Scalable Wastewater Questions and Answers - updated.pdf

Scalable Wastewater Surveillance for Routine and Emerging Infectious Disease Pathogens

Questions & Answers

1. Would a state government public health laboratory, such as a laboratory operating within a state department of public health, be eligible to submit an offer and serve as the prime contractor under this solicitation, provided that the laboratory meets all applicable technical, responsibility, registration, contractual, and performance requirements?

Answer:

There are no restrictions on the request for proposals. State government public health laboratories, such as a laboratory operating within a state department of public health, are eligible to submit an offer.

2. If state government public health laboratories are not eligible to serve as the prime contractor, could you please clarify whether they may participate as a subcontractor or teaming partner to an eligible prime contractor?

Answer:

State government public health laboratories are eligible to participate as a subcontractor.

3. When developing the ddPCR price per test in the pricing table under B.13 (and reproduced on page 67), should we assume that “test” refers to a single pathogen target or that it refers to the entire panel of pathogen targets tested in a given sample?

Answer:

A test would refer to the entire panel of pathogen targets tested in a given sample. In other words, a test refers to all of the ddPCR targets tested per one sample.

4. Technical proposal: sequencing - What are CDC’s selected genomic regions for MeV sequencing? MeV sequencing is required in Task 3: “The contractor shall conduct targeted sequencing on samples for genetic characterization of Measles virus including subclade identification, and other relevant genomic assessments as directed by CDC.

Sequencing shall include selected genomic regions.” (page 8, emphases added).

Answer:

Genotyping of MeV targeting 450 nucleotides of the nucleoprotein (N) gene remains the global standard in MeV genetic analyses. CDC recommends offerors include N450 as an MeV target.

5. The URL provided on p. 22 (RFP IDIQ) or page 19 (RFTOP) in Special Considerations (https://intranet.cdc.gov/od/hcrmo/pdfs/hr/Out_Processing_Checklist.pdf) does not resolve (and appears to be an internal CDC URL). If this is required to prepare our response, please provide a copy?

Answer:

The link is not essential for responding to the solicitation. Following award, if out processing is needed, the form will be provided.

6. Does the RFP allow for a vendor to bid as both “Primary” and “Subcontractor”? If so, does NCEZID have any trepidations or concerns regarding such?

Answer:

A vendor may propose as both the primary contractor and subcontractor. NCEZID has no concerns with this approach.

7. Please confirm the applicable NAICS code (541380, Testing Laboratories) and the $19M size standard, and whether the Government will accept an offeror’s self-certified small-business representation in SAM for this unrestricted acquisition?

Answer:

NAICS code (541380, Testing Laboratories) confirmed.

To be considered small businesses, the organization has to be registered in SAM.gov as such and with the Small Business Administration.

8. For an offeror that is a small business concern, is a Small Business Subcontracting Plan required, given that FAR 52.219-9 does not apply to small business concerns?

Answer:

If the offeror is a small business, then a subcontracting plan is not required?

9. Will the Government provide a pricing template or defined CLIN structure for the Task

Order 1 price proposal? Should sampling kits, shipping, and biorepository shipbacks be priced within the per-sample line items or under the separate program-implementation line (item 0010)?

Answer:

The defined CLIN structure is found on pages 3-5 of the task order solicitation document (A19. RFTOP – Task 1). The program implementation line could cover the sampling kits, shipping, and biorepository shipping.

https://intranet.cdc.gov/od/hcrmo/pdfs/hr/Out_Processing_Checklist.pdf

10. At the IDIQ level (up to 500 facilities, up to 25 pathogen targets, metagenomic sequencing), is any pricing required at this time, or is all pricing limited to Sample Task Order 1?

Answer:

See page seven of IDIQ solicitation. Section B.13 Ordering List by Ordering Period.

11. For Similar Experience and Past Performance, may offerors cite work performed as a subcontractor, and how should offerors reference confidential commercial engagements where the client relationship is subject to a non-disclosure agreement?

Answer:

Yes, offerors may cite work performed as a subcontractor. Additional information, such as testing volume or number of sites served would be valuable. References to confidential engagements could use generic company names to preserve anonymity, with as much detail provided on the tasks completed without any violation of the

NDA.

12. Are the AI Compliance & Risk Management Plan and the Public Health Data Management Plan submitted as separate volumes, and are they excluded from the 35-page IDIQ and 20-page Task Order 1 technical page limits?

Answer:

Yes, the AI Compliance & Risk Management Plan and the Public Health Data Management Plan are separate documents, and they are not included in the page limit.

13. Does the Government have a preferred sample-return logistics model (e.g., utility drop-off at a carrier location versus scheduled courier pickup at the facility)? May offerors propose a hybrid approach that defaults to courier retrieval for any facility that requests it or that is more than a specified distance from a carrier drop point?

Answer:

While there is not a required courier model, the Government prefers scheduled courier pickup at the facility or location of the utility’s choosing. The suggested approach of defaulting to courier retrieval for any facility that requests it or that is more than a specified distance from a carrier drop point, would certainly be acceptable. Ultimately, CDC prefers a courier option that allows for flexibility so that utilities have minimal burden on shipping logistics.

14. Does the Government have any preference or restriction regarding the assignment of the Program Manager role (e.g., full-time dedicated individual versus a dual-hatted senior executive)?

The Government prefers that the Program Manager role be a “Key Personnel” who is a full-time dedicated individual. The government would have to be notified before a “Key Personnel” change occurs.

15. Does CDC anticipate that specialized technology partners or subcontractors could be added by the IDIQ prime after award, subject to the contract terms and applicable Contracting Officer approval?

Answer:

Pending discussion with and approval by CDC's Contracting Office and the Contract Officer of record, it may be possible to add a subcontractor as indicated on

p. 24 section f of the solicitation.

16. Could future task orders potentially accommodate validated alternative sample-preparation, targeted-detection, or sequencing technologies where those technologies meet CDC-defined performance, quality, throughput, reporting, and data requirements?

Answer:

Yes, though the offeror must fulfill requirements for methods written in the RFP.

This includes that samples must be of liquid wastewater influent, quantitative testing must be performed by dPCR, and all genomic data must be filtered of human reads (filter human reads out of any datasets using the sra-human-scrubber (https://github.com/ncbi/sra-human-scrubber) human read removal tool (HRRT), or a tool with equivalent or better performance) prior to submission of any raw sequences to NCBI. Alternative methods should be discussed with CDC prior to implementation, with validation data shared to assess CDC defined requirements.

17. If discussion of the technical capability would be more appropriate with a CDC program or technical representative, would you be willing to direct me to the appropriate contact or industry-engagement mechanism?

Technical capabilities should be discussed in the RFP.

18. IDIQ, page 12 – Does the 30-Day Requirement include design & manufacturing timelines or does the 30-Day development timeline start once the materials are received at the lab?

Answer:

The 30-day requirement for assay adaptability referenced in Requirement Four, section 4.1 is 30 calendar days from the request to update the hybrid capture panel.

19. Task Order 1, page 7: Can you clarify if the first 10 positive samples mean only the first

10 positive measles samples or if the first 10 positive samples mean the first 10 positive samples for ANY of the targets listed in Section 2?

The first 10 positives refer to positive measles samples only.

20. Task Order 1, page 8: Is there flexibility in the 10-day TAT if we need to modify batching to meet the sequencing depth requirement of Section 4.2.1?

Answer:

The 10-day TAT should be met for routine testing. However, if modification needs arise, they shall be communicated to CDC and documented to ensure the exceptions are agreed upon and no penalty on the deliverables are assigned.

21. Does the CDC anticipate awarding a single IDIQ contract to a single offeror, or multiple to multiple offerors?

This is a sole source IDIQ contract.

22. The Pre-solicitation stated “The Government anticipates releasing the solicitation in July 2026, with an anticipated closing date/proposal due date of 30 calendar days from the date of release of the solicitation.” The solicitation was issued August 13, 2026, with a closing date of September 2, 2026. This is 20 days from the date of release of the solicitation. Will the CDC consider changing the solicitation closing date to September 12, 2026?

Answer:

No, the government can not extend the deadline because this requirement needs to take effect this fiscal year.

23. Chart B.13 has the following line items “ddPCR (per test), Genomic Sequencing (per test), Metagenomic Sequencing (per test), Program Implementation” and requires a price per test for each. We have the following questions regarding the completion of this chart:

1. For ddPCR and Genomic Sequencing, different targets may have different prices within the same capability. For example ddPCR for Covid-19 may have a different price than ddPCR for measles virus. Can we add rows / line items to chart B.13 for various targets, and if so, is there a list of targets we should use to complete Chart B.13? Or is providing an average sufficient for the purpose of the Chart B.13, and more specific pricing is expected in individual Task Orders?

2. For Metagenomic Sequencing, can different methods/approaches, and read depths be included as separate rows / line items to capture the difference in price?

3. Program Implementation is priced by contract year. Please confirm whether Program Implementation is intended as a fixed annual price, and whether the proposed annual price is expected to apply regardless of the number of participating facilities included in a Task order, or whether offerors can add rows to show it scaling with facility count. For example, the IDIQ scope contemplates up to 500 facilities while Task Order 1 establishes up to 200.

Answer:

Please see the following responses to each of the questions posed:

1) Multiple pathogen targets are expected to be multiplexed (not single-plex testing) and the pricing details should reflect this. Therefore, average pricing is sufficient.

RFTOP Task Order one delineates the expected ddPCR targets. These are: IAV, IAV subtypes H1, H3, and H5, SARS-COV-2, RSV, and Measles WT virus.

2), Provided that information on each of the methods/approaches for mNGS sequencing is clearly indicated, submitters may use this approach.

3) Program implementation costs are one time for Task Order 1, ut provide flexibility if additional sites need to be onboarded for a future task order. Therefore, offerors can add rows to show scaling with facility count—sites beyond 200 will not be considered for Task Order 1.

24. The section states (IDIQ Section 3.2) “Testing shall only be done by a single laboratory located within the continental United States of America.” Does this apply to all items or capability areas (i.e. PCR, amplicon sequencing and metagenomic sequencing)? Or only the dPCR/ddPCR capability described in item 2?

Yes, this applies to all items and capability areas.

25. This section states (IDIQ Section 3.4) “Research and development costs shall not be covered by this contract.” though it is preceded by language specific to metagenomic sequencing. Requirement Four, 4.1.1, 4.1.3, and 4.1.4 require panel modifications, primer additions, and pathogen expansion on CDC request. How does the CDC intend for assay development and validation of new targets to be funded? Through a separate CLIN, a task order modification, or as an element of the per-test price?

This contract does not fund research and development and does not include assay development.

26. This section states (IDIQ Section 3.3) ‘The contractor shall have the capability to perform untargeted shotgun metagenomic sequencing for an amount of reads per sample identified at the task order level and sequenced on a time frame identified at the task order level.

The contractor shall have the capability to perform hybrid capture or other enrichment and/or depletion methods identified at the task order level to support detection and characterization of both known and emerging pathogens, enabling early recognition of unexpected or novel targets.’ Does a single laboratory need to have both capabilities (untargeted shotgun metagenomic sequencing and hybrid capture/other enrichment/depletion methods) or will one or the other suffice? Can these capabilities be carried out at multiple laboratories?

Answer:

Yes, a single laboratory needs to have both capabilities (untargeted shotgun metagenomic sequencing and hybrid capture/other enrichment/depletion methods).

27. Does the one billion read depth requirement for sequencing apply to only shotgun sequencing or does it extend to hybrid capture and amplicon-based sequencing? Due to the enrichment process integral to hybrid capture and amplicon-based sequencing such extreme depth would likely be unneeded and potentially inefficient for those approaches.

Answer:

This depth requirement is specific to shotgun sequencing (metagenomics). If a hybrid capture approach is used, CDC recognizes this depth would be less efficient overall. As noted in RFTOP Section 3.4.3: “The offeror shall provide CDC with complete and up-to-date written documentation of all sequencing process controls, quality assurance measures including positive and negative controls. At least 90% of sequenced dPCR positive samples with a concentration above a threshold to be determined by the contractor’s validation spike-in studies in the first two months of the start of the Task 1 work, shall have 100% of the defined genomic regions covered at a minimum depth of 50×. Raw sequencing data submitted to CDC shall meet a minimum average base quality standard of Q30, or an equivalent platform-appropriate quality threshold, as documented in the contractor’s sequencing protocol and approved by CDC prior to implementation.”

28. Section 3.6 states that sample remainders “shall not be retained or used by the contractor, unless written permission is granted by CDC.”

1. Could the CDC describe the process, decision criteria, and anticipated turnaround for requesting such written permission?

2. Would the CDC consider granting permission at the task order level for defined categories of public health analysis performed on remainders prior to shipment to the CDC Biorepository?

3. Does “used by the contractor” encompass method development, quality improvement, and assay validation activities performed on remainders in direct support of this contract?

Answer:

1) If the offeror were to request retention or use of remainders and derivatives, they must do so in writing. CDC will review the request, which must include a project proposal/description. Any sample remainders from sites serving tribes will not be used without the tribe’s consent which will be requested by CDC. Criteria for consideration will include public health relevance, described purpose, intended use of data, and populations involved. Anticipated turnaround will depend on each case, but CDC will confirm receipt of the request within 2 business days.

2) This would require permission from CDC prior to any testing. This may be considered.

3) Yes, this includes any use of remainders or derivatives. These may not be used for method development, quality improvement, and assay validation activities without written permission by CDC.

29. Section 5.7.1 states that “All samples and data generated under this contract are the sole property of CDC.”

If the Contractor collects a separately funded sample or aliquot at the same collection event, under an independent agreement with the utility and using supplies not purchased with contract funds, would the CDC consider that sample and any resulting data to be within the scope of Section 5.7? If not, what conditions would the CDC expect the Contractor to observe to keep such activity outside the scope of this contract?

Answer:

If the contractor were to collect a sample from a separately funded program (at the same time as the sample collected for the CDC contract), that separately funded sample would be considered independent and outside the scope of section 5.7.

30. Could the CDC elaborate on the expected approval process for data use (IDIQ Section 5.7.2)?

Does the CDC anticipate a willingness to permit the Contractor and subcontractors to pursue publishing peer-reviewed manuscripts that make use of the data collected on behalf of the CDC?

The expected approval process will depend upon the intended data use (for instance, a website, blog post, or peer-reviewed publication). While the CDC would consider peer-reviewed manuscripts, all data generated are owned by the CDC. Therefore, the data may not be used without CDC approval. A peer-reviewed manuscript should not be started without prior approval from CDC. CDC would make every effort to involve and make aware jurisdictions from which the data in the publication originates.

31. Are the signature pages Exhibit I (page 48), Exhibit II (page 49-50), and CDCL.09 (page 56-57) in Section D – Contract Terms and Conditions, to be included in the Technical Response and count towards the 35-page limit?

No, these pages do not count towards the limit of the technical proposal.

32. CDCH.26 states that the rights in data clauses give the Government “unlimited rights” and expressly notes that “‘Unlimited rights’ is an unlimited license to use, disclose or reproduce the data; it does not give the government ownership of the data.” Section 5.7.1 states that all samples and data are the “sole property of CDC.” Could the CDC clarify which provision governs in the event of an apparent conflict?

Answer:

All samples and data are the sole property of the CDC, and the CDC has unlimited rights to use, disclose or reproduce the data. CDC owns all samples and data generated from this contract. Section 5.7.1 prevails in the event of a conflict of terms.

33. The Proposal Format and Page Limitations states that the Technical Proposal shall not exceed 35 pages. Please confirm whether the “Data Management Plan” and the “Artificial Intelligence (AI) Use Compliance and Risk Management Plan” count against the 35-page Technical Proposal limitation, or whether they are excluded.

Answer:

No, the Data Management Plan and AI Use Compliance and Risk Management Plan does not count towards the limit of the technical proposal.

34. The Price Proposal states “Unless otherwise directed in writing, the Price Proposal shall include, at a minimum:” and no list follows in the text. Please provide the intended list of minimum required Price Proposal contents.

A generalized Price Proposal Content(s) list is provided on pages 65-66

35. The Price Proposal Contents states “The Price Proposal shall include itemization for all proposed pricing including direct labor, materials, supplies, subcontracting, and other direct costs. Offerors shall provide labor categories, labor hours, labor rates, materials, supplies, and any other direct costs associated with each CLIN.”. Where can we reference the aforementioned CLINs?

Answer:

This is a generalized statement and may or may not apply to the specifics of the task(s) being requested for this requirement. The requirement is asking for cost per test and cost per year of implementation.

36. Is an Accessibility Conformance Report or HHS Section 508 checklist required at proposal submission or at the time of deliverable acceptance?

Answer:

Any Section 508 Compliance requirements are applicable to deliverables submitted under the resulting contract/orders. Section 508 requirements are not applicable at the proposal submission phase.

37. Sub-Factor 4 requires a description of three projects “completed within the past five (5) years.” Will the CDC accept ongoing contracts of similar scope, size, and complexity that are substantially performed but not yet complete?

Answer:

CDC is willing to accept descriptions of ongoing contracts as defined, provided >85% of the contracted work is complete as determined by the scope of deliverables of said contract.

38. Box 1 states the request number as 75D301-26-Q-99270. However, page headers throughout the task order state: 75D301-26-Q-79270. Could the CDC clarify which number is correct?

Updated to reflect request number as 75D301-26-Q-99270 throughout the RFTOP.

39. CLINs 0002, 0003, and 0004 (ddPCR Testing for IAV H1, H3, and H5) are each stated at 20,800 samples, the same quantity as CLIN 0001 (ddPCR Testing for IAV). Should offerors assume subtyping is performed on all samples received, or reflexively test for H1,H3, and H5 only on IAV-positive samples? This assumption materially affects the proposed unit price.

The subtyping shall be performed on all samples received

40. Section 2.4 requires results to be submitted to the CDC within 36 hours of sample receipt.

Please confirm whether the 36-hour period runs continuously through weekends and Federal holidays, and what on-time delivery percentage the CDC will consider acceptable performance.

Answer:

The 36-hour period can be flexible for holidays. Weekends should be accounted for in sampling days allowable for sites (for instance, Friday sampling is not ideal).

Holiday sampling and data sharing should be established in collaboration with CDC and shared with utilities ahead of any changes in frequency.

41. This section states (Task Order 1, Section C 3.3.1) ‘Sequencing shall include selected genomic regions.’ Could the CDC provide guidance regarding the genomic regions to be sequenced?

Answer:

The genomic regions will be provided upon the contract award and may be subject to change.

42. Raw sequence data and metadata are to be submitted to the NCBI and the CDC.

Submission to the NCBI is clear, however it is unclear how the CDC prefers to receive the data (Task Order 1, Section C 3.3.3).

A. Does the CDC prefer sharing via an AWS S3 bucket using cross-account replication or via some other sharing method?

B. Does the CDC require raw reads (FASTQ files) only, post human DNA scrubbing, and a metadata manifest? Or, does the CDC require output files from bioinformatics processing (e.g. BAM/CRAM, VCF, or other files).

CDC prefers sharing via cross-account replication using a push from the contractor’s S3 bucket to CDC's S3 bucket. Raw reads, scrubbed of human DNA and a metadata manifest are required in addition to output files from bioinformatics processing.

43. Does the CDC have guidance for how to modify sequencing depth to reflect variation in sewershed population, size, or epidemiological importance (Task Order 1, Section C 4.2.1)?

A. Is the goal a strict linear relationship between sequencing depth and population size (i.e. a population twice as large should accrue twice as many reads as a comparison population)?

B. Does the CDC have a preferred mechanism for scaling sequencing depth based on sewershed characteristics?

C. How would epidemiological importance be defined and would this likely change over the course of the engagement?

D. Do the sequencing depth requirements change if enrichment steps are performed (i.e.

viral capture, probe capture)?

E. Given that the goal of scaling sequencing depth is to ‘enable detection of minority variants’, does the CDC have guidance for a desired limit of detection—for instance, what allele frequency would be an ideal limit of detection?

Answer:

Please see the following responses to each of the questions posed:

A. A strict linear relationship is not necessarily required, though we note that partitioning into "bins" based on catchment area is beneficial such that a larger catchment population size would receive deeper sequencing.

B. At this time CDC does not have a preferred mechanism for scaling sequencing depth on sewershed characteristics.

C. Epidemiological importance definition would vary by pathogen. If using an untargeted sequencing approach, some areas (e.g., with high tourist travel) may be of higher interest given higher potential for pathogen spread.

D. Yes, sequencing depth requirements will change if enrichment is used, given that sensitivity has been enhanced.

E. This is challenging to answer as minority variant detection may vary, regardless of the LoD.

44. While the testing results would never be the output of a generative AI tool, does the CDC have guidance on what level of detail is appropriate to disclose usage of AI outside of the primary deliverable? Examples of use cases for clarification:

A. During the development process of result delivery mechanisms

B. Assisting in data analysis and interpretation C. Machine Learning models included in sequencing instruments or other laboratory equipment (such models are proprietary to the instrumentation company)

Answer:

A. AI could be used to optimize the delivery process using dummy data.

B. AI cannot be used in data analysis and interpretation.

C. CDC owns the data; the data should not be fed into any AI tools that could store the data or use it for learning.