OUSD (R&E) critical technology area(s): Advanced Computing and Software, Biotechnology
Objective: Performers will develop field-portable, low size, weight, and power (SWaP) technology for non-destructive viral identification.
Description: Warfighters are often deployed to emerging disease hotspots. To help mitigate potential exposure risks, DoD entities tasked with force health protection [1] rapidly assess, often on-site, a range of sample types for potential biological threats. Current rapid on-site identification (ID) methods include sequencing [2,3] and lateral flow assays (aka dipstick tests)[4], which destroy both the sample & the organism(s), inhibiting further analysis. While sequencing costs continue to decrease and cheap lateral flow assays continue to increase in organism scope, forward operators often triage the number of sites and samples collected due to resource, personnel, and time constraints[5]. Recent advances in metasurfaces [6,7], optical waveguides [8], microfluidics [9], and (super)high resolution imaging [10], now suggest accurate organism ID and viability maintenance can co-occur; however, current non-destructive systems lack field utility due to their lab-centric designs [7].
This SBIR will address both the significant limitations to rapid, on-site biosurveillance in resource constrained environments and the lab-centric designs for non-destructive pathogen ID by developing human-portable, low size, weight, and power (SWaP) technology to rapidly and non-destructively ID viruses on-site and in the field. Final Phase II prototypes must be: ≤ 1 ft3; ≤ 5 lbs; and ≤ 200-Watt peak power input, with all SWaP requirements inclusive of power delivery mechanisms, software/data processing, consumables, and reagents, and should function with a wide range of simulated clinical samples (e.g., blood, saliva, nasal swabs, etc.) and contrived environmental samples (swipes/wipes, chicken rinse, etc.). Systems should non-destructively ID viruses faster than current state-of-the-art sequencing and lateral flow assays (≤ 15 min per sample, not including sample pre-processing) while maintaining viral infectivity for downstream lab-based analysis. By the end of Phase II systems should ID viruses faster than current state-of-the-art sequencing and lateral flow assays (≤ 15 min per sample), in the field sample pre-processing, if any, should be no more than 20 minutes per sample, and viral ID should be independent of cloud connectivity (e.g., database access, analysis and ID can occur on the device without cloud access).
Phase I
This topic is soliciting Direct to Phase II (DP2) proposals only. To be considered eligible for a DP2 award proposers must demonstrate their technology can achieve the following: (1) rapidly (≤ 45 minutes) identify ≥ 10 different eukaryotic viruses in monoculture across ≥ 5 viral groups (Baltimore classification), (2) differentiate ≥ 5 viruses in a mixed sample with ≥ 2 related viral strains (e.g., FluA H1N1 vs H3N2), and (3) function as a breadboard system with minimal user input. Specific data that directly supports the previous capabilities must be provided. Additionally, proposers must clearly define the testing schema that will be used to satisfy the below sensitivity, specificity, and limits of viral identification metrics. Finally, proposers must describe the developmental pathway of the existing breadboard system to the portable end of DP2 system, production scalability of the platform, potential to adapt the system to sample multiplexing (≥ 10 samples simultaneously), projected final unit cost and cost/test, and technology commercialization plans.
Phase II
This DP2 effort (24 months) will focus on research, development, and testing to develop a portable, in-field, rapid, easily operable viral identification technology. Specifically, performers will utilize existing systems to: (1) increase fidelity of non-destructive ID technology, (2) increase viral diversity assessed, (3) increase sample matrix complexity with simulated clinical and/or environmental samples, and (4) meet SWaP requirements for system portability. Phase II will consist of three demonstrations, including an initial (month 9), interim (month 15) and a final (month 23) demonstration to take place in the field. Technology design reviews will be held at months 3, 11, and 17, with a design lock at month 18. The final technology must demonstrate its operability by non-expert users as well as the ability to demonstrate viral infectivity of collected samples.
Milestones
- Identify viruses from liquid media – monocultures
- Month 9 metric (initial): ≥ 20 viruses (including ≥ 2 related strains from each of ≥ 2 species) representing ≥ 5 viral groups
- Month 15 metric (interim): ≥ 30 viruses (including ≥ 2 related strains from each of ≥ 3 species) representing ≥ 5 viral groups (including enveloped and non-enveloped)
- Month 23 metric (final): ≥ 50 viruses (including ≥ 3 related strains from each of ≥ 4 species) representing ≥ 5 viral groups (including enveloped and non-enveloped)
- Identify viruses from liquid media – mixed cultures
- Month 9 metric (initial): ≥ 5 different mixed samples with ≥ 5 viruses per sample (including ≥ 2 related strains from each of ≥ 2 species) representing ≥ 3 viral groups
- Month 15 metric (interim): ≥ 10 different mixed samples with ≥ 10 viruses per sample (including ≥ 2 related strains from each of ≥ 3 species) representing ≥ 5 viral groups (including enveloped and non-enveloped)
- Month 23 metric (final): ≥ 20 different mixed samples with ≥ 10 viruses per sample (including ≥ 3 related strains from each of ≥ 4 species) representing ≥ 5 viral groups (including enveloped and non-enveloped)
- Identify viruses from clinical (e.g., blood, nasal swabs, saliva), and the environment (e.g., swipe/wipe, chicken rinse) – contrived spiked samples
- Month 9 metric (initial): ≥ 2 different contrived samples (clinical and/or environmental) with ≥ 5 viruses per sample (including ≥ 2 related strains from the same species) representing ≥ 3 viral groups per sample
- Month 15 metric (interim): ≥ 5 different contrived samples (clinical and environmental) with ≥ 5 viruses per sample (including ≥ 2 related strains from the same species) representing ≥ 5 viral groups per sample (including enveloped and non-enveloped)
- Month 23 metric (final): ≥ 10 different contrived samples (clinical and environmental) with ≥ 10 viruses per sample (including ≥ 2 related strains from the same species) representing ≥ 5 viral groups per sample (including enveloped and non-enveloped)
- Identification sensitivity/specificity (per Species)
- Month 9 metric (initial): 90%
- Month 15 metric (interim): 95%
- Month 23 metric (final): 99%
- Identification sensitivity/specificity (per Strain)
- Month 9 metric (initial): 80%
- Month 15 metric (interim): 85%
- Month 23 metric (final): 90%
- Viral Limit of Identification
- Month 9 metric (initial): ≤ 1000 pfu / mL / virus
- Month 15 metric (interim): ≤ 500 pfu / mL / virus
- Month 23 metric (final): ≤ 100 pfu / mL / virus
- Sample input to Answer Time (Minutes)1, volume
- Month 9 metric (initial): ≤ 35, <5mL/sample
- Month 15 metric (interim): ≤ 25, <5mL/sample
- Month 23 metric (final): ≤ 15, <2mL/sample
- Size, Weight, & Power (SWaP)2
- Month 9 metric (initial): ≤ 2 ft3; ≤ 15 lbs; and ≤ 400-Watt peak power input
- Month 15 metric (interim): ≤ 1 ft3; ≤ 10 lbs; and ≤ 250-Watt peak power input
- Month 23 metric (final): ≤ 1 ft3; ≤ 5 lbs; and ≤ 200-Watt peak power input
1Times do not include any pre-processing steps
2All SwaP requirements inclusive of power delivery mechanisms, software/data processing, consumables, and reagents.
Phase II deliverables
- Month 3: Progress report, preliminary design review including description of sample pre-processing
- Month 6: Progress report, initial demonstration plan, cost estimate (per sample)
- Month 9: Initial demonstration
- Month 10: Summary of initial demonstration
- Month 11: Interim design review
- Month 12: Progress report, interim demonstration plan, cost estimate (per sample)
- Month 15: Interim demonstration
- Month 16: Summary of interim demonstration
- Month 17: Critical Design Review
- Month 18: Progress report, technology design lock
- Month 20: Field demo plan; cost estimate (per sample)
- Month 21: Progress report, commercialization plan
- Month 23: Field demonstration
- Month 24: Summary report
DP2 Option
The Phase II option will utilize the fieldable technology from Phase II and add naturally derived environmental samples and decrease the viral limit of detection. Phase II option will consist of two demonstrations, including an interim (month 6) and a final (month 11). A final summary report will include an updated per sample cost estimate, plan for manufacturing, and detailed plan for alternative technology applications and advancements as necessary.
Milestones
- Identify viruses from the environment (e.g., soil, wastewater, aerosol filters) – natural spiked samples
- Month 6 metric (interim):≥ 2 different natural samples with ≥ 5 viruses per sample (including ≥ 2 related strains from the same species) representing ≥ 3 viral groups per sample (including enveloped and non-enveloped)
- Month 11 metric (final): ≥ 10 different natural samples (must include soil and wastewater) with ≥ 15 viruses per sample (including ≥ 2 related strains from the same species) representing ≥ 5 viral groups per sample (including enveloped and non-enveloped)
- Identification Sensitivity/Specificity (per species)
- Month 6 metric (interim): 99%
- Month 11 metric (final): 99%
- Identification Sensitivity/Specificity (per strain)
- Month 6 metric (interim): 95%
- Month 11 metric (final): 99%
- Reproducibility of Virus Identification (Replicate Tests)
- Month 6 metric (interim): 99%
- Month 11 metric (final): 99%
- Viral Limit of Identification
- Month 6 metric (interim): ≤ 10 pfu / sample / virus
- Month 11 metric (final): ≤ 10 pfu / sample / virus
- Sample input to Answer Time (Minutes)
- Month 6 metric (interim): See Phase II Final
- Month 11 metric (final): See Phase II Final
- Size, Weight, & Power (SWaP)
- Month 6 metric (interim): See Phase II Final
- Month 11 metric (final): See Phase II Final
Phase II Option Deliverables:
- Month 1: Progress report and outline for environmental sample acquisition
- Month 3: Progress report
- Month 6: Interim demonstration and report
- Month 9: Progress report
- Month 11: Final demonstration and summary report
Phase III dual use applications
If successful, a system for rapid viral identification would have a range of applications within commercial industry and the US government including the DoD. Determining pathogens that may contaminate products or otherwise pose a health risk requires rapid detection and identification of infectious organisms.
Current methods for monitoring often require samples to be transported back to labs and/or result in the destruction of the sample leading to loss of pathogen viability. Enabling on-site testing would substantially increase the throughput for sample monitoring.
Additionally, such a system would advance the US governments biological surveillance capabilities. Adoption into existing workflows for field sampling & testing is likely.
References
[1] GEIS Strategy FY 2019-2021. Defense Health Agency – Armed Forces Health Surveillance Branch, 03 May 2018.
[2] Gargis, Amy S., et al. "Rapid detection of genetic engineering, structural variation, and antimicrobial resistance markers in bacterial biothreat pathogens by nanopore sequencing." Scientific Reports 9.1 (2019): 13501.
[3] Augustine, Robin, et al. "Loop-mediated isothermal amplification (LAMP): a rapid, sensitive, specific, and cost-effective point-of-care test for coronaviruses in the context of COVID-19 pandemic." Biology 9.8 (2020): 182.
[4] Sohrabi, Hessamaddin, et al. "State of the art: Lateral flow assays toward the point-of-care foodborne pathogenic bacteria detection in food samples." Comprehensive Reviews in Food Science and Food Safety 21.2 (2022): 1868-1912.
[5] Bipartisan Commission on Biodefense. Diagnostics for Biodefense - Flying Blind with No Plan to Land. Washington, DC: Bipartisan Commission on Biodefense; 2020.
[6] Luro, Scott, et al. "Isolating live cells after high-throughput, long-term, time-lapse microscopy." Nature methods 17.1 (2020): 93-100.
[7] Faraji-Dana, MohammadSadegh, et al. "Miniaturized folded metasurface hyperspectral imager." Frontiers in Optics. Optica Publishing Group, 2019.
[8] Hu, Taotao, et al. "A high-resolution miniaturized ultraviolet spectrometer based on arrayed waveguide grating and microring cascade structures." Optics Communications 482 (2021): 126591.
[9] Deng, Tianyang, et al. "Versatile microfluidic platform for automated live-cell hyperspectral imaging applied to cold climate cyanobacterial biofilms." Analytical Chemistry 93.25 (2021): 8764-8773. https://pubmed.ncbi.nlm.nih.gov/34133116/
[10] Amann, Simon, et al. "Design and realization of a miniaturized high resolution computed tomography imaging spectrometer." Journal of the European Optical Society-Rapid Publications 19.2 (2023): 34.
Keywords
Viral Identification, Biodefense, Field-Forward, Low power, Threat Assessment, Biotechnology, Microfluidics, Pathogen, High-throughput
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