Draft PWS.pdf

Title: Wastewater Surveillance Testing Services

C.1 Background and Need

The National Wastewater Surveillance System (NWSS) was established to provide community-level data on infection trends using an approach that is independent of healthcare access and clinical testing capacity. Wastewater data has been used to support state, tribal, local and territorial (STLT) response decision-making, such as resource allocation, siting of mobile testing units, refining health messaging, and near-term forecasting of cases and hospitalizations.

NWSS is a CDC-coordinated surveillance system that is implemented through STLT health departments. By August 2022, 47 state, local, and territorial public health jurisdictions had received funding to support wastewater surveillance activities. However, implementation of this novel surveillance approach requires considerable effort, resources, and coordination at the state and local level, and STLT health departments are already overburdened providing other COVID response activities. Thus, not all funded jurisdictions are able to rapidly implement this novel surveillance approach or provide substantial coverage of the communities in their jurisdictions. Some STLT jurisdictions do not have the capacity to implement wastewater surveillance activities and are lacking access to this valuable source of public health data.

Supplementing STLT capacity through commercial wastewater testing servicee is a critical and urgent need to support the nation's ongoing response to the COVID-19 health emergency.

With the emergence of new variants, there is a sustained risk of surges throughout the US.

Wastewater data can provide an early warning of new surges to allow more time to allocate resources. Wastewater data also provides a robust measure of community infection trends at the height of surges when clinical testing can have insufficient capacity. This testing capacity would allow rapid expansion of the NWSS network to a truly national system providing COVID surveillance data for US territories, tribal nations, and all 50 states.

In summer 2022, a multi-national outbreak of monkeypox emerged with most cases in Europe. NWSS was able to rapidly implement wastewater surveillance for this new pathogen through existing contract mechanism. Wastewater data was a useful tool to confirm the resolution of the outbreak and will be useful to monitor for reemergence. This model of rapid test implementation through commercial laboratories is an effective tool to prepare for future public health responses.

C.2 Project Objectives

The Wastewater Testing Services IDIQ provides the Centers for Disease Control and Prevention (CDC), Division of Foodborne, Waterborne and Environmental Diseases (DFWED), Waterborne Disease

Prevention Branch (WDPB) an “as needed” mechanism to obtain services through the issuance of task orders that support wastewater surveillance testing that aligns with public health priorities for CDC.

The purpose of this requirement is to provide flexible wastewater testing services that complements existing wastewater surveillance networks managed by STLT health departments to support ongoing

COVID and mpox responses and prepare for future public health responses.

• The base service required includes facilitating wastewater sample collection and shipment with select utilities, conducting quantitative SARS-CoV-2 testing and tiled amplicon SARS-CoV-2 sequencing of applicable samples, and timely data submission to CDC.

DRAFT

• The testing period and number of wastewater sites will be scaled as needed, with a minimum order of 100 sites.

• This IDIQ will provide national testing coverage including territories and Tribal communities.

Vendors may bid for Health and Human Services (HHS) regions 1-5, HHS regions 6-10, or all 10

HHS regions.

C.2.1. Adaptability for future responses

• To prepare for future responses, the contract will facilitate ordering additional add-on quantitative

PCR-based tests or tiled amplicon sequencing. This service will be used for pathogens that can be adequately measured using the same sample processing methods as SARS-CoV-2. Research and development costs are not covered by the contract.

• Mpox quantitative PCR-based testing may be ordered as an add-on test using the same processed wastewater samples used for SARS-CoV-2 testing.

C.3 Contract Structure

The basic contract will establish the general scope and ordering period for task orders to be issued against this contract. It is anticipated that multiple task orders will be issued to the contractors for wastewater testing as described in this Scope of Work. Each task order shall have a discrete period of performance independent of the IDIQ contract. Each task order will have a discrete number of wastewater sites, with a minimum of

100 sites and a maximum of 500 sites. For each task order, vendors may bid for HHS regions 1-5, HHS regions 6-10, or all 10 HHS regions (i.e., national coverage). Bids for partial coverage other than as described here will not be considered.

Individual task orders exceeding $3,000 not awarded to all contractors will be competed in accordance with the fair opportunity process described in FAR 16.505(b)(1) unless an exception to fair opportunity in documented in accordance with FAR 16.505(b)(2). All task orders will be solicited by email. Contractors will have a minimum of 10 calendar days to respond.

C.4 Scope of work

The purpose of this contract is to provide wastewater testing services that supplement the existing wastewater surveillance systems in STLT health departments and prepare for future public health responses.

The main requirements for this wastewater testing services IDIQ are:

1. Establish service relationships with selected wastewater testing facilities. Facilities will be selected for testing by CDC in coordination with STLT health departments. Vendors will provide sampling and shipping supplies at no cost to the participating utilities. Wastewater samples will be collected twice per week. Vendors must establish a mechanism to collect the utility metadata required for NWSS data submission

(https://www.cdc.gov/healthywater/surveillance/wastewater-surveillance/data-reporting-analytics.html).

2. Quantitative PCR-based SARS-CoV-2 testing for all samples and data submission to CDC within 36 hours of sample receipt by the vendor. Test method must meet the data submission standards for NWSS (https://www.cdc.gov/healthywater/surveillance/wastewater-surveillance/data-reporting-analytics.html#data-dictionary).

3. Tiled amplicon sequencing of SARS-CoV-2 of all samples that have the minimum SARS-

CoV-2 RNA concentrations necessary to generate high quality sequence data (i.e., Ct ≥ 35).

Raw sequence data must be submitted to CDC within 10 days of sample receipt by the vendor.

4. Add-on testing for mpox and other pathogens based on public health need. These tests will be either quantitative PCR-based assays or tiled amplicon sequencing. Specific testing details will be included in the task order.

C.5 Technical Requirements

5.1 - Requirement 1: Establish wastewater testing services with selected wastewater facilities to support twice weekly sample collection and shipment to the testing laboratory.

Wastewater sites will be selected by CDC and STLT health departments to supplement existing wastewater surveillance systems and provide testing coverage in communities that meet public health priorities. CDC will confirm the utilities’ interest in participating and provide their contact information to the vendor. The number of wastewater sites included in each task order will be scaled to the public health need, with a minimum of 100 and a maximum of 500 sites per task order.

Vendors will provide sampling and shipping kits to each facility in a manner that supports twice weekly sample collection. Instruction for collecting samples, reporting facility metadata as required by NWSS

(https://www.cdc.gov/healthywater/surveillance/wastewater-surveillance/data-reporting-analytics.html#data-dictionary), and packaging the sample for shipment per Department of Transportation shipping regulations shall be provided. Vendors are responsible for maintaining an adequate supply of testing and shipping kits to support the continuous flow of samples during the testing period for each task order. Composite sampling is preferred, but vendors should be able to recieve grab samples as well if the facility does not have a composite autosampler. Sampling and shipping kits, including shipping fees, shall be provided at no cost to the participating facilities. Sample volume shall be sufficient to allow SARS-

CoV-2 testing and sequencing, retesting if necessary, and archiving of no less than 15 ml raw wastewater sample with CDC. Sample remainders should be frozen and shipped on dry ice to the CDC Biorepository every 2-4 weeks.

In addition to sample collection services, vendors will maintain a data management system that facilitates tracking of facility participation and compliance with the sampling schedule. The data system should also track samples from receipt through testing to data reporting. Vendors will be responsible monitoring facility compliance and documenting efforts to support and restore compliance with the sample collection schedule.

Deliverables: to be specified within individual task orders.

5.2 - Requirement 2: SARS-CoV-2 quantitative testing.

The vendor shall conduct laboratory analysis to quantify SARS-CoV-2 RNA (i.e., report results as copies/volume not Ct) via reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) or digital/droplet digital polymerase chain reaction (dPCR or ddPCR). Methods that report only Ct values are not acceptable. The testing protocol must include measurement of recovery efficiency, matrix inhibition evaluation, and human fecal normalization that meet the requirements for the National

Wastewater Surveillance System as described here:

https://www.cdc.gov/healthywater/surveillance/wastewater-surveillance/testing-methods.html. A complete laboratory protocol, including sample processing, nucleic acid extraction, and PCR, must be provided to CDC to ensure proper analysis and interpretation of the results.

Results shall be submitted to CDC within 36 hours of sample receipt by the vendor. Each sample result must include all of the required data fields (NWSS data dictionary link) to be considered complete.

Required QA/QC controls include extraction blanks, negative controls, positive controls, and standard curves (if using RT-qPCR).

SARS-CoV-2 quantitative testing will be included in all task orders. The processing and extraction methods used for this requirement should produce nucleic acid extracts that are appropriate and sufficient for the add-on testing described in requirements 3 through 6.

5.3 - Requirement 3: Add-on SARS-CoV-2 tiled amplicon sequencing.

The vendor shall conduct SARS-CoV-2 sequencing that is appropriate for variant detection. Tiled amplicon methods, such as those used for variant determination in clinical samples, are most appropriate for wastewater samples to overcome challenges of genome fragmentation, short reads, potentially high viral diversity, and the relatively low abundance of viral RNA. The sequencing method should ensure that there is not a drop in coverage for the S-gene. Metagenomic sequencing of total RNA or Sanger sequencing of amplicons is not appropriate or acceptable. Sequence analysis shall be conducted on up to one representative sample (individual or pooled) per week from each participating utility. Only samples that have sufficient SARS-CoV-2 concentrations (e.g., Ct value less than a pre- determined threshold) should be considered for sequencing.

Raw sequence data and sample metadata shall be submitted to the National Center for Biotechnology

Information (NCBI) within 10 days of sample receipt by the vendor.

5.3 – Requirement 4: Add-on mpox virus quantitative testing.

The vendor shall conduct laboratory analysis to quantify mpox virus DNA (i.e., report results as copies/volume not Ct) via reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) or digital/droplet digital polymerase chain reaction (dPCR or ddPCR). Methods that report only Ct values are not acceptable. The non-Variola orthopox assay is preferred

(https://www.cdc.gov/poxvirus/monkeypox/lab-personnel/index.html), but a monkeypox-specific assay is acceptable as long as all positive samples are confirmed with a Clade 2-specific assay. The testing protocol must include measurement of recovery efficiency, matrix inhibition evaluation, and human fecal normalization that meet the requirements for the National Wastewater Surveillance System as described here: https://www.cdc.gov/healthywater/surveillance/wastewater-surveillance/testing-methods.html. A complete laboratory protocol must be provided to CDC to ensure proper analysis and interpretation of the results.

Results shall be submitted to CDC within 36 hours of sample receipt by the vendor. Each sample result must include all of the required data fields (NWSS data dictionary link) to be considered complete.

Required QA/QC controls include extraction blanks, negative controls, positive controls, and standard curves (if using RT-qPCR).

5.3 – Requirement 5: Add-on quantitative PCR-based pathogen testing.

CDC may release task orders to quantify additional pathogens based on public health need. The specific pathogens cannot be anticipated at this time, but consideration for a task order will require that the pathogen is recoverable from wastewater using the same methods that eligible vendors are using for

SARS-CoV-2 and the detectable using PCR-based methods. Test frequency and number will not exceed that of SARS-CoV-2 as described in Requirements 1 and 2. Test frequency and reporting requirements will be detailed in the task order.

Task orders will not include assay development.

5.3 - Requirement 6: Add-on tiled amplicon sequencing for additional pathogens.

CDC may release task orders to sequence mpox or additional pathogens in alignment with requirement 5 based on public health need. To be considered for this requirement, a tiled amplicon approach must be commercially available for the target pathogen. Test frequency and number will not exceed that of SARS-

CoV-2 as described in Requirements 1 and 2. Test frequency and reporting requirements will be detailed in the task order.

Task orders will not include assay development.

5.3 – Requirement 7: Data and program management.

The vendor shall manage their performance to ensure compliance with all requirements of the contract.

The vendor shall assign a Program Manager who will ensure the vendors’s performance complies with all requirements and will be the primary point of contact for the work to be performed. The Program

Manager shall have sufficient corporate authority to direct, execute, and control all elements of the task and ensure that all necessary management, business, contracts, engineering, implementation, and maintenance resources are available and sufficient, both in numbers and qualifications, to successfully perform all the tasks required by the contract.

The vendor shall continuously monitor the performance of this contract, and of all subcontracts, to provide the Government with a timely assessment of program progress and problems and to control contract activities to include Subcontractor and/or vendor activities. This should involve the development and execution of a Communication Plan to include the methodology and approach for communicating status, issues, and risks to CDC through the COR and for communicating with stakeholders outside CDC.

It is imperative that the vendor monitors the facilities for adherence to the testing schedule. The absence of data collection can impair the monitoring of tracking SARS-CoV-2 concentrations in sewage. This is a voluntary program, and a facility may choose to no longer participate, or they may not have the resources to comply with the testing schedule. The vendor shall contact a facility when they miss a collection date.

If a facility misses an entire week of sample collection, the vendor shall notify the project manager with a written correspondence of the interaction with the facility and whether the testing schedule has been resolved. If the vendor cannot contact the facility after three attempts, the vendor should notify CDC. If a facility consistently misses sampling events, the vendor shall notify CDC. CDC may opt to replace non-responsive facilities.

It is imperative that the data received from the vendor are error-free and complete. This includes proper file type, proper file format, accurate column headings, consistent data standards, complete submissions, and accurate data. The technical monitor will notify the vendor if they find data quality issues. The vendor is responsible to isolate and resolve these issues. If the same issue occurs multiple times, the CDC technical monitor may ask for a corrective action plan to resolve the issues. In the corrective action plan, the vendor will provide the steps to be taken to prevent the issue from re-occurring