Amendment_1_RFP_NIAID-DAIDS-NIHAI2015055.pdf

AMENDMENT #1 RFP NIAID-DAIDS-NIHAI2015055 1

Amendment No. 1

NIAID-DAIDS-NIHAI2015055

“External Quality Assurance Program Oversight Laboratory (EQAPOL)”

Solicitation Number: NIAID-DAIDS-NIHAI2015055

Amendment Number: One (1)

Amendment Issue Date: May 17, 2016

Proposal Due Date/Time: Wednesday, August 3, 2016 at 3:00 PM, Local Time

(Unchanged)

Issued By: John R. Manouelian

Contracting Officer

OA/DEA/NIAID/NIH/DHHS

5601 Fishers Lane, Room 3D10, MSC 9821 Bethesda, Maryland 20892-9821

Points of Contact: PRIMARY lorna.finn@nih.gov Lorna Finn, Contract Specialist Phone: 240.669.5153

SECONDARY

manouelj@mail.nih.gov John R. Manouelian, Contracting Officer Phone: 240.669.5152

Please note that we do NOT intend to extend the due date for submission of proposals as a result of this amendment. The date specified for receipt of proposals remains unchanged.

Offerors must acknowledge receipt of this Amendment by identifying the amendment number and the date of the amendment on each copy of the submitted proposal. Failure to receive your acknowledgement 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.

The purpose of Amendment 1 is to: (1) provide responses to questions from potential offerors regarding the solicitation; (2) revise Attachment 1, Statement of Work; (3) revise Attachment 4, Additional Technical Proposal Instructions; and (4) revise Attachment 5, Additional Business Proposal Instructions and Uniform Cost Assumptions.

AMENDMENT #1 RFP NIAID-DAIDS-NIHAI2015055 2

The solicitation is hereby amended to provide the following responses to questions received from potential offerors:

Question 1

1. We have the following questions about the Mucosal EQA effort and sample collection:

a. Should the Mucosal EQA efforts focus on assessing sites’ ability to collect and store their own acquired mucosal samples? Given that sites will be collecting materials from unique donors per site, assessing any functional attributes may be difficult. What functional attributes of mucosal samples are of interest?

b. If a Mucosal EQA program was to be developed to assess collection and storage of samples, would DAIDS be interested in assessing the viability and viable recovery of mucosal samples containing cells? Or cells isolated from mucosal samples stored separately from the “plasma” components? How and what specific parameters does NIH envision assessing for an EQA program to assess the humoral and cellular immune component of the mucosal samples?

c. For Mucosal EQA activities related to mucosal samples, is DAIDS interested in assessing immunological parameters only or also microbiota?

d. Is there any expectation that the EQAPOL site will collect and store mucosal samples? If so, how many samples are we expected to collect per year?

e. For the Mucosal EQA program and repository, what types of samples are of interest?

Is DAIDS interested in mucosal samples containing cells or cell-free samples?

Are biopsies of interest?

Are mucosal samples of interest from the genital tract, GI tract, both or other?

Is DAIDS interested in samples from females, males or both?

The proposal mentions vaccine response. Does this imply that the EQAPOL site will be expected to run a study in recently vaccinated persons? If so, are there specific targeted vaccines that are already FDA-approved? If the site is supposed to collect mucosal samples from HIV-vaccinated volunteers, which vaccine is targeted and how is the trial to be conducted?

Response to Question 1

In response to Questions a-e, the Government does not expect the offeror to propose procedures and provide a budget for a mucosal EQA program, but, rather, as stated in Attachment 3, Statement of Work, Paragraph C., Technical Requirements, item 5., EQA Program to Assess Collection, Storage, and Testing of Mucosal Specimens, “Upon request of the COR, the Contractor shall participate in assay development and validation for mucosal immune factors and assist in development of an EQA program to assess collection, storage, and testing parameters of mucosal specimens for host pathogens (microbiota) or anti-vaccine immune

AMENDMENT #1 RFP NIAID-DAIDS-NIHAI2015055 3

responses.” The Contractor’s participation in and developmental/validation assistance for this activity will be part of the level of effort established under the base activities of the contract.

Because such a program is not currently defined, the Government is interested in the Contractor’s ability in the future to contribute to the development of a mucosal EQA program, and offerors are instructed in Attachment 4, Additional Technical Proposal Instructions, under Section 3, Technical Plan/Approach, item 5, to “Describe experience and/or ability to form collaborations with investigators involved in mucosal collection and immunological assays using mucosal specimens.”

Question 2

Does the Extent of Small Disadvantaged Business Participation apply for this contract?

Response to Question 2

No, the Extent of Small Disadvantaged Business Participation does not apply to this contract.

However, as stated under item 6., Small Business Subcontracting Plan, on page 84 of the solicitation, offerors are required to submit an acceptable subcontracting plan, in accordance with the terms of the clause, entitled, "Small Business Subcontracting Plan," FAR Clause No.

52.219-9, incorporated herein by reference in the Solicitation, See SECTION J - LIST OF ATTACHMENTS, BUSINESS PROPOSAL ATTACHMENTS of this RFP for an example of such a plan…

Question 3

The RFP is not clear in terms of whether subcontractor/consultant effort is included in the FTE cap. On page 15, the text reads: These labor hours/months/years excludes includes/excludes subcontract labor hours/months/years. On the other hand, Attachment 5, page 4 indicates: Please note the number of FTEs includes the effort of subcontractors and consultants. Please confirm if subcontractor/consultant effort is included in the FTE cap.

Response to Question 3

The required number of FTEs (for the base requirement and each option) includes the effort of subcontractors and consultants.

Attachment 5, Additional Business Proposal Instructions and Uniform Cost Assumptions, is hereby revised, by virtue of this amendment, in order to provide the following clarification, under Section 3 – Uniform Cost Assumptions and Section 4 – Options (a revised copy of Attachment 5, Additional Business Proposal Instructions and Uniform Cost Assumptions, which reflects the aforementioned changes, is also included with this amendment): Please note that the number of FTEs required includes the effort of subcontractors and consultants.

Regarding Article F.2. Level of Effort (on page 15 of the solicitation), please be aware that per Part I – The Schedule (on page 4 of the solicitation), the Contract Schedule set forth in Sections B through H…is not an exact representation of the contract document that will be awarded as a result of this solicitation. Since the Contract Schedule set forth in Sections B through H of the solicitation are subject to negotiation, and are intended to provide the offeror with the necessary

AMENDMENT #1 RFP NIAID-DAIDS-NIHAI2015055 4

information to understand the terms and conditions of the resultant contract, we have determined that a revision to Article F.2. Level of Effort is not necessary, particularly since all pertinent information regarding the level of effort requirement is clearly described in Attachment 5, Additional Business Proposal Instructions and Uniform Cost Assumptions. However, please be assured that Article F.2. Level of Effort, of any contract awarded as a result of this requirement, will specify the following: The required number of FTEs (for the base requirement and each option) includes the effort of subcontractors and consultants.

Question 4

For antibody characterization assays, are the samples being tested “serum/plasma” samples or “monoclonal antibodies”?

Response to Question 4

For the purpose of responding to this solicitation, please assume that the samples being tested are “serum/plasma”.

Question 5

Regarding the characterization of Ab responses/function, should we envision characterizing each sample for non-neutralizing activities?

Response to Question 5

No, offerors shall only envision neutralizing antibody activities. For the purpose of responding to this solicitation, please follow the directions described in Attachment 4, Additional Technical Proposal Instructions, Section 3, Technical Plan/Approach, item 6), which requires offerors to “Describe plans and operating procedures for providing an EQA Program for an antibody neutralization assay…”

Question 6

For Options 7-34, is it correct to budget for increased effort as proposed in the table below:

Yr1 Yr2 Yr3 Yr4 Yr5 Yr6 Yr7 Opt 7- A Opt 11- A Opt 15- A Opt 19- A Opt 23- A Opt 27- A Opt 31- A Opt 8-B Opt 12-B Opt 16-B Opt 20-B Opt 24-B Opt 28-B Opt 32-B Opt 9-C Opt 13-C Opt 17-C Opt 21-C Opt 25-C Opt 29-C Opt 33-C Opt 10-D Opt 14-D Opt 18-D Opt 22-D Opt 26-D Opt 30-D Opt 32-D

Where A, B, C and D are as follows:

A. 1 FTE for additional EQA testing to maintain a PBMC Bank and EQA Reagent Repository and additional Mucosal Specimen identification and characterization.

1 FTE for additional EQA testing using ELISpot EQA assays and Flow Cytometry-based Assays.

AMENDMENT #1 RFP NIAID-DAIDS-NIHAI2015055 5

B. 1 FTE for additional EQA testing using Multiplex/Array EQA assays and Antibody Characterization Assays.

C. 1 FTE for additional panel expansion of characterized isolates other than HIV and for establishing and characterizing unique clade-specific HIV virus panels.

D. 1 FTE for Coordinating Optimization Efforts for New Assays and Advising on Assay validation, Regulatory, Compliance, and Statistical Issues.

Response to Question 6

Please be aware that by virtue of this amendment, Attachment 5, Additional Business Proposal Instructions, Section 4 - Options, Options 7-34 to Increase Level of Effort, is hereby revised as follows: (1) the first paragraph has been revised to incorporate the term, “Multiplex Arrays”, and to read more clearly; and (2) the second paragraph, which includes items 1.-4., has been deleted in its entirety. As a result of the foregoing, Attachment 5, Additional Business Proposal Instructions, Section 4 - Options, Options 7-34 to Increase Level of Effort, has been revised to read as follows (a revised copy of Attachment 5, Additional Business Proposal Instructions and Uniform Cost Assumptions, which reflects the aforementioned changes, is also included with this amendment):

Options 7-34 to Increase Level of Effort: The Government may exercise options for increased level of effort (LOE) that may result from unanticipated increases in demand for such things as proficiency testing in areas within the scope of activities supported by the base requirements of the contract, which include: ELISpot EQA program, Flow-Cytometry-based assays, Multiplex Arrays, and/or to expand the panel of characterized HIV isolates and other viral isolates that may be required in order to respond to emerging needs or public health emergencies. Should the Government elect to exercise these options, the Contractor shall provide resources for the unanticipated increase in work volume by 1.00 Full Time Equivalents (FTE) for each option exercised. Each of these options may be exercised up to 4 times per contract year, during Years 1 through 7. The period of performance of an Option for increased level of effort will not exceed the term of the Base Period or Option year in which the Option is exercised. Please note that the number of FTEs required includes the effort of subcontractors and consultants.

For costing purposes, please assume the following labor mix:

Full Time Equivalents (FTEs)

Labor Category Yr 1 Yr 2 Yr 3 Yr 4 Yr 5 Yr 6 Yr 7

Professional Support 0.40 0.40 0.40 0.40 0.40 0.40 0.40

Technical Support 0.60 0.60 0.60 0.60 0.60 0.60 0.60

Total 1.00 1.00 1.00 1.00 1.00 1.00 1.00

NOTE: The labor mix provided above is the Government's estimate and should not be considered restrictive. Offerors should propose the labor mix they consider most appropriate for satisfactory completion of the work.

AMENDMENT #1 RFP NIAID-DAIDS-NIHAI2015055 6

In response to your question, and based on the above revisions, the purpose of these options is to support any unanticipated increase in demand within the scope of activities supported by the base requirements of the contract, for such things as proficiency testing, which may include: ELISpot EQA program, Flow-Cytometry-based assays, Multiplex Arrays, and/or to expand the panel of characterized HIV isolates and other viral isolates that may be required in order to respond to emerging needs or public health emergencies. Therefore, as stated above, should the Government elect to exercise these options, the Contractor shall provide resources for the unanticipated increase in work volume by 1.00 Full Time Equivalents (FTE) for each option exercised. Each of these options may be exercised up to 4 times per contract year, during Years 1 through 7. The period of performance of an Option for increased level of effort will not exceed the term of the Base Period or Option year in which the Option is exercised.

Question 7

For Options 7-34, the business proposal instructions indicate one set of options should be for the following: “1 FTE for additional EQA testing to maintain a PBMC Bank and EQA Reagent Repository and additional Mucosal Specimen identification and characterization. 1 FTE for additional EQA testing using ELISpot EQA assays and Flow Cytometry-based Assays.”

However the FTE information elsewhere indicates that each of Option 7-34 is for 1 FTE total.

Please clarify the FTE allocation for this Option type.

Response to Question 7

Please reference the response provided to Question 6, including the related revisions to Attachment 5, Additional Business Proposal Instructions and Uniform Cost Assumptions. To clarify, should the Government elect to exercise Options 7-34, the Contractor shall provide resources for the unanticipated increase in work volume by 1.00 Full Time Equivalents (FTE) for each option exercised.

Question 8

For Options 7-34, the business proposal instructions indicate a need for “Additional EQA testing”. Is that to indicate the addition of new sites for the EQA programs? If so, how many sites per option?

Response to Question 8

As stated in Attachment 5, Additional Business Proposal Instructions and Uniform Cost Assumptions, the Government may exercise Options 7-34 for increased level of effort that may result from unanticipated increases in demand for such things as proficiency testing in areas within the scope of activities supported by the base requirements of the contract. That being said, the increase in demand may not necessarily be related to the addition of new sites.

Further, as stated in our response to Question 6, the purpose of Options 7-34 is to support any unanticipated increase in demand within the scope of activities supported by the base requirements of the contract, for such things as proficiency testing, which may include: ELISpot EQA program, Flow-Cytometry-based assays, Multiplex Arrays, and/or to expand the panel of characterized HIV isolates and other viral isolates that may be required in order to respond to emerging needs or public health emergencies. Therefore, should the Government elect to

AMENDMENT #1 RFP NIAID-DAIDS-NIHAI2015055 7

exercise these options, the Contractor shall provide resources for the unanticipated increase in work volume by 1.00 Full Time Equivalents (FTE) for each option exercised. Each of these options may be exercised up to 4 times per contract year, during Years 1 through 7. The period of performance of an Option for increased level of effort will not exceed the term of the Base Period or Option year in which the Option is exercised.

Question 9

For Options 7-34, the option types listed frequently include one or more activities (i.e., additional EQA testing using Multiplex/Array EQA assays AND antibody characterization assays). Should the budget reflect completing both of those activities?

Response to Question 9

As stated in our response to Question 6, the purpose of Options 7-34 is to support any unanticipated increase in demand within the scope of activities supported by the base requirements of the contract, for such things as proficiency testing, which may include: ELISpot EQA program, Flow-Cytometry-based assays, Multiplex Arrays, and/or to expand the panel of characterized HIV isolates and other viral isolates that may be required in order to respond to emerging needs or public health emergencies. Therefore, should the Government elect to exercise these options, the Contractor shall provide resources for the unanticipated increase in work volume by 1.00 Full Time Equivalents (FTE) for each option exercised. Each of these options may be exercised up to 4 times per contract year, during Years 1 through 7. The period of performance of an Option for increased level of effort will not exceed the term of the Base Period or Option year in which the Option is exercised. The Government may exercise options for increased level of effort that may result from unanticipated increases in demand for any of the activities supported under the base requirements of the contract. Therefore, in developing their budgets for Options 7-34, the offeror should assume that the unanticipated increase in demand, requiring an increase in level of effort, could be related to any of the activities supported under the base requirements of the contract, (i.e., the offeror should not base their budgets for Options 7-34 on only one specific activity).

Question 10

For Options 7-34, the business proposal instructions indicate a need for additional “panel expansion of characterized isolates other than HIV and for establishing and characterizing unique clade-specific HIV virus panels.” Please clarify the number of new viral isolates per option.

Response to Question 10

Please see our responses to Questions 6 and 9.

Question 11

For Options 7-34, the business proposal instructions indicate a need for additional EQA testing to maintain a PBMC Bank and EQA Reagent Repository and additional Mucosal Specimen identification and characterization. Please clarify the number of test numbers for each PBMC, Reagent and Mucosal Specimen needed per option. Additionally, please clarify the number of tests for each ELISpot and Flow assay per option.

AMENDMENT #1 RFP NIAID-DAIDS-NIHAI2015055 8

Response to Question 11

Please see our responses to Questions 6 and 9.

Question 12

For Options 35-42, how many sites should we assume participate in the HIV incidence assay EQA program?

Response to Questions 12

The offeror shall assume that twice each year 15 U.S. laboratories and 10 international laboratories will participate in the HIV incidence assay EQA program. Attachment 5, Additional Business Proposal Instructions and Uniform Cost Assumptions, Section 4 – Options, has been revised to incorporate this information under Options 35-42 to Increase Level-of-Effort to develop a new EQA program.

In addition, the solicitation has been revised as follows:

Attachment 3, Statement of Work, Paragraph C., Technical Requirements, item 12., Option(s), Options 7-34: Increased Level of Effort, is revised to incorporate the term “Multiplex Arrays”, in the first sentence of the second paragraph (on page 10 of the attachment). As a result of the foregoing, the language for Options 7-34: Increased Level of Effort, is revised to read as follows (a revised copy of Attachment 3, Statement of Work, which reflects the aforementioned changes, is also included with this amendment):

OPTIONS 7 - 34: Increased Level of Effort: The Government may exercise options for increased level of effort that may result from unanticipated increases in demand. Should the Government elect to exercise these options, the Contractor shall provide resources for the unanticipated increase in work volume by 1.00 Full Time Equivalents (FTEs) for each option exercised.

This option provides for an increase in the level of effort to accommodate the addition of 1.00 FTE up to 4 times/year for unanticipated increases in demand for such things as proficiency testing in areas such as ELISpot EQA program, Flow Cytometry-based assays, Multiplex Arrays, and/or to expand the panel of characterized HIV isolates and other viral isolates that may be required to respond to emerging needs or public health emergencies. If the Government elects to exercise this Option, the Contractor shall provide an additional 1.00 FTE per option.

The period of performance of an Option for increased level of effort will not exceed the term of the Base Period or Option year in which the Option is exercised.

Similarly, Attachment 4, Additional Technical Proposal Instructions, Section 7, Options, item 2) Options 7-34: Increase Level of Effort, is revised to incorporate the term “Multiplex Arrays” (on page 6 of the attachment), and shall read as follows:

2) Options 7-34: Increase Level of Effort The Government may exercise options for an increase in the Level-of-Effort to accommodate the

AMENDMENT #1 RFP NIAID-DAIDS-NIHAI2015055 9

addition of 1.00 FTE up to 4 times/year for proficiency testing in areas such as ELISpot EQA program, Flow Cytometry-based assays, Multiplex Arrays, and/or to expand the panel of characterized HIV isolates and other viral isolates that may be required to respond to emerging needs or public health emergencies.

ATTACHMENT 3 – STATEMENT OF WORK

(March 9, 2016) Page 1 of 11

ATTACHMENT 3: STATEMENT OF WORK

EXTERNAL QUALITY ASSURANCE PROGRAM

OVERSIGHT LABORATORY (EQAPOL)

RFP No. NIAID DAIDS-NIHAI2015055

A. BACKGROUND AND INTRODUCTION

The mission of the Division of AIDS (DAIDS), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), is to increase basic knowledge of the pathogenesis and transmission of the human immunodeficiency virus (HIV), support the development of therapies for HIV infection and its complications, and support the development of vaccines and other prevention strategies. Reliable laboratory data are essential to the clinical evaluation of candidate HIV vaccine platforms and immunogens.

Data from multiple laboratories performing assays in support of single or multiple vaccine candidate trials must be accurate and reproducible. The purpose of the External Quality Assurance Program Oversight Laboratory (EQAPOL) is to provide confidence that individual laboratories generate reliable data to support vaccine immunogen advancement. EQAPOL supports these efforts by participating in the development and availability of validated assays, providing common and well-characterized reagents and Standard Operating Procedures (SOPs), and providing External Quality Assurance (EQA) programs to measure and monitor laboratory performance.

The current contract, awarded in 2010 (HHSN272201000045) to Duke University, established proficiency testing programs serving over 60 laboratories in more than 40 sites worldwide and provided a panel of fully characterized viruses from early acute HIV infections to develop new assays and validate assay platforms. The contract also established a peripheral blood mononuclear cell (PBMC) bank and an EQA reagent repository of characterized material that supports EQAPOL proficiency testing programs and are made available to NIAID-supported investigators.

The new contract will support existing activities, develop new assays, and provide assistance in the standardization, validation, and development of new proficiency testing programs. The contract will continue to make materials available to NIAID-sponsored domestic and international investigators. Options will be included to extend the contract for up to six years beyond the base year, to increase level of effort for unanticipated increases in demand, and to develop/implement a new EQA program. Requirement changes from previous EQAPOL competition include an EQA Program for Multiplex/Array, EQA of Mucosal Specimens, and an option for HIV Incidence Assays.

B. SCOPE

This contract’s scope involves quality assurance/quality control (QA/QC) and operational activities, including the following:

QA/QC activities include: (1) providing proficiency testing programs and evaluating the performance of laboratories conducting assays measuring cellular, antibody, and cytokine responses in a variety of tissue types; (2) developing new assays; and (3) acquiring/establishing/characterizing unique clade-specific virus panels. Operational activities include: (1) the maintenance and expansion of a specimen and reagent

(March 9, 2016) Page 2 of 11 repository; (2) the maintenance of a database to support contract activities; and (3) providing advice on assay validation, regulatory compliance and statistical issues.

C. TECHNICAL REQUIREMENTS

Independently and not as an agent of the Government, the Contractor shall furnish all the necessary services, qualified personnel, material, equipment, and facilities, not otherwise provided by the Government as needed to perform the Statement of Work as stated herein.

Work shall follow the DAIDS Guidelines for Good Clinical Laboratory Practice (GCLP) Standards http://www.niaid.nih.gov/LabsAndResources/resources/DAIDSClinRsrch/Documents/gclp .pdf .

Contractor staff shall have appropriate accreditations where applicable (e.g. College of American Pathologists (http://www.cap.org) and/or American Association for Laboratory Accreditation (http://www.a2la.org). When necessary the Contractor shall have local Institutional Review Board (IRB) approval for its activities.

Specifically, the Contractor shall:

1. MAINTAIN AND EXPAND A PERIPHERAL BLOOD MONO-NUCLEAR CELL

(PBMC) BANK AND EQA REAGENT REPOSITORY

a. Maintain a reagent repository consisting of peptides, antigens/antibodies, serum, plasma, viruses, cell lines and other materials used for EQA programs, panel development, or assay development.

b. Maintain a repository consisting of PBMCs from HIV-1 uninfected human volunteers (HIV-1 seronegative, HIV-1 and other infectious disease vaccinated volunteers) and PBMCs from HIV-1 infected/positive human volunteers.

c. Expand and/or replenish this PBMC bank with cells from additional human subjects as directed by the Contract Officer’s Representative (COR).

d. Upon request of the COR characterize PBMC samples:

1) For cytomegalovirus (CMV), Epstein Barr Virus (EBV), hepatitis B titer or other pathogens.

2) Perform molecular based HLA class I typing to 4 digit resolution for A, B and C alleles.

3) Provide immunophenotyping and characterize PBMCs to include assessment of viability and recovery and T cell function as determined by ELISpot and Intracellular cytokine staining (ICS).

4) Include human leukocyte antigen (HLA) Class II and (killer cell immunoglobulin-like receptors) KIR genotyping.

e. Receive, store, ship and inventory PBMC and EQA reagents including:

1) Provide for appropriate storage and 24-hours a day/seven days a week monitoring of refrigerator/freezer conditions by automatic temperature alarm to guarantee continuous proper storage and integrity of cryopreserved PBMC

(March 9, 2016) Page 3 of 11 and EQA reagents to include peptides, antigens, antibodies, serum, plasma, viruses, cell lines.

2) Provide: (a) uninterruptible power to accommodate freezers and refrigerators; (b) continuously monitored central alarm system connected to refrigerators and freezers, and staff to be notified in the event of equipment malfunction; (c) emergency stand-by refrigerators and freezers to be available in case of mechanical failure of storage space; and (d) equipment maintenance services.

3) Ship infectious and non-infectious PBMC and EQA reagents to domestic and international laboratories, using shipping conditions appropriate for preserving the PBMC or EQA reagents. Use biocontainment shipping procedures that comply with International Air Transport Association (IATA) Dangerous Goods Regulations (www.iata.org) for shipment by air transportation or with Department of Transportation (DOT) regulations for shipment by ground transportation, and obtain export permits as required.

4) Establish an inventory control system for PBMC and EQA reagents so that their use and disposition can be monitored.

2. EQA PROGRAM FOR ELISpot

Within 30 calendar days of award provide the COR a plan to design, set up, manage and coordinate an interferon-gamma (IFNγ) ELISpot proficiency program for NIAID supported research laboratories to provide an unbiased assessment of data quality from participating laboratories. Implement the plan within 30 calendar days of COR approval, and update the plan, as needed or requested by the COR. The plan will include the following:

a. Manage and coordinate an ELISpot EQA Program.

b. Design consensus protocols, prepare SOPs and instructions for participating laboratories.

c. Conduct QC and QA of reagents and materials to define standard performance and ensure optimal quality, consistency, reproducibility and lot-to-lot comparability over time.

d. Acquire, aliquot, store, assemble and ship standardized reagents including PBMCs, peptides, controls, evaluation panels and other reagents.

e. Process and evaluate proficiency data received from participating laboratories and the Contractor’s facility to define assay acceptability criteria (pass/fail) for performance assessment. Monitor performance of laboratories over time and report trending analyses to participating laboratories.

f. Work with laboratories as directed by the COR to develop corrective action plans.

3. EQA PROGRAM FOR FLOW CYTOMETRY-BASED ASSAYS

and coordinate a flow cytometry ICS program. Implement the plan within 30

(March 9, 2016) Page 4 of 11 calendar days of COR approval, and update the plan, as needed or requested by the COR. The plan shall include the following:

a. Generate a standardized set of reagents consisting of antigens and antibody cocktails that ensure convenience, stability and standardization.

b. Design specifications and perform QC tests based upon physical properties (appearance, residual moisture, etc.) of the lyophilized reagents to ensure consistency and quality. Determine the standard performance of each lot, document and track the lot-to-lot reproducibility of the reagents.

c. Create a set of instructions and gating templates for these reagents. The instructions shall provide a suggested method that has been validated to provide optimal results. The Contractor shall determine any unique changes that a particular laboratory may have made in comparison to the suggested instructions to be used in case of troubleshooting.

d. Evaluate primary data received from participating laboratories and produced in the Contractor’s facility to define assay acceptability criteria for overall performance assessment. Monitor performance of laboratories over time and report to participating laboratories trending analyses to demonstrate where each laboratory’s data fit in the overall data set. Provide information to the COR to determine the success of the program in maintaining or improving precision across laboratories.

e. Work with NIAID supported laboratories in consultation with the COR to develop a corrective action plan as needed.

f. Upon direction from the COR, design and optimize additional phenotypic and functional flow cytometry panels, design/implement new flow cytometry assays and/or variations of other flow cytometry based assays, design/implement novel T cell assays, and evaluate test results as needed.

4. EQA PROGRAM FOR MULTIPLEX/ARRAY

and coordinate a Luminex cytokine assay EQA program. Implement the plan within 30 calendar days of COR approval, and update the plan, as needed or requested by the COR. The plan shall include the following:

a. Manage and coordinate an EQA program for Luminex cytokine assays to provide participating laboratories with two scheduled evaluations per year. Design consensus protocols and prepare SOPs and instructions for participating laboratories.

b. Acquire, aliquot, store, assemble and ship all necessary reagents and controls to perform a 5-plex Luminex-bead assay to detect IL-2, IL-6, IL-10, TNF alpha and IFNγ. Conduct QC and QA of reagents and materials to define standard performance and ensure optimal quality, consistency, reproducibility and lot-to-lot comparability over time for different rounds of testing.

c. Evaluate primary data received from participating laboratories and the Contractor’s facility to define assay acceptability (pass/fail) criteria for

(March 9, 2016) Page 5 of 11 performance assessment. Monitor performance of laboratories over time and report trending analyses to participating laboratories to demonstrate where each laboratory’s data fit in the overall data set.

d. Work with NIAID supported laboratories, as directed by the COR, to develop corrective action plans as needed.

e. Upon request of the COR, design and implement additional EQA programs for other multiplex/array platforms, e.g. Meso Scale Discovery.

5. EQA PROGRAM TO ASSESS COLLECTION, STORAGE, AND TESTING OF

MUCOSAL SPECIMENS

Upon request of the COR, the Contractor shall participate in assay development and validation for mucosal immune factors and assist in development of an EQA program to assess collection, storage, and testing parameters of mucosal specimens for host pathogens (microbiota) or anti-vaccine immune responses.

6. SUPPORT THE DEVELOPMENT OF ANTIBODY CHARACTERIZATION ASSAYS

AND EQA PROGRAMS

Laboratory assays used to assess candidate vaccine immunogens based on the antibody responses they elicit are continuing to be developed. These include tests to measure neutralizing antibodies and ELISAs to measure binding antibodies in addition to multiplex technologies anti-HIV responses. Various vaccination strategies are likely to produce a variety of antibody isotypes with unique functional abilities, such as antibody dependent cellular cytotoxicity (ADCC), opsonization, fixation of complement, binding of Fc receptors and specific localization of immune mediators (e.g. mucosal immunoglobulin). Assays for these will require a rigorous process of optimization and validation before use in clinical trials. Key reference reagents, development of SOPs, assay validation, and proficiency test panels for newly developed antibody characterization assays are critical.

The Contractor shall:

a. Design and execute a program to provide logistical support for the optimization of new assays by receiving, storing, quality assuring, and redistributing reagents/materials, and tracking shipments to laboratories supporting assay development.

b. Prepare stocks of reagents/materials and necessary cell lines.

c. Prepare and implement a QA/QC plan (including bridging studies and trending analysis) for these reagents/materials and cell lines to ensure lot-to-lot comparability.

d. Develop and distribute SOPs to the laboratories and assist in implementation of the assay in laboratories.

e. Receive and analyze data from the laboratories. Notify laboratories of performance in collaboration with the COR.

(March 9, 2016) Page 6 of 11

f. Provide assistance to participating laboratories as directed by the COR to troubleshoot assay results and protocol deviations, and report outcomes to the

COR.

7. ESTABLISH AND CHARACTERIZE UNIQUE CLADE-SPECIFIC HIV VIRUS

PANELS

The Contractor shall perform the following activities:

a. Receive and catalog source material (e.g. plasma) from NIAID collaborators

(domestic and international) and perform HIV virus characterization. This includes isolating, culturing, propagating, and aliquoting clarified supernatant containing virus for storage, testing, and re-distribution as requested by the COR.

b. Aliquot and store cultured virus as supernatant and/or in defibrinated plasma.

c. Perform HIV viral load assays to support the virus characterization.

d. Characterize selected HIV strains for host co-receptor usage, and perform full length sequencing, sterility testing for endotoxin and mycoplasma, p24, and

TCID50.

e. Store and distribute viruses and/or plasma. Activities shall include reviewing the storage inventory, retrieving the required vials, packaging for safe and proper shipment, and shipment to labs as approved by the COR.

8. OPERATE AND MAINTAIN A CENTRAL WEB DATABASE FOR ACTIVITIES

Operate and maintain a centralized database for the following:

a. Track EQAPOL activities including real time inventory of cells, viral samples, serum, plasma, etc. (including characterization data).

b. Provide an interface to permit participating laboratories to directly provide EQA testing data of primary and processed results.

c. Allow participating laboratories to retrieve their individual test data reports.

d. Store data analyses and statistical analyses; track protocol/assay deviations and tracking performance of laboratories over time (trending analysis).

e. Share technical and scientific documents with laboratories participating in the EQA Programs.

f. Maintain the computerized system security documentation as required by OMB Circular A-130, Appendix III and the Federal Information Security Management Act (FISMA). This shall include a comprehensive assessment of the management, operational, and technical security controls in the system to determine the extent to which the controls are implemented correctly, operating as intended, and producing the desired outcome with respect to meeting a specified set of security requirements for the system. These actions are referred to as System Assessment and Authorization (SA&A). The NIAID Information System Security Officer (ISSO) performs the Assessment to support the NIAID Chief Information

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Officer’s (CIO) decision to authorize operation of an information system and to explicitly accept the risk to NIAID data based on the implementation of an agreed-upon set of security controls.

g. Upon COR approval the Contractor shall place in operation and maintain the system. COR approval shall be required for updates to the system that include hardware and/or software.

h. Although the Contractor may choose to use a different web-based database from the established database, this contract will not cover costs for developing a new database.

9. COORDINATE OPTIMIZATION EFFORTS FOR NEW ASSAYS AND ADVISE ON

ASSAY VALIDATION, REGULATORY, COMPLIANCE, AND STATISTICAL

ISSUES

The Contractor shall provide high-level strategic, product and assay development consulting services to NIAID. The Contractor will perform a complete assessment of the methods, including the validation and “cross-validation” of specific analytical methods performed by NIAID supported laboratories.

The Contractor shall perform the following tasks:

a. Provide advice to NIAID and NIAID-supported laboratory staff in the development, optimization and validation of novel immunological assays needed for candidate vaccine immune monitoring. This advice shall be provided through teleconferences/videoconferences, participation in site visits, writing and reviewing reports, and writing consensus SOPs.

b. Review methods development and validation packages and provide a comprehensive evaluation of the scientific merit and regulatory compliance of these packages. This review shall be provided to the COR in a formal written report within three weeks of receipt of information.

c. Provide recommendations to the COR for additional assay development, assay transfer, or validation necessary to meet regulatory agency requirements.

d. Provide training or guidance templates on biological assay development, validation, HIV diagnostic algorithms, cross validation, and assay transfer methodologies, as requested.

e. At the request of the COR, provide training at investigator meetings and regional training events. Obtain COR pre-approval of training materials at least 3 business days prior to the date of the presentation.

f. At the request of the COR and upon approval of the Contracting Officer, share data and research results with the scientific community at investigator meetings and regional training events.

10. MEETINGS AND TELECONFERENCES

a. Contract Initiation Meeting

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Within 60 calendar days after the effective date of the contract, participate in a one-day Contract Initiation Meeting with the COR, the Contracting Officer and other NIAID personnel designated by the COR, to be held at the Contractor’s site.

The purpose of the Contract Initiation Meeting will be to orient the Contractor to NIAID contract procedures.

b. Monthly Meetings/Teleconferences

Plan and conduct meetings of the Contractor’s Principal Investigator and Project Manager with the COR at a minimum of monthly intervals, either in person or via teleconference, to review overall progress and/or to discuss any matters relevant to the scientific and financial administration of the contract and future activities.

The schedule for those meetings will be established by the COR after contract award. Prepare and distribute the agenda and meeting/teleconference materials to all participants at least one business day prior to the meeting.

c. Annual Site Visit

Arrange for and facilitate annual site visits for NIAID Program staff, the Contracting Officer, and External Advisory Group members (see below) to review and discuss: project progress; problems and obstacles and approaches to overcoming identified problems and obstacles; recommendations for modifications in project timelines, External Advisory Group recommendations, objectives, and research approaches/methodologies based on outcomes to date;

and future plans. These site visits shall be attended by the Principal Investigator, the Contractor’s business representative, and all key personnel. The Contractor shall:

i. Plan and submit the agenda to the COR for approval at least 10 business days before the site visit.

ii. Develop written and oral presentation materials

iii. Arrange the logistics associated with the site visits and for travel costs for non-Government site visit attendees

iv. Prepare and submit Annual Site Visit reports to the COR and Contracting

Officer within 30 calendar days of completion of each annual site visit.

d. Establish an Independent External Advisory Group

Within 3 months of the effective date of the contract, establish an Independent External Advisory Group consisting of 5 members to periodically review performance and progress toward achieving defined technical and strategic goals and milestones based on negotiated objectives. The membership of the Independent External Advisory Group shall be proposed by the Contractor after award, and agreed to by the COR.

11. INITIAL AND FINAL TRANSITION

a. Initial Transition

The Contractor shall be required to receive shipment(s) of characterized PBMCs, virus isolates, and plasma that will be transferred from Duke University in Durham, North Carolina no later than three (3) months from the effective date of the contract. There are approximately 100,000 cryovials (1.8 ml volume size)

(March 9, 2016) Page 9 of 11 with attached bar-coded labels that shall require storage in vapor phase liquid nitrogen. Specifically, the Contractor shall:

i. Within 30 calendar days of the contract effective date, develop and submit, for COR review and approval, a Draft Initial Transition Plan to ensure the storage of the cryovials in the Contractor’s facility no later than three (3) months following the contract effective date. The Draft Initial Transition Plan shall delineate the activities to be undertaken and the timelines for the completion of the cryovial transfer. This plan shall include the procedures to maintain specimen integrity upon receipt of the cryovials to storage in the liquid nitrogen freezers, transfer of all paper and electronic files that contain cryovial specimen characterization data into the Contractor’s inventory database, and QC procedures. Revise the Draft Initial Transition Plan to accommodate COR comments that will be returned within two weeks of receipt, and submit the Final Initial Transition Plan no later than two (2) weeks after receipt of COR comments.

ii. Participate in teleconferences with personnel at Duke University, the COR and his/her designees to: (i) discuss the bar-coded label identifiers on the cryovials and paper/electronic file information for the cryovials; (ii) review the shipping schedule for delivery of cryovials to the Contractor’s facility; and (iii) discuss any issues required to complete the transfer.

b. Final Transition

The Contractor shall prepare and implement a Final Transition Plan to ensure the orderly, efficient and safe transition of all contract activities and materials. This shall include the following:

i. No later than six (6) months prior to the completion date of this contract, develop and submit, for COR review and approval, a Draft Final Transition Plan delineating the transition activities to be undertaken, timelines for the completion of each transition activity, Contractor staff to be assigned and their roles and responsibilities. The Draft Final Transition Plan shall include a listing of and plans for transferring contract-generated materials, e.g., samples, reagents, all paper and electronic regulatory files, databases, software and hardware, SOPs, training plan, and QA/QC plan, and methods proposed to plan and conduct thorough briefings of the new Contractor.

Revise the Draft Final Transition Plan to accommodate COR comments, and submit the Final Transition Plan no later than four (4) months prior to the completion date of the contract.

ii. Implement the approved Final Transition Plan to ensure the completion of all transition activities and the transfer of contract-generated materials to a new contractor by the completion date of the contract.

iii. Maintain contract operations at full staffing levels during the Final Transition period.

[END OF STATEMENT OF WORK (BASE PERIOD)]

12. OPTION(S)

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In addition to the services/quantities outlined above to be provided for the base requirement, Options(s) for additional services/quantities under the contract may be exercised at the discretion of the Government and are defined as follows:

OPTION 1 - 6: Extend the Term of the Contract: The Government may exercise options to extend the period of performance of the contract beyond the base period (Year 1), annually, for a total contract period of up to 7 years. Assume that the scope and types of activities as outlined herein (i.e., for Year 1 of the contract) would be continued for each succeeding annual contract period.

OPTION 7 - 34: Increased Level of Effort: The Government may exercise options for increased level of effort that may result from unanticipated increases in demand.

Should the Government elect to exercise these options, the Contractor shall provide resources for the unanticipated increase in work volume by 1.00 Full Time Equivalents (FTEs) for each option exercised.

This option provides for an increase in the level of effort to accommodate the addition of 1.00 FTE up to 4 times/year for unanticipated increases in demand for such things as proficiency testing in areas such as ELISpot EQA program, Flow Cytometry-based assays, Multiplex Arrays, and/or to expand the panel of characterized HIV isolates and other viral isolates that may be required to respond to emerging needs or public health emergencies. If the Government elects to exercise this Option, the Contractor shall provide an additional 1.00 FTE per option. The period of performance of an Option for increased level of effort will not exceed the term of the Base Period or Option year in which the Option is exercised.

Additionally, Options for expansion of services may be exercised at the discretion of the Government.

OPTION 35-41: Develop/Implement an EQA Program for HIV Incidence Assays

The Government may exercise options for additional level of effort in order to develop/implement an EQA program for HIV incidence assays. If the Government elects to exercise this Option, the Contractor shall provide an additional 2.00 FTEs.

One (1) Option per year may be exercised during years 1 through 7 of contract performance, for a total of seven (7) Options during the life of the contract. The period of performance of an Option for increased level of effort for this purpose will not exceed the term of the Base Period or Option year in which the Option is exercised.

1. Identify appropriate specimens and controls for use in an on-going proficiency testing program of assays in widespread use for the differentiation of recent and long-standing HIV infections. These specimens will be of sufficient volume to maintain the program and be adaptable to suitable specimen matrices for available assays.

2. Design and execute a proficiency test program to externally assess the ability of laboratories to generate accurate, reproducible assay performance data. The immediate focus will be to establish EQA for the leading candidate assay being deployed for incidence estimation, and particularly the CDC’s (LAg) avidity assay.

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3. Provide logistical support by receiving, storing, and provide oversight for quality assurance, and redistributing reagents/materials to the laboratories as well as tracking shipments.

4. Process and statistically evaluate primary data received from participating laboratories and produced in the Contractor’s facility to define assay acceptability (pass/fail) criteria for overall performance assessment. Monitor performance of laboratories over time and report trending analyses to participating laboratories to demonstrate where each laboratory’s data fit in the overall dataset.

5. Work with laboratories as directed by the COR to develop corrective action plans as needed.

[END OF STATEMENT OF WORK – OPTIONS]

ATTACHMENT 4: ADDITIONAL TECHNICAL PROPOSAL INSTRUCTIONS 1

ATTACHMENT 4: ADDITIONAL TECHNICAL PROPOSAL INSTRUCTIONS,

FORMAT FOR TECHNICAL PROPOSAL, and TABLE OF CONTENTS

EXTERNAL QUALITY ASSURANCE PROGRAM OVERSIGHT…