Slide 1: VAX-24 Infant Phase 2 Dose-Finding Study Topline Results
VAX-24 Infant Phase 2 Dose- Finding Study Topline Results March 31, 2025
Slide 2: Forward-Looking Statements
Forward-Looking Statements This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. These statements include, but are not limited to, statements related to the ability of Vaxcyte’s vaccine candidates and platform to achieve the
Slide 3: Vaxcyte Mission Statement
VAXCYTE MISSION STATEMENT We are on a global mission to engineer high- fidelity vaccines that protect humankind from the consequences of bacterial diseases. March 31, 2025 3
Slide 4: Agenda
• INTRODUCTION AND VAX-24 INFANT STUDY RESULTS OVERVIEW Agenda • VAX-24 INFANT PHASE 2 DOSE-FINDING STUDY TOPLINE RESULTS – Disposition and Demographics – Safety and Tolerability Data – Topline Immunogenicity Data ▪ Post-Dose 3 IgG & Interim OPA ▪ Post-Dose 4 Interim IgG • PLANNING FOR INFANT PHASE
Slide 5: Introduction and VAX-24 Infant Study Results Overview
Introduction and VAX-24 Infant Study Results Overview March 31, 2025 5
Slide 6: VAX-24 Phase 2 Infant Study Results Demonstrate Potential to Achieve Broadest Coverage
VAX-24 Phase 2 Infant Study Results and Platform Demonstrate Potential to Achieve Broadest Coverage of Any Infant PCV On-Market Topline study results positive and met objectives Safety and tolerability profile similar to standard-of-care VAX-24 elicited substantial IgG, OPA and memory responses and
Slide 7: Global Health Impact of Pneumococcal Disease Remains Significant
Global Health Impact of Pneumococcal Disease (PD) Remains Significant The U.S. CDC lists drug- Over 150,000 U.S. Globally, Streptococcus resistant Streptococcus hospitalizations annually pneumoniae is the leading pneumoniae as a due to pneumococcal cause of vaccine- “serious threat.” pneumonia. prev
Slide 8: VAX-24 Designed to Provide Broadest Serotype and Disease Coverage in Infants
VAX-24 Designed to Provide Broadest Serotype and Disease Coverage in Infants with Opportunity to Further Expand Coverage with VAX-31 16.00% 14.48% 13.79% 14.00% 13.10% 12.00% 9.66% 10.00% 8.00% 6.21% 6.21% 6.00% 4.83% 4.83% 4.14% 3.45% 4.00% 3.45% 3.45% 2.00% 1.38% 1.38% 1.38% 1.38% 1.38% 0.69% 0.69
Slide 9: VAX-24 Infant Phase 2 Dose-Finding Study Topline Results
VAX-24 Infant Phase 2 Dose-Finding Study Topline Results March 31, 2025 9
Slide 10: Study Design
Study Design March 31, 2025 10
Slide 11: Infant Phase 2 Dose-Finding Clinical Study (N=802)
VAX-24 Infant Phase 2 Dose-Finding Clinical Study (N=802) Randomized, Observer-Blind, Active-Controlled, Dose-Finding, Clinical Study to Evaluate Safety, Tolerability and Immunogenicity of VAX-24 vs. Standard-of-Care (PCV20) in 802 Healthy Infants All 36 VAX-24 subjects from Stage 1 proceeded to Sta
Slide 12: Three VAX-24 Doses Evaluated in Infant Phase 2 Dose-Finding Study
Three VAX-24 Doses Evaluated in Infant Phase 2 Dose-Finding Study Identical to Doses Evaluated in VAX-24 Adult Program 14.5% 13.8% 13.1% % of IPD 9.7% in US children 6.2% 4.8% <5 yrs of age1 3.5% 1.4% 0.7% 0.7% 0.7% 1.4% 1.4% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 3 19F 15B 22F 33F 1
Slide 13: Disposition and Demographics
Disposition and Demographics March 31, 2025 13
Slide 14: Study Disposition
Study Disposition VAX-24 Infant Phase 2 Dose-Finding Study Randomized N = 8021 Vaccinated Vaccinated Vaccinated Vaccinated VAX-24 Low Dose VAX-24 Mid Dose VAX-24 Mixed Dose PCV20 N = 205 N = 201 N = 195 N = 188 Included in Safety Population Included in Safety Population Included in Safety Population
Slide 15: Population Demographics
Population Demographics Generally Balanced Across Cohorts VAX-24 Low Dose VAX-24 Mid Dose VAX-24 Mixed Dose PCV20 Number of Subjects 205 201 195 188 Median Age, days (Q1, Q3)1 64 ( 61, 68 ) 64 ( 61, 68 ) 64 ( 62, 68) 64 ( 62, 68) Sex, n (%) 113 ( 55.1) 103 ( 51.2 ) 94 ( 48.2 ) 87 ( 46.3 ) Female Mal
Slide 16: Safety and Tolerability Data
Safety and Tolerability Data March 31, 2025 16
Slide 17: VAX-24 Well Tolerated Across All Dose Cohorts: Local Solicited AEs
VAX-24 Well Tolerated Across All Dose Cohorts Local Solicited AEs Through 7 Days After Each of Three Primary Doses 100% Mild 90% Moderate 80% Severe 70% 60% 50% 40% 30% 20% 10% 0% Low Mid Mixed PCV20 Low Mid Mixed PCV20 Low Mid Mixed PCV20 Edema* Erythema Tenderness at Injection Site * One occurrenc
Slide 18: VAX-24 Well Tolerated Across All Dose Cohorts: Systemic Solicited AEs
VAX-24 Well Tolerated Across All Dose Cohorts Systemic Solicited AEs Through 7 Days After Each of Three Primary Doses 100% 90% Mild 80% Moderate 70% Severe 60% 50% 40% 30% 20% 10% 0% . Fever* Irritability Decreased Appetite Decreased Sleep Increased Sleep * One occurrence of severe fever redacted to
Slide 19: VAX-24 Well Tolerated Across All Dose Cohorts: Any Solicited AE
VAX-24 Well Tolerated Across All Dose Cohorts Any Solicited AE Through 7 Days After Each Primary Dose 100% Severe Moderate Mild 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% PD1 PD2 PD3 PD1 PD2 PD3 PD1 PD2 PD3 PD1 PD2 PD3 VAX-24 Low VAX-24 Mid VAX-24 Mixed PCV20 March 31, 2025 19
Slide 20: Safety Data from VAX-24 Phase 2 Study
Safety Data from VAX-24 Phase 2 Study Safety Results Similar to PCV20 and Across Cohorts VAX-24 VAX-24 VAX-24 PCV20 Overall Low Dose Mid Dose Mixed Dose NUMBER OF SUBJECTS WITH: 205 201 195 188 789 Unsolicited TEAE, n (%) 186 (90.7) 184 (91.5) 181 (92.8) 176 (93.6) 727 (92.1) Related Unsolicited TEA
Slide 21: Topline Immunogenicity Data
Topline Immunogenicity Data March 31, 2025 21
Slide 22: Criteria for Infant Phase 2 Immunogenicity Measures to Support Phase 3 Advancement
Criteria for Infant Phase 2 Immunogenicity Measures to Support Phase 3 Advancement and Precedent FDA Considerations for Broader-Spectrum Infant PCV Licensure TOTALITY OF DATA1 Phase 2 Target Phase 3 Endpoints Secondary Immunogenicity Endpoints • For common STs: Lower limit (LL) of the • For common S
Slide 23: Demonstrated High Overall Seroconversion Rates Across All Doses
VAX-24 Demonstrated High Overall Seroconversion Rates Across All Doses VAX-24 Low Dose VAX-24 Mid Dose VAX-24 Mixed Dose PCV20 100 % of subjects with predefined IgG levels (>0.35mcg/mL) 80 60 40 20 0 7F 14 15B 11A 10A 19A 18C 6B 6A 9N 20C 19F 22F 33F 12F 23F 17F 9V 3 4 8 5 1 2 Serotypes Common with
Slide 24: PD3 Seroconversion Rates Compared to PCV20
VAX-24 PD3 Seroconversion Rates Compared to PCV20 Met Precedent Phase 2 Non-Inferiority Criteria on 20 of 24 STs at All Doses VAX-24 vs. PCV20: Difference in % of Subjects Meeting Predefined IgG Levels2 % of IPD in US children <5 yrs of age1 VAX-24 Low Dose (1.1mcg) VAX-24 Mid Dose (2.2mcg) VAX-24 M
Slide 25: PD3 IgG GMRs Compared to PCV20
VAX-24 PD3 IgG GMRs Compared to PCV20 Met Target Phase 2 Non-Inferiority Criteria for Point Estimate of >0.6 on 22 of 24 STs at Mid and Mixed Doses % of IPD in US children IgG Geometric Mean Ratios for VAX-24 vs. PCV202 <5 yrs of age1 VAX-24 Low Dose (1.1mcg) VAX-24 Mid Dose (2.2mcg) VAX-24 Mixed Do
Slide 26: PD3 OPA GMT Immune Responses
VAX-24 PD3 OPA GMT Immune Responses OPA is a Key Secondary Endpoint – GMTs >8 Correlated With Effectiveness Against IPD 100000 VAX-24 Low Dose VAX-24 Mid Dose VAX-24 Mixed Dose 10000 PCV 20 OPA GMTs (95% CI) 1000 100 10 1 19F 22F 33F 7F 12F 23F 17F 15B 11A 10A 19A 18C 6B 6A 9N 20B 3 4 8 14 5 1 2 9V
Slide 27: PD4 Interim IgG Immunogenicity Data
PD4 Interim IgG Immunogenicity Data March 31, 2025 27
Slide 28: PD4 Seroconversion Rates
VAX-24 PD4 Seroconversion Rates High IgG Seroconversion Rates Across All Doses VAX-24 Low Dose VAX-24 Mid Dose VAX-24 Mixed Dose PCV20 100 % of subjects with predefined IgG levels (>0.35mcg/mL) 80 60 40 20 0 7F 15B 11A 10A 19A 18C 14 6B 6A 9N 20C 19F 22F 33F 12F 23F 17F 9V 3 4 8 5 1 2 Serotypes Cont
Slide 29: Demonstrated Robust Memory Responses – PD3 vs PD4 IgG GMCs
VAX-24 Demonstrated Robust Memory Responses – PD3 vs PD4 IgG GMCs Robust Booster Responses Elicited at all Doses VAX-24 Mid Dose Post-Dose 3 VAX-24 Mid Dose Post-Dose 4 15 IgG GMCs mcg/mLs (95% CI) 10 5 0 19F 22F 33F 7F 12F 23F 15B 11A 10A 19A 18C 6B 6A 9N 20C 3 4 8 14 5 1 9V 17F 2 Serotypes Contain
Slide 30: PD4 IgG GMRs
VAX-24 PD4 IgG GMRs Met Target Phase 2 Non-Inferiority Criteria for Point Estimate of >0.6 on 19 of 24 STs at Mid and Mixed Doses IgG Geometric Mean Ratios for VAX-24 vs. PCV201 VAX-24 Low Dose (1.1mcg) VAX-24 Mid Dose (2.2mcg) VAX-24 Mixed Dose (2.2mcg/4.4mcg) 14.5% 3 3 3 3 13.8% 19F 19F 19F 19F 13
Slide 31: Planning for Infant Phase 3 Program
Planning for Infant Phase 3 Program March 31, 2025 31
Slide 32: Mid Dose (2.2mcg) Selected as Basis for Advancement
VAX-24 Mid Dose (2.2mcg) Selected as Basis for Advancement Pending VAX-31 Phase 2 Topline Data Readout, Prepare for Phase 3 Study With VAX-24 or VAX-31 PD3 IgG Seroconversion PD3 IgG GMR PD4 IgG GMR % of IPD in US children <5 yrs of age 3 3 14.5% 3 3 19F 19F 13.8% 19F 19F 15B 15B 13.1% 15B/C 15B 22F
Slide 33: Dose-Dependent IgG GMR Responses PD3
VAX-24 Dose-Dependent IgG GMR Responses PD3 IgG Responses for STs Dosed at 1.1mcg, 2.2mcg and 4.4mcg* Indicate Opportunity to Increase Dose IgG GMR 3 6B 7F Dose-Dependent Responses Demonstrate 9V Potential for Optimization 18C 19A 19F GMR 0.0 0.5 1.0 1.5 2.0 2.5 IgG = Immunoglobulin G. *The 7 STs do
Slide 34: IgG GMCs at Mid and Mixed Doses for STs Dosed at 2.2mcg
IgG GMCs at Mid and Mixed Doses for 13 STs Dosed at 2.2mcg Absence of Carrier Suppression Observed Indicate Opportunity to Increase Dose VAX-24 Mid Dose IgG Geometric Mean Concentrations 1-month Post-Dose 3 10 VAX-24 Mixed Dose IgG GMCs mcg/mLs (95% CI) 1 0.1 12F 22F 23F 33F 17F 6A 10A 11A 15B 9N 20
Slide 35: Adult Data Support Carrier-Sparing Platform Ability
Adult Data Support Carrier-Sparing Platform Ability to Add Coverage, Adjust Dose and Improve Immune Responses High/Mixed Dose IgG GMC Comparison: VAX-24 (50-59) vs VAX-31 (50-59) Optimized Optimized Dose Downward Dose Upward in VAX-31 100 in VAX-31 10 IgG GMC 1 0.1 14 31 9N 7C F A A F B F B F F A F
Slide 36: VAX-24 Phase 2 Infant Study Results Demonstrate Potential to Achieve Broadest Coverage
VAX-24 Phase 2 Infant Study Results and Platform Demonstrate Potential to Achieve Broadest Coverage of Any Infant PCV On-Market Topline study results positive and met objectives Safety and tolerability profile similar to standard-of-care VAX-24 elicited substantial IgG, OPA and memory responses and
Slide 37: PCV Franchise and Pipeline Update
PCV Franchise and Pipeline Update March 31, 2025 37
Slide 38: Clinical Development Next Steps and Anticipated Milestones
Clinical Development Next Steps and Anticipated Milestones1 Potential Best-in-Class PCV Franchise for Adult and Infant Segments Population Investigational PCV Key Anticipated Milestones VAX-31 • Following FDA End-of-Phase 2 meeting, initiate Phase 3 pivotal, non-inferiority study by mid-2025 and ann
Slide 39: Pneumococcal Vaccine Market Poised for Significant Growth
Pneumococcal Vaccine Market Poised for Significant Growth Expected to Reach ~$13B by 2027 Driven Primarily by Growth in Adult Market $14 ~$13B PCV MARKET – KEY GROWTH DRIVERS $12 • ACIP recently expanded U.S. universal adult Other PCV Market vaccination by lowering the age to ≥50 years from Growth M
Slide 40: Pipeline of High-Fidelity Vaccines
Pipeline of High-Fidelity Vaccines Broad-Spectrum Conjugate and Novel Protein Vaccines to Prevent or Treat Bacterial Infectious Diseases Preclinical Phase 1 Phase 2 Phase 3 Approved 31-Valent Adults 50+ VAX-31 PCV Candidate Infants 24-Valent VAX-24 Infants PCV Candidate VAX-XL Adults & Infants VAX-X
Slide 41: Q&A with Management
Q&A with Management Grant Pickering Jim Wassil Andrew Guggenhime Chief Executive Officer, Director Executive Vice President and Chief President and Chief Financial Officer and Founder Operating Officer March 31, 2025 41
Slide 42: Vaxcyte
VAXCYTE
Slide 43: Appendix Slides
Appendix Slides VAXCYTE
Slide 44: Study Safety, Tolerability and Immunogenicity Key Outcome Measures
Study Safety, Tolerability and Immunogenicity Key Outcome Measures DAY 7 AFTER EACH 1 MONTH POST-DOSE 1-4; 1 MONTH POST- 1 MONTH POST- 6 MONTHS PD4 DOSE ONGOING DURING DOSE 3 (PD3)* DOSE 4 (PD4)* PRIMARY SERIES SAFETY AND • Solicited local reactions • Unsolicited adverse events (AE) • Serious advers