HomeMy WebLinkAboutSTATE DPH-COVIDNet SARS-CoV-2 Whole Genome Sequencing_A-25-044.pdf Docusign Envelope ID:5641EF79-9606-4E99-9E8B-150FF6844480
COtj County of Fresno Hall of Records, Room 301
2281 Tulare Street
601 Fresno,California
Board of Supervisors 93721-2198
O� 1$56 O Telephone: (559)600-3529
FRV,t' Minute Order Toll Free: 1-800-742-1011
www.fresnocountyca.gov
January 28, 2025
Present: 5- Vice Chairman Garry Bredefeld, Supervisor Luis Chavez, Supervisor Nathan Magsig,
Chairman Buddy Mendes, and Supervisor Brian Pacheco
Agenda No. 51. Public Health File ID: 24-1364
Re: Approve and authorize the Chairman to execute an Agreement with the California Department of Public
Health,for continued participation in the COVID Network of California Laboratories for SARS-CoV-2
Whole Genome Sequencing Services, effective March 1, 2025 through February 29, 2028($0)
A MOTION WAS MADE BY SUPERVISOR MAGSIG,SECONDED BY SUPERVISOR CHAVEZ,
THAT THIS MATTER BE APPROVED AS RECOMMENDED WITH THE CONDITION THAT THE
AGREEMENT INCLUDES A MUTUAL INDEMNIFICATION CLAUSE IN WHICH THE CALIFORNIA
DEPARTMENT OF PUBLIC HEALTH (CDPH)AGREES TO INDEMNIFY THE COUNTY AGAINST
LITIGATION FOR ANY EGREGIOUS ACTS CAUSED BY CDPH RELATIVE TO THE AGREEMENT.
THE MOTION CARRIED BY THE FOLLOWING VOTE:
Ayes: 4- Chavez, Magsig, Mendes, and Pacheco
Noes: 1 - Bredefeld
Agreement No. 25-044
County of Fresno Page 55
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co
Board Agenda Item 51
O 1856 O
DATE: January 28, 2025
TO: Board of Supervisors
SUBMITTED BY: David Luchini, RN, PHN, Director, Department of Public Health
SUBJECT: Agreement with the California Department of Public Health Pertaining to COVID-19
Genome Sequencing Services
RECOMMENDED ACTION(S):
Approve and authorize the Chairman to execute an Agreement with the California Department of
Public Health, for continued participation in the COVID Network of California Laboratories for
SARS-CoV-2 Whole Genome Sequencing Services, effective March 1, 2025 through February 29,
2028 ($0).
There is no additional Net County Cost associated with the recommended action. Approval of the
recommended action will allow the Department to continue participating in the COVID Network of California
Laboratories for SARS-CoV-2 Whole Genome Sequencing (COVIDNet)through the California Department
of Public Health (CDPH). Under this agreement, CDPH will continue to provide laboratory genomic
sequencing in preparing and analyzing movement of the virus and the growth of variants in the County to
support the Department's testing and response to the COVID-19 pandemic. This item is countywide.
ALTERNATIVE ACTION(S):
There are no viable alternative actions. Should your Board not approve the recommended action, the
Department would discontinue providing positive COVID-19 samples to CDPH, hampering efforts to
determine when and where variants are emerging in the County.
FISCAL IMPACT:
There is no increase in Net County Cost associated with the recommended action. This is an approval for a
user participation agreement which does not require a monetary exchange. The Department will be
responsible for all costs associated with processing COVID-19 Specimens. Sufficient appropriations and
estimated revenues for these costs are included in the Department of Public Health Org 5620 FY 2024-25
Adopted Budget.
DISCUSSION:
On April 19, 2022, the Board approved Agreement 22-158 with CDPH, which allowed the County to
participate in COVIDNet and to provide CDPH with COVID-19 testing samples for genomic sequencing data
for epidemiological efforts to control the spread of COVID-19.
COVIDNet was established by the California Testing Task Force as a collaborative effort between CDPH,
the Chan Zuckerberg Biohub, Invitae Corporation, Illumina, diagnostic labs, local public health labs (PHLs),
and academic genomic sequencing experts, to track the spread of the COVID-19 virus in California and
County of Fresno page 1 File Number.24-1364
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File Number:24-1364
characterize new cases and outbreaks using genomic epidemiology. By applying genomic epidemiology
with enhanced testing, intensive contact tracing, and effective isolation, the State of California can execute
an evidence-based public health strategy to successfully contain COVID-19.
This agreement between the County and CDPH is providing a phylogenic tree at no cost to the County. A
phylogenic tree is a means of mapping the evolutionary process of cells within samples of a species. This
phylogenic tree provides a mapping tool to determine the variants of COVID-19 that are present within the
community and is valuable to show how the virus is mutating and evolving over time to educate and guide
the long-term process of combating COVID-19.
The COVID-19 samples will be submitted to CDPH for genome sequencing in order to better inform
outbreak investigations and public health surveillance. These samples will provide the County with key data
to determine when and where outbreaks are occurring as well as the evolution of COVID-19 growth and
variants as the disease continues throughout the County. COVIDNet will use the genomic sequencing data
to generate and maintain a timely and comprehensive phylogenetic tree of California COVID-19 viruses
through the COVIDNet partnership and apply such data for use as warranted for local outbreaks and
contract tracing investigations.
The term of the Agreement shall remain in effect for three years, unless one or both parties wish to
terminate the Agreement upon 30 days advanced written notice. The agreement deviates from the County's
model contract as this agreement contains a one-way indemnification in favor of the State.
REFERENCE MATERIAL:
BAI #40, April 19, 2022
ATTACHMENTS INCLUDED AND/OR ON FILE:
On file with Clerk-Agreement with CDPH
CAO ANALYST:
Ron Alexander
County of Fresno page 2 File Number.24-1364
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Agreement No. 25-044
COVIDNet Participation Agreement
This COVID Network of California Laboratories for SARS-CoV-2 Whole Genome Sequencing
("COVIDNet") Participation Agreement ("Agreement") sets forth the understandings and obligations of
the County of Fresno [Laboratory] ("Participant"), and the California
Department of Public Health ("CDPH") (collectively, "Parties") with respect to their participation in
COVIDNet. Participant shall check all applicable boxes in Section IV of this Agreement to indicate their
involvement in COVIDNet.
I. Supersession: This Agreement supersedes any prior COVIDNet Agreement between CDPH
and Participant.
II. Definitions: For purposes of this Agreement, the following definitions shall apply:
a. COVID-19 Specimen: "COVID-19 Specimen" means a respiratory or other medical
specimen that was tested by industry standard practices for SARS-CoV-2 virus where
this virus was detected (i.e., a SARS-CoV-2 positive specimen).
b. Diagnostic Testing Lab: "Diagnostic Testing Lab" means a CLIA-certified laboratory within
California which is authorized to test specimens originating from California that can
provide COVID-19 Specimens and/or Samples to a Sequencing Lab, as defined herein.
c. Disclosure: "Disclosure" means the release, transfer, provision of, access to, or divulging
in any other manner of information.
d. COVIDNet Partner Data: "COVIDNet Partner Data" means any COVID-19 Specimen
and/or Sample, as defined herein, received by Participant either from or belonging to
another COVIDNet participant, as well as any information or data associated with the
COVID-19 Specimen and/or Sample, including the date of collection and 3-digit zip code.
e. Participant Data: "Participant Data" means any COVID-19 Specimen and/or Sample, as
defined herein, received from Participant and any information or data associated with the
Sample, including the date of collection and 3-digit zip code.
f. Sample: "Sample" means the extracted total nucleic acid or viral RNA from a SARS-CoV-
2 Specimen.
g. Sample Code or Coded Identifier: "Sample Code" or "Coded Identifier" means a de-
identified unique identifier which corresponds to a specific COVID-19 Specimen.
COVIDNet Participation Agreement (updated 9-2024) Page 1 of 7
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h. Sequencing: "Sequencing" as used herein denotes the process performed by a
Sequencing Lab, as defined herein, to determine the order of nucleotides from a Sample,
as defined herein.
i. Sequencing Lab: "Sequencing Lab" means CDPH, or another California laboratory
member of COVIDNet, which will provide genomic sequencing of COVID-19 Samples.
j. Use: "Use" means the sharing, employment, application, utilization, examination, or
analysis of information.
k. Workforce Member: "Workforce Member" means an employee, agent, volunteer, trainee,
or other person, whose conduct, in the performance of work for Participant, is under the
direct control of Participant, whether or not they are paid by Participant.
III. Background and Purpose:
CDPH seeks to conduct and/or facilitate whole genome sequencing ("WGS") of COVID-19
Specimens to better inform outbreak investigations and public health surveillance.
COVIDNet strives to transform how laboratory scientists and epidemiologists approach the
detection, characterization, and investigation of SARS-CoV-2 virus transmission and
containment, allowing California health jurisdictions to better trace and track outbreaks,
including those that would have previously gone undetected, to inform public health action
pursuant to Health and Safety Code section 100325. COVIDNet will use WGS data to
generate and maintain a timely and sufficiently comprehensive phylogenetic tree of California
SARS-CoV-2 viruses through the COVIDNet partnerships and apply such data for use as
warranted for local outbreaks and contact tracing investigations.
IV. Participant Responsibilities:
❑ A. General Requirements: Participant agrees to:
1. Work cooperatively with CDPH and all COVIDNet Participants;
2. Communicate with CDPH and COVIDNet Participants, as needed, any obstacles,
barriers, or hindrances that will or may impede fulfilling COVID-19 Specimen
Processing or Sequencing in the agreed upon timeframe or otherwise; and
3. Comply with CDPH instructions for transporting specimens to CDPH for
sequencing, and to provide requested metadata to CDPH regarding specimens
submitted for sequencing.
COVIDNet Participation Agreement (updated 9-2024) Page 2 of 7
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® B. Diagnostic Testing Lab: Participant shall serve as a Diagnostic Testing Lab, as
defined above, for COVIDNet. Participant agrees:
1. Participant is a Diagnostic Testing Lab that is CLIA-certified and registered with
the CDPH Laboratory Field Services as authorized to test specimens originating
from California that has the ability to provide COVID- 19 Specimens or Samples to
CDPH for genomic sequencing;
2. Participant believes it can supply approximately 100 COVID-19 Specimen or
Samples per month to CDPH to be sequenced. Participant and CDPH acknowledge
this amount is an estimate and may be subject to change based on availability and
condition of COVID-19 Specimens or Samples; and
3. Participant shall submit COVID-19 Specimens or Samples to CDPH for genomic
sequencing. Participant is solely responsible for the cost of transportation of
Samples to CDPH. Participant shall ensure that the COVID-19 Specimens and/or
Samples are properly handled and transported in accordance with industry
standard practices for such Samples.
C. Sequencing Lab: Participant shall serve as a Sequencing Lab, as defined above,
for COVIDNet.
1. Participant shall serve as its own Sequencing Lab. Participant agrees:
a) Participant anticipates an ability to sequence approximately
Samples per month. Participant and CDPH acknowledge this
amount is an estimate and may be subject to change based on
availability and condition of Samples;
b) Participant shall follow industry standards in sequencing Samples;
c) Participant shall upload resulting raw sequence data files (either
FASTQ or BAM files)to Terra cloud environment set up by CDPH or
other mutually agreed upon sequence repository; and
d) Participant is solely responsible for all costs associated with
sequencing Specimen.
COVIDNet Participation Agreement (updated 9-2024) Page 3 of 7
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2. Participant is available to assist other COVIDNet participants with genomic
sequencing. Participant agrees:
a) Participant anticipates an ability to sequence approximately
Samples per month for other COVIDNet participants. Participant and
CDPH acknowledge this amount is an estimate and may be subject
to change based on availability and condition of Samples;
b) Participant, and its workforce members and agents, shall not attempt
re-identification of COVIDNet Partner Data, including utilization of
any publicly available or non-publicly available sources;
c) Participant shall work directly with CDPH and/or a COVIDNet
Diagnostic Testing Lab that sends the Samples to be sequenced,
including to arrange payment, transportation, and any legal
agreements, when required; and
d) Participant shall upload resulting raw sequence data files (either
FASTQ or BAM files) to Terra cloud environment set up by CDPH or
other mutually agreed upon sequence repository transmitted via
email by the points of contacts listed in Section VII.
V. CDPH Responsibilities: To the extent practicable, CDPH shall be available for consultation
with Participant regarding obligations under this Agreement, including sequencing,
bioinformatics, and data analysis.
VI. COVIDNet Partner Data: If Participant receives COVIDNet Partner Data from participating
COVIDNet labs, Participant, and their workforce members and agents, shall not attempt re-
identification of COVIDNet Partner Data, including by using any publicly available or non-
publicly available sources. Participant, and its workforce members and agents, shall
safeguard the COVIDNet Partner Data to which they have access from unauthorized use.
Participant, and its workforce members and agents, shall not use any COVIDNet Partner
Data for any purpose other than carrying out the Participant's obligations under this
Agreement, under a direct agreement with another COVIDNet participant, or as otherwise
required by law. Participant shall implement administrative, physical, and technical
safeguards that reasonably and appropriately protect the privacy, security, integrity, and
availability of COVIDNet Partner Data.
COVIDNet Participation Agreement (updated 9-2024) Page 4 of 7
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VII. Key Contacts: The following individuals shall be responsible for overseeing their respective
Party's performance under this Agreement:
A. For CDPH:
Debra A. Wadford, PhD
Chief, Viral and Rickettsial Disease Laboratory
Infectious Diseases Laboratory Division
Center for Laboratory Sciences
California Department of Public Health
Debra.Wadford(a)_cdph.ca.gov
VRDL.Mail(a�cdph.ca.gov
B. For Participant:
Name: Jeff Bulawit
Title: Sr. Public Health Microbiologist
Organization: County of Fresno, Department of Public Health
Email Address: ibulawit(c�fresnocountyca.gov
VIII. Term of Agreement: Unless otherwise terminated earlier in accordance with the provisions
set forth herein, this Agreement shall remain in effect for three (3) years after the latest
signature date in the signature block below. After three (3) years, this Agreement will expire
without further action. If the parties wish to extend this Agreement, they may do so by
reviewing, updating, and reauthorizing this Agreement. If one or both of the parties wish to
terminate this Agreement prematurely, they may do so upon 30 days advanced written notice
to the Program Contact of the respective Party in Section VII. Any amendment to this
Agreement shall be in writing signed by all Parties. Participant shall securely return, or upon
CDPH approval, destroy any specimens/samples that they have received from other
participants prior to termination of this Agreement and certify in writing specimens have been
securely returned or destroyed, including the date and method used. If return or destruction
is not feasible, Participant shall provide a written explanation to CDPH.
COVIDNet Participation Agreement (updated 9-2024) Page 5 of 7
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IX. Indemnification: Participant hereby agrees to indemnify, hold harmless, and defend the
CDPH from and against any and all claims, losses, liabilities, damages, costs and other
expenses (including attorneys' fees) that result from or arise out of negligent act or omission
or willful misconduct of Participant, its officers, workforce members or agents relative to this
Agreement, to the extent Participant is responsible for the claim, loss, liability, damage, cost
and other expenses.
CDPH hereby agrees to indemnify, hold harmless, and defend the Participant from and
against any and all claims, losses, liabilities, damages, costs and other expenses (including
attorneys' fees) that result from or arise out of negligent act or omission or willful misconduct
of CDPH, its officers, workforce members or agents relative to this Agreement, to the extent
CDPH is responsible for the claim, loss, liability, damage, cost and other expenses.
X. Transfer of Rights: Participant has no right and shall not delegate, assign, or otherwise
transfer or delegate any of its rights or obligations under this Agreement to any other person
or entity. Any such transfer of rights shall be null and void.
XI. No Third-Party Beneficiaries: Nothing express or implied in the terms and conditions of this
Agreement is intended to confer, nor shall anything herein confer, upon any person other
than CDPH or Participant, any rights, remedies, obligations or liabilities whatsoever.
XII. Interpretation: The terms and conditions in this Agreement shall be interpreted as broadly
as necessary to implement and comply with regulations and applicable State and Federal
laws. The parties agree that any ambiguity in the terms and conditions of this Agreement
shall be resolved in favor of a meaning that complies and is consistent with Federal and State
laws.
XIII. Survival: The respective rights and obligations of Participant under Sections VII I and X of this
Agreement shall survive the termination or expiration of this Agreement.
XIV. Entire Agreement: This Agreement, including all attachments, constitutes the entire
agreement between CDPH and Participant. Any and all modifications of this Agreement must
be in writing and signed by all parties. Any oral representations or agreements between the
parties shall be of no force or effect.
XV. Severability: The invalidity in whole or in part of any provisions of this Agreement shall not
void or affect the validity of any other provisions of this Agreement.
XVI. Choice of Law and Venue: The laws of the state of California will govern any dispute from or
relating to this Agreement. The parties submit to the exclusive jurisdiction of the state of
California and federal courts for or in Sacramento and agree that any legal action or
proceeding relating to the Agreement may only be brought in those courts.
[This space intentionally left blank—Continued on next page.]
COVIDNet Participation Agreement (updated 9-2024) Page 6 of 7
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XVII. Signatures:
IN WITNESS,WHEREOF, the Parties have executed this Agreement as follows:
On behalf of County of Fresno [Participant], the undersigned individual hereby attests that
he or she is authorized to enter into this Agreement and agrees to abide by and enforce all the terms
specified herein.
Ernest Buddy Mendes (Print Name) Date
Chairman of the Board of Supervisors of the County of Fresno ATTEST:
BERNICE E.SEIDEL
Address: Clerk of the Board of Supervisors
County of Fresno,State of California
County of Fresno, Department of Public Health
By_ Deputy
1221 Fulton Street, 6th Floor
Fresno, CA 93721
On behalf of CDPH, the undersigned individual hereby attests that he or she is authorized to enter into
this Agreement and agrees to all the terms specified herein.
DocuSigned by:
Ql l ryp� 2/11/2025
—a�rrFe-rr�r��aa
Anthony Tran, Dr.PH., MPH, D(ABMM), MT(ASCP) Date
Director, State Public Laboratory Director
Deputy Director, Center for Laboratory Sciences
California Department of Public Health
850 Marina Bay Parkway
Richmond, CA 94804
Return Executed Agreement to:
Debra A. Wadford, PhD
Chief, Viral and Rickettsial Disease Laboratory
Infectious Diseases Laboratory Division
Center for Laboratory Sciences
California Department of Public Health
850 Marina Bay Parkway
Richmond, CA 94804
Debra.Wadford6D-cdph.ca.gov
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