Janssen Vaccines & Prevention B.V.* Clinical Protocol Protocol Title A Randomized, Double-blind, Placebo-controlled Phase 3 Study to Assess the Efficacy and Safety of Ad26.COV2.S for the Prevention of SARS-CoV-2-mediated COVID-19 in Adults Aged 18 Years and Older ENSEMBLE 2 Protocol VAC31518COV3009; Phase 3 AMENDMENT 3 VAC31518 (JNJ-78436735) * Janssen Vaccines & Prevention B.V. is a Janssen pharmaceutical company of Johnson & Johnson and is hereafter referred to as the sponsor of the study. The sponsor is identified on the Contact Information page that accompanies the protocol. United States (US) sites of this study will be conducted under US Food & Drug Administration Investigational New Drug (IND) regulations (21 CFR Part 312). Regulatory Agency Identifier Number: IND: 22657 EudraCT: 2020-003643-29 Status: Approved Date: 18 December 2020 EDMS number: EDMS-RIM-96655, 4.0 GCP Compliance: This study will be conducted in compliance with Good Clinical Practice, and applicable regulatory requirements. Confidentiality Statement The information provided herein contains Company trade secrets, commercial or financial information that the Company customarily holds close and treats as confidential. The information is being provided under the assurance that the recipient will maintain the confidentiality of the information under applicable statutes, regulations, rules, protective orders or otherwise. CONFIDENTIAL – FOIA Exemptions Apply in U.S. 1 Status: Approved, Date: 18 December 2020 VAC31518 (JNJ-78436735) Clinical Protocol VAC31518COV3009 Amendment 3 PROTOCOL AMENDMENT SUMMARY OF CHANGES TABLE DOCUMENT HISTORY Document Date Amendment 3 This document Amendment 2 27 November 2020 Amendment 1 25 September 2020 Original Protocol 22 August 2020 Amendment 3 (This document) Overall Rationale for the Amendment: The main purpose of this amendment is to outline the procedures to be followed in the event that an investigator receives a request to unblind study participants who may become eligible to receive an authorized/licensed COVID-19 vaccine if/when these become available. The purpose is to ensure (1) that the participants are informed that there is no data on the safety of receiving two different COVID-19 vaccines, (2) that in the event the participant is unblinded, no further study vaccination will be permitted, (3) that unblinded participants will continue to be followed in this study in line with the Schedules of Activities, and that safety, efficacy, and immunogenicity evaluations will continue to be performed, although the data will be analyzed separately from the point of unblinding. The changes made to the clinical protocol of study VAC31518COV3009 are listed below, including the rationale of each change and a list of all applicable sections. Section number Description of Change Brief Rationale and Name 1.1 Synopsis Clarification of procedures for To ensure that if participants 6.3 Measures to Minimize Bias: unblinding of study participants become eligible to receive an Randomization and Blinding who may become eligible to receive authorized/licensed COVID-19 6.6 Continued Access to Study an authorized/licensed COVID-19 vaccine, they are aware of the Vaccine After the End of the Study vaccine during the course of the potential options and ramifications, 7.1 Discontinuation of Study study. including the lack of safety data of vaccination the authorized/licensed vaccine in 9.9 Analyses for cohort unblinded participants that have received a due to administration of an 1-dose or 2-dose Ad26.COV2.S authorized/licensed COVID-19 vaccine, and that no further study vaccine. vaccination will be permitted; that unblinded participants will continue to be followed throughout the study for safety, efficacy and immunogenicity assessments, although the data will be analyzed separately from the point of unblinding. 7.1 Discontinuation of Study Clarification that study vaccination Clarification vaccination will be discontinued in participants with molecularly confirmed SARS-CoV-2 infection, regardless of symptomatic or asymptomatic. CONFIDENTIAL – FOIA Exemptions Apply in U.S. 2 Status: Approved, Date: 18 December 2020 VAC31518 (JNJ-78436735) Clinical Protocol VAC31518COV3009 Amendment 3 Section number Description of Change Brief Rationale and Name 1.1 Synopsis psVNA was removed from the Due to lack of sensitivity of the 3 OBJECTIVES AND protocol. evaluated psVNA, the assay has ENDPOINTS been removed from the protocol wtVNA will be used to support the 8.1.4 Immunogenicity Assessments exploratory immunogenicity wtVNA is currently only qualified endpoint. and not validated and can therefore not be used to support a secondary immunogenicity endpoint unless validated. 5.1 Inclusion Criteria Inclusion criterion 4 was updated to Clarification include a timeframe for criteria a and b for stable/well-controlled HIV infection. In addition, it was clarified that participants with stable/well-controlled HIV infection that are on stable ART are included if nationwide guidelines require transition from one ART regimen to another, within a period of less than 6 months 5.2 Exclusion Criteria Exclusion criterion 4 updated for Clarification clarification. Throughout the protocol Minor errors and inconsistencies Correction of minor errors and were corrected, and minor inconsistencies. Minor clarifications were added clarifications are made. throughout the protocol. CONFIDENTIAL – FOIA Exemptions Apply in U.S. 3 Status: Approved, Date: 18 December 2020 VAC31518 (JNJ-78436735) Clinical Protocol VAC31518COV3009 Amendment 3 TABLE OF CONTENTS PROTOCOL AMENDMENT SUMMARY OF CHANGES TABLE ............................................................... 2 TABLE OF CONTENTS ............................................................................................................................... 4 LIST OF IN-TEXT TABLES AND FIGURES ................................................................................................ 6 1. PROTOCOL SUMMARY ..................................................................................................................... 7 1.1. Synopsis........................................................................................................................................... 7 1.2. Schema .......................................................................................................................................... 22 1.3. Schedules of Activities ................................................................................................................... 23 1.3.1. All Participants ............................................................................................................................ 23 1.3.2. Participants With (Suspected) COVID-19................................................................................... 28 2. INTRODUCTION................................................................................................................................ 31 2.1. Study Rationale.............................................................................................................................. 34 2.2. Background .................................................................................................................................... 36 2.3. Benefit-Risk Assessment ............................................................................................................... 39 2.3.1 Risks Related to Study Participation .......................................................................................... 40 2.3.2 Benefits of Study Participation.................................................................................................... 44 2.3.3 Benefit-Risk Assessment of Study Participation ........................................................................ 44 3. OBJECTIVES AND ENDPOINTS ..................................................................................................... 46 4. STUDY DESIGN ................................................................................................................................ 50 4.1. Overall Design................................................................................................................................ 50 4.2. Scientific Rationale for Study Design............................................................................................. 54 4.2.1. Study-Specific Ethical Design Considerations ........................................................................... 55 4.3. Justification for Dose...................................................................................................................... 56 4.4. End-of-study Definition................................................................................................................... 57 5. STUDY POPULATION ...................................................................................................................... 57 5.1. Inclusion Criteria ............................................................................................................................ 57 5.2. Exclusion Criteria ........................................................................................................................... 60 5.3. Lifestyle Considerations................................................................................................................. 62 5.4. Screen Failures .............................................................................................................................