Draft Clear DX Reagents SOW_05162022.docx

Department of Veterans Affairs Public Health National Program Office Public Health Biorepository Palo Alto, CA 94304

SCOPE OF WORK for Clear DX WGS SARS-CoV-2 Reagents (IDIQ)

1. BACKGROUND:

The VA Public Health National Program Office (PHNPO) and the VA Public Health Biorepository (PHB) have a requirement for recurrent purchase of Clear DX WGS SARS-CoV-2 Reagents.

Mark Holodniy, M.D. is the Director of PHNPO, formerly Public Health Surveillance and Research (PHSR), the PHB and the Public Health Reference Laboratory (PHRL). PHNPO is responsible in VA for national public health surveillance, national outbreak and lookback investigations, and national clinical and public health laboratory testing. PH collaborates with other VHA program offices including National Center for Patient Safety (NCPS), Pathology and Laboratory Medicine Services (P&LMS), the Clinical Emergency Response Team (CERT), Office of Research (ORD) and supports VHA clinical care activities at all VA sites. PHNPO has numerous ongoing collaborations with the Centers for Disease Control and Prevention (CDC), Department of Defense (DoD), and the Armed Forces Health Surveillance Center. PHRL serves as the primary VHA reference microbiology laboratory to test for, and aid in the diagnosis of unusual pathogens; confirm atypical laboratory test results; test epidemiologically significant specimens with potential public health implications; and test for infectious diseases of public health consequence that are too rare or unusual for other VHA clinical laboratories to maintain testing capacity.

The unprecedented COVID-19 pandemic has created a need for VA nationwide testing. Currently, PHRL receives specimens from throughout VHA daily for a variety of clinical and epidemiological evaluations is also a valuable partner to Centers of Disease Control and Prevention (CDC). PHRL has been certified to participate in PulseNET (foodborne illness detection), CaliciNET (norovirus detection and sequencing), Influenza Division for Influenza detection and subtyping, and ArboNET (vector-borne viral infection detection like dengue or zika viruses). Data from these analyzed samples maintains an important partnership between CDC and VA as each works to best understand current and future threats to public health.

At the peak of the pandemic, PHRL tested between 5,000-20,000 Veteran clinical samples for COVID-19 per month. Beyond the diagnosis of COVID-19 infection, PHNPO and PHRL are responsible for the ongoing sequencing of COVID-19 virus strains, to determine if these emerging strains can cause reinfection or render current COVID-19 vaccines ineffective. PHRL is currently processing 1000 sequences per month.

PHB is located at the VA Palo Alto Health Care System in Palo Alto, California. This biorepository was created to store primary and remnant samples for operational investigations, IRB approved studies, and IRB approved secondary research purposes supporting studies in the prevention, diagnosis, and treatment of a wide range of serious and life-threatening illnesses, particularly of new and emerging infectious diseases. PHB is also the primary national biorepository for all COVID-19.

2. PROJECT SCOPE:

This is a request for the reagents and supplies to perform COVID-19 sequencing on the Clear LABs DX instrument. This instrument is used to test patient samples (from Palo Alto and other VA Facilities) for Covid-19 and other infectious agents. This machine addresses our need for higher throughput with an US FDA EUA approved assay since our sample testing volume has increased substantially due to the Covid-19 pandemic and will continue to increase for the unforeseen future. In addition, the instrument will allow us to determine Covid-19 virus sequences from patient samples in order to track development of new strains and those associated with vaccine failure.

3. DEFINITIONS:

COR – Contracting Officer’s Representative PHNPO – Public Health National Program Office PHSR – Public Health Surveillance and Research CDC – Centers for Disease Control and Prevention PHRL – Public Health Reference Laboratory

4. SITE AND DELIVERY LOCATIONS:

Department of Veterans Affairs, Public Health Reference Laboratory, 3801 Miranda Avenue, MB-400, Palo Alto, CA 94304

5. Objectives

This request will provide the purchase of the reagents and supplies for COVID-19 testing and sequencing.

6. Project Management Plan

No project management is required for this purchase.

7. Project Deliverables and Tasks*

a. Clear DX reagent subscription DX mode

b. Clear DX WGS reagent Subscription WGS mode

8. Reporting Requirements and Deliverables

a. Vendor will provide reagents and supplies.

b. COR will certify all deliverables

9. PHASING AND INSTALLATION SCHEDULE:

Delivery at rate of need.

10. GOVERNMENT-FURNISHED PROPERTY

None

11. GOVERNMENT FURNISHED INFORMATION

None