Performance Work Statement (PWS) for

Genomic Differentiation of Bacterial and/or Viral Diseases

1.0 General Information

1.1 Introduction

The U.S. Naval Medical Research Unit (NAMRU) INDO PACIFIC aims to monitor and characterize emerging and re-emerging infectious diseases of importance to warfighter health and to develop mitigation strategies against threats to warfighter health and medical readiness in the Indo-Pacific region.

1.2 Objectives

The objectives of this contract are to obtain services to (i) improve standardized laboratory procedures to detect biothreat agents, arboviruses, and antibiotic resistant organisms from contrived, environmental, zoonotic or patient samples, (ii) develop detailed consensus genomes for an expanded subset of regional pathogens of concern, and (iii) provide bioinformatic platform to identify novel emerging and re-emerging infectious diseases in the region in samples collected as part of the NAMRU INDO PACIFIC Biosurveillance program.

1.3 Scope of Work

The Contractor shall provide all personnel, materials, facilities, licenses, and other supplies and nonpersonal services including local agreements and assist with ethical research approvals necessary to conduct research services as defined in this PWS. This is a non-personal services award for non-severable services.

1.4. Background

NAMRU INDO PACIFIC has implemented an Armed Forces Health Surveillance Division’s Global Emerging Infections Surveillance (GEIS) program to monitor and address emerging and re-emerging pathogens in the Indo-Pacific region. This program establishes robust surveillance networks to detect and characterize novel pathogens. Through collaboration with host-nation partners, NAMRU INDO PACIFIC collects human and animal samples containing pathogens of interest for analysis using Next Generation Sequencing (NGS). Advanced sequencing bioinformatics is then employed to analyze and interpret the raw data, providing critical insights into pathogen genomics and epidemiology.

To date, NAMRU INDO PACIFIC’s collaborators supporting the surveillance networks include, but are not limited to the following:

1. Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit laboratory, Vientiane, Laos

2. Institut Pasteur du Laos, Vientiane, Laos

3. Tropical Infectious Diseases Research & Education Centre at the University Malaysia, Kuala

Lumpur, Malaysia

4. Monash University, Selangor, Malaysia

5. National Defence University of Malaysia, Kuala Lumpur, Malaysia

6. University of Malaysia Sabah, Sabah, Malaysia

7. The Malaysian Armed Forces sites in Malaysia

8. Institute of Malariology, Parasitology and Entomology Quy Nhon, Hanoi, Vietnam

9. Vietnam Institute of Animal and Veterinary Science, Vietnam

10. Various locations in and around Metro Manila, Philippines

11. Hanyang University, Seoul, South Korea.

12. The National Defense Medical Center and other Taiwanese military locations in Taiwan

13. Central Public Health Laboratory, Port Moresby, Papua New Guinea

14. University of Florida, Gainesville, USA

1.5 Applicable Protocol(s), Standard Operating Procedures (SOPs), Publication(s)

1.5.1 IRB HRPO.NAMRUIP.2025.0003 protocol titled, “Genomic Differentiation of Bacterial versus

Viral Diseases Across Asia and Oceania” and HRPO.NAMRUIP.2024.0005 protocol titled, “Phylogenetic Analysis of Korean Severe Fever and Thrombocytopenia Syndrome Virus Samples since 2013”.

1.5.2 Other protocols may be added when deemed necessary and appropriate by NAMRU INDO

PACIFIC Project Officer (PO).

2.0 Requirements

2.1 The contractor bears primary responsibility for the research.

2.2. All correspondence, deliverables, and conversations with representatives of the U.S. Government will be in proficient English.

2.3 The Contractor shall implement the study protocol(s) (1.5 above) and monitor that implementation follows approved protocol. The study protocol to be used shall be confirmed by NAMRU INDO PACIFIC PO. For any deviations that occur from approved protocol, the Contractor shall report deviation to PO and the Contracting Officer’s Representative (COR) within two business days. The Contractor shall

2.3.1 Provide managerial, supervisory, administrative and logistical support to execute the protocol. In addition, the Contractor shall provide the necessary personnel, materials, equipment, consumables, facilities, licenses – and all other direct and indirect costs associated with this project.

2.3.2 Assist NAMRU INDO PACIFIC to obtain regulatory and ethical approval from local internal institutional review board (IRB) at the selected study sites/locations where work is to be performed and any other required local approvals. Approvals must be obtained in writing.

2.3.3 Assist NAMRU INDO PACIFIC PO in obtaining Department of the Navy IRB approvals and

Human Research Protections Program (HRPP) reviews and Command Level Administrative review (CLAR) by providing local partner human use and non-human study ethical approvals and any changes and amendments to the study protocols and study related documents for U.S.

Government review as directed by the NAMRU INDO PACIFIC PO and/or the head of the NAMRU INDO PACIFIC HRPP. No samples shall be sequenced and/or data analyzed until after IRB, HRPP, and CLAR approvals and all other required approvals have been received in writing.

2.3.4 Work with local partners at each site to optimize Standard Operating Procedures (SOPs) improving detection efficiencies from samples collected for sequencing where needed for activities such as: collecting samples, transporting samples to laboratories for testing, reporting sequencing results, and storing bioinformatic data. This shall include designing and implementing all required training for local personnel.

2.3.5 Upon notification and receipt of the HRPP approval, and CLAR approval if applicable, for the research protocol from the NAMRU INDO PACIFIC PO, complete the following research activities:

2.3.5.1 Oversee the training of staff to don/doff of personal protective equipment (PPE) properly in the laboratory, perform sample-library preparation for sequencing, process serum/whole blood samples according to good clinical practices (GCPs), and onboard new SOPs as needed.

2.3.5.2 Handle all samples according to study protocol(s) in coordination with instructions for each protocol, ensuring local safety requirements and established standard laboratory operating procedures are adhered to.

2.3.5.3 Provide on-site training to laboratory staff at NAMRU INDO PACIFIC’s collaborating sites (up to three sites), to (1) implement sequencing methodologies via a contamination prevention and control strategy to include genetic barcoding procedures with GCPs and quality control procedures, (2) conduct custom hybridization-enrichment, amplicon-based, and metagenomics MinION and/or Illumina-based sequencing on site, as appropriate for the site, (3) and analyze genomics data from sequencing by bioinformatics that can identify, classify and define known and new mutations in known pathogens or characterize near-neighbor novel emerging pathogens, to include protocols for the identification of viral, parasitic, and/or bacterial targets. Where prior training on sites has occurred, conduct refresher training and quality control (QC) & quality assurance (QA).

2.3.5.4 Provide and/or upgrade an integrated system for concurrent molecular sequencing of both bacterial and/or viral diseases at each laboratory to include (1) modified molecular sequencing workflow SOPs tailored for each site’s specific laboratory setup as needed, (2) sample processing and extraction equipment of nucleic acids from human, animal, and vector respiratory and blood/serum or other biological samples as needed, (3) hybridization-enrichment and amplicon-based MinION and/or Illumina sequencing equipment and supplies, and (4) bioinformatics software and hardware. The hybridization-enrichment sequencing methodology shall contain pathogen-specific enrichment probes customized for the pathogens known or suspected to be endemic at each of the study sites, as determined in collaboration with the NAMRU INDO PACIFIC and local laboratory partners. Any equipment acquired and invoiced as cost reimbursable items by the Contractor shall be U.S. Government (USG) property and shall be returned to USG at the end of the contract. Equipment acquired shall be installed, serviced and maintained per manufacturer’s guidelines. The Contractor shall provide documentation to PO and COR for the shipping, delivery, and receipt for equipment within 24-hours of delivery to the partner site(s). The Contractor shall provide reports for professional installation, service, and maintenance of the equipment.

2.3.5.5 Complete NGS of at least 100 samples to characterize SARS-CoV-2, Influenza A/B, Respiratory Syncytial Virus (RSV), Dengue Virus, Plasmodium species, Adenovirus, novel human Coronaviruses, other febrile diseases, and antibiotic resistant or biothreat pathogens.

In addition, these results will assist in developing quality-controlled genomes of pathogens and identifying variants and sequence polymorphisms. Sample selection for testing shall be agreed upon with NAMRU INDO PACIFIC PO and local laboratory partners.

2.3.5.6 Ensure that NAMRU INDO PACIFIC COR and PO are informed during quarterly meetings if any specific project goals cannot be achieved or if any problems are encountered to completing tasks in this PWS.

2.3.5.7 Ensure that all data records are maintained and shared with NAMRU INDO PACIFIC PO and only among collaborating institutions. The data must be approved for presentation or publication by the NAMRU INDO PACIFIC Public Affairs Officer (PAO) including NAMRU INDO PACIFIC internal approvals. All electronic records shall be stored in secure computerized system that contains layered passwords for protection and hard copy documents in a locked and secured room.

2.3.5.8 Provide sequencing reports, Fasta files, and any other related information requested by NAMRU INDO PACIFIC PO on a quarterly basis.

2.3.5.9 Provide trip reports documenting tasks performed and subsequent sequencing results.

2.3.5.10 Provide a mid-year technical report and a final technical report.

3.0 Place of Performance

The work to be performed under this contract shall be in the United States. The locations for the sequencing and bioinformatic work shall be selected by mutual agreement between the Contractor and NAMRU INDO PACIFIC. Potential sites for wet-lab sequencing training/sample processing include but are not limited to those mention in Section 1.4 above. Dry-lab analyses could occur on-site and/or remotely from the USA.

4.0 Deliverables

4.1 Kickoff meeting; The Contractor shall host a kickoff meeting no later than two weeks after task order award to present research and management plans, timeline for performance of tasks, introduce key and supporting personnel, and identify any coordination and potential risks for the performance of the tasks.

4.2 All study protocols, initial and any subsequent versions, as approved by the country/local IRB.

4.3 Quarterly Teleconference Meeting and Minutes: The Contractor shall arrange monthly meetings and provide progress updates on all aspects of the Contractors’ progress towards completing the tasks. The contractor shall generate and deliver a summary (e.g., meeting minutes) of the information shared at each teleconference meeting.

4.4 Sequencing reports, Fasta files, and other related information requested by PO; The Contractor shall provide sequencing reports, Fasta files, and other related information requested on a quarterly basis.

4.5 Trip reports: The Contractor shall submit trip reports to detail tasks performed during the trip.

Details shall include the site visited, the personnel in attendance, any trainings that were conducted, and tasks performed during the trip.

4.6 Technical Progress Reports: The Contractor shall deliver one (1) written mid-year report, due by the 10th working day after the end of six (6) months, and one (1) written final annual report due at the end of the period of performance. Each written report shall contain:

4.6.1 A cover page that includes the contract/task order, “contract number”, title: “[title]”, and report number (e.g., R1, July – Dec 2026).

4.6.2 Report to provide detailed description of number of events supported and contract achievements

(e.g., sequencing and/or bioinformatic tasks performed, training conducted etc.), any problems identified related to the execution of the project, and any other pertinent data beneficial for interpretation of the data or successful execution of the project.

4.6.3 Reports shall be cumulative- meaning the Final report will include R1 information. All reports are the property of the U.S. Navy.

Table of deliverables

Deliverable Frequency # of Copies Medium/Format Submit To

Kickoff meeting Once within two weeks of task order award (TOA)

Verbal communication in English. Minutes in English

NAMRU

INDO

PACIFIC PO

& COR

Protocol approval and final study protocol version as approved by the country/local IRB.

Once upon approval. One Word document, written in English

PO and COR

Teleconference Progress Reports

Quarterly One Verbal communication via teleconferencing; Meeting minutes to be provided in Word document in English

PO and COR

Sequencing reports, Fasta files, and other related information requested

Quarterly One Word document, written in English

PO and COR

Trip Reports Within seven days of returning from the trip

One Word document, written in English

PO and COR

R1 Report Within 6 months and 10 days of TOA

One Word document, written in English

PO and COR

Final Report At the end of the period of performance (PoP).

One Word document, written in English

PO and COR

4. PERFORMANCE REQUIREMENTS SUMMARY

PWS

Paragraph

Performance Standard and AQL

Quality Assurance Method

Acceptance

2.3.2 Obtain Local and regulatory approvals or

approval modifications to include IRB and/or IACUC protocol clearance.

Monitoring by

NAMRU INDO

PACIFIC PO and

COR

Receipt of approved IRB protocol and any other required local and regulatory approvals. 0% variance.

2.3.3 Obtain HRPP and CLAR approvals. Monitoring by

PO and COR

Receipt of HRPP and CLAR approvals. 0% variance.

2.3.5.3 Provide on-site training to laboratory staff at

NAMRU INDO PACIFIC’s collaborating sites (at three sites).

Monitoring by PO and COR

0% variance. Both positive and negative performance shall be documented.

2.3.5.5 Complete next generation sequencing of 90

samples.

Monitoring by PO and COR

Deviation of 3 samples (i.e.

must sequence 87 samples).

Both positive and negative performance shall be documented.

2.3.5.8 Provide Sequencing reports, Fasta files and

any other related information requested by

NAMRU INDO PACIFIC PO

Monitoring by PO and COR

Within 5 days of due date.

Both positive and negative performance shall be documented.

2.3.5.10 Mid-year and final reports. Monitoring by

PO and COR

Within 5 days of due date.

Both positive and negative performance shall be documented.

5.0 Special Qualifications and Training

5.1 Full proficiency in English relating to correspondence, reports, manuscripts(s) and conversations with NAMRU INDO PACIFIC (e.g., during NAMRU INDO PACIFIC PO field site visits). All correspondence shall be in English. Documents in a foreign language shall be translated to English and both original and translated copies shall be delivered.

5.2 The Contractor shall ensure that all project personnel are appropriately trained for the required tasks. All team members are required to complete appropriate research training from the Collaborative Institutional Training Initiative (CITI) (http://www.citiprogram.org) or from another institution approved by NAMRU INDO PACIFIC PO. The Contractor shall provide CITI (or another institution as approved by NAMRU INDO PACIFIC PO) certificates (upon request) confirming training requirements for all Contractor and Subcontractor (if applicable) investigators and staff involved in research for this effort.

5.3 The Contractor shall ensure that all project personnel complete training on Research Integrity, education, and misconduct. The training material shall be provided by NAMRU INDO PACIFIC.

The Contractor shall provide a list of names and dates to record the completion of such training.

At NAMRU INDO PACIFIC’s approval, equivalent training other than that provided by NAMRU INDO PACIFIC may be considered acceptable.

6.0 Contractor Travel Approval

The Contractor shall submit to the PO and COR a trip request authorization at least two months before anticipated travel. This is to ensure that all letters of support, coordination with visiting laboratory, local ethical approvals, IACUC and/or HRPO protocols that cover sequencing of human subject samples, animal samples, and entomological samples are submitted and approved.

7.0 Data Rights

All reports are property of the U.S. Navy. The Contractor shall not release to the public any information regarding the medical research or resulting data without the review and approval of the NAMRU INDO PACIFIC PAO. The approval process may include blanket approval for some types of information releases.

The Contractor shall submit to the NAMRU INDO PACIFIC PO and COR, or Contracting Officer for review and approval, in line with NAMRU INDO PACIFIC PAO requirements, prior to public disclosure any written publications or public relations materials (including proposed public announcements, flyers, posters, audiovisual materials, newspaper, advertisements, or mailed advertisements) which are targeted primarily to the scope of contract services or policies and programs of the Contractor.

The U.S. Government has unlimited rights to all documents/material/reports produced under this contract.

All documents and materials, to include the source codes of any software, produced under this contract shall be U.S. Government owned and are the property of the U.S. Government with all rights and privileges of ownership/copyright belonging exclusively to the U.S. Government. These documents and materials may not be used or sold by the Contractor without written permission from the Contracting Officer. All materials supplied to the U.S. Government shall be the sole property of the U.S. Government and may not be used for any other purpose. This right does not abrogate any other U.S. Government rights.

8.0 Research Integrity

All parties agree to the definitions, protocol, and processes for research integrity as explained in BUMEDINST 6500.3B and DoD Instruction 3210.7.

9.0 Organizational Conflict of Interest

Contractor personnel performing work under this contract may receive, have access to, or participate in the development of proprietary information. The Contractor shall notify the Contracting Officer immediately whenever it becomes aware that such access or participation may result in any actual or potential organizational conflict of interest (OCI) and shall promptly submit a plan to the Contracting Officer to avoid or mitigate any such OCI. The Contractor’s mitigation plan will be determined to be acceptable solely at the discretion of the Contracting Officer and in the event the Contracting Officer unilaterally determines that any such OCI cannot be satisfactorily avoided or mitigated, the Contracting Officer may affect other remedies as he or she deems necessary, including prohibiting the Contractor from participation in subsequent contracted requirements which may be affected by the OCI.

10.0 Invoicing and Payments

All payments will be in U.S. dollars, the United States currency. Invoices shall be submitted for payment on a quarterly basis.

11.0 Protection of Human Subjects

All parties agree to the definitions, protocol, and processes for protection of human subjects in research as explained in DFARS clause 252.235-7004 (Federal Register Volume 74 Number 144, 29 July 2009) as specified below.

a) Definitions. As used in this clause--

1) Assurance of compliance means a written assurance that an institution will comply with requirements of 32 CFR Part 219, as well as the terms of the assurance, which the Human Research Protection Official determines to be appropriate for the research supported by the Department of Defense (DoD) component

(32 CFR 219.103).

2) Human Research Protection Official (HRPO) means the individual designated by the head of the applicable DoD component and identified in the component's Human Research Protection Management Plan as the official who is responsible for the oversight and execution of the requirements of this clause, although some DoD components may use a different title for this position.

3) Human subject means a living individual about whom an investigator (whether professional or student) conducting research obtains data through intervention or interaction with the individual, or identifiable private information (32 CFR 219.102(f)). For example, this could include the use of human organs, tissue, and body fluids from individually identifiable living human subjects as well as graphic, written, or recorded information derived from individually identifiable living human subjects.

4) Institution means any public or private entity or agency (32 CFR 219.102(b)).

5) Institutional Review Board (IRB) means a board established for the purposes expressed in 32 CFR Part 219 (32 CFR 219.102(g)).

6) IRB approval means the determination of the IRB that the research has been reviewed and may be conducted at an institution within the constraints set forth by the IRB and by other institutional and Federal requirements (32 CFR 219.102(h)).

7) Research means a systematic investigation, including research, development, testing, and evaluation, designed to develop or contribute to generalizable knowledge. Activities that meet this definition constitute research for purposes of 32 CFR Part 219, whether they are conducted or supported under a program that is considered research for other purposes. For example, some demonstration and service programs may include research activities (32 CFR 219.102(d)).

b) The Contractor shall oversee the execution of the research to ensure compliance with this clause. The Contractor shall comply fully with 32 CFR Part 219 and DoD Directive 3216.02, applicable DoD component policies, 10 U.S.C. 980, and, when applicable, Food and Drug Administration policies and regulations.

c) The Contractor shall not commence performance of research involving human subjects that is covered under 32 CFR Part 219 or that meets exemption criteria under 32 CFR 219.101(b), or expend funding on such effort, until and unless the conditions of either the following paragraph (c)(1) or (c)(2) have been met:

1) The Contractor furnishes to the HRPO, with a copy to the Contracting Officer, an assurance of compliance and IRB approval and receives notification from the Contracting Officer that the HRPO has approved the assurance as appropriate for the research under the Statement of Work and that the HRPO has reviewed the protocol and accepted the IRB approval for compliance with the DoD component policies. The Contractor may furnish evidence of an existing assurance of compliance for acceptance by the HRPO, if an appropriate assurance has been approved in connection with previous research. The Contractor shall notify the Contracting Officer immediately of any suspensions or terminations of the assurance.

2) The Contractor furnishes to the HRPO, with a copy to the Contracting Officer, a determination that the human research proposed meets exemption criteria in 32 CFR 219.101(b) and receives written notification from the Contracting Officer that the exemption is determined acceptable. The determination shall include citation of the exemption category under 32 CFR 219.101(b) and a rationale statement. In the event of a disagreement regarding the Contractor's furnished exemption determination, the HRPO retains final judgment on what research activities or classes of research are covered or are exempt under the contract.

d) DoD staff, consultants, and advisory groups may independently review and inspect the Contractor's research and research procedures involving human subjects and based on such findings, DoD may prohibit research that presents unacceptable hazards or otherwise fails to comply with DoD procedures.

e) Failure of the Contractor to comply with the requirements of this clause will result in the issuance of a stop-work order under Federal Acquisition Regulation clause 52.242-15 to immediately suspend, in whole or in part, work and further payment under this contract, or will result in other issuance of suspension of work and further payment for as long as determined necessary at the discretion of the Contracting Officer.

f) The Contractor shall include the substance of this clause, including this paragraph (f), in all subcontracts that may include research involving human subjects in accordance with 32 CFR Part 219, DoD Directive 3216.02, and 10 U.S.C. 980, including research that meets exemption criteria under 32 CFR 219.101(b). This clause does not apply to subcontracts that involve only the use of cadaver materials.

(End of clause)