HomeMy WebLinkAboutSTATE DPH-COVIDNet SARS-CoV-2 Whole Genome Sequencing Initiative_A-22-158.pdf coU County of Fresno Hall of Records,Room 301
2281 Tulare Street
1111 Fresno,California
Board of Supervisors 93721-2198
O Telephone:(559)600-3529
FREC-1 Minute Order Toll Free: 1-800-742-1011
www.co.fresno.ca.us
April 19, 2022
Present: 5- Supervisor Steve Brandau, Supervisor Nathan Magsig, Supervisor Buddy Mendes,
Chairman Brian Pacheco,and Vice Chairman Sal Quintero
Agenda No. 40. Public Health File ID: 22-0011
Re: Approve and authorize the Chairman to execute a retroactive 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 1,2022 through
February 28,2025($0)
APPROVED AS RECOMMENDED
Ayes: 5- Brandau, Magsig, Mendes, Pacheco, and Quintero
Agreement No.22-158
County of Fresno Page 41
coU��
Board Agenda Item 40
0 18j6 0
FRE`3
DATE: April 19, 2022
TO: Board of Supervisors
SUBMITTED BY: David Luchini, RN, PHN, Director, Department of Public Health
SUBJECT: Retroactive 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 a retroactive 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, 2022
through February 28,2025 ($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 for genomic sequencing, which will
end the Department's efforts to map the relationship among the variants of COVID-19 samples, hampering
efforts to determine when and where variants are emerging in the County.
RETROACTIVE AGREEMENT:
The recommended agreement was originally scheduled to come before the Board on February 22, 2022.
However, the agenda item had to be pulled due to the delay in obtaining approval from CDPH's legal team to
amend the agreement to add mutual indemnification and self-insurance language, requested by Fresno
County Human Resource Risk Management(HR Risk). After several discussions with CDPH, the
recommended agreement was finalized on March 1, 2022. The Fresno County Public Health Laboratory,
Quest, and Labcorp submit a total of 25 COVID-19 samples weekly to COVIDNet for whole genome
sequencing.
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 2021-22
County of Fresno page 1 File Number:22.0011
File Number:22-0011
Adopted Budget.
DISCUSSION:
On February 19, 2021, the County Administrative Officer, acting as the Emergency Services Director,
signed Agreement D-21-056 with CDPH 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.
On May 11, 2021, your Board ratified the Agreement, allowing the continuation of services through February
28, 2022.
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
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 contact
tracing investigations.
The term of the Agreement shall remain in effect for 3 years, unless one or both parties wish to terminate
the Agreement upon 30 days advanced written notice. The Agreement contains a mutual indemnification
clause where the County agrees to indemnify CDPH for any claims arising from the agreement and the
County's self-insurance language requested by HR Risk.
REFERENCE MATERIAL:
BAI #41, May 11, 2021
ATTACHMENTS INCLUDED AND/OR ON FILE:
On file with Clerk-CDPH COVIDNet Participation Agreement
CAO ANALYST:
Ron Alexander
County of Fresno page 2 File Number:22-0011
Agreement No. 22-158
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,
either directly or indirectly through a Processing 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. Processing Lab: "Processing Lab" means a California laboratory which can provide the
viral RNA extract or Sample, as defined herein, from a COVID-19 Specimen.
g. Sample: "Sample" means the extracted total nucleic acid or viral RNA from a SARS-CoV-
2 specimen.
h. 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 9-2021) Page 1 of 8
i. 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.
j. Sequencing Lab: "Sequencing Lab" means CDPH, Biohub, or another California
laboratory member of COVIDNet which will provide genomic sequencing of COVID-19
Samples.
k. Use: "Use" means the sharing, employment, application, utilization, examination, or
analysis of information.
I. 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 in order 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, in order 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; 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 9-2021) Page 2 of 8
® 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 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. Processing Lab: Participant shall serve as a Processing Lab, as defined above, for
COVIDNet.
❑ 1. Participant shall serve as its own Processing Lab. Participant agrees:
a) Participant shall follow industry standards in extracting total nucleic
acid or viral RNA from the Specimen;
b) Participant is solely responsible for all costs associated with
processing COVID-19 Specimen; and
c) Participant will either sequence resulting Samples (extracted total
nucleic acid or viral RNA) or will ship Samples to CDPH for
sequencing.
❑ 2. Participant is available to assist CDPH with total nucleic acid or viral
RNA extraction. Participant agrees:
a) Participant shall work directly with CDPH to arrange transportation
of COVID-19 Specimens .to Participant's site for extraction of total
nucleic acid or viral RNA from COVID-19 Specimens.
COVIDNet Participation Agreement(updated 9-2021) Page 3 of 8
D. 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.
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 COVIDNet
Diagnostic Testing Lab or Processing 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.
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.
COVIDNet Participation Agreement(updated 9-2021) Page 4 of 8
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.
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 Branch
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: jbulawit(a)-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 from March 1, 2022.
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 9-2021) Page 5 of 8
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 directly or indirectly out of or in
connection with any negligent act or omission or willful misconduct of Participant, its officers,
workforce members or agents relative to this Agreement.
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 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.
XVII. Insurance Requirements: Without limiting the indemnification obligation of Participant as
stated herein, it is understood and agreed that the Parties shall each maintain, at their sole
expense, insurance policies or self-insurance programs including, but not limited to, an
insurance pooling arrangement and/or Joint Powers Agreement including general liability,
automotive liability, and professional, cyber, and workers' compensation.. Evidence of
insurance, e.g., Certificates of Insurance, public-liability letters, or other similar
documentation, shall be provided at the request of either party under this Agreement. Each
party shall provide a Waiver of Subrogation under the Worker's Compensation policy in favor
of the other party as applicable to and available under that party's insurance program.
COVIDNet Participation Agreement(updated 9-2021) Page 6 of 8
Parties understand and accept the following:
A. In accordance with Government Code section 11007.4, the State of California has
elected to be self-insured for liability exposures. Under this form of insurance, the
State and its employees acting in the course and scope of their employment are
insured for tort liability arising out of official State business. All claims against the
State of California based on tort liability should be presented as a government
claim to the Government Claims Program, P.O. Box 989052 MS 414, West
Sacramento, CA 95798-9052. (Gov. Code section 900, et. seq.) Internet link:
https://www.dgs.ca.gov/ORI M/Services/Page-Content/Office-of-Risk-and-
Insurance-Management-Services-List-Folder/File-a-Government-Claim.
B. The State of California has also elected to be insured for its motor vehicle liability
exposures through the State Motor Vehicle Liability Self-Insurance Program
(VELSIP). This program provides liability coverage arising out of the operations of
motor vehicles used by state employees for official state business (California
Vehicle Code Sections 17000 and 17001). Motor vehicle liability claims against the
State of California should be presented to the Office of Risk and Insurance
Management, P.O. Box 989052 MS-403, West Sacramento, CA 95798-9052,
(800) 900-3634, claims@dgs.ca.gov. If your motor vehicle liability claim is not
resolved within six months from the date of loss, California law requires you to file
a formal claim with the Government Claims Program, P.O. Box 989052 MS 414,
West Sacramento, CA 95798-9052. (Gov. Code section 900, et. seq.) Internet link:
https://www.dgs.ca.gov/ORIM/Services/Page-Content/Office-of-Risk-and-
Insurance- Management-Services-List-Folder/File-a-Government-Claim.
The State of California has a Master Agreement with the State Compensation Insurance
Fund regarding workers' compensation benefits for all state employees, as required by
the Labor Code.
[This space intentionally left blank— Continued on next page.]
COVIDNet Participation Agreement(updated 9-2021) Page 7 of 8
XVIII. 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.
L, 6 q I? a
Brian Pacheco (Print Name) Date
Chairman of the Board of Supervisors of the County of Fresno ATTEST:
Address: BERNICE E.SEIDEL
Clerk of the Board of Supervisors
County of Fresno, Department of Public Health County of Fresno,State of California
1221 Fulton Street, 6th Floor By ��� � Deputy
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.
04/26/2022
Paul Kimsey, PhD Date
Deputy Director, State Public Laboratory Director
Office of the State Public Health Laboratory Director
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 Branch
California Department of Public Health
850 Marina Bay Parkway
Richmond, CA 94804
Debra.Wadford(,U_)cdph.ca.gov
COVIDNet Participation Agreement(updated 9-2021) Page 8 of 8