSGGIYNEQFF CIVRVQTGANNLFF-CASTSSGGIYNEQFF 8 HD2 1501-YF45 TCM CASTSSGGIYNEQFF CIVRVQTGANNLFF-CASTSSGGIYNEQFF 8 HD2 1501-YF45 TCM CASTSSGGIYNEQFF CIVRVQTGANNLFF-CASTSSGGIYNEQFF 8 HD2 1501-YF45 TCM CASTSSGGIYNEQFF CIVRVQTGANNLFF-CASTSSGGIYNEQFF 8 HD2 1501-YF45 TCM CATSDFPVVGVNYGYTF CALVSNSGYALNF-CATSDFPVVGVNYGYTF 1 HD3 0407-YF54 TCM CATSREVSRGQYF CATSREVSRGQYF 1 HD3 1501-YF91 TCM CAVFTVEAGRDEAFF CAFVPFGGAQKLVF-CAVFTVEAGRDEAFF 2 HD2 1501-YF45 TCM CSAGVRVEGEQFF CAERTSGGYQKVTF-CSAGVRVEGEQFF 2 HD2 1501-YF45 TCM CSAISGSVYNEQFF CIVRVPVVNNNDMRF-CSAISGSVYNEQFF 1 HD2 1501-YF45 TCM CSAKFTTGRKETQYF CAFISDGQKLLF-CSAKFTTGRKETQYF 1 HD3 1501-YF45 TCM CSAKMRVGGELFF CSAKMRVGGELFF 3 HD2 1501-YF45 TCM CSAKMTSGASYEQYF CATDAYTDKLIF-CSAKMTSGASYEQYF 1 HD3 1501-YF45 TCM CSALVRTGDQQPQHF CAAGGRGGNTGKLIF-CSALVRTGDQQPQHF 1 HD2 1501-YF45 TCM CSANPRTGYNQPQHF CAVRDRGGFGNVLHC-CSANPRTGYNQPQHF 3 HD2 1501-YF45 TCM CSANPRTGYNQPQHF CAVRDRGGFGNVLHC-CSANPRTGYNQPQHF 3 HD2 1501-YF45 TCM CSANPRTGYNQPQHF CAVRDRGGFGNVLHC-CSANPRTGYNQPQHF 3 HD3 1501-YF45 TCM CSANVRVEGEQYF CAAIRGTYKYIF-CSANVRVEGEQYF 1 HD2 1501-YF45 TCM CSAQMRTGGSGNTIYF CLVETGNTGKLIF-CSAQMRTGGSGNTIYF 1 HD2 1501-YF45 TCM CSARAITARYEQYF CSARAITARYEQYF 2 HD2 1501-YF45 TCM CSARAITARYEQYF CSARAITARYEQYF 2 HD2 1501-YF45 TCM CSARALTTVAEAFF CIVPPGGGADGLTF-CSARALTTVAEAFF 1 HD3 1501-YF45 TCM CSARATSGGASEQYF CSARATSGGASEQYF 13 HD3 1501-YF45 TCM CSARATSGGASEQYF CSARATSGGASEQYF 13 HD3 1501-YF45 TCM CSARATSGGASEQYF CSARATSGGASEQYF 13 HD3 1501-YF45 TCM CSARATSGGASEQYF CSARATSGGASEQYF 13 HD3 1501-YF45 TCM CSARATSGGASEQYF CAASGAL_GYNKLIF-CSARATSGGASEQYF 13 HD3 1501-YF45 TCM CSARATSGGASEQYF CSARATSGGASEQYF 13 HD3 0407-YF54 TCM CSARDEGAKNIQYF CSARDEGAKNIQYF 1 HD3 0407-YF54 TCM CSARDWQGQRNTEAFF CAVNGYGNKLVF-CSARDWQGQRNTEAFF 3 HD3 0407-YF54 TCM CSAREIQGARNTEAFF CAVNGGDDKIIF-CSAREIQGARNTEAFF 7 HD3 0407-YF54 TCM CSAREIQGARNTEAFF CAVNGGDDKIIF-CSAREIQGARNTEAFF 7 HD3 0407-YF54 TCM CSAREIQGARNTEAFF CAVNGGDDKIIF-CSAREIQGARNTEAFF 7 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD3 0407-YF54 TCM CSAREIQGARNTEAFF CAVNGGDDKIIF-CSAREIQGARNTEAFF 7 HD3 0407-YF54 TCM CSARGLQRRNTEAFF CAVNDRDDKIIF-CSARGLQRRNTEAFF 3 HD3 1501-YF91 TCM CSARGRIANYGYTF CAAPLSGSARQLTF-CSARGRIANYGYTF 7 HD3 1501-YF45 TCM CSARILTGEDSPLHF CSARILTGEDSPLHF 2 HD3 1501-YF45 TCM CSARILTSNNSPLHF CATDARTTDSWGKLQF-CSARILTSNNSPLHF 1 HD2 1501-YF45 TCM CSARLLVNGEQFF CALTFSASKIIF-CSARLLVNGEQFF 1 HD2 1501-YF45 TCM CSARLSGSIGEQFF CSARLSGSIGEQFF 3 HD2 1501-YF45 TCM CSARPPTLGQTNTEAFF CIVRLPISGNTPLVF-CSARPPTLGQTNTEAFF 1 HD2 1501-YF45 TCM CSARRGEASYEQYF CAGHPRGYALNF-CSARRGEASYEQYF 1 HD2 1501-YF45 TCM CSARRTSILNEQYF CAAP*TAQGGKLIF- CSARRTSILNEQYF;CALDSRDAGKSTF - CSARRTSILNEQYF 1 HD2 1501-YF45 TCM CSARSRTGWGTEAFF CAGSSYGQNFVF-CSARSRTGWGTEAFF 2 HD3 0407-YF54 TCM CSARVADRGTTRNTEAFF CSARVADRGTTRNTEAFF 3 HD3 0407-YF54 TCM CSARVADRGTTRNTEAFF CAVNRGDDKIIF-CSARVADRGTTRNTEAFF 3 HD3 1501-YF45 TCM CSARVGSVIGNTIYF CAAFAYSGAGSYQLTF-CSARVGSVIGNTIYF 1 HD3 1501-YF45 TCM CSARVIAGAYEQYF CAASGAGGTSYGKLTF-CSARVIAGAYEQYF 1 HD2 1501-YF45 TCM CSARVLAGGPYVEQYF CVVSEGNAGNMLTF-CSARVLAGGPYVEQYF 1 HD2 1501-YF45 TCM CSARVLSGGPQETQYF CAGRPYNFNKFYF-CSARVLSGGPQETQYF 1 HD2 1501-YF45 TCM CSARVLTGNNQPQHF CALNYRKTF-CSARVLTGNNQPQHF 2 HD2 1501-YF45 TCM CSARVLTISSYTF CAAHNDMRF-CSARVLTISSYTF 1 HD2 1501-YF45 TCM CSARVLVAGELFF CAVDAGGTSYGKLTF-CSARVLVAGELFF 1 HD3 1501-YF45 TCM CSARVSGFNEQFF CAENTPQAGTALIF-CSARVSGFNEQFF 1 HD2 1501-YF45 TCM CSARVTAINTGELFF CIARNTGFQKLVF-CSARVTAINTGELFF 1 HD3 0407-YF54 TCM CSARVVQGRRNTEAFF CAVNNRDDKIIF-CSARVVQGRRNTEAFF 16 HD3 1501-YF45 TCM CSARVVTGSDQPQHF CIVRSINNAGNMLTF-CSARVVTGSDQPQHF 1 HD3 1501-YF45 TCM CSARVVVGDTQYF CALDNAGGTSYGKLTF-CSARVVVGDTQYF 1 HD2 1501-YF45 TCM CSASAGSLGQPQHF CAENKNQGGKLIF-CSASAGSLGQPQHF 1 HD2 1501-YF45 TCM CSASFTSGGWTDTQYF CAVVYMEYGNKLVF-CSASFTSGGWTDTQYF 1 HD2 1501-YF45 TCM CSASLVTGGTGELFF CLVGGNTNAGKSTF- CSASLVTGGTGELFF;CLVGGNTNAGKSTF - CSASLVTGGTGELFF 1 HD2 1501-YF45 TCM CSASPLTGDEETQYF WGLPGQ_RALTF-CSASPLTGDEETQYF 1 HD2 1501-YF45 TCM CSASQGAVGNTIYF CAENRNAGNMLTF-CSASQGAVGNTIYF 3 HD2 1501-YF45 TCM CSASQGAVGNTIYF CAENRNAGNMLTF-CSASQGAVGNTIYF 3 HD2 1501-YF45 TCM CSASQGAVGNTIYF CAV**ML_NNRKLIW-CSASQGAVGNTIYF 3 HD2 1501-YF45 TCM CSASRGYTGELFF CANAGGTSYGKLTF-CSASRGYTGELFF 1 HD2 1501-YF45 TCM CSASSGTVSGNTIYF CAENKAAGNKLTF-CSASSGTVSGNTIYF 2 HD2 1501-YF45 TCM CSASSGTVSGNTIYF CAENKAAGNKLTF-CSASSGTVSGNTIYF 2 HD2 1501-YF45 TCM CSASTGSLGQPQHF CAENRNQGGKLIF-CSASTGSLGQPQHF 1 HD2 1501-YF45 TCM CSASVLAGGYNEQFF CALNYGANNLFF-CSASVLAGGYNEQFF 1 HD3 1501-YF45 TCM CSASVVTNQPQHF CAYRSSDYKLSF-CSASVVTNQPQHF 1 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD2 1501-YF45 TCM CSATQMSVGELFF CAENRAAGNKLTF-CSATQMSVGELFF 1 HD3 1501-YF45 TCM CSATTGSNSGNTIYF CAENGNAGNMLTF-CSATTGSNSGNTIYF 1 HD3 1501-YF91 TCM CSAWDRANYGYTF CIVRVERDDKIIF-CSAWDRANYGYTF 4 HD3 1501-YF91 TCM CSAWDRANYGYTF CIVRVERDDKIIF-CSAWDRANYGYTF 4 HD2 1501-YF45 TCM CSVAGLYNEQFF CIVRVLAGANNLFF-CSVAGLYNEQFF 1 HD2 0407-YF80 TCM CSVEGTSGRGEQFF CSVEGTSGRGEQFF 19 HD2 0407-YF80 TCM CSVEGTSGRGEQFF CSVEGTSGRGEQFF 19 HD2 1501-YF45 TCM CSVEGTSGRGEQFF CIVRPSAGNTGKLIF-CSVEGTSGRGEQFF 19 HD3 1501-YF91 TCM CSVEGTSGRGEQFF CALSEGDQGGKLIF-CSVEGTSGRGEQFF 19 HD3 1501-YF91 TCM CSVEGTSGRGEQFF CSVEGTSGRGEQFF 19 HD3 1501-YF91 TCM CSVEGTSGRGEQFF CSVEGTSGRGEQFF 19 HD3 1501-YF45 TCM CSVEGTSGRGEQFF CSVEGTSGRGEQFF 19 HD3 1501-YF45 TCM CSVEGTSGRGEQFF CSVEGTSGRGEQFF 19 HD3 1501-YF45 TCM CSVEVRVGGTEAFF CIIHGSSNTGKLIF-CSVEVRVGGTEAFF 1 HD2 1501-YF45 TCM CSVGDRVGTGELFF CIAIGGATNKLIF-CSVGDRVGTGELFF 1 HD2 1501-YF45 TCM CSVNYRTGMNTEAFF CIVGSGNTGKLIF-CSVNYRTGMNTEAFF 1 HD2 0407-YF80 TCM CVVEGQTEAFF CVVEGQTEAFF 1 HD3 1501-YF45 TEM CASDLRDR_VRYYGYTF CIVKVQTGANNLFF-CASDLRDR_VRYYGYTF 1 HD2 0407-YF80 TEM CASEGGGSGANVLTF CASEGGGSGANVLTF 3 HD2 0407-YF80 TEM CASEGGGSGANVLTF CASEGGGSGANVLTF 3 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD2 0407-YF80 TEM CASGTGSSGANVLTF CASGTGSSGANVLTF 9 HD2 0407-YF80 TEM CASGTGSSGANVLTF CASGTGSSGANVLTF 9 HD2 0407-YF80 TEM CASGTGSSGANVLTF CVVSSRHTDKLIF- CASGTGSSGANVLTF;CALITQGGSEKLVF - CASGTGSSGANVLTF 9 HD2 0407-YF80 TEM CASGTGSSGANVLTF CASGTGSSGANVLTF 9 HD2 0407-YF80 TEM CASGTGSSGANVLTF CASGTGSSGANVLTF 9 HD2 0407-YF80 TEM CASGTGSSGANVLTF CASGTGSSGANVLTF 9 HD2 1501-YF45 TEM CASHPGTSIAGELFF CAVGSSGNTGKLIF-CASHPGTSIAGELFF 1 HD2 0407-YF80 TEM CASIGGGEGNEQFF CASIGGGEGNEQFF 5 HD2 1501-YF45 TEM CASIKIGVLGYGYTF CVVSFLW_GYNKLIF-CASIKIGVLGYGYTF 12 HD2 1501-YF45 TEM CASIKIGVLGYGYTF CASIKIGVLGYGYTF 12 HD2 1501-YF45 TEM CASIKIGVLGYGYTF CASIKIGVLGYGYTF 12 HD2 1501-YF45 TEM CASIKIGVLGYGYTF CVVSFLW_GYNKLIF-CASIKIGVLGYGYTF 12 HD2 1501-YF45 TEM CASIKIGVLGYGYTF CVVSFLW_GYNKLIF-CASIKIGVLGYGYTF 12 HD3 1501-YF91 TEM CASKHRPDSYEQYF CAASEEMDSSYKLIF-CASKHRPDSYEQYF 2 HD2 1501-YF45 TEM CASKMDSWTNTEAFF CAYRSAGTGNQFYF-CASKMDSWTNTEAFF 1 HD2 0407-YF80 TEM CASPKSSGSTDTQYF CASPKSSGSTDTQYF 14 HD2 0407-YF80 TEM CASPKSSGSTDTQYF CASPKSSGSTDTQYF 14 HD2 0407-YF80 TEM CASPKSSGSTDTQYF CALITQGGSEKLVF-CASPKSSGSTDTQYF 14 HD2 0407-YF80 TEM CASPKSSGSTDTQYF CASPKSSGSTDTQYF 14 HD2 0407-YF80 TEM CASPKSSGSTDTQYF CASPKSSGSTDTQYF 14 HD2 0407-YF80 TEM CASPKSSGSTDTQYF CASPKSSGSTDTQYF 14 HD2 0407-YF80 TEM CASPKSSGSTDTQYF CASPKSSGSTDTQYF 14 HD2 0407-YF80 TEM CASPKSSGSTDTQYF CASPKSSGSTDTQYF 14 HD2 0407-YF80 TEM CASPKSSGSTDTQYF CASPKSSGSTDTQYF 14 HD2 0407-YF80 TEM CASPKSSGSTDTQYF CASPKSSGSTDTQYF 14 HD2 0407-YF80 TEM CASPKSSGSTDTQYF CASPKSSGSTDTQYF 14 HD2 1501-YF45 TEM CASQTGASVTYEQYF CIVRVAAGNTGKLIF-CASQTGASVTYEQYF 9 HD3 1501-YF45 TEM CASRDLYGYTF CIVRVAAEAAGNKLTF-CASRDLYGYTF 3 HD2 0407-YF80 TEM CASRWDGNSPLHF CASRWDGNSPLHF 6 HD2 1501-YF45 TEM CASSEGHIPMNTEAFF CIVRVAAGQSGYALNF-CASSEGHIPMNTEAFF 5 HD2 1501-YF45 TEM CASSEGHIPMNTEAFF CIVRVAAGQSGYALNF-CASSEGHIPMNTEAFF 5 HD2 1501-YF45 TEM CASSEGHIPMNTEAFF CIVRVAAGQSGYALNF-CASSEGHIPMNTEAFF 5 HD2 1501-YF45 TEM CASSEGHIPMNTEAFF CIVRVAAGQSGYALNF-CASSEGHIPMNTEAFF 5 HD3 0407-YF54 TEM CASSFGTGVDEAFF CAGRNGGSQGNLIF-CASSFGTGVDEAFF 1 HD2 0407-YF80 TEM CASSFSSGTAGPPLHF CASSFSSGTAGPPLHF 1 HD2 1501-YF45 TEM CASSKGSTSGSYNEQFF CIVRVVAGNEKLTF-CASSKGSTSGSYNEQFF 1 HD3 0407-YF54 TEM CASSLAGGFYEQYF CAVREDDKIIF-CASSLAGGFYEQYF 1 HD2 1501-YF45 TEM CASSLAGTVNTEAFF CIVKGTGTASKLTF-CASSLAGTVNTEAFF 2 HD2 1501-YF45 TEM CASSLAGVGPGGYEQFF CAPPDQAGTALIF-CASSLAGVGPGGYEQFF 2 HD2 1501-YF45 TEM CASSLAVTVRSSNYGYTF CIVRVQTGANNLFF-CASSLAVTVRSSNYGYTF 3 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD2 1501-YF45 TEM CASSLEPVRDTEAFF CAGSAINSGGSNYKLTF-CASSLEPVRDTEAFF 1 HD2 1501-YF45 TEM CASSLGFSMTDRGYTF CIVRPSAGNTGKLIF-CASSLGFSMTDRGYTF 3 HD2 1501-YF45 TEM CASSLGFSMTDRGYTF CIVRPSAGNTGKLIF- CASSLGFSMTDRGYTF;CAENNGQLGDKIIF - CASSLGFSMTDRGYTF 3 HD2 1501-YF45 TEM CASSLGFVAGKELFF CIVSALSGNTGKLIF-CASSLGFVAGKELFF 2 HD2 1501-YF45 TEM CASSLGFVAGKELFF CIVSALSGNTGKLIF-CASSLGFVAGKELFF 2 HD2 1501-YF45 TEM CASSLGGTVNTEAFF CIGKHTGTASKLTF-CASSLGGTVNTEAFF 1 HD2 1501-YF45 TEM CASSLGPGLAGETQYF CIVTPLSGYALNF-CASSLGPGLAGETQYF 1 HD2 0407-YF80 TEM CASSLGSAGANVLTF CAVERQGSGNTGKLIF-CASSLGSAGANVLTF 3 HD2 0407-YF80 TEM CASSLGSAGANVLTF CALITQGGSEKLVF- CASSLGSAGANVLTF;CAPDNYGQNFVF - CASSLGSAGANVLTF 3 HD2 1501-YF45 TEM CASSLGSLAGSYNEQFF CIVRVRAGNTPLVF-CASSLGSLAGSYNEQFF 4 HD2 1501-YF45 TEM CASSLGSLAGSYNEQFF CIVRVRAGNTPLVF-CASSLGSLAGSYNEQFF 4 HD2 1501-YF45 TEM CASSLGTSYRAPYEQYF CIGWSSGDKLTF-CASSLGTSYRAPYEQYF 1 HD2 0407-YF80 TEM CASSLNPLGPWT_GD*GTNE KLFF CVVSSRHTDKLIF- CASSLNPLGPWT_GD*GTNEKLFF 1 HD2 0407-YF80 TEM CASSLNTGVKQPQHF CASSLNTGVKQPQHF 2 HD2 0407-YF80 TEM CASSLNTGVKQPQHF CASSLNTGVKQPQHF 2 HD2 1501-YF45 TEM CASSLQM*A_RTTDTQYF CAGSGGSYIPTF-CASSLQM*A_RTTDTQYF 1 HD2 1501-YF45 TEM CASSLSRQGAREQFF CAMREGPYNFNKFYF-CASSLSRQGAREQFF 3 HD2 1501-YF45 TEM CASSLSRQGAREQFF CAMREGPYNFNKFYF-CASSLSRQGAREQFF 3 HD2 1501-YF45 TEM CASSLTAGRGAGGANVLTF CIVSRAGSYQLTF- CASSLTAGRGAGGANVLTF;CAFIMYSGGGADGL TF-CASSLTAGRGAGGANVLTF 2 HD2 1501-YF45 TEM CASSLTAGRGAGGANVLTF CIVSRAGSYQLTF-CASSLTAGRGAGGANVLTF 2 HD2 1501-YF45 TEM CASSLTQGRNSPLHF CADGSGNTGKLIF-CASSLTQGRNSPLHF 1 HD3 1501-YF45 TEM CASSLVQLNTEAFF CIVRVYAGNMLTF-CASSLVQLNTEAFF 2 HD3 1501-YF45 TEM CASSMTVQGAIGANVLTF CAGAGGTSYGKLTF-CASSMTVQGAIGANVLTF 5 HD3 0407-YF54 TEM CASSNGA_NTGELFF CAVNNGGNKLVF-CASSNGA_NTGELFF 2 HD3 1501-YF45 TEM CASSNLRGSEQYF CALSEGPNNAGNMLTF-CASSNLRGSEQYF 1 HD2 1501-YF45 TEM CASSPGGLSTEAFF CAVQQE_TPLVF-CASSPGGLSTEAFF 4 HD2 1501-YF45 TEM CASSPGGLSTEAFF CAVQQE_TPLVF-CASSPGGLSTEAFF 4 HD3 1501-YF45 TEM CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 14 HD3 0407-YF54 TEM CASSPQGPSYEQYF CAVSGRTGAGSYQLTF-CASSPQGPSYEQYF 1 HD3 0407-YF54 TEM CASSPSLGDTQYF CAFMKPFPGGTSYGKLTF-CASSPSLGDTQYF 1 HD2 1501-YF45 TEM CASSPSRPGGPLSYEQYF CATVDNQGGKLIF-CASSPSRPGGPLSYEQYF 3 HD2 1501-YF45 TEM CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 15 HD2 1501-YF45 TEM CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 15 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD2 1501-YF45 TEM CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 15 HD3 0407-YF54 TEM CASSPTSGRGYEQYF CALIGDDMRF-CASSPTSGRGYEQYF 2 HD2 1501-YF45 TEM CASSQERLTYTGELFF CIVRVGAGSARQLTF-CASSQERLTYTGELFF 1 HD2 1501-YF45 TEM CASSQQQGLNTEAFF CALGGFKTIF- CASSQQQGLNTEAFF;CALGGFKTIF - CASSQQQGLNTEAFF 7 HD2 1501-YF45 TEM CASSQQQGLNTEAFF CALGGFKTIF- CASSQQQGLNTEAFF;CALGGFKTIF - CASSQQQGLNTEAFF 7 HD2 1501-YF45 TEM CASSQQQGLNTEAFF CALGGFKTIF- CASSQQQGLNTEAFF;CALGGFKTIF - CASSQQQGLNTEAFF 7 HD2 1501-YF45 TEM CASSQQQGLNTEAFF CALGGFKTIF-CASSQQQGLNTEAFF 7 HD2 1501-YF45 TEM CASSQQQGLNTEAFF CALGGFKTIF-CASSQQQGLNTEAFF 7 HD2 1501-YF45 TEM CASSQRQGINTEAFF CVVSVGKFSDGQKLLF- CASSQRQGINTEAFF;CIVRSAGNMLTF - CASSQRQGINTEAFF 3 HD2 1501-YF45 TEM CASSQRQGINTEAFF CVVSVGKFSDGQKLLF-CASSQRQGINTEAFF 3 HD3 0407-YF54 TEM CASSQSIDRNNYGYTF CASSQSIDRNNYGYTF 1 HD2 1501-YF45 TEM CASSQSRQSAYEQYF CAMREGPYNFNKFYF-CASSQSRQSAYEQYF 1 HD2 1501-YF45 TEM CASSSGASTPGYEQYF CIVRSAGNMLTF-CASSSGASTPGYEQYF 5 HD2 1501-YF45 TEM CASSSGGLNTEAFF CAVGRQGGGADGLTF-CASSSGGLNTEAFF 2 HD2 1501-YF45 TEM CASSSGGSVSNEQFF CIVRPSSGNTGKLIF-CASSSGGSVSNEQFF 1 HD2 1501-YF45 TEM CASSSMGLAGGLTGELFF CAGRTNTGNQFYF- CASSSMGLAGGLTGELFF;CALVNRDNARLMF - CASSSMGLAGGLTGELFF 12 HD2 1501-YF45 TEM CASSSMGLAGGLTGELFF CAGRTNTGNQFYF- CASSSMGLAGGLTGELFF;CALVNRDNARLMF - CASSSMGLAGGLTGELFF 12 HD2 1501-YF45 TEM CASSSMGLAGGLTGELFF CAGRTNTGNQFYF- CASSSMGLAGGLTGELFF;CAGRTNTGNQFYF - CASSSMGLAGGLTGELFF 12 HD2 1501-YF45 TEM CASSSMGLAGGLTGELFF CAGRTNTGNQFYF-CASSSMGLAGGLTGELFF 12 HD2 1501-YF45 TEM CASSSMGLAGGLTGELFF CAGRTNTGNQFYF- CASSSMGLAGGLTGELFF;CALVNRDNARLMF - CASSSMGLAGGLTGELFF 12 HD3 1501-YF91 TEM CASSSQNYGYTF CIVTFRR_GADGLTF-CASSSQNYGYTF 1 HD3 1501-YF45 TEM CASSSRQGLNTEAFF CIPPLA_DDKIIF-CASSSRQGLNTEAFF 1 HD2 1501-YF45 TEM CASSSTTDGYTF CASSSTTDGYTF 7 HD2 1501-YF45 TEM CASSSTTDGYTF CASSSTTDGYTF 7 HD2 1501-YF45 TEM CASSTGGLTTEAFF CAVGAQGGGADGLTF-CASSTGGLTTEAFF 3 HD2 1501-YF45 TEM CASSTGSTTPNNEQFF CILKTSGSRLTF-CASSTGSTTPNNEQFF 2 HD2 1501-YF45 TEM CASSTLLAGAPPTDTQYF CAVSHRSGYSTLTF-CASSTLLAGAPPTDTQYF 2 HD3 1501-YF45 TEM CASSTQGLITEAFF CASSTQGLITEAFF 8 HD3 1501-YF45 TEM CASSTQGLITEAFF CASSTQGLITEAFF 8 HD3 1501-YF45 TEM CASSTQGLITEAFF CASSTQGLITEAFF 8 HD2 1501-YF45 TEM CASSVAGSVNTEAFF CAMSPTGGTSYGKLTF-CASSVAGSVNTEAFF 1 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD2 1501-YF45 TEM CASSVAGTVNTEAFF CIVKNTGTASKLTF-CASSVAGTVNTEAFF 2 HD2 1501-YF45 TEM CASSVAGTVNTEAFF CIVKNTGTASKLTF-CASSVAGTVNTEAFF 2 HD2 1501-YF45 TEM CASSVGMGSTDTQYF CAVQAWDKIIF-CASSVGMGSTDTQYF 7 HD2 1501-YF45 TEM CASSVGMGSTDTQYF CAVQAWDKIIF-CASSVGMGSTDTQYF 7 HD2 1501-YF45 TEM CASSVGMGSTDTQYF CAVQAWDKIIF-CASSVGMGSTDTQYF 7 HD2 1501-YF45 TEM CASSVGMGSTDTQYF CAVQAWDKIIF-CASSVGMGSTDTQYF 7 HD2 1501-YF45 TEM CASSVGMGSTDTQYF CAVQAWDKIIF-CASSVGMGSTDTQYF 7 HD3 1501-YF45 TEM CASSVGSVSGGTGELFF CAMSHTGFQKLVF-CASSVGSVSGGTGELFF 2 HD2 1501-YF45 TEM CASSYEAG_ANNEQFF CAVRGTSYGKLTF-CASSYEAG_ANNEQFF 1 HD3 1501-YF91 TEM CASSYGMWYGYTF CALSEPGGGSEKLVF-CASSYGMWYGYTF 1 HD2 1501-YF45 TEM CASSYSTGGAAKNIQYF CAGPGDSSYKLIF-CASSYSTGGAAKNIQYF 2 HD2 1501-YF45 TEM CASSYSTGGAAKNIQYF CAGPGDSSYKLIF-CASSYSTGGAAKNIQYF 2 HD2 1501-YF45 TEM CASTSSGGIYNEQFF CIVRVQTGANNLFF-CASTSSGGIYNEQFF 8 HD2 1501-YF45 TEM CASTSSGGIYNEQFF CIVRVQTGANNLFF-CASTSSGGIYNEQFF 8 HD2 1501-YF45 TEM CASTSSGGIYNEQFF CIVRVQTGANNLFF-CASTSSGGIYNEQFF 8 HD2 1501-YF45 TEM CASTSSGGIYNEQFF CIVRVQTGANNLFF-CASTSSGGIYNEQFF 8 HD2 0407-YF80 TEM CATNHGGSGANVLTF CATNHGGSGANVLTF 1 HD2 0407-YF80 TEM CATSSDRVREKLFF CATSSDRVREKLFF 1 HD2 1501-YF45 TEM CSAGVRVEGEQFF CAERTSGGYQKVTF- CSAGVRVEGEQFF;CAERTSGGYQKVTF - CSAGVRVEGEQFF 2 HD2 1501-YF45 TEM CSAHQGNGYTF CAASHGFQKLVF- CSAHQGNGYTF;CIALPAGGTSYGKLTF - CSAHQGNGYTF 3 HD2 1501-YF45 TEM CSAHQGNGYTF CAASHGFQKLVF-CSAHQGNGYTF 3 HD2 1501-YF45 TEM CSAIQGVVWDTQYF CILKAPISGNTPLVF-CSAIQGVVWDTQYF 1 HD2 1501-YF45 TEM CSAPARTGTTEQYF CAAPSGNTGKLIF-CSAPARTGTTEQYF 1 HD2 1501-YF45 TEM CSAPVGSLGQPQHF CAENRAAGNKLTF-CSAPVGSLGQPQHF 1 HD3 1501-YF45 TEM CSAPVIVGGEQYF CAACSNDYKLSF-CSAPVIVGGEQYF 1 HD2 1501-YF45 TEM CSARAPAFAYNEQFF CIVRVEGGNNRKLIW-CSARAPAFAYNEQFF 1 HD3 1501-YF45 TEM CSARATSGGASEQYF CSARATSGGASEQYF 13 HD2 1501-YF45 TEM CSARAVTGDNSPLHF CAMTGSARQLTF- CSARAVTGDNSPLHF;CAMTGSARQLTF - CSARAVTGDNSPLHF 1 HD2 1501-YF45 TEM CSARAVVGGYEQYF CAYRSRYPYNTDKLIF- CSARAVVGGYEQYF;CAGGLTQGGSEKLVF - CSARAVVGGYEQYF 2 HD2 1501-YF45 TEM CSARDDGEQFF CIVRVAGRSINTDKLIF-CSARDDGEQFF 1 HD2 1501-YF45 TEM CSARDLGQSYGYTF CIVRGPVGGNKLTF-CSARDLGQSYGYTF 1 HD3 0407-YF54 TEM CSARDLQGARNTEAFF CSARDLQGARNTEAFF 1 HD3 0407-YF54 TEM CSARDRQGRNTEAFF CAVTLNNNDMRF-CSARDRQGRNTEAFF 1 HD3 0407-YF54 TEM CSARDVQGRRNTEAFF CAVNMGDDKIIF-CSARDVQGRRNTEAFF 1 HD3 0407-YF54 TEM CSARDWQGARNTEAFF CAVNSNFNKFYF-CSARDWQGARNTEAFF 4 HD3 0407-YF54 TEM CSARDWQGARNTEAFF CAVNSNFNKFYF-CSARDWQGARNTEAFF 4 HD3 0407-YF54 TEM CSARDWQGQRNTEAFF CAVNGYGNKLVF-CSARDWQGQRNTEAFF 3 HD3 0407-YF54 TEM CSAREIQGARNTEAFF CAVNGGDDKIIF-CSAREIQGARNTEAFF 7 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD3 0407-YF54 TEM CSAREIQGARNTEAFF CAVNGGDDKIIF-CSAREIQGARNTEAFF 7 HD3 0407-YF54 TEM CSARGLQRRNTEAFF CAVNDRDDKIIF-CSARGLQRRNTEAFF 3 HD3 0407-YF54 TEM CSARGLQRRNTEAFF CAVNDRDDKIIF-CSARGLQRRNTEAFF 3 HD3 1501-YF91 TEM CSARGRIANYGYTF CAAPLSGSARQLTF-CSARGRIANYGYTF 7 HD3 1501-YF91 TEM CSARGRIANYGYTF CAAPLSGSARQLTF-CSARGRIANYGYTF 7 HD3 0407-YF54 TEM CSARGTGGAKSYTF CSARGTGGAKSYTF 1 HD3 1501-YF45 TEM CSARILTGEDSPLHF CSARILTGEDSPLHF 2 HD2 1501-YF45 TEM CSARISNLNQETQYF CAVRDGSAYNTDKLIF-CSARISNLNQETQYF 2 HD3 1501-YF45 TEM CSARLLSSYNSPLHF CATVNAGGTSYGKLTF-CSARLLSSYNSPLHF 1 HD2 1501-YF45 TEM CSARLSGSIGEQFF CSARLSGSIGEQFF 3 HD2 1501-YF45 TEM CSARPRTGGEQYF CAMSVTNPFHNAGNMLTF-CSARPRTGGEQYF 1 HD2 1501-YF45 TEM CSARTLAGGPGETQYF CALSVIQGAQKLVF-CSARTLAGGPGETQYF 1 HD2 1501-YF45 TEM CSARTRVGGEQYF CAVLIGGATNKLIF- CSARTRVGGEQYF;CAFPPRDDKIIF - CSARTRVGGEQYF 2 HD2 1501-YF45 TEM CSARTRVGGEQYF CAVLIGGATNKLIF-CSARTRVGGEQYF 2 HD3 0407-YF54 TEM CSARVADRGTTRNTEAFF CAVNRGDDKIIF-CSARVADRGTTRNTEAFF 3 HD3 1501-YF45 TEM CSARVGSLPGNTIYF CSARVGSLPGNTIYF 1 HD2 1501-YF45 TEM CSARVITGGGEQYF CAVSDRNGNKLVF-CSARVITGGGEQYF 1 HD2 1501-YF45 TEM CSARVLTGNNQPQHF CALNYRKTF- CSARVLTGNNQPQHF;CAENGSGNTGKLIF - CSARVLTGNNQPQHF 2 HD2 1501-YF45 TEM CSARVLTYNSPLHF CAGEPYNTDKLIF-CSARVLTYNSPLHF 1 HD3 1501-YF45 TEM CSARVLVGQETQYF CALTYSGYSTLTF-CSARVLVGQETQYF 1 HD3 1501-YF45 TEM CSARVRVEGEQYF CGADGNTGNQFYF-CSARVRVEGEQYF 1 HD3 1501-YF45 TEM CSARVRVQGTQYF CARDSSGGSNYKLTF-CSARVRVQGTQYF 1 HD3 0407-YF54 TEM CSARVVQGRRNTEAFF CAVNNRDDKIIF-CSARVVQGRRNTEAFF 16 HD3 0407-YF54 TEM CSARVVQGRRNTEAFF CAVNNRDDKIIF-CSARVVQGRRNTEAFF 16 HD3 0407-YF54 TEM CSARVVQGRRNTEAFF CAVNNRDDKIIF-CSARVVQGRRNTEAFF 16 HD3 0407-YF54 TEM CSARVVQGRRNTEAFF CAVNNRDDKIIF-CSARVVQGRRNTEAFF 16 HD3 0407-YF54 TEM CSARVVQGRRNTEAFF CAVNNRDDKIIF-CSARVVQGRRNTEAFF 16 HD3 0407-YF54 TEM CSARVVQGRRNTEAFF CAVNNRDDKIIF-CSARVVQGRRNTEAFF 16 HD3 0407-YF54 TEM CSARVVQGRRNTEAFF CAVNNRDDKIIF-CSARVVQGRRNTEAFF 16 HD3 0407-YF54 TEM CSARVVQGRRNTEAFF CAVNNRDDKIIF-CSARVVQGRRNTEAFF 16 HD3 0407-YF54 TEM CSARVVQGRRNTEAFF CAVNNRDDKIIF-CSARVVQGRRNTEAFF 16 HD3 0407-YF54 TEM CSARVVQGRRNTEAFF CSARVVQGRRNTEAFF 16 HD3 0407-YF54 TEM CSARVVQGRRNTEAFF CAVNNRDDKIIF-CSARVVQGRRNTEAFF 16 HD2 1501-YF45 TEM CSARVVSGSGIQYF CAVVREETSGSRLTF-CSARVVSGSGIQYF 1 HD2 1501-YF45 TEM CSARVYVGSEQFF CSARVYVGSEQFF 1 HD2 1501-YF45 TEM CSASARVGGELFF CAASRPDSWGKLQF-CSASARVGGELFF 3 HD2 1501-YF45 TEM CSASARVGGELFF CAVLLRL_ATNKLIF-CSASARVGGELFF 3 HD2 1501-YF45 TEM CSASAVVGNIQYF CAPSETDKLIF-CSASAVVGNIQYF 1 HD2 1501-YF45 TEM CSASPLSGGANYEQYF CAVKNAGGTSYGKLTF- CSASPLSGGANYEQYF;CAVKNAGGTSYGKLTF - CSASPLSGGANYEQYF 1 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD2 1501-YF45 TEM CSASPRVEGEQYF CIVRGNQFYF-CSASPRVEGEQYF 2 HD2 1501-YF45 TEM CSASQGTASGNTIYF CAENMAAGNKLTF-CSASQGTASGNTIYF 1 HD2 1501-YF45 TEM CSASVRTGDNQPQHF CAGRFQGAQKLVF-CSASVRTGDNQPQHF 1 HD3 1501-YF45 TEM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD2 1501-YF45 TEM CSASYMTGVGTQYF CATGYLMGGATNKLIF-CSASYMTGVGTQYF 2 HD2 1501-YF45 TEM CSASYMTGVGTQYF CATGYLMGGATNKLIF-CSASYMTGVGTQYF 2 HD2 1501-YF45 TEM CSATIRTGAGVEQYF CALSEAYGSGNTGKLIF-CSATIRTGAGVEQYF 1 HD2 1501-YF45 TEM CSATLRTGANTEAFF CIVPGTYKYIF-CSATLRTGANTEAFF 1 HD2 1501-YF45 TEM CSAYQRVAGELFF CAFNGLGDSWGKLQF-CSAYQRVAGELFF 1 HD2 1501-YF45 TEM CSGKAVSGSNQPQHF CALSGYMGGSEKLVF-CSGKAVSGSNQPQHF 1 HD2 1501-YF45 TEM CSVEDRAGGTEAFF CAVRVYSSASKIIF-CSVEDRAGGTEAFF 1 HD3 1501-YF45 TEM CSVEGTSGRGEQFF CAGQGYNQGGKLIF-CSVEGTSGRGEQFF 19 HD3 1501-YF45 TEM CSVEGTSGRGEQFF CSVEGTSGRGEQFF 19 HD3 1501-YF45 TEM CSVEGTSGRGEQFF CSVEGTSGRGEQFF 19 HD3 1501-YF45 TEM CSVEGTSGRGEQFF CSVEGTSGRGEQFF 19 HD3 1501-YF45 TEM CSVEGTSGRGEQFF CSVEGTSGRGEQFF 19 HD3 1501-YF45 TEM CSVEGTSGRGEQFF CALTLNSGNTPLVF-CSVEGTSGRGEQFF 19 HD3 1501-YF45 TEM CSVEGTSGRGEQFF CAGQGYNQGGKLIF-CSVEGTSGRGEQFF 19 HD3 1501-YF45 TEM CSVEGTSGRGEQFF CSVEGTSGRGEQFF 19 HD3 1501-YF45 TEM CSVEGTSGRGEQFF CSVEGTSGRGEQFF 19 HD2 1501-YF45 TEM CSVGNRVGSRELFF CIVRVPSPSAGNMLTF-CSVGNRVGSRELFF 1 HD3 1501-YF45 TEM CSVRTGQVTGELFF CAGQEGIQ_GGADGLTF-CSVRTGQVTGELFF 3 HD2 1501-YF45 TEM CSVSDRVGSDTIYF CLVGAGNTGKLIF-CSVSDRVGSDTIYF 1 HD3 1501-YF91 Naïve CASASVAGGTYEQYF CALSEGDQGGKLIF-CASASVAGGTYEQYF 6 HD3 1501-YF91 Naive CASASVAGGTYEQYF CALSEGDQGGKLIF-CASASVAGGTYEQYF 6 HD2 1501-YF45 Naive CASQTGASVTYEQYF CIVRVAAGNTGKLIF-CASQTGASVTYEQYF 9 HD2 1501-YF45 Naive CASQTGASVTYEQYF CIVRVAAGNTGKLIF-CASQTGASVTYEQYF 9 HD2 1501-YF45 Naive CASQTGASVTYEQYF CIVRVAAGNTGKLIF-CASQTGASVTYEQYF 9 HD3 1501-YF91 Naive CASRPEDEPQHF CALSEGDQGGKLIF-CASRPEDEPQHF 1 HD2 0407-YF80 Naive CASRWDGNSPLHF CASRWDGNSPLHF 6 HD3 0407-YF54 Naive CASSFLAGANEQFF CAVNNRDDKIIF-CASSFLAGANEQFF 1 HD3 1501-YF91 Naive CASSLDFNSPLHF CASSLDFNSPLHF 1 HD3 0407-YF54 Naive CASSLLGQTEAFF CASSLLGQTEAFF 1 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD3 1501-YF91 Naive CASSLSAGGRDEQFF CAESQGGYQKVTF-CASSLSAGGRDEQFF 2 HD2 1501-YF45 Naive CASSLSRQGAREQFF CAMREGPYNFNKFYF-CASSLSRQGAREQFF 3 HD3 1501-YF45 Naive CASSMTVQGAIGANVLTF CAGAGGTSYGKLTF-CASSMTVQGAIGANVLTF 5 HD3 1501-YF91 Naive CASSPFLGAVDTQYF CAFMIDNARLMF-CASSPFLGAVDTQYF 1 HD2 1501-YF45 Naive CASSPLSGGAYKTQYF CALRGGGADGLTF-CASSPLSGGAYKTQYF 1 HD3 1501-YF45 Naive CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 14 HD2 1501-YF45 Naive CASSPSRPGGPLSYEQYF CASSPSRPGGPLSYEQYF 3 HD2 1501-YF45 Naive CASSPSRPGGPLSYEQYF CATVDNQGGKLIF-CASSPSRPGGPLSYEQYF 3 HD2 1501-YF45 Naive CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 15 HD2 1501-YF45 Naive CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 15 HD2 1501-YF45 Naive CASSPTGLGDYGYTF CIALPAGGTSYGKLTF- CASSPTGLGDYGYTF;CIALPAGGTSYGKLTF - CASSPTGLGDYGYTF 15 HD3 1501-YF91 Naive CASSQDLGFENSPLHF CAVGAR_TYKYIF-CASSQDLGFENSPLHF 4 HD3 1501-YF91 Naive CASSQDRSGGSYNSPLHF CAVGNQFYF- CASSQDRSGGSYNSPLHF;CAVVTGNQFYF - CASSQDRSGGSYNSPLHF 1 HD3 1501-YF91 Naive CASSQDVGGEIGNSPLHF CASSQDVGGEIGNSPLHF 4 HD3 1501-YF91 Naive CASSQDVGGEIGNSPLHF CALSEGDQGGKLIF- CASSQDVGGEIGNSPLHF;CAQIGFGNVLHC - CASSQDVGGEIGNSPLHF 4 HD3 1501-YF91 Naive CASSQEGGGYEQYF CASSQEGGGYEQYF 1 HD3 1501-YF91 Naive CASSQGTGGVVVEKLFF CAQIGFGNVLHC-CASSQGTGGVVVEKLFF 1 HD2 1501-YF45 Naive CASSQRQGINTEAFF CVVSVGKFSDGQKLLF-CASSQRQGINTEAFF 3 HD3 1501-YF91 Naive CASSSDRGGSNQPQHF CALSDMDSSYKLIF-CASSSDRGGSNQPQHF 1 HD2 0407-YF80 Naive CASSSGGATNEKLFF CASSSGGATNEKLFF 1 HD3 1501-YF45 Naive CASSSGLAIEQYF CIVRVGNYGQNFVF-CASSSGLAIEQYF 3 HD3 1501-YF45 Naive CASSVGSVSGGTGELFF CAMSHTGFQKLVF-CASSVGSVSGGTGELFF 2 HD3 1501-YF91 Naive CATSVRETQYF CVTGQGGANNLFF-CATSVRETQYF 1 HD3 1501-YF91 Naive CAVFTVEAGRDEAFF CAFVPFGGAQKLVF-CAVFTVEAGRDEAFF 2 HD3 1501-YF45 Naive CAWSLRQAAAPLHF CALIGDDMRF- CAWSLRQAAAPLHF;CALSEGANTGGFKTIF - CAWSLRQAAAPLHF 1 HD3 1501-YF45 Naive CSAKMRVGGELFF CSAKMRVGGELFF 3 HD2 1501-YF45 Naive CSANRGAVSNQPQHF CIVRNSGNTPLVF-CSANRGAVSNQPQHF 1 HD2 1501-YF45 Naive CSANVATNSPLHF CGADMGGAGTASKLTF-CSANVATNSPLHF 1 HD3 1501-YF45 Naive CSARATSGGASEQYF CIVRNNAGNMLTF-CSARATSGGASEQYF 13 HD3 1501-YF45 Naive CSARATSGGASEQYF CAASGAL_GYNKLIF-CSARATSGGASEQYF 13 HD3 0407-YF54 Naive CSARDWQGARNTEAFF CAVNSNFNKFYF-CSARDWQGARNTEAFF 4 HD3 0407-YF54 Naive CSARDWQGARNTEAFF CAVNSNFNKFYF-CSARDWQGARNTEAFF 4 HD3 0407-YF54 Naive CSARDWQGQRNTEAFF CAVNGYGNKLVF-CSARDWQGQRNTEAFF 3 HD3 0407-YF54 Naive CSAREIQGARNTEAFF CAVNGGDDKIIF-CSAREIQGARNTEAFF 7 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD3 1501-YF91 Naive CSARGRIANYGYTF CAAPLSGSARQLTF-CSARGRIANYGYTF 7 HD3 1501-YF91 Naive CSARGRIANYGYTF CAAPLSGSARQLTF-CSARGRIANYGYTF 7 HD3 1501-YF91 Naive CSARGRIANYGYTF CAAPLSGSARQLTF-CSARGRIANYGYTF 7 HD3 1501-YF91 Naive CSARGRIANYGYTF CAAPLSGSARQLTF- CSARGRIANYGYTF;CAASFNAGNNRKLIW - CSARGRIANYGYTF 7 HD3 0407-YF54 Naive CSARHLQGNRNTEAFF CAVEGQGGGYNKLIF-CSARHLQGNRNTEAFF 2 HD3 1501-YF45 Naive CSARVGSLADTQYF CAVHSGNTPLVF-CSARVGSLADTQYF 1 HD3 0407-YF54 Naive CSARVVQGRRNTEAFF CAVNNRDDKIIF-CSARVVQGRRNTEAFF 16 HD3 0407-YF54 Naive CSARVVQGRRNTEAFF CAVNNRDDKIIF-CSARVVQGRRNTEAFF 16 HD2 1501-YF45 Naive CSASARVGGELFF CAVLLRL_ATNKLIF-CSASARVGGELFF 3 HD2 1501-YF45 Naive CSASPRVEGEQYF CIVRGNQFYF-CSASPRVEGEQYF 2 HD3 1501-YF45 Naive CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 Naive CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 Naive CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 Naive CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF91 Naive CSAWDRANYGYTF CIVRVERDDKIIF-CSAWDRANYGYTF 4 HD3 1501-YF91 Naive CSAWDRANYGYTF CIVRVERDDKIIF-CSAWDRANYGYTF 4 HD2 1501-YF45 TEMRA CASIKIGVLGYGYTF CASIKIGVLGYGYTF 12 HD2 1501-YF45 TEMRA CASIKIGVLGYGYTF CVVSFLW_GYNKLIF-CASIKIGVLGYGYTF 12 HD3 1501-YF45 TEMRA CASSHRGLEQPQHF CASSHRGLEQPQHF 1 HD3 0407-YF54 TEMRA CASSIGTARVEKLFF CASSIGTARVEKLFF 1 HD3 1501-YF91 TEMRA CASSLSAGGRDEQFF CASSLSAGGRDEQFF 2 HD2 1501-YF45 TEMRA CASSLSALSGNTIYF CAASAISNSGGSNYKLTF- CASSLSALSGNTIYF;CAMREGPYNFNKFYF - CASSLSALSGNTIYF 1 HD3 0407-YF54 TEMRA CASSNGA_NTGELFF CAVNNGGNKLVF-CASSNGA_NTGELFF 2 HD2 1501-YF45 TEMRA CASSPGTSVADTQYF CAFRNTGNQFYF- CASSPGTSVADTQYF;CAAPIKAAGNKLTF - CASSPGTSVADTQYF 1 HD3 1501-YF45 TEMRA CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 14 HD3 1501-YF45 TEMRA CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 14 HD2 1501-YF45 TEMRA CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 15 HD2 1501-YF45 TEMRA CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 15 HD2 1501-YF45 TEMRA CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 15 HD2 1501-YF45 TEMRA CASSSGASTPGYEQYF CIVRSAGNMLTF-CASSSGASTPGYEQYF 5 HD3 1501-YF45 TEMRA CASSSGLAIEQYF CIVRVGNYGQNFVF-CASSSGLAIEQYF 3 HD3 1501-YF45 TEMRA CASSSSGGIYNEQFF CIVKVQTGANNLFF-CASSSSGGIYNEQFF 4 HD2 1501-YF45 TEMRA CASSTGSTTPNNEQFF CILKTSGSRLTF-CASSTGSTTPNNEQFF 2 HD2 1501-YF45 TEMRA CASSTLLAGAPPTDTQYF CAVSHRSGYSTLTF- CASSTLLAGAPPTDTQYF;CATDAIQ_DYKLSF - CASSTLLAGAPPTDTQYF 2 HD3 1501-YF45 TEMRA CASSTQGLITEAFF CASSTQGLITEAFF 8 HD2 1501-YF45 TEMRA CASSVGMGSTDTQYF CAVQAWDKIIF-CASSVGMGSTDTQYF 7 HD3 1501-YF45 TEMRA CSARATSGGASEQYF CSARATSGGASEQYF 13 HD3 1501-YF45 TEMRA CSARATSGGASEQYF CAASGAL_GYNKLIF-CSARATSGGASEQYF 13 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD2 1501-YF45 TEMRA CSARAVVGGYEQYF CAYRSRYPYNTDKLIF- CSARAVVGGYEQYF;CAGGLTQGGSEKLVF - CSARAVVGGYEQYF 2 HD3 0407-YF54 TEMRA CSARDYQGDRNTEAFF CAVPLRSNDYKLSF-CSARDYQGDRNTEAFF 1 HD2 1501-YF45 TEMRA CSARESLAGAREQYF CIVLRPPGNTPLVF-CSARESLAGAREQYF 1 HD3 0407-YF54 TEMRA CSARHLQGNRNTEAFF CAVEGQGGGYNKLIF-CSARHLQGNRNTEAFF 2 HD2 1501-YF45 TEMRA CSARISNLNQETQYF CAVRDGSAYNTDKLIF-CSARISNLNQETQYF 2 HD2 1501-YF45 TEMRA CSARLSGSIGEQFF CSARLSGSIGEQFF 3 HD2 1501-YF45 TEMRA CSARMDSLNTGELFF CILKAPISGNTPLVF-CSARMDSLNTGELFF 1 HD2 1501-YF45 TEMRA CSARSRTGWGTEAFF CAPDR_NQFYF-CSARSRTGWGTEAFF 2 HD3 1501-YF45 TEMRA CSARVIVAGELFF CSARVIVAGELFF 1 HD2 1501-YF45 TEMRA CSARVLTNEKLFF CAVYNDMRF-CSARVLTNEKLFF 1 HD3 1501-YF45 TEMRA CSARVQTSGEQYF CSARVQTSGEQYF 1 HD3 0407-YF54 TEMRA CSARVVQGRRNTEAFF CAVNNRDDKIIF-CSARVVQGRRNTEAFF 16 HD3 0407-YF54 TEMRA CSARVVQGRRNTEAFF CSARVVQGRRNTEAFF 16 HD3 1501-YF45 TEMRA CSASIRTGDNQPQHF CAASGRAQKLVF-CSASIRTGDNQPQHF 1 HD3 1501-YF45 TEMRA CSASYLTGSYNEQFF CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEMRA CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEMRA CSASYLTGSYNEQFF CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEMRA CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEMRA CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEMRA CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEMRA CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEMRA CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEMRA CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEMRA CSASYLTGSYNEQFF CSASYLTGSYNEQFF 55 HD3 1501-YF45 TEMRA CSVEGTSGRGEQFF CSVEGTSGRGEQFF 19 HD2 1501-YF45 TMN CASIKIGVLGYGYTF CVVSFLW_GYNKLIF-CASIKIGVLGYGYTF 12 HD2 1501-YF45 TMN CASIKIGVLGYGYTF CVVSFLW_GYNKLIF-CASIKIGVLGYGYTF 12 HD2 1501-YF45 TMN CASSEQSLNNYNEQFF CALSPFSGGYNKLIF-CASSEQSLNNYNEQFF 1 HD2 1501-YF45 TMN CASSLAGTVNTEAFF CIVKGTGTASKLTF-CASSLAGTVNTEAFF 2 HD2 1501-YF45 TMN CASSLAVTVRSSNYGYTF CIVRVQTGANNLFF-CASSLAVTVRSSNYGYTF 3 HD2 1501-YF45 TMN CASSPRQGLNTEAFF CAAKGLK_SGYALNF-CASSPRQGLNTEAFF 1 HD2 1501-YF45 TMN CASSQQQGLNTEAFF CALGGFKTIF-CASSQQQGLNTEAFF 7 HD2 1501-YF45 TMN CASSSTTDGYTF CAGEVLV_YNKLIF-CASSSTTDGYTF 7 HD2 1501-YF45 TMN CSAHQGNGYTF CAASHGFQKLVF-CSAHQGNGYTF 3 HD3 1501-YF45 TMN CASIIGTP_SGNTIYF CAMRGSGGGADGLTF-CASIIGTP_SGNTIYF 1 HD3 1501-YF45 TMN CASSLVQLNTEAFF CIVRVYAGNMLTF-CASSLVQLNTEAFF 2 HD3 1501-YF45 TMN CASSMTVQGAIGANVLTF CAGAGGTSYGKLTF-CASSMTVQGAIGANVLTF 5 HD3 1501-YF45 TMN CASSPGSSTSSYNEQFF CIVRPSSGNTPLVF-CASSPGSSTSSYNEQFF 1 HD3 1501-YF45 TMN CASTKSGGVYNEQFF CIVRVQTGANNLFF-CASTKSGGVYNEQFF 2 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD3 1501-YF45 TMN CASTLSGGLYNEQFF KGRDDKIIF-CASTLSGGLYNEQFF 1 HD3 1501-YF45 TMN CSARATSGGASEQYF CSARATSGGASEQYF 13 HD3 1501-YF45 TMN CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TMN CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TMN CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TMN CSVEGTSGRGEQFF CSVEGTSGRGEQFF 19 HD3 1501-YF45 TMN CSVRTGQVTGELFF CAENNNNARLMF-CSVRTGQVTGELFF 3 HD2 1501-YF45 TSCM CASIKIGVLGYGYTF CVVSFLW_GYNKLIF-CASIKIGVLGYGYTF 12 HD2 1501-YF45 TSCM CASQTGASVTYEQYF CIVRVAAGNTGKLIF-CASQTGASVTYEQYF 9 HD2 1501-YF45 TSCM CASQTGASVTYEQYF CIVRVAAGNTGKLIF-CASQTGASVTYEQYF 9 HD2 1501-YF45 TSCM CASSKTSGLQSYNEQFF CILRPNYGGSQGNLIF-CASSKTSGLQSYNEQFF 2 HD3 1501-YF45 TSCM CASSLALRDRGSIQPQHF CVVSAVGGTYKYIF-CASSLALRDRGSIQPQHF 1 HD3 1501-YF45 TSCM CASSLEAGLSTDTQYF CASSLEAGLSTDTQYF 4 HD3 1501-YF45 TSCM CASSLEAGLSTDTQYF CASSLEAGLSTDTQYF 4 HD3 1501-YF45 TSCM CASSLGFMNTEAFF CIVRVVTNAGKSTF-CASSLGFMNTEAFF 1 HD2 1501-YF45 TSCM CASSLGSLAGSYNEQFF CIVRVRAGNTPLVF-CASSLGSLAGSYNEQFF 4 HD3 1501-YF45 TSCM CASSLHGGTVSTEAFF CIVREAGGFKTIF-CASSLHGGTVSTEAFF 1 HD3 1501-YF45 TSCM CASSMTVQGAIGANVLTF CAGAGGTSYGKLTF-CASSMTVQGAIGANVLTF 5 HD3 1501-YF45 TSCM CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 14 HD2 1501-YF45 TSCM CASSSGASTPGYEQYF CIVRSAGNMLTF-CASSSGASTPGYEQYF 5 HD2 1501-YF45 TSCM CASSSMGLAGGLTGELFF CAGRTNTGNQFYF-CASSSMGLAGGLTGELFF 12 HD3 1501-YF45 TSCM CASTPTGTVGGTQYF CIVRVGAGGTSYGKLTF-CASTPTGTVGGTQYF 1 HD3 1501-YF45 TSCM CSAKMRVGGELFF CALSEAGL_FGNEKLTF-CSAKMRVGGELFF 3 HD3 1501-YF45 TSCM CSALDRVGGEQYF CAVLPGR_GNKLTF-CSALDRVGGEQYF 1 HD3 1501-YF45 TSCM CSARALSTGEQYF CSARALSTGEQYF 2 HD3 1501-YF45 TSCM CSARALSTGEQYF CSARALSTGEQYF 2 HD3 1501-YF45 TSCM CSARATSGGASEQYF CSARATSGGASEQYF 13 HD3 1501-YF45 TSCM CSARGQGVLGELFF CLVGATGSARQLTF-CSARGQGVLGELFF 1 HD3 1501-YF45 TSCM CSARLSDGTMRSEAFF CAMVTSHGKLTF-CSARLSDGTMRSEAFF 1 HD2 1501-YF45 TSCM CSARVPQQGLAHNEQFF CIVRVANSGNTPLVF-CSARVPQQGLAHNEQFF 1 HD3 1501-YF45 TSCM CSARVQTSGPQHF CAVANDMRF-CSARVQTSGPQHF 1 HD3 1501-YF45 TSCM CSARVVSNQPQHF CIAGGNTDKLIF-CSARVVSNQPQHF 1 HD3 1501-YF45 TSCM CSARYVTGNTGELFF CIVGSSNTGKLIF-CSARYVTGNTGELFF 1 HD3 1501-YF45 TSCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TSCM CSASYLTGSYNEQFF CSASYLTGSYNEQFF 55 HD3 1501-YF45 TSCM CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 55 HD3 1501-YF45 TSCM CSVRTGQVTGELFF CAENNNNARLMF-CSVRTGQVTGELFF 3 HD2 1501-YF45 TSCM CSVSDRVGWDTEAFF CAGTLTF-CSVSDRVGWDTEAFF 1 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint Table S5: YF45 tetramer+ T cells before and 14 days after YFV vaccination Donor specificity visit TCRb TCRa-TCRb clone size HD2 1501-YF45 d14 post CASNHRLPYNSPLHF CIVRSSNTGNQFYF- CASNHRLPYNSPLHF;CIVRSSNTGNQFYF - CASNHRLPYNSPLHF 1 HD3 1501-YF45 d14 post CASSFGTPLGGELFF CASSFGTPLGGELFF 1 HD3 1501-YF45 d14 post CASSFLKPGQAHYGYTF CASSFLKPGQAHYGYTF 1 HD3 1501-YF45 d14 post CASSFPMNTEAFF CASSFPMNTEAFF 1 HD3 1501-YF45 d14 post CASSFPRGQNINQPQHF CIVRVGAQGAQKLVF-CASSFPRGQNINQPQHF 3 HD3 1501-YF45 d14 post CASSFPRGQNINQPQHF CIVRVGAQGAQKLVF-CASSFPRGQNINQPQHF 3 HD3 1501-YF45 d14 post CASSFPRGQNINQPQHF CIVRVGAQGAQKLVF-CASSFPRGQNINQPQHF 3 HD2 1501-YF45 d14 post CASSKTSGLQSYNEQFF CILRPNYGGSQGNLIF- CASSKTSGLQSYNEQFF;CILRPNYGGSQGNLIF -CASSKTSGLQSYNEQFF 1 HD2 1501-YF45 d14 post CASSLAGTVNTEAFF CIVKGTGTASKLTF- CASSLAGTVNTEAFF;CIVKGTGTASKLTF - CASSLAGTVNTEAFF 1 HD3 1501-YF45 d14 post CASSLAQQGNTEAFF CIVRVGASNTGKLIF-CASSLAQQGNTEAFF 5 HD3 1501-YF45 d14 post CASSLAQQGNTEAFF CIVRVGASNTGKLIF-CASSLAQQGNTEAFF 5 HD3 1501-YF45 d14 post CASSLAQQGNTEAFF CIGGRK_QGNLIF- CASSLAQQGNTEAFF;CIVRVGASNTGKLIF - CASSLAQQGNTEAFF 5 HD3 1501-YF45 d14 post CASSLAQQGNTEAFF CIVRVGASNTGKLIF-CASSLAQQGNTEAFF 5 HD3 1501-YF45 d14 post CASSLAQQGNTEAFF CIVRVGASNTGKLIF-CASSLAQQGNTEAFF 5 HD2 1501-YF45 d14 post CASSLAVTVRSSNYGYTF CIVRVQTGANNLFF-CASSLAVTVRSSNYGYTF 4 HD2 1501-YF45 d14 post CASSLAVTVRSSNYGYTF CIVRVQTGANNLFF- CASSLAVTVRSSNYGYTF;FIVRVQTGANNLFF - CASSLAVTVRSSNYGYTF 4 HD2 1501-YF45 d14 post CASSLAVTVRSSNYGYTF CIVRVQTGANNLFF- CASSLAVTVRSSNYGYTF;CIVRVQTGANNLFF - CASSLAVTVRSSNYGYTF 4 HD2 1501-YF45 d14 post CASSLAVTVRSSNYGYTF CIVRVQTGANNLFF-CASSLAVTVRSSNYGYTF 4 HD3 1501-YF45 d14 post CASSLDYNEQFF CASSLDYNEQFF 1 HD3 1501-YF45 d14 post CASSLEAGLSTDTQYF CVVIPNW_ANNLFF-CASSLEAGLSTDTQYF 1 HD3 1501-YF45 d14 post CASSLEWRGAQMRPFF CAVRLMNYGGSQGNLIF- CASSLEWRGAQMRPFF 1 HD3 1501-YF45 d14 post CASSLGFMNTEAFF CIVRVVTNAGKSTF-CASSLGFMNTEAFF 2 HD3 1501-YF45 d14 post CASSLGFMNTEAFF CIVRVVTNAGKSTF-CASSLGFMNTEAFF 2 HD2 1501-YF45 d14 post CASSLGFSMTDRGYTF CIVRPSAGNTGKLIF- CASSLGFSMTDRGYTF;CAENNGQLGDKIIF - CASSLGFSMTDRGYTF 1 HD3 1501-YF45 d14 post CASSLGGIESGYTF CAMREGNNFNKFYF-CASSLGGIESGYTF 1 HD3 1501-YF45 d14 post CASSLGKTTSGNTIYF CAMREVNNARLMF-CASSLGKTTSGNTIYF 1 HD3 1501-YF45 d14 post CASSLGQVLFTDTQYF CIVRPLGGAQKLVF-CASSLGQVLFTDTQYF 1 HD2 1501-YF45 d14 post CASSLGSLAGSYNEQFF CIVRVRAGNTPLVF-CASSLGSLAGSYNEQFF 4 HD2 1501-YF45 d14 post CASSLGSLAGSYNEQFF CIVRVRAGNTPLVF-CASSLGSLAGSYNEQFF 4 HD2 1501-YF45 d14 post CASSLGSLAGSYNEQFF CIVRVRAGNTPLVF- CASSLGSLAGSYNEQFF;CIALPAGGTSYGKLTF -CASSLGSLAGSYNEQFF 4 HD2 1501-YF45 d14 post CASSLGSLAGSYNEQFF CIVRVRAGNTPLVF-CASSLGSLAGSYNEQFF 4 HD3 1501-YF45 d14 post CASSLGSVPPGNTIYF CIVRVSGGGGADGLTF-CASSLGSVPPGNTIYF 1 HD3 1501-YF45 d14 post CASSLHGGTVSTEAFF CIVREAGGFKTIF-CASSLHGGTVSTEAFF 1 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD3 1501-YF45 d14 post CASSLNPLAGGLTGELFF CIVKAGTALIF-CASSLNPLAGGLTGELFF 1 HD2 1501-YF45 d14 post CASSLQPGQVSYEQYF CIVRVGYGQNFVF-CASSLQPGQVSYEQYF 1 HD2 1501-YF45 d14 post CASSLTQGRNSPLHF CADGSGNTGKLIF-CASSLTQGRNSPLHF 1 HD3 1501-YF45 d14 post CASSLVQLNTEAFF CIVRVYAGNMLTF-CASSLVQLNTEAFF 2 HD3 1501-YF45 d14 post CASSLVQLNTEAFF CIVRVYAGNMLTF-CASSLVQLNTEAFF 2 HD3 1501-YF45 d14 post CASSMTVQGAIGANVLTF CAGAGGTSYGKLTF-CASSMTVQGAIGANVLTF 3 HD3 1501-YF45 d14 post CASSMTVQGAIGANVLTF CAGAGGTSYGKLTF-CASSMTVQGAIGANVLTF 3 HD3 1501-YF45 d14 post CASSMTVQGAIGANVLTF CAGAGGTSYGKLTF-CASSMTVQGAIGANVLTF 3 HD3 1501-YF45 d14 post CASSPEGPTYF CIVRVAAISGGYNKLIF-CASSPEGPTYF 1 HD3 1501-YF45 d14 post CASSPNLWVPHEQFF CIVRVAGDTGRRALTF-CASSPNLWVPHEQFF 1 HD3 1501-YF45 d14 post CASSPPGQVNTEAFF CIGKNTGTASKLTF-CASSPPGQVNTEAFF 3 HD3 1501-YF45 d14 post CASSPPGQVNTEAFF CIGKNTGTASKLTF-CASSPPGQVNTEAFF 3 HD3 1501-YF45 d14 post CASSPPGQVNTEAFF CIGKNTGTASKLTF-CASSPPGQVNTEAFF 3 HD3 1501-YF45 d14 post CASSPQDSLGVYNEQFF CASSPQDSLGVYNEQFF 2 HD3 1501-YF45 d14 post CASSPQDSLGVYNEQFF CAENRPGV_SSASKIIF- CASSPQDSLGVYNEQFF 2 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF- CASSPQGPLINEQFF;CIVRNNAGNMLTF - CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF- CASSPQGPLINEQFF;CIVRNNAGNMLTF - CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 HD3 1501-YF45 d14 post CASSPQGPLINEQFF CIVRNNAGNMLTF-CASSPQGPLINEQFF 26 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD2 1501-YF45 d14 post CASSPTGLGDYGYTF CIALPAGGTSYGKLTF- CASSPTGLGDYGYTF;CIVRVQTGANNLFF - CASSPTGLGDYGYTF 6 HD2 1501-YF45 d14 post CASSPTGLGDYGYTF CIALPAGGTSYGKLTF- CASSPTGLGDYGYTF;CIALPAGGTSYGKLTF - CASSPTGLGDYGYTF 6 HD2 1501-YF45 d14 post CASSPTGLGDYGYTF CIALPAGGTSYGKLTF- CASSPTGLGDYGYTF;CIALPAGGTSYGKLTF - CASSPTGLGDYGYTF 6 HD2 1501-YF45 d14 post CASSPTGLGDYGYTF CIALPAGGTSYGKLTF- CASSPTGLGDYGYTF;CIALPAGGTSYGKLTF - CASSPTGLGDYGYTF 6 HD2 1501-YF45 d14 post CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 6 HD2 1501-YF45 d14 post CASSPTGLGDYGYTF CIALPAGGTSYGKLTF-CASSPTGLGDYGYTF 6 HD3 1501-YF45 d14 post CASSPYWTVTDSPLHF CIVRSNTDKLIF- CASSPYWTVTDSPLHF;CIWHE_LFYF - CASSPYWTVTDSPLHF 2 HD3 1501-YF45 d14 post CASSPYWTVTDSPLHF CIVRSNTDKLIF-CASSPYWTVTDSPLHF 2 HD2 1501-YF45 d14 post CASSQARQGTPEAFF GFGNVLHC- CASSQARQGTPEAFF;CAMREGPFSGGYNKLIF -CASSQARQGTPEAFF 1 HD3 1501-YF45 d14 post CASSQGGLNTEAFF CASSQGGLNTEAFF 1 HD2 1501-YF45 d14 post CASSQNVGIVYEQYF CALSRNSGNTPLVF-CASSQNVGIVYEQYF 1 HD2 1501-YF45 d14 post CASSQRQGINTEAFF CVVSVGKFSDGQKLLF-CASSQRQGINTEAFF 3 HD2 1501-YF45 d14 post CASSQRQGINTEAFF CVVSVGKFSDGQKLLF- CASSQRQGINTEAFF;CIVRSAGNMLTF - CASSQRQGINTEAFF 3 HD2 1501-YF45 d14 post CASSQRQGINTEAFF CVVSVGKFSDGQKLLF-CASSQRQGINTEAFF 3 HD3 1501-YF45 d14 post CASSQSGGVYNEQFF CIVKVQTGANNLFF-CASSQSGGVYNEQFF 1 HD3 1501-YF45 d14 post CASSRWTGPLGQETQYF CAPGR_DKIIF-CASSRWTGPLGQETQYF 1 HD2 1501-YF45 d14 post CASSSGASTPGYEQYF CIVRSAGNMLTF- CASSSGASTPGYEQYF;CIVRGAGNMLTF - CASSSGASTPGYEQYF 2 HD2 1501-YF45 d14 post CASSSGASTPGYEQYF CIVRSAGNMLTF-CASSSGASTPGYEQYF 2 HD2 1501-YF45 d14 post CASSSGEIPRSYEQYF CIVRVAGSARQLTF-CASSSGEIPRSYEQYF 2 HD2 1501-YF45 d14 post CASSSGEIPRSYEQYF CASSSGEIPRSYEQYF 2 HD3 1501-YF45 d14 post CASSSGLAIEQYF CIVRVGNYGQNFVF-CASSSGLAIEQYF 3 HD3 1501-YF45 d14 post CASSSGLAIEQYF CIVRVGNYGQNFVF-CASSSGLAIEQYF 3 HD3 1501-YF45 d14 post CASSSGLAIEQYF CIVRVGNYGQNFVF-CASSSGLAIEQYF 3 HD3 1501-YF45 d14 post CASSSPGLNTEAFF CALCTGGGNKLTF-CASSSPGLNTEAFF 3 HD3 1501-YF45 d14 post CASSSPGLNTEAFF CALCTGGGNKLTF-CASSSPGLNTEAFF 3 HD3 1501-YF45 d14 post CASSSPGLNTEAFF CALCTGGGNKLTF-CASSSPGLNTEAFF 3 HD3 1501-YF45 d14 post CASSSRQGLNTEAFF CIPPLA_DDKIIF-CASSSRQGLNTEAFF 1 HD3 1501-YF45 d14 post CASSSSGGIYNEQFF CIVKVQTGANNLFF-CASSSSGGIYNEQFF 2 HD3 1501-YF45 d14 post CASSSSGGIYNEQFF CIVKVQTGANNLFF-CASSSSGGIYNEQFF 2 HD2 1501-YF45 d14 post CASSSTTDGYTF CASSSTTDGYTF 4 HD2 1501-YF45 d14 post CASSSTTDGYTF CASSSTTDGYTF 4 HD2 1501-YF45 d14 post CASSSTTDGYTF CASSSTTDGYTF 4 HD2 1501-YF45 d14 post CASSSTTDGYTF CASSSTTDGYTF 4 HD3 1501-YF45 d14 post CASSSVPGPNTEAFF CALLNYGQNFVF-CASSSVPGPNTEAFF 2 HD3 1501-YF45 d14 post CASSSVPGPNTEAFF CASSSVPGPNTEAFF 2 HD2 1501-YF45 d14 post CASSTGGLTTEAFF CASSTGGLTTEAFF 3 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD2 1501-YF45 d14 post CASSTGGLTTEAFF CASSTGGLTTEAFF 3 HD2 1501-YF45 d14 post CASSTGGLTTEAFF CASSTGGLTTEAFF 3 HD2 1501-YF45 d14 post CASSTGSTTPNNEQFF CILKTSGSRLTF- CASSTGSTTPNNEQFF;CILKTSGSRLTF - CASSTGSTTPNNEQFF 3 HD2 1501-YF45 d14 post CASSTGSTTPNNEQFF CILKTSGSRLTF- CASSTGSTTPNNEQFF;CILKTSGSRLTF - CASSTGSTTPNNEQFF 3 HD2 1501-YF45 d14 post CASSTGSTTPNNEQFF CILKTSGSRLTF- CASSTGSTTPNNEQFF;CILKTSGSRLTF - CASSTGSTTPNNEQFF 3 HD3 1501-YF45 d14 post CASSTQGLITEAFF CASSTQGLITEAFF 4 HD3 1501-YF45 d14 post CASSTQGLITEAFF CASSTQGLITEAFF 4 HD3 1501-YF45 d14 post CASSTQGLITEAFF CAPSTGGGNKLTF-CASSTQGLITEAFF 4 HD3 1501-YF45 d14 post CASSTQGLITEAFF CASSTQGLITEAFF 4 HD2 1501-YF45 d14 post CASSVAGTVNTEAFF CIVKNTGTASKLTF-CASSVAGTVNTEAFF 1 HD3 1501-YF45 d14 post CASSVGIGSTDTQYF CAVQAWVTGGGNKLTF-CASSVGIGSTDTQYF 1 HD3 1501-YF45 d14 post CASSVGSVSGGTGELFF CAMSHTGFQKLVF- CASSVGSVSGGTGELFF;CIVKAGTALIF - CASSVGSVSGGTGELFF 1 HD3 1501-YF45 d14 post CASTAGPLDTEAFF CASTAGPLDTEAFF 1 HD3 1501-YF45 d14 post CASTKSGGVYNEQFF CIVRVQTGANNLFF- CASTKSGGVYNEQFF;CIVRVQTGANNLFF - CASTKSGGVYNEQFF 2 HD3 1501-YF45 d14 post CASTKSGGVYNEQFF CIVRVQTGANNLFF-CASTKSGGVYNEQFF 2 HD3 1501-YF45 d14 post CASTLSGGLYNEQFF KGRDDKIIF- CASTLSGGLYNEQFF;CIVRPQTGANNLFF - CASTLSGGLYNEQFF 1 HD2 1501-YF45 d14 post CASTSSGGIYNEQFF CIVRVQTGANNLFF-CASTSSGGIYNEQFF 2 HD2 1501-YF45 d14 post CASTSSGGIYNEQFF CIVRVQTGANNLFF-CASTSSGGIYNEQFF 2 HD2 1501-YF45 d14 post CATGPKRGLSDTQYF CATGPKRGLSDTQYF 1 HD2 1501-YF45 d14 post CATSDFPVVGVNYGYTF CALVSNSGYALNF-CATSDFPVVGVNYGYTF 1 HD2 1501-YF45 d14 post CSAGGRVGTGELFF CIVRVGNNNDMRF- CSAGGRVGTGELFF;CIVRVGNNNDMRF - CSAGGRVGTGELFF 1 HD2 1501-YF45 d14 post CSAIAGPAYNEQFF CIVRSTGNKLTF-CSAIAGPAYNEQFF 3 HD2 1501-YF45 d14 post CSAIAGPAYNEQFF CIVRSTGNKLTF- CSAIAGPAYNEQFF;CIVRSTGNKLTF - CSAIAGPAYNEQFF 3 HD2 1501-YF45 d14 post CSAIAGPAYNEQFF CIVRSTGNKLTF-CSAIAGPAYNEQFF 3 HD2 1501-YF45 d14 post CSANPRVEGTQYF CAIPSQFYF-CSANPRVEGTQYF 1 HD3 1501-YF45 d14 post CSANVRVEGEQYF CAAIRGTYKYIF-CSANVRVEGEQYF 1 HD2 1501-YF45 d14 post CSAQPHITSEQYF TTRPGYSTLTF-CSAQPHITSEQYF 2 HD2 1501-YF45 d14 post CSAQPHITSEQYF TTRPGYSTLTF-CSAQPHITSEQYF 2 HD2 1501-YF45 d14 post CSARAITARYEQYF CSARAITARYEQYF 1 HD3 1501-YF45 d14 post CSARALSTGEQYF CSARALSTGEQYF 7 HD3 1501-YF45 d14 post CSARALSTGEQYF CSARALSTGEQYF 7 HD3 1501-YF45 d14 post CSARALSTGEQYF CSARALSTGEQYF 7 HD3 1501-YF45 d14 post CSARALSTGEQYF CSARALSTGEQYF 7 HD3 1501-YF45 d14 post CSARALSTGEQYF CSARALSTGEQYF 7 HD3 1501-YF45 d14 post CSARALSTGEQYF CSARALSTGEQYF 7 HD3 1501-YF45 d14 post CSARALSTGEQYF CSARALSTGEQYF 7 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD3 1501-YF45 d14 post CSARARVGGEAFF CAVEPQLNNAGGTSYGKLTF- CSARARVGGEAFF 1 HD2 1501-YF45 d14 post CSARAVSGGSTDTQYF CVVSAWYSSASKIIF-CSARAVSGGSTDTQYF 1 HD2 1501-YF45 d14 post CSARAVTGDNSPLHF CAMTGSARQLTF- CSARAVTGDNSPLHF;CAMTGSARQLTF - CSARAVTGDNSPLHF 4 HD2 1501-YF45 d14 post CSARAVTGDNSPLHF CAMTGSARQLTF- CSARAVTGDNSPLHF;CAMTGSARQLTF - CSARAVTGDNSPLHF 4 HD2 1501-YF45 d14 post CSARAVTGDNSPLHF CAMTGSARQLTF- CSARAVTGDNSPLHF;CAMTGSARQLTF - CSARAVTGDNSPLHF 4 HD2 1501-YF45 d14 post CSARAVTGDNSPLHF CAMTGSARQLTF- CSARAVTGDNSPLHF;CAMTGSARQLTF - CSARAVTGDNSPLHF 4 HD2 1501-YF45 d14 post CSARAVVGGYEQYF CAYRSRYPYNTDKLIF- CSARAVVGGYEQYF;CAGGLTQGGSEKLVF - CSARAVVGGYEQYF 1 HD3 1501-YF45 d14 post CSARGQGVLGELFF CLVGATGSARQLTF- CSARGQGVLGELFF;CLVGATGSARQLTF - CSARGQGVLGELFF 2 HD3 1501-YF45 d14 post CSARGQGVLGELFF CLVGATGSARQLTF-CSARGQGVLGELFF 2 HD3 1501-YF45 d14 post CSARGRVGGEQYF CAAPGHSNYQLIW-CSARGRVGGEQYF 1 HD3 1501-YF45 d14 post CSARLGNTNNEQFF CIVRATGNQFYF-CSARLGNTNNEQFF 4 HD3 1501-YF45 d14 post CSARLGNTNNEQFF CIVRATGNQFYF-CSARLGNTNNEQFF 4 HD3 1501-YF45 d14 post CSARLGNTNNEQFF CIVRATGNQFYF-CSARLGNTNNEQFF 4 HD3 1501-YF45 d14 post CSARLGNTNNEQFF CIVRATGNQFYF-CSARLGNTNNEQFF 4 HD3 1501-YF45 d14 post CSARLRTGWDSPLHF CAQGGRNNYGQNFVF- CSARLRTGWDSPLHF;CLVGATGSARQLTF - CSARLRTGWDSPLHF 2 HD3 1501-YF45 d14 post CSARLRTGWDSPLHF CAQGGRNNYGQNFVF-CSARLRTGWDSPLHF 2 HD2 1501-YF45 d14 post CSARLSGSIGEQFF CSARLSGSIGEQFF 1 HD2 1501-YF45 d14 post CSARPGSIETQYF CSARPGSIETQYF 1 HD2 1501-YF45 d14 post CSARPPTLGQTNTEAFF CIVRLPISGNTPLVF-CSARPPTLGQTNTEAFF 1 HD2 1501-YF45 d14 post CSARPRTGGEQYF CALIRNSGNTPLVF- CSARPRTGGEQYF;CAMSVTNPFHNAGNMLTF - CSARPRTGGEQYF 2 HD2 1501-YF45 d14 post CSARPRTGGEQYF CALIRNSGNTPLVF- CSARPRTGGEQYF;CAMSVTNPFHNAGNMLTF - CSARPRTGGEQYF 2 HD2 1501-YF45 d14 post CSARQGSLNTQYF CIVRVLAGGTSYGKLTF-CSARQGSLNTQYF 1 HD3 1501-YF45 d14 post CSARQGVVNEQFF CIVRATGNQFYF- CSARQGVVNEQFF;CIVRATGNQFYF - CSARQGVVNEQFF 1 HD2 1501-YF45 d14 post CSARRTSILNEQYF CALDSRDAGKSTF-CSARRTSILNEQYF 1 HD2 1501-YF45 d14 post CSARTISGGSTDTQYF CVVSSYYSSASKIIF- CSARTISGGSTDTQYF;CIVRSTGNKLTF - CSARTISGGSTDTQYF 1 HD3 1501-YF45 d14 post CSARTRVGNSPLHF CAVDNTNAGKSTF-CSARTRVGNSPLHF 1 HD3 1501-YF45 d14 post CSARVLAGGPGEQYF CSARVLAGGPGEQYF 1 HD2 1501-YF45 d14 post CSARVLSSYNSPLHF CAVSVSYLDGGTSYGKLTF- CSARVLSSYNSPLHF;CAVSVSYLDGGTSYGKL TF-CSARVLSSYNSPLHF 1 HD3 1501-YF45 d14 post CSARVLTVGEQYF CPHP-CSARVLTVGEQYF 1 HD3 1501-YF45 d14 post CSARVLVGNTIYF CASYRDDKIIF-CSARVLVGNTIYF 1 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD3 1501-YF45 d14 post CSARVVVGDTQYF CALDNAGGTSYGKLTF-CSARVVVGDTQYF 3 HD3 1501-YF45 d14 post CSASGGSNSGNTIYF CAENRNAGNMLTF-CSASGGSNSGNTIYF 1 HD3 1501-YF45 d14 post CSASLRTGQNQPQHF CASGSSNTGKLIF-CSASLRTGQNQPQHF 6 HD3 1501-YF45 d14 post CSASLRTGQNQPQHF CASGSSNTGKLIF-CSASLRTGQNQPQHF 6 HD3 1501-YF45 d14 post CSASLRTGQNQPQHF CAESVGLH_NAGKSTF-CSASLRTGQNQPQHF 6 HD3 1501-YF45 d14 post CSASLRTGQNQPQHF CAESVGLH_NAGKSTF-CSASLRTGQNQPQHF 6 HD3 1501-YF45 d14 post CSASLRTGQNQPQHF CASGSSNTGKLIF-CSASLRTGQNQPQHF 6 HD3 1501-YF45 d14 post CSASLRTGQNQPQHF CASGSSNTGKLIF-CSASLRTGQNQPQHF 6 HD2 1501-YF45 d14 post CSASPLTGDEETQYF CAVRGRLGGGYNKLIF-CSASPLTGDEETQYF 1 HD2 1501-YF45 d14 post CSASPRVYGEQYF CIVRVGSWNAGNMLTF- CSASPRVYGEQYF;CIVRVQTGANNLFF - CSASPRVYGEQYF 1 HD3 1501-YF45 d14 post CSASQRTGSSGNTIYF CILGSSNTGKLIF- CSASQRTGSSGNTIYF;CILGSSNTGKLIF - CSASQRTGSSGNTIYF 2 HD2 1501-YF45 d14 post CSASVVTGTFGEQYF CAGTNNDMRF- CSASVVTGTFGEQYF;CAGTNNDMRF - CSASVVTGTFGEQYF 1 HD2 1501-YF45 d14 post CSASWTSFGEQYF CIVLTSGTYKYIF-CSASWTSFGEQYF 1 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD3 1501-YF45 d14 post CSASYLTGSYNEQFF CAGQGYNQGGKLIF-CSASYLTGSYNEQFF 30 HD3 1501-YF45 d14 post CSATLRTLGEQFF CSATLRTLGEQFF 1 HD3 1501-YF45 d14 post CSATSLVTSRTGIQQYF CATDPYSSNTGKLIF-CSATSLVTSRTGIQQYF 1 HD3 1501-YF45 d14 post CSATTLSGGGRETQYF CALSDGGYQKVTF-CSATTLSGGGRETQYF 2 HD3 1501-YF45 d14 post CSATTLSGGGRETQYF CALSDGGYQKVTF-CSATTLSGGGRETQYF 2 HD2 1501-YF45 d14 post CSATVRTGGEQYF CSATVRTGGEQYF 1 HD3 1501-YF45 d14 post CSAVVGSVMRSPLHF CALTPLNSGGSNYKLTF-CSAVVGSVMRSPLHF 1 HD3 1501-YF45 d14 post CSTLDRVGGGELFF CLVGLPGSSNTGKLIF-CSTLDRVGGGELFF 1 HD3 1501-YF45 d14 post CSVADRVGTGELFF CIVPGSTPLVF-CSVADRVGTGELFF 1 HD2 1501-YF45 d14 post CSVAWRVGTGELFF CIVSSGNTGKLIF-CSVAWRVGTGELFF 1 HD3 1501-YF45 d14 post CSVGARVNTGELFF CIAFSGNTPLVF- CSVGARVNTGELFF;CIAFSVNTPLVF - CSVGARVNTGELFF 1 HD3 1501-YF45 d14 post CSVGNRWARVVGSGNTIYF CIVRVSHKAAGNKLTF- CSVGNRWARVVGSGNTIYF 1 HD3 1501-YF45 d14 post CSVGQASNTGELFF CIVRVAVNAGNMLTF-CSVGQASNTGELFF 1 HD3 1501-YF45 d14 post CSVLHRVGGTEAFF CAGPVGSSNTGKLIF-CSVLHRVGGTEAFF 1 HD3 1501-YF45 d14 post CSVQIGRVGGEQFF CIVRPLNTGNQFYF- CSVQIGRVGGEQFF;SMVLGANSKLTF - CSVQIGRVGGEQFF 1 HD3 1501-YF45 d14 post CSVRRGNGQGDTEAFF CALFSSNTGKLIF-CSVRRGNGQGDTEAFF 1 HD3 1501-YF45 d14 post CSVRTGQVTGELFF CSVRTGQVTGELFF 1 HD2 1501-YF45 d14 post CSVSDRVGSDTIYF CLVGAGNTGKLIF- CSVSDRVGSDTIYF;GFQKLVF - CSVSDRVGSDTIYF 1 HD2 1501-YF45 d14 post CSVSGLAGGGEQFF CIALKAAGNKLTF- CSVSGLAGGGEQFF;CIVRVQTGANNLFF - CSVSGLAGGGEQFF 1 HD2 1501-YF45 d14 post CSVVVRTGGNQPQHF CALSGNNNARLMF- CSVVVRTGGNQPQHF;CALSGNNNARLMF - CSVVVRTGGNQPQHF 1 HD3 1501-YF45 pre-vac CASGFLAPGQTSGNTIYF CASGFLAPGQTSGNTIYF 1 HD2 1501-YF45 pre-vac CASRDRFRTDTQYF CAASVAGTYKYIF-CASRDRFRTDTQYF 1 HD2 1501-YF45 pre-vac CASREGPGPRNKNYGYTF CASREGPGPRNKNYGYTF 1 HD2 1501-YF45 pre-vac CASRKGTGTNEKLFF CIVISGAGGTSYGKLTF-CASRKGTGTNEKLFF 1 HD3 1501-YF45 pre-vac CASRPRQTEQFF CILSQGGSQGNLIF- CASRPRQTEQFF;CILSQGGSQGNLIF - CASRPRQTEQFF 1 HD2 1501-YF45 pre-vac CASSASGTSLYEQYF CASSASGTSLYEQYF 1 HD2 1501-YF45 pre-vac CASSEQPLDYGYTF CIVRVAGSGGYQKVTF-CASSEQPLDYGYTF 1 HD2 1501-YF45 pre-vac CASSFTTDTQYF CFTFSGGYQKVTF-CASSFTTDTQYF 1 HD2 1501-YF45 pre-vac CASSGRLAPNEQFF CAMTSTGFQKLVF- CASSGRLAPNEQFF;CAMTSTGFQKLVF - CASSGRLAPNEQFF 1 HD2 1501-YF45 pre-vac CASSLASAQETQYF CAMRGNQAGTALIF-CASSLASAQETQYF 1 HD2 1501-YF45 pre-vac CASSLDVVTDTQYF CASSLDVVTDTQYF 1 HD2 1501-YF45 pre-vac CASSLERAPWEKLFF CASSLERAPWEKLFF 1 HD3 1501-YF45 pre-vac CASSLGASGGAAGEQFF CAVRDAYGGSQGNLIF- CASSLGASGGAAGEQFF 1 HD2 1501-YF45 pre-vac CASSLGVDEQYF CAASASYNTDKLIF-CASSLGVDEQYF 1 HD2 1501-YF45 pre-vac CASSMWARWPNTEAFF CILRAVLLGNNNDMRF- CASSMWARWPNTEAFF;CILRAVLLGNNNDMRF -CASSMWARWPNTEAFF 1 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD2 1501-YF45 pre-vac CASSPFLGPGVQPQHF CIVRGLAAQKLVF- CASSPFLGPGVQPQHF;CIVRGLAAQKLVF - CASSPFLGPGVQPQHF 1 HD2 1501-YF45 pre-vac CASSPGGYRQETQYF CAFMKRGNNARLMF-CASSPGGYRQETQYF 1 HD2 1501-YF45 pre-vac CASSPGLAGSGTGELFF CASSPGLAGSGTGELFF 1 HD2 1501-YF45 pre-vac CASSPVLHTQYF CAYRSAGAQKLVF- CASSPVLHTQYF;CAYRSAGAQKLVF - CASSPVLHTQYF 1 HD2 1501-YF45 pre-vac CASSPVVLANQETQYF CAVGRSGGSYIPTF- CASSPVVLANQETQYF;CAVGRSGGSYIPTF - CASSPVVLANQETQYF 1 HD2 1501-YF45 pre-vac CASSQDKLRGGETQYF CAVISNAGGTSYGKLTF- CASSQDKLRGGETQYF 1 HD2 1501-YF45 pre-vac CASSQVPGGSEQYF CIVRVAGIGGNTPLVF- CASSQVPGGSEQYF;CIVRVAGIGGNTPLVF - CASSQVPGGSEQYF 1 HD3 1501-YF45 pre-vac CASSQVTQLSTEAFF CIVRVGYNARLMF-CASSQVTQLSTEAFF 1 HD2 1501-YF45 pre-vac CASSRAVQPGQGATNEKLFF CAASLMDSNYQLIW- CASSRAVQPGQGATNEKLFF 1 HD3 1501-YF45 pre-vac CASSRDLIGTEAFF CIVRVYTGNQFYF-CASSRDLIGTEAFF 1 HD2 1501-YF45 pre-vac CASSRTGWYEQYF CALAVTTGNQFYF-CASSRTGWYEQYF 1 HD2 1501-YF45 pre-vac CASSTFGQGSTGNTEAFF CASSTFGQGSTGNTEAFF 1 HD3 1501-YF45 pre-vac CASSVQGLNTEAFF CAPQMDSSYKLIF-CASSVQGLNTEAFF 1 HD2 1501-YF45 pre-vac CASSYKENYGYTF CAMSPNYGNNRLAF-CASSYKENYGYTF 1 HD3 1501-YF45 pre-vac CASTPSRTGGYNEQFF CAERRGSGGSNYKLTF- CASTPSRTGGYNEQFF 1 HD2 1501-YF45 pre-vac CASWGNYGYTF CIVRVAVLSGANNLFF- CASWGNYGYTF;CIVRVSVLSGANNLFF - CASWGNYGYTF 1 HD3 1501-YF45 pre-vac CATRLAGGLQGYNEQFF CAFLMDSNYQLIW-CATRLAGGLQGYNEQFF 1 HD2 1501-YF45 pre-vac CATSEGPFRRNIQYF CVVLKPDNFNKFYF-CATSEGPFRRNIQYF 1 HD2 1501-YF45 pre-vac CATVGTGGDVRGDEAFF CATVGTGGDVRGDEAFF 1 HD2 1501-YF45 pre-vac CSAALLGTGGGGYTF CIVRGLNAGNMLTF- CSAALLGTGGGGYTF;CIVRGLAAQKLVF - CSAALLGTGGGGYTF 1 HD2 1501-YF45 pre-vac CSAAPGDSYNEQFF CAVRVPSWGKLQF-CSAAPGDSYNEQFF 1 HD3 1501-YF45 pre-vac CSAGGRPGEQYF CSAGGRPGEQYF 1 HD3 1501-YF45 pre-vac CSAGQRTNTGELFF CIVMSGNTPLVF-CSAGQRTNTGELFF 1 HD2 1501-YF45 pre-vac CSAIVLVSGEQYF CVVSDFKDKLSF- CSAIVLVSGEQYF;CVVSDFKDKLSF - CSAIVLVSGEQYF 1 HD2 1501-YF45 pre-vac CSAKMLTGNQPQHF CAFGDSNYQLIW-CSAKMLTGNQPQHF 1 HD2 1501-YF45 pre-vac CSAKVLAAFQETQYF CVVSGGYSGNTGKLIF- CSAKVLAAFQETQYF;CVVSGGYSGNTGKLIF - CSAKVLAAFQETQYF 1 HD3 1501-YF45 pre-vac CSALVRTGDQQPQHF CAAGGRGGNTGKLIF-CSALVRTGDQQPQHF 1 HD2 1501-YF45 pre-vac CSAPILAGQGQKLFF CILGRDDKIIF- CSAPILAGQGQKLFF;CILGRDDKIIF - CSAPILAGQGQKLFF 1 HD3 1501-YF45 pre-vac CSAPPLSGGQETQYF CAVRPYDSWGKLQF- CSAPPLSGGQETQYF;CAVGPYDSWGKLQF - CSAPPLSGGQETQYF 1 HD3 1501-YF45 pre-vac CSAPTRVEGPQHF CVVSSPNSGYALNF- CSAPTRVEGPQHF;CVVSSPNSGYALNF - CSAPTRVEGPQHF 1 HD2 1501-YF45 pre-vac CSAPVIAGRADTQYF CSAPVIAGRADTQYF 1 HD2 1501-YF45 pre-vac CSARAGTGAFEQYF CAVYDYKLSF-CSARAGTGAFEQYF 1 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD2 1501-YF45 pre-vac CSARAIAFGGEQYF CAGPNSNSGYALNF-CSARAIAFGGEQYF 1 HD3 1501-YF45 pre-vac CSARALTVYNSPLHF CAASAGGGAGGTSYGKLTF- CSARALTVYNSPLHF;CAASAGGGAGGTSYGRL TF-CSARALTVYNSPLHF 1 HD2 1501-YF45 pre-vac CSARASRIGTDTQYF CAGLNTGGFKTIF- CSARASRIGTDTQYF;CAGLNTGGFKTIF - CSARASRIGTDTQYF 1 HD2 1501-YF45 pre-vac CSARDLGLAEETQYF CALGGSQGNLIF- CSARDLGLAEETQYF;CAVYDYKLSF - CSARDLGLAEETQYF 1 HD2 1501-YF45 pre-vac CSARDLTILTDTQYF CIVRVEANAGGTSYGKLTF- CSARDLTILTDTQYF 1 HD2 1501-YF45 pre-vac CSARGVVGRNSPLHF CALSAAGGTSYGKLTF-CSARGVVGRNSPLHF 1 HD2 1501-YF45 pre-vac CSARILAGGPYNEQFF CAVRSYNTDKLIF-CSARILAGGPYNEQFF 1 HD2 1501-YF45 pre-vac CSARLRVSSETQYF CAYRSGYRDDKIIF-CSARLRVSSETQYF 1 HD2 1501-YF45 pre-vac CSARPLTNSPLHF CVVSDSGNQFYF- CSARPLTNSPLHF;CVVSDSGNQFYF - CSARPLTNSPLHF 1 HD2 1501-YF45 pre-vac CSARPLTTMKTQYF CSARPLTTMKTQYF 1 HD2 1501-YF45 pre-vac CSARRAVISYEQYF CIVRPPTGNQFYF- CSARRAVISYEQYF;CAFRKASGTYKYIF - CSARRAVISYEQYF 1 HD2 1501-YF45 pre-vac CSARSRVGGAQHF CAGSVYNTDKLIF-CSARSRVGGAQHF 1 HD2 1501-YF45 pre-vac CSARTGSIYNSPLHF CALKAAGNKLTF-CSARTGSIYNSPLHF 1 HD2 1501-YF45 pre-vac CSARVGANYGYTF CAPRDSGGYQKVTF-CSARVGANYGYTF 1 HD2 1501-YF45 pre-vac CSARVGSIMDTQYF CAVRPRSGNTPLVF-CSARVGSIMDTQYF 1 HD3 1501-YF45 pre-vac CSARVGSIQETQYF CAVRGAGGTSYGKLTF-CSARVGSIQETQYF 1 HD2 1501-YF45 pre-vac CSARVGSISTLHF CAYRTGNTGKLIF-CSARVGSISTLHF 1 HD2 1501-YF45 pre-vac CSARVGSLLAQYF CAVRSPGGGADGLTF-CSARVGSLLAQYF 1 HD3 1501-YF45 pre-vac CSARVGSLLETQYF CAYRAGNQFYF-CSARVGSLLETQYF 1 HD2 1501-YF45 pre-vac CSARVGSLNTIYF CAVNQAGTALIF- CSARVGSLNTIYF;CAVNQAGTALIF - CSARVGSLNTIYF 1 HD2 1501-YF45 pre-vac CSARVGSLPDTQYF CAGRPNAGGTSYGKLTF-CSARVGSLPDTQYF 1 HD2 1501-YF45 pre-vac CSARVGSLQETQYF CAVPSGSARQLTF-CSARVGSLQETQYF 3 HD2 1501-YF45 pre-vac CSARVGSLQETQYF CSARVGSLQETQYF 3 HD3 1501-YF45 pre-vac CSARVGSLQETQYF CAVQGTGGFKTIF-CSARVGSLQETQYF 3 HD2 1501-YF45 pre-vac CSARVGSLTAQYF CAGPGGGADGLTF-CSARVGSLTAQYF 1 HD2 1501-YF45 pre-vac CSARVGSLTDTQYF CAVRGLSGGSNYKLTF- CSARVGSLTDTQYF;CAVRGLSGGSNYKLTF - CSARVGSLTDTQYF 2 HD2 1501-YF45 pre-vac CSARVGSLTDTQYF CVVTNSNSGYALNF- CSARVGSLTDTQYF;CVVTNSNSGYALNF - CSARVGSLTDTQYF 2 HD2 1501-YF45 pre-vac CSARVGSLVETQYF CVVRANSNSGYALNF- CSARVGSLVETQYF;CVVRANSNSGYALNF - CSARVGSLVETQYF 1 HD3 1501-YF45 pre-vac CSARVGSVQPHEQYF CSARVGSVQPHEQYF 1 HD3 1501-YF45 pre-vac CSARVGSVVGNTIYF CAVLNRDDKIIF-CSARVGSVVGNTIYF 1 HD2 1501-YF45 pre-vac CSARVGTNYGYTF CALPQGAQKLVF- CSARVGTNYGYTF;CALPQGAQKLVF - CSARVGTNYGYTF 1 HD3 1501-YF45 pre-vac CSARVIAGAYEQYF CAASGAGGTSYGKLTF-CSARVIAGAYEQYF 1 HD3 1501-YF45 pre-vac CSARVLAGASGETQYF CAVEEAAGNKLTF-CSARVLAGASGETQYF 1 HD2 1501-YF45 pre-vac CSARVLAGGPGETQYF CAVKGYNTDKLIF-CSARVLAGGPGETQYF 1 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD3 1501-YF45 pre-vac CSARVLAGGPRDTQYF CALSAPRAQKLVF-CSARVLAGGPRDTQYF 1 HD2 1501-YF45 pre-vac CSARVLAGHPGETQYF CSARVLAGHPGETQYF 1 HD2 1501-YF45 pre-vac CSARVLAGRADTQYF CAAFFSDGQKLLF- CSARVLAGRADTQYF;CAAFFSDGQKLLF - CSARVLAGRADTQYF 1 HD2 1501-YF45 pre-vac CSARVLAGRPQETQYF CAVSERTGGTSYGKLTF- CSARVLAGRPQETQYF;CAVSERTGGTSYGKLT F-CSARVLAGRPQETQYF 1 HD2 1501-YF45 pre-vac CSARVLAGVGEQFF CAVKDNYGQNFVF-CSARVLAGVGEQFF 1 HD2 1501-YF45 pre-vac CSARVLAGVSTDTQYF CAVRASTDSWGKLQF- CSARVLAGVSTDTQYF;CAVFWW_YNKLIF - CSARVLAGVSTDTQYF 1 HD2 1501-YF45 pre-vac CSARVLIGQETQYF CAAINTNAGKSTF- CSARVLIGQETQYF;CAINTLAGGTSYGKLTF - CSARVLIGQETQYF 1 HD2 1501-YF45 pre-vac CSARVLPSTDTQYF CAVEDPLTTDSWGKLQF-CSARVLPSTDTQYF 1 HD2 1501-YF45 pre-vac CSARVLSGGVRETQYF CSARVLSGGVRETQYF 1 HD3 1501-YF45 pre-vac CSARVLTGGNSPLHF CAGSPQGGSEKLVF-CSARVLTGGNSPLHF 1 HD2 1501-YF45 pre-vac CSARVLTGNQPQHF CAAMDSNYQLIW-CSARVLTGNQPQHF 1 HD2 1501-YF45 pre-vac CSARVLVGYEQYF CAVAQGGSEKLVF-CSARVLVGYEQYF 1 HD3 1501-YF45 pre-vac CSARVRADYNSPLHF CAVIDYNQGGKLIF- CSARVRADYNSPLHF;CAHGRGSQGNLIF - CSARVRADYNSPLHF 1 HD3 1501-YF45 pre-vac CSARVRTDLGSPLHF CIALNAGGTSYGKLTF-CSARVRTDLGSPLHF 1 HD3 1501-YF45 pre-vac CSARVRVRGTQYF CGADYDNDMRF- CSARVRVRGTQYF;CGADYDNDMRF - CSARVRVRGTQYF 1 HD3 1501-YF45 pre-vac CSARVVAWNSPLHF CAMAGNRDDKIIF- CSARVVAWNSPLHF;LGPDSWGKLQF - CSARVVAWNSPLHF 1 HD2 1501-YF45 pre-vac CSARVVINSPLHF CAVSVAGGADGLTF- CSARVVINSPLHF;CAVSVAGGADGLTF - CSARVVINSPLHF 1 HD3 1501-YF45 pre-vac CSARVVTGDNSPLHF CAGPYAGGTSYGKLTF-CSARVVTGDNSPLHF 1 HD3 1501-YF45 pre-vac CSARVVTGDSPLHF CAVGTGGTSYGKLTF-CSARVVTGDSPLHF 1 HD2 1501-YF45 pre-vac CSARVVTGIGQPQHF CSARVVTGIGQPQHF 1 HD3 1501-YF45 pre-vac CSARVVTGSDQPQHF CALILLLDSNYQLIW-CSARVVTGSDQPQHF 1 HD2 1501-YF45 pre-vac CSARVVVEGPQHF CATDVNAGGTSYGKLTF-CSARVVVEGPQHF 1 HD3 1501-YF45 pre-vac CSARVVVGDTQYF CALDNAGGTSYGKLTF-CSARVVVGDTQYF 3 HD3 1501-YF45 pre-vac CSARVVVGDTQYF CALDNAGGTSYGKLTF-CSARVVVGDTQYF 3 HD2 1501-YF45 pre-vac CSARVVVNQPQHF CAASPLNAGGTSYGKLTF-CSARVVVNQPQHF 1 HD2 1501-YF45 pre-vac CSASGVAGGEDGYTF CAASSYYNDYKLSF-CSASGVAGGEDGYTF 1 HD2 1501-YF45 pre-vac CSASLRVYGEQFF CGAGGTSYGKLTF- CSASLRVYGEQFF;CGAGGTSYGKLTF - CSASLRVYGEQFF 1 HD2 1501-YF45 pre-vac CSASPLVGNTQYF CASNTGFQKLVF-CSASPLVGNTQYF 1 HD3 1501-YF45 pre-vac CSASQRTGSSGNTIYF CILGSSNTGKLIF- CSASQRTGSSGNTIYF;CILGSSNTGKLIF - CSASQRTGSSGNTIYF 2 HD2 1501-YF45 pre-vac CSASVLQGAFEQYF CAVGLDARLMF-CSASVLQGAFEQYF 1 HD3 1501-YF45 pre-vac CSASVVTGDQPQHF CAVLYSGAGSYQLTF-CSASVVTGDQPQHF 6 HD3 1501-YF45 pre-vac CSASVVTGDQPQHF CAVLYSGAGSYQLTF- CSASVVTGDQPQHF;CIVRA*YGNKLVF - CSASVVTGDQPQHF 6 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint HD3 1501-YF45 pre-vac CSASVVTGDQPQHF CSASVVTGDQPQHF 6 HD3 1501-YF45 pre-vac CSASVVTGDQPQHF CSASVVTGDQPQHF 6 HD3 1501-YF45 pre-vac CSASVVTGDQPQHF CAVLYSGAGSYQLTF-CSASVVTGDQPQHF 6 HD3 1501-YF45 pre-vac CSASVVTGDQPQHF CAVLYSGAGSYQLTF-CSASVVTGDQPQHF 6 HD3 1501-YF45 pre-vac CSATTRVEGSQYF CIVRVQGGVGNQFYF-CSATTRVEGSQYF 1 HD2 1501-YF45 pre-vac CSAWVLVQGAQYF CAVETPYNTDKLIF-CSAWVLVQGAQYF 1 HD2 1501-YF45 pre-vac CSGLVVSARPDTQYF CSGLVVSARPDTQYF 1 HD3 1501-YF45 pre-vac CSPVGTGDEKLFF CAVRAANQAGTALIF-CSPVGTGDEKLFF 1 HD3 1501-YF45 pre-vac CSVEGTSGRGEQFF CSVEGTSGRGEQFF 1 HD3 1501-YF45 pre-vac CSVEMAVRSGEQYF CIVRGGKLIF-CSVEMAVRSGEQYF 1 HD2 1501-YF45 pre-vac CSVGMGTVTTYEQYF CAASKRGSGNTGKLIF-CSVGMGTVTTYEQYF 1 HD2 1501-YF45 pre-vac CSVPSGGDGYTF CIVRVATYGQNFVF-CSVPSGGDGYTF 1 HD3 1501-YF45 pre-vac CSVQHRVGGEQFF CAVSSSNTGKLIF-CSVQHRVGGEQFF 1 HD2 1501-YF45 pre-vac CSVTDRVGSYEQYF CSVTDRVGSYEQYF 1 HD2 1501-YF45 pre-vac CSVVFRVEGGYTF CAVGGYYGGATNKLIF-CSVVFRVEGGYTF 1 HD3 1501-YF45 pre-vac RSVEGTSGRGEQFF RSVEGTSGRGEQFF 1 Table S6: Longitudinal follow-up visits ID Sex Total YFV doses Vaccine dates Longitudinal visit dates HD1 M 2 8/25/2016, 9/8/2017 8/28/17 12/4/18 HD2 F 2 9/12/2016, 5/26/2017 5/12/17 4/11/19 12/14/21 5/25/23 HD3 M 2 1/4/2017, 8/11/2017 8/2/17 8/29/19 6/15/23 HD4 M 1 5/22/17 8/14/17 4/23/18 1/30/20 9/8/21 HD5 F 1 4/21/17 6/22/17 2/7/19 2/13/20 9/27/21 4/6/23 .CC-BY-NC-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted March 14, 2024. ; https://doi.org/10.1101/2024.03.11.584523doi: bioRxiv preprint