DARPA-BAA-16-35.pdf

Broad Agency Announcement INTERfering and Co-Evolving Prevention and Therapy

BIOLOGICAL TECHNOLOGIES OFFICE

DARPA-BAA-16-35

April 28, 2016

DARPA-BAA-16-35, INTERCEPT

TABLE OF CONTENTS

PART I: OVERVIEW INFORMATION

PART II: FULL TEXT OF ANNOUNCEMENT

1. Funding Opportunity Description

1.1. PROGRAM OVERVIEW

1.2. PROGRAM METRICS

2. Award Information

3. Eligibility Information

3.1. ELIGIBLE APPLICANTS

3.2. COST SHARING/MATCHING

4. Application and Submission Information

4.1. ADDRESS TO REQUEST APPLICATION PACKAGE

4.2. CONTENT AND FORM OF APPLICATION SUBMISSION

4.3. FORMATTING CHARACTERISTICS

4.4. SUBMISSION DATES AND TIMES

4.5. FUNDING RESTRICTIONS

4.6. OTHER SUBMISSION REQUIREMENTS (If applicable. If there are none, write “Not Applicable.”)

5. Application Review Information

5.1. EVALUATION CRITERIA

5.2. REVIEW AND SELECTION PROCESS

6. Award Administration Information

6.1. SELECTION NOTICES

6.2. ADMINISTRATIVE AND NATIONAL POLICY REQUIREMENTS

6.3. REPORTING

6.4. ELECTRONIC SYSTEMS

7. Agency Contacts

8. Other Information

8.1. INTELLECTUAL PROPERTY

9. APPENDIX 1 – Volume II checklist

PART I: OVERVIEW INFORMATION

Federal Agency Name – Defense Advanced Research Projects Agency (DARPA), Biological Technologies Office

Funding Opportunity Title – INTERfering and Co-Evolving Prevention and Therapy

Announcement Type – Initial announcement Funding Opportunity Number – DARPA-BAA-16-35 Catalog of Federal Domestic Assistance Numbers (CFDA) – “12.910 Research and Technology Development” Dates o Posting Date (Date Posted to FBO and/or Grants.gov – to be completed by

CMO)

o Proposal Abstract Due Date – Thursday, May 19 4:00 PM ET o Proposal Due Date – Thursday, July 7, 2016 4:00 PM ET o Proposers’ Day – Thursday, April 28, 2016

Concise description of the funding opportunity - DARPA is soliciting innovative proposals for research to explore and develop therapeutic interfering particles as a novel approach to address infections from fast evolving viral pathogens.

Anticipated individual awards - Multiple awards are anticipated.

Types of instruments that may be awarded - Procurement Contract, Cooperative

Agreement, Grant, or Other Transaction.

Agency contact o Points of Contact James Gimlett, Ph.D. Program manager Biological Technologies Office (BTO)

The BAA Coordinator for this effort may be reached at:

DARPA-BAA-16-35@darpa.mil

DARPA/BTO

ATTN: DARPA-BAA-16-35

675 North Randolph Street Arlington, VA 22203-2114 mailto:DARPA-BAA-16-35@darpa.mil

PART II: FULL TEXT OF ANNOUNCEMENT

1. Funding Opportunity Description

The Defense Advanced Research Projects Agency often selects its research efforts through the Broad Agency Announcement (BAA) process. This BAA is being issued, and any resultant selection will be made, using procedures under Federal Acquisition Regulation (FAR) 35.016 and the Department of Defense Grant and Agreement Regulatory System (DoDGARS) Part 22 for Grants and Cooperative Agreements. Any negotiations and/or awards will use procedures under FAR 15.4, Contract Pricing, as specified in the BAA (including DoDGARS Part 22 for Grants and Cooperative Agreements). Proposals received as a result of this BAA shall be evaluated in accordance with evaluation criteria specified herein through a scientific review process.

DARPA BAAs are posted on the Federal Business Opportunities (FedBizOpps) website at https://www.fbo.gov and, as applicable, the Grants.gov website at http://www.grants.gov. The following information is for those wishing to respond to the BAA.

DARPA is soliciting innovative research proposals to explore and evaluate the potential of a radically different therapeutic and preventative approach to combat and outpace fast-evolving viral pathogens based on viral therapeutic interfering particles.

1.1. PROGRAM OVERVIEW

Current preventive and therapeutic approaches to address viral pathogens, including vaccines and anti-virals, are designed to target the virus in its circulating state or at the time of diagnosis.

However, pathogens mutate and evolve over time, becoming resistant to many therapies. Fast-evolving viruses with changing/heterogeneous surface antigens or complex immunopathogenesis among multiple serotypes (e.g., influenza and dengue, respectively) are particularly challenging.

The current paradigm of static therapeutics and preventives relies on repeated and time-consuming development, manufacturing, and testing of new therapies and vaccines. This results in major health response gaps, economic burden, and limited capability to respond rapidly to emerging strains and bio threats. For many viral diseases there are no approved vaccines and few (if any) therapeutic options. The goal of the INTERfering and Co-Evolving Prevention and Therapy (INTERCEPT) program is to explore and evaluate virus-based therapeutic interfering particles (TIPs) that parasitize, interfere, and co-evolve with viral targets as a means of adaptively preventing, controlling, and eliminating acute or chronic infection.

The novel path explored in this program is based upon previously reported Defective Interfering Particles (DIPs), viral-derived particles with partially deleted genomes that arise during a natural infection. DIPs lack genes encoding replication enzymes and capsid proteins, and thus require co-infection with the wildtype parent virus to replicate and mobilize.1 DIPs have been isolated from numerous viral infections and shown to interfere with the replication and packaging processes through stoichiometric competition for essential viral components.2 It has been

1 Huang, A. S. & Baltimore, D. (1970). Defective viral particles and viral disease processes. Nature (Review).

https://www.fbo.gov/ http://www.grants.gov/ suggested that DIPs may have therapeutic and protective potential and may serve as a broad range treatment approach to combat respiratory infections. For example, a cloned Influenza-A DIP was effective in protecting from infection by Influenza-A, as well as by heterologous respiratory viruses in small animal models.3 In addition, given their transmission potential, it has been proposed that interfering viral particles may serve as anti-viral therapies to reduce disease incidence and thus control epidemics.4

The INTERCEPT program aims to explore and evaluate the potential of TIPs as a therapeutic and/or preventive approach for the long term control of a broad range of fast-evolving viruses.

The program will address the key technical challenges and risks of TIP safety, efficacy, long-term co-evolution, and generalizability, by leveraging novel molecular and genetic design tools, high throughput genomic technologies, and advanced computational methods in a multidisciplinary, multi-team effort.

To explore the TIP concept as a potential therapeutic and/or preventive platform that can keep pace with fast-evolving pathogens, INTERCEPT will address four fundamental questions:

1. Safety & efficacy: Can TIPs be built that are safe and out-compete the pathogen to control infections short-term?

2. Co-evolution: Can TIPs evolve and keep pace with evolving pathogens to control an infection long-term?

3. Population-scale efficacy: Can TIPs co-transmit alongside pathogen to help control the spread of infectious disease across populations?

4. Generalizability: Can the TIP concept be extended across multiple viruses and for multiple acute and chronic infectious diseases?

DARPA anticipates that the INTERCEPT program will encompass a four year effort organized in two phases of two years duration each. During the Phase I period, performer teams will establish proof-of-concept of TIPs safety, broad range efficacy, and initial TIP-pathogen co-evolution using in vitro and in vivo models of viral infection, as well as mathematical models of TIP-pathogen-host dynamics. The Phase II period will focus on the validation of long-term TIP safety and efficacy, long-term co-evolution studies, and TIP co-transmission dynamics for population-scale disease control.

INTERCEPT research objectives are structured along three Technical Areas (TAs), to be addressed concurrently: (1) TIP development and in vitro screening; (2) TIP optimization and in vitro and in vivo assessment of long-term safety; efficacy, and co-evolution with parent wildtype virus; and (3) mathematical modeling of TIP-pathogen-host dynamics to support TIP optimal design and predict TIP long-term safety, efficacy, co-evolution and co-transmission.

2 Dimmock N.J. & Easton A.J. (2014). Defective interfering influenza virus RNAs: time to reevaluate their clinical potential as broad-spectrum antivirals? J Virol (Review).

3 Easton AJ, Dimmock NJ. (2015). Cloned Defective Interfering Influenza RNA and a Possible Pan-Specific Treatment of Respiratory Virus Diseases. Viruses (Review).

4 Metzger, V. T., Lloyd-Smith, J. O. & Weinberger, L. S. (2011). Autonomous targeting of infectious superspreaders using engineered transmissible therapies. PLoS Comput Biol.

Proposers must address one of the following:

All three Technical Areas;

Technical Areas 2 and 3; or Technical Area 3.

Proposals that focus solely on Technical Area 1 or solely on Technical Area 2 will not be considered for funding. Proposers selected to pursue Technical Area 3 independently must identify one or more collaborators with whom they could team with to address Technical Area 2 before the end of the first year of contract.

Milestones will be negotiated between proposers and DARPA and structured to provide early validation results (see Table 2, page 14 for notional metrics); Phase II of the program will focus on those pathogens of interest and TIP approaches that successfully meet initial safety and efficacy targets and are most likely to advance the TIP platform.

Proposals involving multiple teams and/or experimental approaches should be structured as unified efforts that address the program Technical Areas in parallel, in an integrated manner.

Technical Area 1 (TA1): TIP engineering and screening

Studies within this Technical Area aim to generate TIP prototypes demonstrating safety and broad range efficacy in short term in vitro assays. Proposers should select one or more pathogens from the provided list of viral pathogens of interest (Table 1), and describe a technical approach for building several virus-specific TIP prototype candidates, and for testing the TIPs for short-term safety and efficacy using conventional in vitro methods. Proposers should justify choice of virus candidates using data, models, and reasoned explanations, based on: (1) likelihood of successful TIP therapy; (2) plausible path for TIP design, development, and optimization; and (3) availability or ease of developing suitable models for testing. The INTERCEPT program aims to explore the TIP approach for either or both chronic and acute infectious diseases (see Table 1).

TIP design: Proposers should outline a detailed approach to generate TIPs using state-of-the-art cloning and molecular techniques. For the purpose of this BAA, TIPs are defined as engineered virus-like particles that depend on the wildtype parent virus to replicate and mobilize. Proposers should consider TIP designs that adhere to the following criteria: (1) contain parental viral proteins; (2) contain part of the parental viral genome; (3) require complementation by a non-defective homologous virus for replication; (4) interfere specifically with replication of the parental wildtype virus; and (5) target the same cell/tissue as the parental wildtype virus.

Approaches to TIP generation may include (but are not limited) to: (a) random deletion libraries;

(b) site-directed deletions; (c) alterations of naturally emerging DI particles; (d) reverse genetics;

and (e) hybrid approaches involving multiple techniques. TIPs should also be designed to enable tracking of specific TIP candidates and TIP molecular sequences (i.e. through molecular tagging, barcoding, fluorescent labeling, or other). Proposers should identify adequate methods to package, isolate and/or enrich TIPs from parental wildtype virus populations.

TIP efficacy: Proposers should describe how they will quantitatively assess TIP candidates for their ability to reduce viral load using established in vitro assays (e.g., viral infectivity assays, ratio of TIP to viral genomes, and viral particle counts) at various multiplicity of infections (MOI) and for a range of TIP concentrations. Proposers should also describe how they will investigate mechanisms for TIP-mediated interference of viral replication, such as competition for essential viral components or activation of anti-viral immunity pathways. In addition, proposers should describe a plan to assess the TIP prototype candidates for broad efficacy across pathogen strain variants within a given species (e.g., HIV strain variants) and/or within a genus sub-group (e.g., multiple dengue serotypes).

TIP safety: A key safety requirement is that TIPs cannot replicate in uninfected cells and should remain dormant until the host cell is co-infected by the associated wildtype pathogen. Proposers should plan to investigate if TIP prototypes affect cell viability, and whether TIPs are transcriptionally silent, do not replicate, and are not mobilized either in the absence of the wildtype virus or in the presence of viral strains unrelated to the parent virus. These assessments should be conducted at various multiplicity of infections (MOI), for a range of TIP concentrations, and when exposed pre- and post-infection with the wildtype virus.

TIP prototype molecular design and testing may be further optimized based on design parameter requirements predicted from modeling studies in Technical Area 3 and on long-term in vitro and/or in vivo assessment studies from Technical Area 2.

Table 1. Viral pathogens of interest, including the National Institute of Allergy and Infectious Diseases category A, B, and C pathogens for which limited vaccines or therapies are available.

(http://www.niaid.nih.gov/topics/BiodefenseRelated/Biodefense/Pages/CatA.aspx).

HIGH PRIORITY VIRAL PATHOGHENS

Dengue SARS-CoV Ebola JC virus Zika MERS-CoV Crimean Congo HV BK virus Hantaviruses Lassa Lujo Chapare Nipah Junin Machupo Guanarito Hendra Sabia Caliciviruses West Nile Rift Valley Fever St. Louis encephalitis LaCrosse encephalitis California encephalitis

Western equine encephalitis

Eastern equine encephalitis

Enterovirus 68 Enterovirus 71

Chikungunya Hepatitis C Herpes simplex HIV Japanese encephalitis

Venezuelan equine encephalitis

Influenza Hepatitis E

Crimean Congo Hemorrhagic Fever

Marburg Severe Fever with Thrombocytopenia Syndrome

Heartland

Omsk Hemorrhagic Fever

Alkhurma virus Kyasanur Forest Tickborne encephalitis complex flaviviruses

By the end of Phase I (year 2), performers are expected to have completed the proposed in vitro efficacy and safety studies with one or more rounds of optimization of virus-specific TIP candidates for each selected pathogen. Performers should demonstrate broad-range efficacy of optimized TIPs across multiple pathogen strain variants and/or within various pathogen http://www.niaid.nih.gov/topics/BiodefenseRelated/Biodefense/Pages/CatA.aspx serotypes. Proposers should provide yearly intermediate metrics and milestones specific to their proposed approach (see Table 2). The proposed number and depth of proposed studies should allow for completion within the 24-month Phase I period. TA1 efforts may continue into years 3 and 4 if further TIP optimizations are prescribed based upon the empirical testing results of TA2 and the modeling results of TA3.

Technical Area 2 (TA2): Optimization for long-term TIP safety, efficacy, and co-evolution

Studies under this Technical Area should address the long-term efficacy, safety, evolutionary stability, and transmission of TIP prototypes developed in TA1, and the long-term effects of TIPs on wildtype virus evolution, persistence, and transmission. Proposers may choose to test selected TIP prototypes directly in animal models, without previous assessment in long-term dynamic in vitro systems (this selected path should be fully justified).

Long-term in vitro monitoring: Traditional in vitro cell culture systems may not be suitable for continuous, long-term assessment of virus and TIP co-evolution. Proposers should devise dynamic, in vitro platforms that sustain continuous virus evolution for extended periods of time (weeks to months). The proposed system should enable continuous operation and control of critical parameters while closely emulating physiological conditions (e.g., maintain a steady state target cell population and exponential or otherwise appropriate growth/replication of wildtype virus and TIPs). The proposed dynamic in vitro system should be used to assess wildtype virus- TIP co-evolution in a time-dependent and systematic manner. In the context of this BAA, co-evolution of wildtype virus and TIP is defined as the accumulation of hereditary genetic changes during the lifespan of both wildtype virus and TIP, arising from replication errors and adaptations to changing environment, including TIP and the wildtype virus selective pressures.

In addition, the dynamic in vitro system should be used to optimize and/or select for TIP candidates with high efficacy (e.g., isolating and enriching for promising low frequency TIP candidates, implementing controlled selective pressures, or other proposed techniques).

Examples of dynamic in vitro systems may include, but are not limited to: (1) bioreactors that sustain continuous feeding of healthy cells and removal of dead cells with controlled wildtype virus and TIP removal; (2) high-throughput microfluidic systems that can track viral evolution at the single cell level; and (3) organ-on-a-chip infection models (provided the system has been developed previously and is available for use with minimal modifications). The use of continuous cell passaging may be used only if well-justified.

Quantifying virus and TIP co-evolution: Proposers should outline approaches to quantify wildtype virus and TIP genetic diversity at given time points, as well as longitudinal diversification, TIP genetic stability, and wildtype virus escape via monitoring of mutation rates, recombination rates, replication rates, stoichiometric competition, and/or other parameters established by the proposer. Appropriate approaches, including possible use of markers, reporters, and new sequencing technologies, as well as experimental controls should be described. Proposers should provide a plan to assess and quantify the long-term stability, safety, and efficacy of TIP prototypes in the dynamic in vitro system under different conditions, e.g., different target cell lines, various times of TIP introduction, multiple MOIs and/or other parameters established by the proposer. Long-term, wide-range efficacy against pathogen-related strains also should be addressed in the dynamic in vitro system. The exploration of TIP cocktails to broaden TIP efficacy to a range of viral strains and/or serotypes, and to prevent viral escape, is encouraged.

Long-term in vivo assessment: Proposers should describe appropriate animal models of chronic and/or acute infection and a reasonable plan to investigate TIP safety, stability, co-evolution, and efficacy at varied TIP dose range and exposure times pre- and/or post-infection. Proposers should determine the most promising TIP prototype or TIP prototype cocktails to be tested in animal models based on in vitro results from TA1 and/or TA2 safety and efficacy studies. TIP prototype selection and animal study design (e.g., TIP dose and exposure time range to be tested) may also be informed by within-host mathematical model predictions from TA3.

In vivo safety and stability: Animal studies should address any potential long-term toxicity of selected TIP candidates in the absence of parent virus and/or in the presence of non-parent virus.

TIP safety monitoring may include, but is not limited to: (1) adverse effects on host health; (2) innate and adaptive host immune responses; (3) TIP distribution and specificity to target cells/tissues; (4) TIP activation in the absence of parent wildtype virus; and (5) TIP clearance from the host. Studies addressing TIP stability in the presence of wildtype parent virus may include, but are not limited to: (1) TIP genome recombination and reversion to an infectious state; (2) TIP genome co-packaging with wildtype virus; and (3) TIP diversification from parent wildtype virus (e.g., TIP no longer competes for viral factors). Appropriate metrics to determine TIP safety and stability in vivo should be established by the proposer.

In vivo efficacy: Proposers should provide sound approaches to quantify long-term efficacy of TIP prototypes in chronic animal models of infection and/or short-term efficacy in acute animal models of infection. These studies should examine dose-dependent kinetics of TIP activation, stoichiometric competition, and efficacy (e.g., reduced viral replication/titers, clinical improvement, reduced viral shedding, and increased viral clearance) as a function of days post infection (dpi) and viral MOI. In addition, suitable routes of TIP delivery should be identified and/or investigated (e.g., intranasal, intramuscular, and/or intradermal). Proposers should explore TIP feasibility as a preventive modality in acute and/or chronic infection settings, for example, by testing TIP latency, physical stability (i.e., half-life), and competition when administered within a measured timeframe prior to infection with wildtype virus. TIP preventive or therapeutic efficacy may depend on cell/tissue/organ tropism, routes of administration, viral MOI, and dose and timing parameters, all of which should be explained in the experimental approach. Proposers should outline appropriate metrics to determine in vivo efficacy.

Virus, TIP, and host immune response dynamics: Proposers should provide a well-reasoned approach to study co-evolution between wildtype virus and TIP under the influence of the host immune response. Studies that exploit non-traditional technologies are strongly encouraged.

These may include, but are not limited to, longitudinal assessment of TIP and wildtype virus evolution at the single molecule level, advanced imaging and metrics to quantify wildtype virus and TIP amplification within the host, and tracking single molecule mutation trajectories (e.g., single molecule labeling, virus reporters, and real-time detection by whole body imaging). These studies may also be informed by within-host mathematical model predictions from TA3.

TIP transmission: Transmission studies to assess TIP efficacy to control disease spread at the population level may be explored in experimental animal models of chronic and/or acute infection. Such studies should address wildtype virus and TIP co-transmission kinetics, and identify relevant parameters involved. These may include, but are not limited to: (1) wildtype virus and TIP load thresholds for co-transmission; (2) mechanisms of co-transmission; and (3) kinetics of co-transmission (including cell/tissue/organ tropism).

Vector-mediated mechanisms: Proposers are encouraged to explore vector-mediated (e.g., mosquito) TIP transmission and evolution. It has been suggested that DIPs, while reducing infectivity, may enhance persistence of wildtype virus infections (e.g., for certain flaviviruses) in cell culture and in vivo.5,6 Proposers should address whether and how TIPs may affect wildtype virus persistence within the host, and/or within the vector using appropriate models. Proposals that describe approaches for reducing TIP-mediated long-term persistence of the wildtype virus, and TIP-mediated suppression of wildtype virus in the vector, are encouraged. Proposers should provide a well-reasoned plan to study wildtype virus and TIP co-evolution, stability, and persistence, as well as mechanisms of co-transmission within vectors and associated reservoirs.

These studies also may be informed by population-level mathematical model predictions from

TA3.

Proposers must identify all animal study vendors and facilities, including the appropriate biosafety level (BSL), and provide a letter of intent for each subcontractor at the time of proposal submission. Contracted service vendors should demonstrate capability for accommodating the animal species to be tested as outlined in proposed experimental plan, including small and large animals.

Human use studies will be considered if proposers: (1) describe a feasible path by which they can obtain the prerequisite toxicity, safety, and dosage data from animal studies; (2) outline a detailed plan for obtaining all necessary human use approvals within the program time frame;

and (3) provide a well-reasoned plan to address TA3 with results obtained from human subjects (i.e. develop in silico models of TIP safety, efficacy, and co-evolution).

TA2 studies may span the 4-year program duration. The outputs of TA2 should include empirical, quantitative data on TIP long-term stability, safety, efficacy, and co-evolution dynamics with the pathogen. Data from these experiments should inform the in silico model developments in TA3 and also may inform TIP design optimization in TA1. Proposers should outline reasonable yearly program metrics and milestones, such as those suggested in Table 3.

5 Salas-Benito J.S. and De Nova-Ocampo M. (2015). Viral Interference and Persistence in Mosquito-Borne Flaviviruses. Journal of Immunology Research (Review).

6 Ke R et al. (2013). Phylodynamic Analysis of the Emergence and Epidemiological Impact of Transmissible Defective Dengue Viruses. PLoS Pathogens.

Technical Area 3 (TA3): Mathematical modeling

Mathematical models have been reported that describe dynamics of wildtype virus and DIPs at the single cell, host, and population levels. 4,6,7,8 A critical component of the INTERCEPT program is the development of a quantitative, multiscale, in silico model that can map and predict long-term co-evolutionary dynamics of the wildtype virus, TIP, and host interactions.

Proposers may leverage and build upon existing mathematical models of viral evolution and transmission. It is expected that models developed in the INTERCEPT program will move beyond the standard pathogen-host dynamics to include TIP dynamics, and to account for the large spectrum of wildtype virus and TIP variants that co-exist at any given time within the host and in a population.

Single cell modeling: Proposers should describe their approach to building computational tools to simulate intracellular wildtype virus and TIP dynamics as well as the cell output of wildtype virus and TIP progeny. These models should aim to capture the kinetics of wildtype virus and TIP replication, wildtype virus and TIP production ratios, TIP persistence, TIP interference, molecular dynamics of competition between wildtype virus and TIP, mutational rates and evolution of wildtype virus and TIP within a cell, cell-to-cell variability, and/or other parameters relevant to the system.

Within-host modeling: Proposers should describe their approach to modeling the long-term co-evolution of wildtype virus and TIP, as well as TIP safety and efficacy within a host. Model outputs may include, but are not limited to: (1) TIP impact on viral loads (efficacy) as a function of TIP dosage and time of intervention; (2) probability of wildtype virus escape under TIP selective pressure; (3) probability of a TIP to revert to virulence (e.g., recombination between wildtype virus and TIP or other means); (4) TIP impact on viral persistence; and (5) within-host TIP spatial dynamics (e.g., distribution to target organ). The role of host immune response as a natural selection pressure on long-term wildtype virus and TIP co-evolutionary dynamics should be incorporated into the models. The mathematical models should also describe cell and host variability and their potential impact to TIP design and requisites for optimal TIP-to-virus production ratios.

Population modeling: Proposers should describe their approach to population-scale modeling of TIP dynamics within a population. These models should predict TIP impacts on viral transmission dynamics and the potential to control disease spread. Models should predict wildtype virus and TIP long-term co-evolution rates and trajectories within a population, wildtype virus and TIP co-transmission dynamics, and/or the role of vectors on co-evolution and co-transmission dynamics (e.g., mosquito-borne diseases). Data from population-level modeling should further inform TIP design and constraints to enable TIP effectiveness across populations (e.g., provide the TIP-to-virus stoichiometric production ratio across viral strains required for population-scale disease control). Proposer should provide a plan for generalizing these multi-scale models for applicability to other viruses and associated TIPs. Models may also describe

7 Reichl U et al. (2016). Modeling the intracellular replication of influenza A virus in the presence of defective interfering RNAs. Virus Research.

8 Ke R and Loyd-Smith J. (2012). Evolutionary Analysis of Human Immunodeficiency Virus Type 1 Therapies Based on Conditionally Replicating Vectors. PLOS Comp Bio.

and predict TIP capability as a complementary therapy to traditional anti-viral therapies and/or vaccines, or for slowing disease progression while the host mounts an effective immune response.

Studies in this Technical Area may span the entire 4-years duration of the program. It is expected that TA3 will be informed by empirical data obtained in TA1 and TA2, but proposers are also encouraged to utilize any accessible pre-existing retrospective datasets from animal and human infectious diseases studies that may assist in analysis and validation of the models generated.

Data and results obtained from the in silico models should guide optimal TIP design and dosage parameters for TIP optimization in TA1 and TA2. Proposers should outline reasonable yearly program metrics and milestones, such as those suggested in Table 4.

Data Sharing:

Proposers must ensure all technical data items (including experimental findings, processed data, methods of processing, research reports, and publications) and software (source code and executables) generated from INTERCEPT program funding are made available to DARPA.

Regularly submitted reports (e.g., monthly or quarterly) should contain all relevant project data, including (but not limited to) raw and analyzed data and any necessary annotations and interpretations. Data obtained from human volunteers must be provided in a coded format that protects subject identities, but must contain diagnosis (signs/symptoms), interventions, technical observations, diagnostic tests/results, and outcomes. All raw data and metadata should be recorded appropriately following approved experimental standards.

DARPA intends to share data items within the INTERCEPT performer community to promote program goals. To facilitate sharing and exchange of data items, performers will be required enter an Associate Contractor Agreement (ACA); an ACA clause will be included in the contract or agreement awarded.

To gain enhanced scientific value from open collaboration in fundamental research, DARPA may seek permission to share some or all program generated data with the broader research community as open data (with permission to access, reuse, and redistribute under appropriate licensing terms) to the extent permitted by applicable law and regulations (e.g., privacy, security, and export control).

The proposers must describe a plan to share data with teams both internally to the INTERCEPT performer group and externally with the broader research community. Proposers should demonstrate an understanding of data file types, sizes, annotations, and other metadata components associated with the experiment(s) proposed. Proposers should indicate the extent of their team's familiarity with open data and open-access journals. Proposers should provide timelines for dataset availability to the broader research community.

Period of Performance:

DARPA anticipates that the INTERCEPT program will provide up to four years of funding for research and development to be performed in two phase periods of 2 years each.

1.1.1. Phase I

Phase I efforts aim to establish proof-of-concept TIP safety, broad-range efficacy, and short-term co-evolution capability. By the end of Phase I performers will be expected to:

1. Demonstrate proof-of-concept that engineered and optimized TIP prototypes are safe and can effectively outcompete the virus(es) of choice in vitro and/or in vivo.

2. Demonstrate understanding of TIP molecular mechanisms.

3. Provide initial evidence of TIP short-term coevolution with the pathogen.

4. Demonstrate TIP efficacy against a broad range of viral strains and/or subtypes closely related to the parental wildtype virus.

5. Demonstrate initial in silico models that describe virus and TIP dynamics at the single cell level, and long-term safety, efficacy, and co-evolutionary stability at the host level.

1.1.2. Phase II

Phase II efforts aim to explore TIPs safety, efficacy, and co-evolution in long-term assessments.

Phase II efforts also aim to evaluate TIP transmissibility and use in population-scale control of disease. By the end of Phase II performers will be expected to:

1. Demonstrate long-term safety and efficacy of optimized TIP(s) in a dynamic in vitro system and in animal models of chronic and/or acute infection.

2. Demonstrate long-term co-evolution of wildtype virus and TIP, and establish proof-of-concept TIP co-transmission in animal models.

3. Demonstrate TIP long-term stability and efficacy, and, for vector-borne pathogens, dynamics of virus and TIP co-transmission and co-evolution within the vector.

4. Demonstrate host-scale in silico models that describe and integrate dynamics among TIP, wildtype virus, and host immune response.

5. Demonstrate population-scale models that predict long-term TIP safety, efficacy, and evolution within a population, and define critical feedback metrics for population-level virus control via TIP co-transmission.

1.2. PROGRAM METRICS

In order for the Government to evaluate the effectiveness of a proposed solution in achieving the stated program objectives, proposers should note that the Government hereby promulgates the following program metrics that may serve as a guideline for assessing program progress, risk and impact. Although the following program metrics are provided, proposers should note that the Government has identified these goals with the intention of bounding the scope of effort, while affording the maximum flexibility, creativity, and innovation in proposing solutions to the stated problem. Proposers may offer more appropriate and specific metrics for their particular use case and technical approach, including intermediate metrics (i.e. every 6 months, or sooner) to help further evaluate progress. Final metrics are to be negotiated at time of contracting.

Table 2: Milestones, Deliverables, and Program Metrics for TA1

Phase Milestones and Deliverables Program Metric Initial TIP prototypes that:

Out-compete virus in vitro Cannot replicate, and mobilize in absence of parent wildtype virus

Mechanisms of TIP functional efficacy elucidated (Encouraged)

Quantitative measures of:

Short-term TIP efficacy for a range of virus

MOI and TIP doses Short-term TIP safety in cell culture for a range of virus MOI and TIP doses Broad-range efficacy to out-compete multiple virus strain variants

I

TIP design strategies for targeting a second or third selected viruses of one or more broad types (based on Baltimore classification) (Optional)

(Same as above for a second and/or third virus-specific TIP in vitro)

II Further optimization of TIP prototypes:

Genome sequences of Phase I TIPs further optimized based on modelling data (TA3) Long-term evaluation of safety and efficacy in bioreactor and/or animal models

(Same as above, to include all progressive improvements with advancing optimizations)

Table 3: Milestones, Deliverables, and Program Metrics for TA2

Phase Milestones and Deliverables Program Metric Demonstrated dynamic in vitro system capable of maintaining long-term viral infection Demonstrated TIP efficacy in vitro Assessed wildtype virus and TIP co-evolution in vitro

Sustained steady-state infection for at least 1 month based on cell and molecular studies

Quantitative measure of long term safety and efficacy (metrics established by the proposer)

Quantitative assessment of long term co-evolution (metrics established by the proposer)

I

Demonstrated initial TIP safety and stability in animal models

TIPs are not toxic, and do not over-stimulate an immune response as demonstrated by histopathology, immunological studies, and/or other metric established by the proposer

Quantitative measure of TIPs stability and clearance over a period determined by proposer (e.g. two weeks for acute infection, or two months for chronic infection)

Demonstrated TIP efficacy and co-evolution at different TIP doses and viral strains in continuous dynamic in vitro systems

Quantitative measure of long-term efficacy established and justified by proposer (e.g., TIP-mediated stable reduction of virus loads at least 90% for at least 4 months)

Quantitative measures of pathogen and TIP co-evolution (e.g., rates of mutations, recombination events, or other determined by the proposer)

II

Demonstrated long-term TIP safety and efficacy in animal models of chronic /acute infection Assessment of co-evolution and co-transmission in animal models of chronic /acute infection Demonstrated TIP stability and co-evolution in vector-born viral infection

Quantitative measure of long-term TIPs safety and efficacy in animal models of chronic/acute infection

Quantitative measure of pathogen and TIP co-evolution (e.g., rates of mutation, emergence of virus and TIP variants, or other determined by the proposer)

Quantitative measure of pathogen and TIP co-transmission (e.g., ratios of TIP-to-pathogen loads in target organ during transmission studies)

Quantitative measure of TIP loads and TIP-virus co-evolution in vector studies

Table 4: Milestones, Deliverables, and Program Metrics for TA3

Phase Milestones and Deliverables Program Metric Cell scale models that predict parameters for TIPs safety and efficacy:

TIP-virus dynamics as a function of

TIP dosage and time of intervention Probability of TIP reversion to virulence

Model predicts:

Critical parameters for TIP out-competition (TIP/pathogen genomic ratios, TIP length, sequence, stoichiometric ratios) Safety (e.g., probability of TIP and virus recombination and TIP reversion to infectious particle) Kinetic variability across various cell types Quantitative predictions feed back to TA1 and TA2 and guide TIP design and dosage parameters

I

Host-scale models that predict long-term safety and efficacy of TIPs:

Within-host co-evolutionary stability Within-host spatial and temporal dynamics of TIPs and pathogen TIP and pathogen co-evolution dynamics

Model predicts:

Critical parameters for long-term TIP stability at target organ

(e.g., dosage, time of introduction, or other) Critical parameters for long-term efficacy (e.g., dosage, time of introduction, or other) Probability of virus escape under TIP evolutionary pressure Inter-host variability Quantitative predictions feed back to TA1 and TA2 on TIP optimal design constraints and dosage parameters for long-term stability and efficacy

Host-scale models incorporate host immune response with TIP-to-pathogen dynamic models generated in Phase I

Model predicts:

Effect of host immune response on long-term TIP and pathogen co-evolutionary dynamics and TIP stability Probability of virus escape from TIP under selective pressure of host immune response Probability of TIP cocktails to enable broad efficacy of TIPs across viral strains and serotypes Probability of TIP cocktails to prevent viral escape

Population-scale models of pathogen and TIP co-evolution and co-transmission dynamics across population

Model predicts:

Critical parameters for TIP safety and efficacy across populations for acute and/or chronic infections Relevant parameters in TIP design and dosage to control pathogen escape at the population level Critical parameters for optimal co-transmission dynamics for pathogen control across a population (reduce incidence) Quantitative predictions feed back to TA1 and TA2 on TIP optimal design and dosage parameters for optimal TIP transmission to serve as long-term, single-shot therapies

II

Vector-based disease models that predict co-transmission and co-evolution dynamics of pathogen and TIP

Model predicts:

Critical parameters for TIP co-transmission with pathogen within vector and host Probability to reduce epidemic as compared to other therapies or vaccines Probability of TIP stability and virus escape within vector and reservoir

2. Award Information

Multiple awards are possible. The amount of resources made available under this BAA will depend on the quality of the proposals received and the availability of funds.

The Government reserves the right to select for negotiation all, some, one, or none of the proposals received in response to this solicitation, and to make awards without discussions with proposers. The Government also reserves the right to conduct discussions if it is later determined to be necessary. If warranted, portions of resulting awards may be segregated into pre-priced options. Additionally, DARPA reserves the right to accept proposals in their entirety or to select only portions of proposals for award. In the event that DARPA desires to award only portions of a proposal, negotiations may be opened with that proposer. The Government reserves the right to fund proposals in phases with options for continued work at the end of one or more of the phases.

Awards under this BAA will be made to proposers on the basis of the evaluation criteria listed below (see section labeled “Application Review Information”, Sec. 5.), and program balance to provide overall value to the Government. The Government reserves the right to request any additional, necessary documentation once it makes the award instrument determination. Such additional information may include but is not limited to Representations and Certifications. The Government reserves the right to remove proposers from award consideration should the parties fail to reach agreement on award terms, conditions and cost/price within a reasonable time or the proposer fails to timely provide requested additional information. Proposals identified for negotiation may result in a procurement contract, grant, cooperative agreement, or other transaction depending upon the nature of the work proposed, the required degree of interaction between parties, whether or not the research is classified as Fundamental Research, and other factors.

In all cases, the Government contracting officer shall have sole discretion to select award instrument type and to negotiate all instrument terms and conditions with selectees. Proposers are advised that regardless of the instrument type proposed, DARPA personnel, in consultation with the Government contracting officer, may select other award instruments, as they deem appropriate. DARPA will apply publication or other restrictions, as necessary, if it determines that the research resulting from the proposed effort will present a high likelihood of disclosing performance characteristics of military systems or manufacturing technologies that are unique and critical to defense. Any award resulting from such a determination will include a requirement for DARPA permission before publishing any information or results on the program. For more information on publication restrictions, see the section below on Fundamental Research.

Fundamental Research

It is DoD policy that the publication of products of fundamental research will remain unrestricted to the maximum extent possible. National Security Decision Directive (NSDD) 189 established the national policy for controlling the flow of scientific, technical, and engineering information produced in federally funded fundamental research at colleges, universities, and laboratories. The Directive defines fundamental research as follows:

'Fundamental research' means basic and applied research in science and engineering, the results of which ordinarily are published and shared broadly within the scientific community, as distinguished from proprietary research and from industrial development, design, production, and product utilization, the results of which ordinarily are restricted for proprietary or national security reasons.

As of the date of publication of this BAA, the Government expects that program goals as described herein may be met by proposers intending to perform fundamental research. The Government does not anticipate applying publication restrictions of any kind to individual awards for fundamental research that may result from this BAA. Notwithstanding this statement of expectation, the Government is not prohibited from considering and selecting research proposals that, while perhaps not qualifying as fundamental research under the foregoing definition, still meet the BAA criteria for submissions. If proposals are selected for award that offer other than a fundamental research solution, the Government will either work with the proposer to modify the proposed statement of work to bring the research back into line with fundamental research or else the proposer will agree to restrictions in order to receive an award.

Proposers should indicate in their proposal whether they believe the scope of the research included in their proposal is fundamental or not. While proposers should clearly explain the intended results of their research, the Government shall have sole discretion to select award instrument type and to negotiate all instrument terms and conditions with selectees. Appropriate clauses will be included in resultant awards for non-fundamental research to prescribe publication requirements and other restrictions, as appropriate.

For certain research projects, it may be possible that although the research being performed by the prime contractor is restricted research, a subawardee may be conducting fundamental research. In those cases, it is the prime contractor’s responsibility to explain in its proposal why its subawardee’s effort is fundamental research.

The following statement or similar provision will be incorporated into any resultant non-fundamental research procurement contract or other transaction:

There shall be no dissemination or publication, except within and between the contractor and any subawardees, of information developed under this contract or contained in the reports to be furnished pursuant to this contract without prior written approval of DARPA’s Public Release Center (DARPA/PRC). All technical reports will be given proper review by appropriate authority to determine which Distribution Statement is to be applied prior to the initial distribution of these reports by the contractor. With regard to subawardee proposals for Fundamental Research, papers resulting from unclassified fundamental research are exempt from prepublication controls and this review requirement, pursuant to DoD Instruction 5230.27 dated October 6, 1987.

When submitting material for written approval for open publication, the contractor/awardee must submit a request for public release to the DARPA/PRC and include the following information: (1) Document Information: document title, document author, short plain-language description of technology discussed in the material (approx.

30 words), number of pages (or minutes of video) and document type (e.g., briefing, report, abstract, article, or paper); (2) Event Information: event type (conference, principal investigator meeting, article or paper), event date, desired date for DARPA's approval; (3) DARPA Sponsor: DARPA Program Manager, DARPA office, and contract number; and (4) Contractor/Awardee's Information: POC name, email and phone. Allow four weeks for processing; due dates under four weeks require a justification. Unusual electronic file formats may require additional processing time. Requests may be sent either via email to public_release_center@darpa.mil or by mail at 675 North Randolph Street, Arlington VA 22203-2114, telephone (571) 218-4235. Refer to the following for link for information about DARPA’s public release process: http://www.darpa.mil/work-with-us/contract-management/public-release.”

3. Eligibility Information

All responsible sources capable of satisfying the Government’s needs may submit a proposal that shall be considered by DARPA.

3.1. ELIGIBLE APPLICANTS

3.1.1. Federally Funded Research and Development Centers (FFRDCs) and Government Entities

Federally Funded Research and Development Centers (FFRDCs) and Government entities (e.g., Government/National laboratories, military educational institutions, etc.) are subject to applicable direct competition limitations and cannot propose to this BAA in any capacity unless they meet the following conditions: (1) FFRDCs must clearly demonstrate that the proposed work is not otherwise available from the private sector; and (2) FFRDCs must provide a letter on official letterhead from their sponsoring organization citing the specific authority establishing their eligibility to propose to Government solicitations and compete with industry, and their compliance with the associated FFRDC sponsor agreement’s terms and conditions. This information is required for FFRDCs proposing to be prime contractors or subawardees.

Government entities must clearly demonstrate that the work is not otherwise available from the private sector and provide written documentation citing the specific statutory authority and contractual authority, if relevant, establishing their ability to propose to Government solicitations. At the present time, DARPA does not consider 15 U.S.C. § 3710a to be sufficient legal authority to show eligibility.