Vaxcyte : December Investor Presentation

Corporate Presentation

December 3, 2024

VAXCYTE MISSION STATEMENT

We are on a global mission to engineer high- fidelity vaccines that protect humankind from the consequences of bacterial diseases.

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Highlights: Potential Best-in-Class Pneumococcal Conjugate Vaccine (PCV) Franchise

Positive Phase 1/2 Adult Data for VAX-31 and VAX-24 Validate Potential of Site-Specific, Carrier-Sparing Platform

POTENTIAL BEST-IN-CLASS PCV

FRANCHISE

• Scalable, site-specific platform enabling broader-spectrumcarrier- sparing PCVs
• Adult Indication
• • VAX-31: Advancing to Phase 3 program based on the positive Phase 1/2 data; received FDA Breakthrough Therapy designation
  • Broadest-spectrumPCV in clinic; designed to cover >95% of IPD, including currently circulating and historically prevalent strains, in U.S. adults aged 50 and older
• Pediatric Indication: VAX-24 and VAX-31 advancing in parallel
• • VAX-24: Enrollment complete in Phase 2 infant study
  • VAX-31: Enrolling subjects in Phase 2 study

HIGHLY ATTRACTIVE

PCV MARKET

• Well-defined~$8B market segment poised for substantial growth
• • Age range in US expanded to include adults ≥ 50 years of age; and
  • As more developed countries adopt or expand universal vaccination of adults
• Leverages established surrogate immune endpoints as basis for full approval, negating need for field efficacy studies
• Serotype and disease spectrum of coverage is the primary adoption driver, yet incumbents limited by carrier suppression

EXCLUSIVE CELL-FREE	ALIGNED CRITICAL
PLATFORM	RESOURCES
• Vaxcyte PCV Franchise	• Strategic alignment with Lonza
- Leverages site-specific conjugation to	- Global commercial manufacturing
expose protective T- and B-cell antigens	agreement to produce VAX-31 and VAX-24
- Enables carrier-sparing conjugates that	key components
honor well-understood PCV MOA	- Building out capacity to satisfy global PCV
• Permits production of "tough-to-	demand for commercial markets
make" antigens	• Seasoned management team,
• Platform unlocks large market	directors and advisors
opportunities	• $3.3 billion in cash, cash equivalents
- VAX-A1: Novel Group A Strep vaccine	and investments as of 9/30/24
- VAX-PG: Novel periodontitis vaccine
- VAX-GI: Novel Shigella vaccine

SOC = Standard-of-Care, IPD = Invasive Pneumococcal Disease, MOA = Mechanism of Action.

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Experienced Team with Track Record in Vaccines and Biopharma

Management Team

	Grant Pickering, MBA			Andrew Guggenhime, MBA			Jim Wassil, MS, MBA
	CEO & Co-Founder			President & CFO			EVP & COO

Jeff Fairman, PhD

Sally Bolmer

Harp Dhaliwal, MBA

Mark Wiggins, MBA

VP Research & Co-Founder

SVP Regulatory Affairs

SVP Commercial Mfg & Supply Chain

CBO

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Cell-Free Protein Synthesis Platform Unlocks Multiple Vaccine Applications

Design and Produce Proteins Beyond Reach of Conventional Methods

CELL-FREE PROTEIN

SYNTHESIS

• Transcriptional & translational (ribosomal) machinery from E. coli stored as a frozen
  "extract"
• Produces singular protein of interest at high yields
• Enables site-specific conjugation via insertion of multiple nnAA conjugation anchors
• Permits protein production in non- physiological conditions

SPEED, FLEXIBILITY, SCALABILITY

• Rapidly screen vaccine candidates
• Flexible reaction conditions
• Scaled to 1000L using standard equipment

SUPERIOR CONJUGATE VACCINES

• Site-specificallyattach antigens onto protein carriers designed to:
• • Enable consistent exposure of T-cell epitopes and/or B-cell epitopes on protein carrier
  • Avoid off-target effects
  • Enable use of less protein carrier without sacrificing immunogenicity
  • Enable broader- spectrum vaccines

NOVEL PROTEIN

VACCINES

• Able to produce
  "tough-to-make" protein antigens that conform to target pathogens
• Increased likelihood of protective immune response

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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

Novel Group A	VAX-A1		Adults & Infants
Strep Vaccine

Novel Therapeutic	VAX-PG		Adults
Periodontitis Vaccine

Novel Shigella Vaccine	VAX-GI		Adults & Infants

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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

31-valent PCV candidate

• Following FDA End-of-Phase 2 meeting, initiate Phase 3 pivotal, non-inferiority study by mid-2025 and announce topline safety, tolerability and immunogenicity data in 2026.
• Initiate remaining Phase 3 studies in 2025 and 2026.

Adults

VAX-24	• Announce topline safety, tolerability and immunogenicity data from
24-valent PCV candidate	primary three-dose immunization series of Phase 2 study, which is
	fully enrolled with 802 healthy infants, by end of 1Q:2025, followed
	by topline data from booster dose by end of 2025.

	VAX-31	• Announce topline safety, tolerability and immunogenicity data
Infants	31-valent PCV candidate	from primary three-dose immunization series of Phase 2 study,
	which is enrolling subjects, in mid-2026, followed by topline data
		from booster dose approximately nine months later.
(1) Guidance as of November 12, 2024.

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PCV Opportunity

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Global Health Impact of Pneumococcal Disease Remains Significant

ABOUT STREPTOCOCCUS

PNEUMONIAE

Streptococcus pneumoniae is the

most common pathogen causing

pneumococcal disease (PD)

A

• Non-invasivePD includes otitis media, sinusitis, pneumonia
• Invasive PD (IPD) includes bacteremia, meningitis
• Pneumococci cause over 50% of bacterial meningitis cases in the U.S.

CURRENT ~$8 BILLION GLOBAL VACCINE CATEGORY

Vaccinations are recommended globally for infants and adults to prevent PD1,2

Routine SOC schedule in the U.S.:

• Infants :

• Prevnar 20® (PCV20) x 4 doses; or

- Vaxneuvance (PCV15) x 4 doses

• Adults aged 50 and older (single dose):
• • PCV20 or CapvaxiveTM (PCV21); or
  • PCV15 & Pneumovax® 23 (PPV23)

GLOBAL INCIDENCE & IMPACT

OF PD STILL SUBSTANTIAL

Global incidence driven by emerging serotypes not covered by currently available vaccines

• In the U.S. alone, over 150K hospitalizations occur annually3
• Streptococcus pneumoniae is the leading cause of vaccine preventable deaths globally in children under five4
• ~300k children under five years old die annually worldwide due to Streptococcus pneumoniae5

1. https://www.cdc.gov/pneumococcal/hcp/vaccine-recommendations/,(2) https://www.cdc.gov/pinkbook/hcp/table-of-contents/chapter-17-pneumococcal-disease.html.

1. GBD 2019 Diseases and Injuries Collaborators.. Lancet 2020; 396: 1204-22. Supplementary Appendix 2.
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8677503/table/T2/,https://www.cdc.gov/pneumococcal/php/surveillance/index.html#:~:text=Global%20trends,deaths%20occur%20in%20developing%20countries.

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ACIP Recommendations Reinforce Need for Broader-Spectrum PCVs

Advisory Committee on Immunization Practices (ACIP)

Pneumococcal Vaccine Recommendations

PREVNAR 20 (PCV20)

Infant Routine Use	Children Catch-Up	Risk Conditions1	Adult Routine Use	Adult Catch-Up2
Ages 2 - 23 months	Ages 2 - 6 years	Ages 6 - 49 years	Ages 50+ years	Ages 65+ years

CAPVAXIVE (PCV21) ADULTS ONLY

Risk Conditions1	Adult Routine Use	Adult Catch-Up2
Ages 19 - 49 years	Ages 50+ years	Ages 65+ years

VAXNEUVANCE (PCV15)

Infant Routine Use

Ages 2 - 23 months

Children Catch-Up

Ages 2 - 6 years

Risk Conditions1

Ages 6 - 49 years

Adult Routine Use

Ages 50+ years

	Continued Inclusion of PPSV23
PLUS PNEUMOVAX 23 (PPSV23)	Driven by Lack of Broader-
Spectrum PCV
(1) No prior vaccination with PCV13, PCV15 or PCV20.
(2) Shared clinical decision-making is recommended regarding use of a supplemental PCV21 or PCV20 dose for adults aged ≥65 years who have completed their recommended vaccine series with both PCV13 and PPSV23.

Sources: 1. https://stacks.cdc.gov/view/cdc/133252, 2.https://www.cdc.gov/pneumococcal/hcp/vaccinerecommendations/index.html?CDC_AA_refVal=https%3A%2F%2Fwww.cdc.gov%2Fvaccines%2Fvpd%2Fpneumo%2Fhcp%2Frecommendations.htm,

3. https://www.cdc.gov/pneumococcal/hcp/vaccine-recommendations/,4. https://www.cdc.gov/mmwr/volumes/72/rr/rr7203a1.htm.

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