Amendment II_CDC-RFA-CK22-2204.pdf

Centers for Disease Control and Prevention

National Center for Emerging and Zoonotic Infectious Diseases

US Public Health Pathogens Genomics Centers of Excellence

CDC-RFA-CK22-2204

05/17/2022

AMENDMENT 1 – This amendment provides a) clarification under the Eligibility Section located on Page 35 and b) Provides a cutoff date for submission of questions of 5/1/2022 at the bottom of page 2 and c) clarifies where Q& A documents will be available for applicant review.

AMENDMENT 2 - This amendment changes pages 35-36 to include full eligibility information.

It also corrects funding amounts on pages 3 and 33 from $7,000,000 to $6,200,00 and on pages 4 and 33 from $7,000,000 to $6,000,000. This amendment also amends page 27 from “For research proposed or anticipated, an application must describe the following” to read “An application must describe the following:”

Table of Contents A. Funding Opportunity Description

B. Award Information

C. Eligibility Information

D. Required Registrations

E. Review and Selection Process

F. Award Administration Information

G. Agency Contacts

H. Other Information

I. Glossary

Part I. Overview Applicants must go to the synopsis page of this announcement at www.grants.gov and click on the "Subscribe" button link to ensure they receive notifications of any changes to CDC-RFA- CK22-2204. Applicants also must provide an e-mail address to www.grants.gov to receive notifications of changes.

A. Federal Agency Name:

Centers for Disease Control and Prevention (CDC) B. Notice of Funding Opportunity (NOFO) Title:

US Public Health Pathogens Genomics Centers of Excellence C. Announcement Type: New - Type 1:

This announcement is only for non-research activities supported by CDC. If research is proposed, the application will not be considered. For this purpose, research is defined at https://www.gpo.gov/fdsys/pkg/CFR-2007-title42-vol1/pdf/CFR-2007-title42-vol1-sec52- 2.pdf. Guidance on how CDC interprets the definition of research in the context of public health can be found at https://www.hhs.gov/ohrp/regulations-and-policy/regulations/45-cfr- 46/index.html (See section 45 CFR 46.102(d)).

Please note for this particular NOFO, CDC-RFA-CK22-2204, research activities are allowable and will be subject to all applicable laws, regulations and policy requirements.

Note research and human subjects protection requirements inserted throughout this NOFO. All instructions pertaining to research should be addressed and followed as indicated in this NOFO. Please refer to the Strategies and Activities for more details.

D. Agency Notice of Funding Opportunity Number:

CDC-RFA-CK22-2204

https://www.grants.gov/ https://www.grants.gov/ https://www.gpo.gov/fdsys/pkg/CFR-2007-title42-vol1/pdf/CFR-2007-title42-vol1-sec52-2.pdf https://www.gpo.gov/fdsys/pkg/CFR-2007-title42-vol1/pdf/CFR-2007-title42-vol1-sec52-2.pdf https://www.hhs.gov/ohrp/regulations-and-policy/regulations/45-cfr-46/index.html https://www.hhs.gov/ohrp/regulations-and-policy/regulations/45-cfr-46/index.html

E. Assistance Listings Number:

93.084 F. Dates:

1. Due Date for Letter of Intent (LOI):

04/17/2022 Recommended but not Required Although a letter of intent is not required, is not binding, and does not enter into the review of a subsequent application, the information that it contains allows CDC staff to estimate the potential review workload and plan the review.

By the date listed in the Application and Submission Information section of this NOFO, prospective applicants are asked to submit a letter of intent that includes the following information:

Name of the applicant organization Descriptive title of proposed application Name, address, and telephone number of the PD(s)/PI(s) Names of other key personnel Participating institutions Number and title of this notice of funding opportunity

The letter of intent should be sent to:

Gregory Anderson, MPH, MS Extramural Research Program Office Office of the Associate Director of Science National Center for HIV, Viral Hepatitis, STD and TB Prevention Centers for Disease Control and Prevention U.S. Department of Health and Human Services 1600 Clifton Road, MS US8-1 Atlanta, GA 30333 Telephone: 404-718-8833 Email: GAnderson@cdc.gov

2. Due Date for Applications:

05/17/2022 11:59 p.m. U.S. Eastern Standard Time, at www.grants.gov.

Due Date for Informational Conference Call:

March 31, 2022 Time, 2:00 pm ET; Phone Number 1-866-620-0420; Passcode: 8943360 Questions and answers from the conference call and information on any updates to the NOFO will be posted at www.cdc.gov/amd and on Grants.gov. All questions must be received by 5/1/2022 in order to be included in the Q& A document.

mailto:GAnderson@cdc.go https://www.grants.gov/

F. Executive Summary:

Summary Paragraph This NOFO includes three components, two Mandatory and one Optional. The underlying objective of the Pathogen Genomics Centers of Excellence (PGCoE) network NOFO is to foster and improve innovation and technical capacity in pathogen genomics, molecular epidemiology, and bioinformatics to better prevent, control and respond to microbial threats of public health importance. Partnership and collaboration between academia, public health and the private sector is at the core of this objective. The Centers of Excellence network is intended to enable the public health system to better respond to infectious disease threats with resilience, flexibility and the latest practical advances in laboratory technology, scientific computing, and applied research. This cooperative agreement will fund the establishment of several centers of excellence, each consisting of a combination of a health department and one or more academic institutions with the purpose of working together as a network to establish a platform to develop and identify relevant areas of genomics and related technologies, adapt them for use in public health, and pilot their application in actual settings. The network of health departments with their academic partners is expected to also implement three other high-level strategies: education of the public health workforce, including bioinformaticians, microbiologists, and epidemiologists, preparing to respond to infectious threats, and responding to infectious threats.

a. Eligible Applicants:

Open Competition

b. NOFO Type:

CA (Cooperative Agreement)

c. Approximate Number of Awards Mandatory Components (Core, Response Implementation): 6 awards Optional Component (Lead PGCoE for Education): 1 award (to a recipient of a Mandatory Components (Core, Response Implementation) award)

d. Total Period of Performance Funding:

$185,000,000

e. Average One Year Award Amount:

$6,200,000 $4,000,000 (Mandatory Component, Core); $2,000,000 Mandatory Component (Response Implementation); $1,000,000 (Optional Component)

If applying for both the Mandatory Components (Core, Response Implementation) and Optional Component (Lead PGCoE for Education), a separate Budget and Budget Narrative must be included for each component (Mandatory Component (Core), Mandatory Component (Response Implementation) and Optional Component (Lead PGCoE for Education)).

Awards issued under this NOFO are contingent upon availability of funds and a sufficient number of meritorious applications. Because the nature and scope of the proposed work will vary from application to application, it is also anticipated that the size and duration of each award may also vary. The total amount awarded and the number of awards will depend upon the number, quality, duration and cost of the applications received.

Average One Year Award Amount for Mandatory Components (Core, Response Implementation) and Optional Component (Lead PGCoE for Education) is as follows:

Year 1:

Average per site for Mandatory Components (Core, Response Implementation): $6,000,000 $4,000,000/award for Mandatory Component (Core) with approximate amounts for each strategy as follows $3,500,000 for Translation $400,000 for Education $100,000 for Response Base

$2,000,000/award for Mandatory Component (Response Implementation)

In addition, one site will be awarded approximately $1,000,000/award for Optional Component (Lead PGCoE for Education)

Throughout the project period, CDC will continue the award based on the availability of funds, the evidence of satisfactory progress by the recipient (as documented in required reports), and the determination that continued funding is in the best interest of the federal government. The total number of years for which federal support has been approved (project period) will be shown in the “Notice of Award.” This information does not constitute a commitment by the federal government to fund the entire period. The total period of performance comprises the initial competitive segment and any subsequent non-competitive continuation award(s).

f. Total Period of Performance Length:

g. Estimated Award Date:

September 30, 2022

h. Cost Sharing and / or Matching Requirements:

No Cost sharing or matching funds are not required for this program. Although no statutory matching requirement for this NOFO exists, leveraging other resources and related ongoing efforts to promote sustainability is strongly encouraged as long as there is no scientific, budgetary, percent effort or other overlap with any other funded projects.

Part II. Full Text A. Funding Opportunity Description

1. Background

a. Overview Rapid advances in genomic technologies are transforming public health, particularly the prevention and control of infectious diseases. “Next-generation sequencing”, bioinformatics, and genomic epidemiology are improving understanding of pathogen transmission and clinical features including of foodborne illness, tuberculosis, influenza, SARS-CoV-2, and antimicrobial drug resistant organisms. Bringing these advances into everyday public health is a priority and can also present a challenge, especially given the continued rapid evolution of genomics, bioinformatics, and related technologies. This NOFO envisions three components:

Mandatory Component (Core; all applications must address) has a three-pronged strategy:

• Translation: developing, identifying, refining, evaluating, piloting, and implementing technologies and practices relevant to public health

• Education: developing practical training for public health professionals

• Response Base: developing capacity to respond to infectious disease threats

Mandatory Component (Response Implementation; all applications must address):

• Responding to infectious disease threats by applying genomic technologies and synthesizing diverse data

Optional Component (Lead PGCoE for Education; applicant may choose to address):

• Lead network educational activities and develop an online training program

All PGCoEs to be supported by this NOFO are expected to address the Mandatory Components (Core, Response Implementation) and one center is also expected to address the Optional Component (Lead PGCoE for Education) by pairing public health agencies with academic centers, utilizing strengths of both. The public health agencies will be the prime recipients of their respective awards and are expected to bring deep understanding of public health priorities and practice as well as needs of the public health workforce. The academic centers (sub-recipients) are expected to bring expertise in microbial genomics and genomic epidemiology and access to innovation and novel, relevant technologies. The intent is for these groups to work synergistically together, accelerating the application of genomics and related technologies in public health, focusing initially on the U.S. but with an eye towards making innovations globally accessible. The PGCoE are expected to work together as a network, and with CDC, its programs, and other partners to implement the strategies and activities described in this NOFO.

The translational strategy will be the main, ongoing focus of the PGCoE network and relies on developing and identifying technologies and approaches that have relevance for public health, adapting and evaluating those for use in public health, piloting those in real-life public health settings and, if applicable, assisting in implementing those in the public health system. In this sense, the PGCoE network is expected to be a U.S. public health system technology “incubator."

The educational strategy (mandatory and optional components) relies on identifying relevant educational needs of public health bioinformaticians, microbiologists, and epidemiologists and developing training to address these needs. Training that is developed will be mostly online and asynchronous, although some in-person training may also be supported.

The response strategy relies on contributing to the overarching response to infectious disease threats in a flexible and rapid manner. This assistance may include, for example, assisting with sequencing or analysis of sequence data, synthesis of data from a variety of sources, and reports of findings.

Statutory Authorities PUBLIC LAW 117–2, the AMERICAN RESCUE PLAN ACT OF 2021, (PUBL002.PS (congress.gov)), Section 2402;

ARP SEC. 2402. FUNDING FOR SARS–COV–2 GENOMIC SEQUENCING AND

SURVEILLANCE.

(a) In General.—In addition to amounts otherwise available, there is appropriated to the Secretary for fiscal year 2021 out of any money in the Treasury not otherwise appropriated, $1,750,000,000, to remain available until expended, to strengthen and expand activities and workforce related to genomic sequencing, analytics, and disease surveillance.

(b) Use Of Funds.—From amounts appropriated by subsection (a), the Secretary, acting through the Director of the Centers for Disease Control and Prevention, shall—

(1) conduct, expand, and improve activities to sequence genomes, identify mutations, and survey the circulation and transmission of viruses and other organisms, including strains of SARS– CoV–2;

(2) award grants or cooperative agreements to State, local, Tribal, or territorial public health departments or public health laboratories—

(A) to increase their capacity to sequence genomes of circulating strains of viruses and other organisms, including SARS–CoV–2;

(B) to identify mutations in viruses and other organisms, including SARS–CoV–2;

(C) to use genomic sequencing to identify outbreaks and clusters of diseases or infections, including COVID–19; and

(D) to develop effective disease response strategies based on genomic sequencing and surveillance data;

(3) enhance and expand the informatics capabilities of the public health workforce; and

(4) award grants for the construction, alteration, or renovation of facilities to improve genomic sequencing and surveillance capabilities at the State and local level.

c. Healthy People 2030 Public Health Infrastructure (https://health.gov/healthypeople/objectives-and-data/browse-objectives/public-health-infrastructure) Health IT (https://health.gov/healthypeople/objectives-and-data/browse-objectives/health-it) Global Health (https://health.gov/healthypeople/objectives-and-data/browse-objectives/global-health) Workforce Development (https://health.gov/healthypeople/objectives-and-data/browse-objectives/public-health-infrastructure/increase-use-core-and-discipline-specific-competencies-drive-workforce-development-phi-r03)

d. Other National Public Health Priorities and Strategies To increase the use of pathogen genomics in the US public health system as articulated in the American Rescue Plan Act of 2021, Section 2402.

e. Relevant Work

1. Armstrong GL, MacCannell DR, Taylor J, et al. Pathogen genomics in public health. N Engl J Med 2019;381:2569-80. This review describes how microbial genomics was impacting public health practice in the United States before the start of the COVID-19 pandemic.

2. Kubota KA, Wolfgang WJ, Baker DJ, et al. PulseNet and the changing paradigm of https://www.congress.gov/117/plaws/publ2/PLAW-117publ2.pdf https://www.congress.gov/117/plaws/publ2/PLAW-117publ2.pdf https://health.gov/healthypeople/objectives-and-data/browse-objectives/public-health-infrastructure https://health.gov/healthypeople/objectives-and-data/browse-objectives/public-health-infrastructure https://health.gov/healthypeople/objectives-and-data/browse-objectives/health-it https://health.gov/healthypeople/objectives-and-data/browse-objectives/global-health https://health.gov/healthypeople/objectives-and-data/browse-objectives/global-health https://health.gov/healthypeople/objectives-and-data/browse-objectives/public-health-infrastructure/increase-use-core-and-discipline-specific-competencies-drive-workforce-development-phi-r03 https://health.gov/healthypeople/objectives-and-data/browse-objectives/public-health-infrastructure/increase-use-core-and-discipline-specific-competencies-drive-workforce-development-phi-r03 https://health.gov/healthypeople/objectives-and-data/browse-objectives/public-health-infrastructure/increase-use-core-and-discipline-specific-competencies-drive-workforce-development-phi-r03 laboratory-based surveillance for foodborne diseases. Pub Health Rep 2019;134(2 Suppl):22S- 28S. PulseNet (https://www.cdc.gov/pulsenet) is a flagship program for molecular surveillance in the United States public health system and switched several years ago from PFGE to whole-genome sequencing.

3. Zhou B, Deng YM, Barnes JR, et al. Multiplex Reverse Transcription-PCR for Simultaneous Surveillance of Influenza A and B Viruses. J Clin Microbiol 2017:3492-3501.

4. Shepard SS, Meno S, Bahl J, Wilson MM, Barnes J, Neuhaus E. Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler. BMC Genomics. 2016 Sep 5;17(1):708.

5. Rambo-Martin BL, Keller MW, Wilson MM, et al. Influenza A Virus Field Surveillance at a Swine-Human Interface. mSphere. 2020;5(1):e00822-19. Sequencing is a core part of viral surveillance of influenza in the United States and elsewhere, and also plays a key role in investigations such as those in the third reference.

6. https://www.cdc.gov/amd. The Advanced Molecular Detection (AMD) program has supported the adoption of sequencing in the US public health system since 2014. The AMD web site provides information on some of the many activities supported by the program, both internally at CDC and externally, including support for SARS-CoV-2 sequencing and training.

2. CDC Project Description Bold indicates period of performance outcome.

CDC-RFA-CK22-2204 Logic Model: US Public Health Pathogens Genomics Centers of Excellence Bold indicates period of performance outcome Strategies and Activities

Short-term Outcomes

Intermediate Outcomes

Long-Term Outcomes

Mandatory Component (Core)

1. Translate Innovations to Public Health

a) develop networked approaches and support and encourage use of reproducible methods and open standards

b) identify gaps in use of genomic epidemiology

c) develop, identify, adapt, pilot, and

Networked function with established “platform” for collaborative work between and beyond centers

Improved understanding of current state of genomic epidemiology in public health

Increased use of new and refined laboratory and bioinformatics

Greater use of genomic technologies to address infectious public health threats

Improved interoperability of microbial genomic and other surveillance, clinical and public health relevant information

Increased use of common tools and applications across network sites and beyond

Improved prevention of infectious diseases

Improved detection and characterization of emerging and re-emerging infectious diseases

Improved response to emerging and re-emerging infectious diseases

Improved response to outbreaks of infectious diseases http://www.cdc.gov/amd implement technologies and applications for public health

d) assist in implementing technologies broadly in the US and aligning with global efforts

2. Educate Public Health Workforce

Lead or assist in training activities

3. Response Base

Prepare to respond to infectious disease threats

Mandatory Component (Response Implementation)

Perform sequencing and other applications, analysis, and data synthesis during emergencies from infectious agents

Optional Component (Lead PGCoE for Education)

Identify relevant educational needs, lead education efforts of the network and develop online tools

Increased capacity to sequence pathogens and to analyze genomic data

Increased capacity to link microbial genomic, clinical, and epidemiologic data and analyze linked data

Increased speed of adoption of relevant genomic technologies in US public health

Increased availability of educational materials and approaches

Networked activity supported by established systems for data sharing, analysis, review, and reporting

Improved discovery of transmission, risk factors, and outcomes of pathogens of public health importance

Increase in US public health personnel with proficiency and expertise in use of genomics and genomic epidemiology

Greater alignment of US and global microbial genomics and genomic epidemiology efforts

Rapid scale-up of genomic epidemiology capabilities in emergencies from infectious agents

Lower burden of infectious diseases

Improved national-level capacity and coordination against infectious disease threats

Improved use of microbial genomic and epidemiologic data in global public health training

i. Purpose This NOFO will implement a Mandatory Component (Core) with three-pronged strategy: 1) translation of pathogen genomic technologies and innovations into the U.S. public health system;

2) training of the public health workforce in genomics and genomic epidemiology; and 3) preparation for response to infectious threats. If and when needed this NOFO will implement Mandatory Component (Response Implementation) to respond to infectious threats. This NOFO will also implement an Optional Component (Lead PGCoE for Education) to lead education activities of the network and develop online training.

ii. Outcomes The overall outcomes will focus on:

• Establishing “platform” for collaborative work between and beyond centers

• Improving understanding of the current state of genomic epidemiology in public health

• Increasing use of new and refined laboratory and bioinformatics tools

• Increasing capacity to sequence pathogens and to analyze genomic data

• Increasing capacity to link microbial genomic, clinical, and epidemiologic data and analyze linked data

• Increasing speed of adoption of relevant genomic technologies in US public health

• Increasing availability of educational materials and approaches

• Establishing systems for data sharing, analysis, review and reporting

• Greater use of genomic technologies to address public health threats

• Improving interoperability of microbial genomic and other surveillance, clinical and public health relevant systems and information

• Increasing use of common tools and applications across network sites and beyond

• Improving discovery of transmission, risk factors, and outcomes of pathogens of public health importance

• Increasing in US public health personnel with proficiency and expertise in use of genomics and genomic epidemiology

• Greater alignment of US and global microbial genomics and genomic epidemiology efforts

• Rapid scale-up of genomic epidemiology capabilities in emergencies from infectious agents

iii. Strategies and Activities Each funded prime recipient is expected to develop, with an academic partner or partners, a U.S.

Pathogen Genomics Center of Excellence (PGCoE) to pursue three crosscutting strategies (Mandatory Component (Core)): 1) translation of innovations to public health; 2) education of the public health workforce; and 3) preparation for response to infectious disease threats. In addition, each funded prime recipient is expected to propose a strategy of response to infectious disease threats (Mandatory Component (Response Implementation) to be funded and implemented if and when needed. In addition, one prime recipient will be funded to be the Lead PGCoE for Education and lead the network in workforce education activities (Optional Component (Lead PGCoE for Education)). The Mandatory Component (Core) Translation and Response Base strategies and the Mandatory Component (Response Implementation) may contain research activities. The Mandatory Component (Core) Education strategy and the Optional Component (Lead PGCoE for Education) may not include research activities.

The PGCoEs are expected to operate collaboratively as a network and will be expected to collaborate with CDC and CDC-funded entities, including other partners and health departments.

This collaboration is intended to ensure synergy and policy coordination toward achieving the expected outcomes consistent with this cooperative agreement. The network is intended to actively assist stakeholders in CDC-supported partnerships (e.g., other grants, cooperative agreements), support communication channels, and provide peer-to-peer technical assistance (TA) to relevant entities, that include other state and local public health departments, academic partners, the community, and other stakeholders.

A coordinating group for the PGCoE network will include representatives of each funded site and CDC personnel. The coordinating group will consider emergent public health priorities and advancements in public health genomics, coordinate implementation and operation of the network activities among the sites and within the scope of the cooperative agreement, and foster coordination across PGCoEs and with CDC programs. The coordinating group will not include consensus decision making and will not provide advice or recommendations to CDC. Over the period of performance of the cooperative agreement, a networked approach with collaboration across sites will be expected. Specific projects may involve one or several sites, and there may be “core” projects in which all sites are participants. Activities of the network will fall within five broad topic areas:

1. Wet laboratory methods development and validation, proficiency testing, technologies, and applications

2. Bioinformatics technologies and applications, as well as related technologies

3. Data standardization/data security/data stewardship/data integration and reporting/data linkage/data science/data analytics/data visualization including of genomic, epidemiologic, clinical, biological, environmental, geospatial, behavioral, social and other types of data together

4. Genomic surveillance, monitoring, analysis, data synthesis, and response

5. Field applications and investigations

To ensure that PGCoE activities align with the CDC mission, collaboration between the PGCoE personnel and CDC technical advisors, including from programs focused on specific pathogens or groups of pathogens, is required. Project plans will be assessed at least annually by appropriate CDC technical advisors; to the extent projects are proposed that may implicate research activities governed by applicable laws, regulations and policies, those proposals are expected to comply with those laws, regulations and policies.

Applicants should propose activities for each of the three main strategies of the (Mandatory Component (Core) and for the strategy of the Mandatory Component (Response Implementation). Applicants interested in being considered for the Optional Component (Lead PGCoE for Education) should propose how they would lead the network in workforce education activities.

The Project Narrative and Budgets should focus in a detailed way on site-specific projects in the first year. Applicants are encouraged to propose projects that highlight and build upon particular areas of expertise of the PGCoE applicant partners (health department and academic). The application should discuss ways that these projects could be further developed and implemented over the period of performance and across the network and beyond. Applications may address host genomics, if the main focus is for its use in understanding and responding to infectious disease threats. The Project Narrative and Budget for the first year should include a landscape analysis on gaps, needs, and opportunities for relevant genomics (and related) technologies in the U.S. public health system. This landscape analysis will contribute to a Roadmap for pathogen genomics (and related technologies) and genomic epidemiology in public health.

Work of the network is intended to meet the needs of public health and to align with the strategic direction of CDC programs, and to incorporate new technologies and approaches from the rapidly evolving field of genomics. Therefore, the network and individual PGCoEs are expected to be agile and flexible in identifying, implementing, and amending specific activities, to the extent consistent with the terms of this cooperative agreement. Annually, by way of the PGCoE cooperative agreement continuation planning and process, projects will be evaluated and amended as necessary in light of public health priorities, advancement in the field and emerging issues and infectious threats.

Applicants should describe how the network will benefit from the applicant’s expertise within the five broad topic areas for network activities.

Applicants should also describe how the network will benefit from their unique scientific environment, subject populations, or collaborative arrangements.

The Project Narrative should follow the format specified in the H. Other Information section of this NOFO. The protection of human subjects should also be described in the Strategies and Activities section of the Project Narrative, including a single institutional review board (IRB) plan, using the Public Health Service (PHS) Human Subjects and Clinical Trials Information format (a sample of the format can be found on page 238 at https://grants.nih.gov/grants/how-to-apply-application-guide/forms-g/general-forms-g.pdf).

Protections for Human Subjects and Animals If any proposed research involves human subjects but does not involve one of the eight categories of research that are exempt under 45 CFR Part 46, the proposal must include the justification for the involvement of human subjects and the proposed protections from research risk relating to their participation according to the following five criteria: 1) risk to subjects, 2) adequacy of protection against risks, 3) potential benefits to the subjects and others, 4) importance of the knowledge to be gained, and 5) data and safety monitoring for clinical trials.

https://grants.nih.gov/grants/how-to-apply-application-guide/forms-g/general-forms-g.pdf

For research that involves human subjects and meets the criteria for one or more of the eight categories of research that are exempt under 45 CFR Part 46, include the following: 1) the justification for the exemption, 2) human subjects involvement and characteristics, and 3) sources of materials. For additional information on the content of the Human Subjects section, please refer to https://grants.nih.gov/grants/how-to-apply-application-guide/forms-g/general-forms-g.pdf.

Activities involving the use of animals conducted under this NOFO shall be in compliance with the PHS Policy on Humane Care and Use of Laboratory Animals, the current edition of the “Guide for the Care and Use of Laboratory Animals (the Guide), the Animal Welfare Act and Regulations (Title 9 Code of Federal Regulations part 1), and all applicable local, state, or other federal regulations. The PGCoE and any sub-awardee shall have an approved Animal Welfare Assurance on file with the Office of Laboratory Animal Welfare (OLAW), at the time of contract award. Accreditation of the PGCoE or sub-awardee by the Association for the Assessment and Accreditation of Laboratory Animal Care International (AAALAC) is preferred. If animal species regulated by the United States Department of Agriculture (USDA) are to be used, the PGCoE or sub-awardee shall be registered with the Secretary of Agriculture of the United States in accordance with the following Federal regulations 7 U.S.C 2136 and 9 CFR sections 2.25-2.28 respectively.

Applicants are required to respond to all three strategies of the Mandatory Component (Core) and to the one strategy of the Mandatory Component (Response Implementation). Applicants may choose to respond to the Optional Component (Lead PGCoE for Education).

A separate Narrative and Budget are required each component and strategy as follows:

I. Mandatory Component (Core)

a. Translation (one narrative and budget)

b. Education (one narrative and budget)

c. Response Base (one narrative and budget)

II. Mandatory Component (Response Implementation) (one narrative and budget) III. Optional Component (Lead PGCoE for Education) (one narrative and budget)

Mandatory Component (Core)

Strategy 1: Translation. Translate innovations in pathogen genomics and genomic epidemiology to public health

a) Develop networked approaches and support and encourage the use of reproducible methods and open standards.

Work with the other centers as part of a network. Provide representation to the coordinating group. Establish processes and procedures that will allow for coordinated efforts within and beyond the network of centers, such as data use agreements, memoranda of understanding, and

IRB protocols.

b) Identify gaps in and opportunities for use of genomic epidemiology in public health.

All applicants should indicate how they will perform a landscape analysis for the following 5 broad areas relevant to genomic epidemiology. Recipients will be expected to coordinate with other centers and will receive technical assistance and input from CDC, including pathogen-focused programs on these landscape analyses.

1. Wet laboratory methods development and validation, proficiency testing, technologies, and applications

2. Bioinformatics technologies and applications, as well as related technologies

3. Data standardization/data security/data stewardship/data integration and reporting/data linkage/data science/data analytics/data visualization including of genomic, epidemiologic, clinical, biological, environmental, geospatial, behavioral, social and other types of data together

4. Genomic surveillance, monitoring, analysis, data synthesis, and response

5. Field applications and investigations

c) Develop, identify, adapt, pilot, and implement technologies and applications for public health.

This may include relevant genomic and other “-omics” (e.g., host genomics, transcriptomics, proteomics, metabolomics) technologies and applications.

The PGCoE network is expected to function as a technology and innovation “incubator” for pathogen genomics in public health. To this end, all PGCoEs are expected to establish and maintain a research and evaluation “platform” that allows them to readily develop or identify, adapt, pilot, evaluate, and implement technologies and applications within 5 broad areas:

1. Wet laboratory methods development and validation, proficiency testing, technologies, and applications

2. Bioinformatics technologies and applications, as well as related technologies

3. Data standardization/data security/data stewardship/data integration and reporting/data linkage/data science/data analytics/data visualization including of genomic, epidemiologic, clinical, biological, environmental, geospatial, behavioral, social and other types of data together

4. Genomic surveillance, monitoring, analysis, data synthesis, and response

5. Field applications and investigations

Applicants should describe their capacity to conduct activities in these five broad topic areas, and how their specialized expertise within the five main topic areas relevant to pathogen genomics may contribute to the overall capacity of the network.

Applicants should also describe how the network will benefit from the applicant’s unique scientific environment, subject populations, or collaborative arrangements.

Sites should describe how they will establish a research program that will allow them, in an ongoing and flexible way, to develop or identify, adapt, pilot, evaluate, and implement technologies and applications for use in public health that align with the activities set out in this cooperative agreement. This should include provision for human subjects research protocols that will allow enrollment of participants, collection of specimens, banking of specimens, testing of banked specimens, and collection of clinical and other participant data. The proposed research projects should be guided by public health needs. Applicants should also clearly articulate how the research program will ensure compliance with applicable regulatory requirements for proposed research activities.

Applicants should propose an initial research and non-research project or projects that include all 5 of these broad topic areas. Applicants are expected to propose activities in all 5 broad topic areas, but to highlight in the application the areas in which they have particular expertise. Applications should focus in a detailed way on site-specific projects in the first year. The application should discuss ways that this project or projects could be further developed over the period of performance and across the network and beyond.

Applications should describe projects in the Project Narrative using the format specified in the H. Other Information. section of this NOFO.

Applications should include working with other network sites to evaluate novel bioinformatics platforms.

The following are examples of types of projects that might be considered. These are only provided as examples and applicants should not limit themselves to proposals that fall within the scope of these:

• Data integration and analytics. Integrating genomic data with epidemiologic data and analyzing the two types of data together are high priorities for US public health. A site may propose to pilot and scale up methods for better achieving this integration. Such a project could be used, for example, to evaluate technologies for integrating data or might serve to evaluate what aspects of this integration are most valuable to public health.

• Increasing the availability and accessibility of genomic data. Projects that improve the ability of sites to make public health genomic data (and its metadata) available for use by other organizations (e.g., researchers, industry) or that make the data or analyses of the data more accessible to public health workers or to the general public would fall within the scope of this cooperative agreement.

• Other methods for improving the use of genomics in public health. Applicants are encouraged to think creatively about projects that could result in the improved use of genomics and other relevant, related technologies in public health.

Applicants should consider the following when selecting and proposing their activities:

• Potential for public health impact: An overarching objective of the cooperative agreement is to improve the use of pathogen genomics in the U.S. public health system (i.e., federal, state, territorial, local, and tribal public health agencies). As such, projects whose results have the potential to improve public health either immediately, or in the future, will be prioritized. A framework assessing potential public-health impact is given below (“Framework for evaluating potential public health impact”). The network will have leeway to support some projects that will advance more upstream (i.e., more basic science) priorities in the absence of clear public health benefit, but these are expected to be a minor part of the project portfolio.

• Scalability: For many of the anticipated projects, the ultimate impact will depend on the ability to alter public health practice in the United States and elsewhere. Projects that can be integrated into routine public health workflows and that make use of equipment and other infrastructure already commonly found in public health agencies are most likely to be scalable. Projects that are difficult to implement or that require technical support not typically found in public health agencies are not necessarily scalable.

• Applicability beyond the U.S. setting: Whereas the primary objective of this cooperative agreement is to improve U.S. public health, it is desired that it also yields products or findings that can have an impact beyond the United States.

• Scope of implementation: Projects need not be ones with potential to be implemented separately in many sites. For example, a proposal to develop or expand a web site or service that is useful to public health in making use of genomic data would be of interest.

d) Assist in implementing technologies broadly in the U.S. and aligning with global efforts.

The application should discuss ways that projects could be further developed and implemented over the period of performance and across the network and beyond.

Strategy 2: Education. Educate the Public Health Workforce.

a.) Lead or assist in training activities b.) Educate state, local, territorial and other non-Federal public health workforce in pathogen genomics and genomic epidemiology All centers will be expected, in collaboration with the Lead PGCoE for Education (see Optional Component (Lead PGCoE for Education) described below) and with CDC, to contribute to development of online training resources and other training activities.

• Lead an online course or training. Provide a high-level outline of the curriculum for the course(s) and describe how the proposed courses are relevant to public health practice.

• Assist in training. Describe expertise or resources that the applicant could bring to the network to assist in an educational project led by a different center.

• Other educational activities may be proposed as well.

Strategy 3: Response Base. Prepare to Respond to Infectious Threats a.) Prepare to respond to infectious threats and respond to infectious threats

Applications should describe foundational activities such as preparing data use agreements, memoranda of understanding and IRB protocols to allow rapid scale-up of efforts across the network.

Mandatory Component (Response Implementation): Perform sequencing and other applications, analysis, and data synthesis during emergencies from infectious agents.

Response implementation consistent with the terms of this cooperative agreement may be funded via post-award supplements should infectious threat conditions warrant.

Implement activities in response to an infectious threat. Plan the types of experiments, research studies, and non-research activities that could be done in the event of an infectious threat, including analyzing and synthesizing data to inform public health action.

Applications should include working with other network sites to analyze and synthesize pathogen genomic and other diverse data and preparing informational reports. The network is expected to make informational reports public. This data synthesis activity will provide an objective overview of recent information for use by local, state, and federal public health agencies. These network data synthesis reports are not intended to provide recommendations.

Applications should describe response implementation activities in 5 broad areas:

1. Wet laboratory methods development and validation, proficiency testing, technologies, and applications

2. Bioinformatics technologies and applications, as well as related technologies

3. Data standardization/data security/data stewardship/data integration and reporting/data linkage/data science/data analytics/data visualization including of genomic, epidemiologic, clinical, biological, environmental, geospatial, behavioral, social and other types of data together

4. Genomic surveillance, monitoring, analysis, data synthesis, and response

5. Field applications and investigations

Specific activities, consistent with the terms of this cooperative agreement, may include but are not limited to the following:

• In collaboration with relevant subject-matter groups from CDC, develop or adapt methods for sequencing the pathogen or for applying other molecular subtyping.

• Contribute to pathogen sequencing efforts or analysis of sequence data.

• Enroll study participants, test clinical specimens, test banked specimens, collect clinical, epidemiologic and other data.

• Develop and integrate bioinformatic solutions to rapidly analyze, interpret, visualize, integrate, and share pathogen genomic information.

• Expand networks of partnerships across public health, academia and the private sector that can be rapidly engaged for infectious threats.

• Perform ongoing analysis of genomic and epidemiologic surveillance data as well as other relevant information such as surveillance data from other countries and information in preprints and publications.

• Interpret all these data for their implications for public health.

• Provide regular and timely reports to public health and, as appropriate, relevant third parties, including advisory committees (e.g., CDC Board of Scientific Counselors), in response to infectious threats.

These activities should provide coordinated, rapid, and scalable actions in responding to infectious threats. Following initial award, a Network Response Plan will be developed collaboratively with the coordinating group.

Applicants should describe how they would use their expertise in areas that may be useful during responses to infectious threats.

The following are examples of contributions such a network might have provided had one been in place during past infectious disease threats. During such responses, the network will be expected to work in collaboration with the relevant federal/state/local public health agencies so that these actions may more directly impact the response. Applicants are encouraged to consider, in addition to these examples, how their expertise would be useful during infectious disease threats.

• SARS-CoV-2 emergence:

o Working with state/local public health agencies to sequence samples as part of surveillance or outbreak investigations, either in the public health agency’s laboratory or at an outside laboratory.

o Analyzing publicly available data on circulating SARS-CoV-2 variants at the national, state, or local level, and presenting these data in ways that make them useful to public health.

o Projecting the course of variant emergence in the United States.

o Reviewing available data on emerging variants from a variety of sources, including publications, pre-prints, and other relevant public or non-public sources.

o Creating regular, publicly available summaries of these various sources of information to be used by public health agencies and other interested parties.

o Assessing the role of host genomics factors in infection, transmission, disease severity and outcomes.

• Zika emergence in the Americas o Assistance to US states and partners (including overseas partners) in sequencing specimens and analysis of available genomic data.

o Assessment of the risk of importation of the virus.

• Emergence of Candida auris o Assistance with sequencing and analysis of the data.

o Real-time summary of C. auris sequence data submitted to the National Center for Biotechnology Information (NCBI). This could be a simple webpage that is auto populated and resides with the centers of excellence.

o Development and piloting of new workflows for sequencing and analysis of the sequence data. For example, the project could evaluate measures of genomic relatedness and whether those can be used to infer transmission between healthcare facilities.

Optional Component (Lead PGCoE for Education)

In order to apply for Lead PGCoE (Optional Component (Lead PGCoE for Education)), an applicant must apply for both of the Mandatory Components (Core and Response Implementation).

The Work Plan for the Optional Component (Lead PGCoE for Education) must address the following activities:

• Identify relevant educational needs for the public health workforce, with focus on microbiologists, bioinformaticians, and epidemiologists

• Lead education efforts of the network o Provide leadership for educational activities of the network.

o Pilot and evaluate educational materials, including online training.

• Develop online training o Act as the host for the network's online training. In this capacity, the site will need to operate or have access to a robust online educational platform and have resources that enable the network members to create training courses or modules for the platform.

o Engage with CDC, relevant partner organizations (e.g., Association of Public Health Laboratories, Council of State and Territorial Epidemiologists, American Society for Microbiology, National Association of County and City Health Officials, American Public Health Association, Public Health Alliance for Genomic Epidemiology), and other health departments and academic institutions to expand training, cross-appointments, sharing of best practices and uses of genomic data.

o Develop and/or work to offer online, freely available training platform focused specifically on the use of genomics in public health. Training should address the needs of microbiologists, bioinformaticians, and epidemiologists working in public health.

o Include, as part of training, the opportunity to receive continuing education credits in the relevant disciplines (e.g., PACE, CME, or other accreditation).

Addendum: Framework for evaluating potential public health impact

In developing their applications, applicants should consider the following questions which get at the potential public health impact of particular projects. The term “intervention” below refers to what is being proposed, be it a diagnostic protocol, a surveillance tool, data system, or any other proposed outcome.

• Would the intervention have a direct impact on public health? This is usually the easiest type of justification to explain. This impact may be immediate, as with an intervention that enabled early detection of outbreaks, or delayed, as in one that slows transmission of infectious diseases.

• Would the intervention result in better data for decision-making? For example, a project might improve the collection of data that would be useful in establishing a baseline for surveillance.