Amendment 3 - HHS-NIH-NIAID-BAA2022-1.pdf

HHS-NIH-NIAID-BAA2022-1

Page 1 of 10 Amendment Three (3)

NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES (NIAID)

2022 DMID Omnibus Broad Agency Announcement (BAA):

No. HHS-NIH-NIAID-BAA2022-1

Solicitation Amendment Three (3)

Issuing Office: OFFICE OF ACQUISITIONS

National Institute of Allergy and Infectious Diseases (NIAID) 5601 Fishers Lane, MSC 9821 Bethesda, MD 20892-9821

Solicitation Number: HHS-NIH-NIAID-BAA2022-1

Date of Solicitation Issuance: January 18, 2022

Date of Amendment One Issuance: February 14, 2022

Date of Amendment Two Issuance: February 17, 2022

Date of Amendment Three Issuance: March 16, 2022

Number of Pages: Ten (10) pages

Proposal Due Dates: The hour and date specified for receipt of offers for each

Research Area remains unchanged:

RESEARCH

AREA

NIAID

DIVISION

TITLE PROPOSALS DUE*

DMID

Development of Vaccine Candidates for Biodefense, Antimicrobial Resistant (AMR) Infections and Emerging Infectious Diseases

April 18, 2022

Development of Therapeutic Candidates for Biodefense, Antimicrobial Resistant (AMR) Infections and Emerging

The Antiviral Program for Pandemics (APP): Development of Antivirals for Specific RNA Viral Families of Pandemic Potential

March 18, 2022

Development of In Vitro Diagnostics for Biodefense, Antimicrobial Resistant Infections (AMR), and Emerging

Page 2 of 10 Amendment Three (3)

* Proposals must be received before 3:00 PM Eastern Time on the date specified herein.

Contracting Office Points of Contact:

Primary Contact:

Julie Rodriguez, Contracting Officer Email: julie.rodriguez@nih.gov Phone: 301-761-7735

Secondary Contact:

Brian Madgey, Contracting Officer Email: brian.madgey@nih.gov Phone: 240-627-3712

Offerors MUST acknowledge receipt of the amendment by Amendment number(s) and date of the amendment. Failure to receive your acknowledgment of this amendment may result in the rejection of your proposal.

Except as provided herein, all terms and conditions of the solicitation remain unchanged and in full force and effect.

PURPOSE OF SOLICITATION AMENDMENT #1

The purpose of Amendment One is to:

1. Update the “Date Offers Due” in Beta Sam to April 18, 2022, at 3:00pm EST for Research Areas 001, 002, and 004. Please note that the “Date Offers Due” for Research Area 003 remains unchanged as March 18, 2022, at 3:00pm EST;

2. Provide a cut-off date of April 1, 2022 for questions from potential offerors under Research Areas 001, 002, and 004; and

3. Provide the NIAID’s response to questions received regarding the solicitation. The responses are offered for information only and do not modify or become part of this solicitation. Additional amendments may be provided as needed to address further questions and their related responses.

Please note, in the questions/responses below, specific organizational names have been removed or replaced where possible as well as other minor adjustments.

GOVERNMENT’S RESPONSES:

The Government’s responses to questions received regarding this solicitation are as follows:

I. GENERAL QUESTIONS APPLICABLE TO ALL RESEARCH AREAS:

QUESTION 1: On page 78 of the solicitation, it states to use NIH Form 2043 as the first page of the pricing proposal. However, Form 2043 does not answer all of the questions that are listed as mandatory directly thereunder (e.g., item 7 - statement certifying actual costs). Do we create two

Page 3 of 10 Amendment Three (3) cover pages, one using Form 2043 and the other answering the remainder of the questions not captured on Form 2043?

RESPONSE: Yes, you may submit both the 2043 form and a separate second page to address all the information.

QUESTION 2: Regarding letters of support from collaborators, we did not find any language in the BAA about such letters. Are these allowable, and if so, would they be included in the Technical proposal at the end of Section 5 (Scientific and Technical Personnel)?

RESPONSE: Please see BAA Section 4.3.3.1.16 - Subcontractors, which requests that a commitment letter be provided as part of the Business Proposal for all subcontractors. Elements of the commitment letter are included in that section.

QUESTION 3: Our SAM registration is still being processed and we are concerned that it will take them time to do so and we will miss our deadline to file our application.

RESPONSE: The BAA and FAR 4.1102 require offerors to be registered and active in SAM at the time of offer submission. Potential offerors should comply with this requirement to avoid disqualification and rejection of their proposal. We are unable to provide any assistance with this issue as SAM.gov is not administered by the NIAID.

QUESTION 4: Where the costing states “Direct Labor excluding overhead, fringe benefits etc”, does this mean we can only charge the Direct Labor element of a person working on the project?

RESPONSE: No; Direct labor should be a separate element in the business proposal, but charges for overhead and fringe benefits are allowable. Note that a logical and consistent method for the allocation of indirect costs to intermediate and final cost objectives is required. See

4.3.3.1.13 - Adequate Accounting System.

QUESTION 5: We are not sure we understand the salary limitation. Could you provide more detail about this?

RESPONSE: The Consolidated Appropriations Act, 2021, restricts the amount of direct salary to Executive Level II of the Federal Executive pay scale. The Office of Personnel Management released new salary levels for the Executive Pay Scale and effective January 2, 2022, the salary limitation for Executive Level II is $203,700. The salary rate limitation does not restrict the salary that an organization may pay an individual working under an HHS contract or order and does not apply to fringe benefits or associated indirect costs; it merely limits the portion of that salary that may be paid with contract funds. Please see Section 4.3.3.1.5 - Salary Rate Limitation of the solicitation. The HHS Salary Limitation here: https://grants.nih.gov/grants/guide/notice-files/NOT-OD-22-076.html. More information is available at:

https://www.hhs.gov/grants/contracts/contract-policies-regulations/salary-ratelimitation/ index.html#Q3 (see Question 3 and answer).

QUESTION 6: We need to determine whether we can charge our manpower & facilities at our traditional charge out rates? OR whether we can only charge direct costs and then a % of the overhead element?

Page 4 of 10 Amendment Three (3)

RESPONSE: Resulting awards will be cost type contracts. As such, contractors will be reimbursed for all costs incurred in performance of the work including actual salaries paid and any indirect rates that apply to those salaries. Please see 4.3.3.1.3 – Certified Cost or Pricing Data, Section 2. Cost Elements.

QUESTION 7: For the Business Proposal, does the solicitation operate under the assumption that proposed work would be fully funded by this contract?

RESPONSE: The initial funding shall be for the base period only; contract options will be fully funded only if exercised. In addition, cost sharing is permitted, but not required, for proposals under this solicitation. See 4.3.3.1.21 - Cost Sharing (p. 92). Cost sharing is a cost-reimbursement contract in which the Government and the Offeror negotiate the share of the project costs eligible for reimbursement under the contract. A cost sharing contract may be used when the contractor agrees to absorb a portion of the costs, in the expectation of substantial compensating benefits. The contractor receives no fee and is reimbursed only for the negotiated portion of its allowable costs.

QUESTION 8: We have a question about the product development plan. The solicitation includes two different descriptions for what is required for the product development plan - first on pages 19-20 and again on page 51. Both are attached here. Which set of instructions should we follow, or should we follow both by including all requirements?

RESPONSE: Page 51 is the sample SOW that may be used when proposing to RA 001, 002, or

004. Page 19 contains the requirements for the PDP.

QUESTION 9: Work plan and technical discussions sections sound very similar. Could you please clarify the differences between these two sections?

RESPONSE: The requirements for the technical proposal is located in Section 4.3.2 - TECHNICAL PROPOSAL INSTRUCTIONS. The Work Plan refers to the proposed detailed work packages that will be executed to reach the milestones and complete the deliverables of the contract. As noted in BAA Section 3.5.1, the Work Plan describes the studies to be performed at each stage of the project within the 5-year term of award in order to implement the PDP and advance the product through Phase 1 clinical testing. Technical Discussions refers to summary data, figures, and graphs to date.

QUESTION 10: Regarding this NIAID BAA2022-1 announcement, would the IP be shared or would it belong to the product developer ?

RESPONSE: Any data that is developed under this acquisition will be covered by the general data rights and/or additional data rights clauses which will be incorporated into the contract award. In addition to the general clauses for R&D requirements, FAR 52.227-11 Patent Rights – Ownership by Contractor will be included. Please also refer to IP section of the BAA (page 92 of the BAA solicitation, Section 4.3.3.1.20 - Intellectual Property).

QUESTION 11: Where can we find more information on the nature of the deliverables that have to be delivered to NIH and the Government oversight and control as part of such contract?

RESPONSE: Please refer to Section 3.5. and 3.5.1 of the BAA.

Page 5 of 10 Amendment Three (3)

QUESTION 12: We understand that proposals are submitted via the NIH electronic Contract Proposal Submission portal. Are any registrations (e.g., DUNS, SAM, etc.) required for submission? Was there a webinar about this opportunity that we can access?

RESPONSE: Please refer to the BAA solicitation for a full list of requirements. A DUNS number is required. See BAA solicitation Section 4.3.1.1 - Authorized Official. The completed Representations and Certifications from SAM must be included with the Business Proposal. See BAA solicitation Section 4.2.1 - Representations, Certifications, and Other Statements of Offerors. There is no webinar available regarding this opportunity.

QUESTION 13: Is it only FAR based contracts or are OTA allowable or negotiable?

RESPONSE: This Broad Agency Announcement and any resultant contract award(s) are subject to the FAR. OTA is not permitted.

QUESTION 14: We have some questions on the instructions. Can we still submit questions regarding this solicitation?

RESPONSE: You may still submit general questions, or questions under Research Areas 001, 002, and 004. Questions related to Research Area 003 were due no later than March 1.

QUESTION 15: Is there a specific order you would like all the items in for the business proposal?

RESPONSE: It is recommended that the business proposal consist of a cover page, a table of contents, and the information requested in the Business Proposal Instructions as specified in Section 4.3.3. There is no specific order required.

QUESTION 16: It seems the excel budget spreadsheet is included separately, so is not included in the Business Proposal – yes?

RESPONSE: Offerors may include pdf copies of the excel budget as part of the business proposal. However, the excel version should also be submitted separately.

QUESTION 17: Is the Certification Regarding Tax Matters to be included in the Business Proposal?

RESPONSE: Yes.

QUESTION 18: Is the Disclosure of Lobbying Activities required and if so is this to be included in the Business Proposal?

RESPONSE: Yes.

QUESTION 19: Certified Cost or Pricing Data – Is this just the one-page certification that was included in the forms? Is there anything else here you are looking for?

RESPONSE: Please refer to Section 4.3.3.1.3 – Certified Cost or Pricing Data.

Page 6 of 10 Amendment Three (3)

QUESTION 20: For “Post-award Requirements” (section 3.4.6, p. 23): “Offerors are instructed to address responsibility for complying with these requirements in the proposed SOW for the Technical Proposal.” Is there a particular place under the example SOW on p. 51 where this should be addressed?

RESPONSE: As this section is “Post-award Requirements” (see Section 3.4.6), at the time of application submission you need not submit any documentation to address this. Instructions for submitting the documentation associated with post-award requirements will be provided during negotiations if offered an award.

QUESTION 21: For “Section 4: Technical Discussions,” could you provide more guidance on what to include that is not already addressed in Section 3 (SOW), Section 4 (Scientific and Technical Personnel), Section 6 (Project Management), Section 7 (Facilities, Equipment, and Other Resources), Section 8 (Other Considerations), Section 9 (Human Subjects), and Section 10 (Vertebrate Animal Section)? Page 52 indicates that for Section 4: Technical Discussions, “your proposal be organized in accordance with the order of your SOW and the technical evaluation criteria provided in Section 6.” Should Section 4: Technical Discussions be organized according to the SOW on p. 51 or based on the technical evaluation criteria provided in Section 6: Scientific and Technical Merit, Scientific and Technical Personnel, Project Management, and Organizational Facilities, Equipment, and Other Resources? It seems that these criteria are redundant with other Sections of the technical proposal.

RESPONSE: Technical Discussions generally includes background information relating to medical need, rationale or justification of the vaccine approach and development pathway. This may include short summaries of scientific descriptions of critical immunogenic components, adjuvants if applicable and other critical components that justify the proposed vaccine development approach and strategy. This may include but not necessarily require descriptions of key personnel or institutional expertise/technology. The Technical Discussion section generally is a high-level summary which can range from a single page to several pages. Please include detailed information as it relates to Project Management, Organizational Facilities, Equipment and Other Resources in other sections such as Sections 6 and 7.

QUESTION 22: Where do we include requirements that do not fall under Sections 1-7, Human Subjects, or Vertebrate Animal Section of the Technical Proposal? Ex. Possession, Use and Transfer of Select Biological Agents or Toxins; Enhancing Reproducibility Through Rigor and Transparency; Dual Use Research of Concern; Obtaining and Disseminating Biomedical Research Resources; and Electronic and Information Technology Accessibility. Should these be listed under Section 8: Other Considerations?

RESPONSE: Yes, human subjects, vertebrate animal sections, and all other information can be placed in Section 8. Other Considerations.

QUESTION 23: For “Financial Conflicts of Interest” indicated on p. 109, do we include these in the technical proposal or business proposal?

RESPONSE: “Financial Conflicts of Interest” should be included in the business proposal.

Page 7 of 10 Amendment Three (3)

II. RESEARCH AREA SPECIFIC QUESTIONS

1) RESEARCH AREA 001:

QUESTION 1: Our research group has a question regarding the applicability of a rapid-acting influenza vaccine that does NOT contain an antigen or an immunogen, but instead acts through a non-specific resistance mechanism for Research Area 001. The BAA states that it will not support development of adjuvants in the absence of a companion product (page 8 of the BAA). Does our proposed product fall into this excluded category?

RESPONSE: Research Area 001 focuses on the advancement of a promising lead vaccine candidate from pre-clinical testing through evaluation in a clinical trial. Section 3.3.1.2 defines the criteria of a lead vaccine candidate. As the proposed lead candidate does not include an identified antigen or immunogen (Section 3.3.1.2.1), the proposed product is excluded from this BAA.

QUESTION 2: Is there a limit to the number of subjects in a proposed Phase 1 clinical trial under

RA 001?

RESPONSE: The number limit of subjects in a Phase I Clinical Trial is 120 individuals for Research Area 001. However, in practice the typical number is 60-80 subjects for such a trial. If a Phase I trial exceeds 100 subjects, then a Data and Safety Monitoring Board (DSMB) will be required rather than a Safety Monitoring Committee (SMC).

QUESTION 3: Would a proposal that focuses on development of a lead vaccine candidate to A.

baumannii be considered responsive to this BAA?

RESPONSE: A. baumannii is considered responsive to Research Area 001 of the BAA.

QUESTION 4: Page 51 provides an example Statement of Work (SOW) for Research Areas 001, 002, and 003. We noticed that “Efficacy Studies” and “Animal Safety Studies” are listed twice under Technical Requirements as items 1. and 2., respectively, and items 3.a. and 3.b., respectively. Should these two items be addressed twice as indicated or only once, either as items

1. and 2., respectively, or items 3.a. and 3.b., respectively?

RESPONSE: Refer to page 7 of the BAA, defining the Technical Approach for Research Area 001, which states that Research Area 001 focuses on the advancement of a promising lead vaccine candidate from preclinical testing through evaluation in a clinical trial. A lead vaccine candidate is defined by the following criteria (a partial list has been provided directly below):

1. Antigen/immunogen design and technology platform selection completed (both well characterized)

2. Preliminary data that demonstrates proof-of-concept immunogenicity in relevant animal model(s)

3. Prefer, but do not require, evidence of proof-of-concept efficacy data in a relevant animal model.

In your proposal, you should provide, for items 1. and 2., any data that you may have currently that is related to the lead vaccine candidate’s efficacy and/or safety as part of the Product Development Plan. For item 3.a. and 3.b., respectively, you should provide any data you have in

Page 8 of 10 Amendment Three (3) which the vaccine product substance or drug has been tested for efficacy or in GLP toxicology studies. If not completed, please provide the proposed plans for these studies.

2) RESEARCH AREA 002:

QUESTION 1: Would a post-symptomatic antidote to botulinum neurotoxin fit into research area 2, as a Tier 1 select agent?

RESPONSE: Research Area 002 will support lead optimization, pre-clinical (IND enabling) studies and clinical trials that include Phase 1 and Phase 2 studies or confirmatory trials no greater than 120 subjects. The scope of support differs depending on the stage of the project being proposed. Refer to Section 3.3.2.1 – Technical Objectives for details describing the development phases in-scope of Research Area 002, and Section 3.3.2.3 - Additional Requirements for phase-appropriate evidence that therapeutic candidates must demonstrate.

QUESTION 2: Is an anti-Cdiff therapeutic derived from probiotic yeast, which is genetically modified, no longer considered “Probiotics” so that it would be responsive to Research Area 002?

RESPONSE: The proposed product is a live biotherapeutic product based on a yeast so it is considered a probiotic for the purposes of this solicitation. Please refer to Section 3.3.2.4 that states that development of probiotics and other microbiome related products is not supported.

QUESTION 3: Since area 002 allows for support of Phase 1 and Phase 2 trials we want to ask if NIAID will consider the pediatric development of an antibiotic in scope for this solicitation.

RESPONSE: Yes; Research Area 002 supports clinical trials of Phase 1 and/or Phase 2 with no larger 120 subjects.

QUESTION 4: The BAA indicates that contracts will not support development of licensed drugs for other indications. However, because we would only be considering adjunctive therapy (not monotherapy) with these FDA-approved treatments, we wonder if it would be allowable to propose such studies, or perhaps they would be best left to alternative approaches?

RESPONSE: Due to the competitive nature of the BAA, the NIAID is unable to offer advice or feedback regarding a specific technical approach. Refer to Section 3.3.2.4 for studies which are not supported by the contract. Developing a therapeutic candidate that has not been approved or licensed by a US or non-US regulatory agency is in scope. Research Area 002 will support lead optimization, pre-clinical (IND enabling) studies and clinical trials that include Phase 1 and Phase 2 studies or confirmatory trials no greater than 120 subjects. The scope of support differs depending on the stage of the project being proposed. Refer to Section 3.3.2.1 – Technical Objectives for details describing the development phases in-scope of Research Area 002, and Section 3.3.2.3 – Additional Requirements for phase-appropriate evidence that therapeutic candidates must demonstrate.

QUESTION 5: Is tuberculosis and drug resistant tuberculosis in scope?

RESPONSE: Yes, tuberculosis including drug-resistant TB is in scope for RA 002.

Page 9 of 10 Amendment Three (3)

QUESTION 6: Our concern is that our drug might not be supported under this BAA, based on a bullet point in Section 3.3.2.4 because the drug is currently being marketed under NDAs for both community-acquired bacterial pneumonia (CABP) and ABSSSI (acute bacterial skin and skin structure infections). Could you please advise?

RESPONSE: BAA Section 3.3.2.4 – “Contracts awarded under this Research Area will NOT support” indicates that development of products licensed/approved by the US and non-US regulatory agencies (e.g. FDA, EMA) for additional clinical indications is not supported.

QUESTION 7: Can you confirm the eligibility of a Lassa virus therapeutic for post-Phase 1 nonclinical and Phase 2 clinical studies as a submission to Research Area 002? Lassa is listed as an RA 003 eligible virus. Does that mean it is no longer eligible for RA 002? Our candidate is too advanced for RA 003.

RESPONSE: Lassa virus is a pathogen of interest for both Research Areas (RA) 002 and 003.

Please consider therapeutic candidate’s attributes and development phase specified in Sections

3.3.2.1 and 3.3.3.1 – Technical Objectives of the two RAs to determine the most appropriate research area for the potential proposal.

QUESTION 8: Would a small molecule that strongly prevents the growth of SARS-CoV-2, influenza virus and RSV in the lung of mice after its intranasal administration be responsive to Research Area 002 or 003? The small molecule is an immunostimulatory molecule that acts on innate immunity.

RESPONSE: Since this drug candidate acts on host innate immunity, it is suitable for Research Area 002, but not in scope of Research Area 003. Please refer to Section 3.3.2.3 – Additional Requirements and Section 3.3.2.4 – Contracts awarded under this Research Area will NOT support to determine if the drug candidate has demonstrated phase-appropriate evidence.

QUESTION 9: Would it be responsive to only propose a GMP manufacturing campaign and conduct of a Phase 2 trial?

RESPONSE: Research Area 002 will support lead optimization, pre-clinical (IND enabling) studies and clinical trials that include Phase 1 and Phase 2 studies or confirmatory trials no greater than 120 subjects. The scope of support differs depending on the stage of the project being proposed. Refer to Section 3.3.2.1 – Technical Objectives for details describing the development phases in-scope of Research Area 002, and Section 3.3.2.3 - Additional Requirements for phase-appropriate evidence that therapeutic candidates must demonstrate.

3) RESEARCH AREA 004:

QUESTION 1: What do you define as a “portable sequencer”? Does this include desktop sequencing devices such as from Illumina (NextSeq)…or is this solely for a system like Oxford nanopore?

RESPONSE: ‘Portable’ does not mean solely the system from Oxford Nanopore. ‘Portable’ is intended to mean small footprint and ease of use for diverse laboratories and other locations.

Page 10 of 10 Amendment Three (3)

QUESTION 2: The BAA notes that proposals that have >5 mins manual sample processing would not be considered. Is this applicable for proposals in ALL 3 research objectives under this call, including the third objective?

RESPONSE: Total sample processing time (manual plus automated) may take more than 5 min. It is hoped that by the end of the program, the amount of hands-on time (manual processing) after sample withdrawal from collection tube would be < 5 min; this holds for all three research objectives.

QUESTION 3: Additional point on manual steps: Would it be okay to have manual steps in between workflow steps, simple things like loading, adding etc., totaling not greater than 5 minutes.

RESPONSE: It is acceptable to have manual steps in between workflow steps, totaling not more than 5 min.

QUESTION 4: Is there a target definition for a “moderate throughput” that the diagnostic is expected to meet?

RESPONSE: Moderate throughput means 10 samples up to 96-well sample processing, per clinical laboratory work shift.

QUESTION 5: Could you please clarify the expectations on the following terminology? Smaller volume of blood (pg.17) to detect BSI – are there specific maximum volumes in mind?

RESPONSE: There are no maximum volumes above which the submission would be unresponsive.

QUESTION 5a: “Greater clinical sensitivity” (pg. 17) to detect pathogen analyte from whole blood - Is there a target sensitivity?

RESPONSE: There is no minimum requirement below which the submission would be unresponsive.

QUESTION 5b: Turnaround time -is the expectation a total of 6 hours for ID (4 hrs) + AST (2 hrs) if we want to propose including both?

RESPONSE: Efforts to include both bacterial ID and AST would be expected to complete this in approximately 6 hours.

QUESTION 5c: Phenotypic antimicrobial resistance characterization -we interpret detection of resistance genes and correlation to a genotype-phenotypic database using well-characterized specimens in lieu of growing pathogens for phenotypic ID to be compliant with the intent of the BAA and consistent with the TAT and NGS requirement.

RESPONSE: It is acceptable to detect resistance genes and validate these with a genotype-phenotype database using well-characterized specimens in lieu of growing pathogens for straight phenotypic ID and consistent with TAT and NGS requirements.