HomeMy WebLinkAbout11 - Water Quality Testing Storm Drains-TributariesITEM II
TO: Members of the Newport Beach City Council
FROM: Dave Kiff, Assistant City Manager
SUBJECT: Contract with the University of California: Water Quality Testing in
Storm Drains and Tributaries to Newport Bay
RECOMMENDED Authorize the Mayor to execute a $36,179 sole- source contract with the Regents
ACTION: of the University of California for the testing of storm drains and tributaries to
Newport Bay for the presence of human viruses and bacteria.
BACKGROUND: While most of Newport Bay's waters routinely test "clean, " several locations in
Newport Bay often show bacteria levels higher than allowed by State law (AB
411, Wayne, 1997) for water contact recreational activities like swimming and
wading. These areas include:
43rd Street Beach (Channel Place Park)
Arches Marina (PCH and Newport Boulevard)
Santa Ana/ Delhi Channel
San Diego Creek at Jamboree
Big Canyon Wash
Back Bay Drain /East Side of Newport Dunes
The Orange County Health Care Agency's Environmental Health Division
(HCA) tests these six areas and about 30 more (see the map within this staff
report) at least once a week. if the areas exceed AB 411 standards for total
coliforni, fecal coliforni, or enterococcus, the County directs that the waters be posted
as potentially unsafe for water contact recreation. A posting is separate from a
closure. Per AB 411, the latter occurs when HCA suspects or knows of a sewage
spill or leak. The sign on the left is a closure sign - the sign on the right is a
posting sign.
Beach Closure
KEEP OUT
•
SEWAGE CONTAMINATED
WATER
® RU�W.1�Y.,y�WL{LLNW
ueacn
WARNING!
1AVISO!
l05 wNL4Fkt X NL,EniY F,4ttN
�[�O�.PLF�Laq
The three bacteria listed above are known as indicator bacteria, meaning that they
may indicate the presence of a human pathogen like a virus. The key word is may -
for we do not know with certainty whether or not a virus is always attached to or
near the indicator bacteria. Nor do we know the source of the indicator bacteria
- the bacteria may be present due to bird droppings, pet waste, garden fertilizer,
or other decomposing organic matter.
Determining the source of the bacteria is an expensive challenge, with differing
ways on how such sourcing can be done. These methods include:
• Genetic Fingerprinting. This methodology takes unknown bacteria from
the water, determines the bacteria's DNA pattern, and then attempts to
match that pattern to a pattern from bacteria from a known source.
• Antibiotic Resistance. This method takes unknown bacteria from the
water, determines how the bacteria reacts to up to eight common
antibiotics, and then attempts to match the reaction patterns with bacteria
from known sources.
Newport Bay Study Area
Sant Ana• Ihi Chwannel
Ww Olb
B
lego
ree
�II
e
an n v.m
vvvuuva
ughn's Launch
n, N•'*•^
i g Canyon Wash
Ywa uu.a
Northstar Beach
o. �... v.�e.
oe•..
SM.
an...n �
Y.n
IPI•on•al
.•
sndim.a.. once
. dtln
y Dr. Pipe
43
PM B.lat.
�
a
hine h
.a oa shore
ac
u M.E.W.N
ua
Sth 3 St.
I ...
s. Vac lub
19th t
each
L$eac
xAve.
ease. vmn. . Ih L B
Le i " ark Ave.
WRea PI.,
arnet�ve.
rand Canal
Oq W.ee
..e.. Saphirt
B hi. Cwmmm
ve.Abalo eve.
Yu.a
Harbor Patrol Beach
T
Alvarado
Ba Isle
_
cP.on. pl M. dam
WNe• Pu'
N St. Beac` — Rocky P[. Beach
Pacific Ocean
Better than merely using indicator bacteria, the City has embarked upon a
limited testing program of actual viruses within Newport Bay. These tests are
expensive, costing more than $1,000 per test. Last summer, the City contracted
for viral testing with Dr. Rachel Noble of the Southern California Coastal Water
Research Project (SCCWR), a Westminster -based joint- powers agency set up to
do water quality research. Dr. Sunny Jiang of the University of California, Irvine,
joined Dr. Noble in these efforts.
Drs. Noble and Jiang tested the following areas for human enteric virus particles:
43rd Street Beach (Channel Place Park)
Arches Marina
Bayshore Beach
— Santa Ana Delhi Channel (near Mesa and near University)
San Diego Creek (near Campus and near Michelson)
Big Canyon Wash
Back Bay Drain /East Side of Newport Dunes
During two distinct periods of testing last summer, Drs. Noble and Jiang's data
showed no detectable levels of human enteric viruses in any area EXCEPT the
Santa Ana Delhi Channel. Five of six tested samples from the Santa Ana Delhi
Channel tested positive for the presence of human enteric viruses. The City paid
for this testing using a grant from the State Water Resources Control Board.
As Summer 2001 approached, the City planned additional testing efforts and
received another $400,000 in State grants to do so. The City's Summer 2001
water quality testing program includes:
• Antibiotic Resistance Testing in West Newport. A joint OC Health Care
Agency -City effort (which began in August and will continue into October)
will attempt to determine the source of chronic bacteria problems around
Newport Island.
• Swimmer Contribution Study. A City- Regional Board -OCSD effort
(completed in late August) will attempt to determine if there is a link
between swimmers and fecal coliform in a high -use swimming area.
• Vessel Waste Study. A City- Regional Board -OC HCA effort (planned for
this fall) will attempt to determine the extent of illegal waste discharges from
boaters into Newport Harbor.
• Baywide Bacteria and Virus Testing. In an attempt to determine if
contamination levels have changed since 2000, the City and the Regional
Board have directed the completion of a 3 -week study in mid -to late- August
that re -tests six locations in the Bay for human viruses, coliphage, and the
three bacterial indicators.
This Baywide Bacteria and Virus Testing effort, again conducted for the City by
Dr. Jiang of UCI, followed the Scope of Work shown on the next page. Readers
will see that Dr. Jiang tested six different sites in the Bay, all of which were tested
during the 2000 studies. Dr. Jiang has added an infectivity component to her
study in an attempt to determine to what extent, if any, virus particles detected
in the Bay had the ability to infect humans.
Baywide Sampling Scope of Work - Summer 2001
A study design team oversees all four of the Summer 2001 studies -this team
includes staff from OC HCA, the Regional Board, and Newport Beach resident
Dr. Jack Skinner, and me. When the results are compiled by Dr. Jiang and
reviewed by the Study team, the data shall
become publicly available.
The total cost of the Baywide Bacti /Virus Sampling is $36,179.00. This amount
includes UCI's mandatory 50% charge for overhead. We did not anticipate this
overhead charge when the Sampling protocol was originally envisioned, since
we were told that it can be waived for certain contracts. UCI, however, denied
this waiver for the City. As such, the contract once envisioned to be less than
$30,000 and able to be authorized by the City
Manager is now over $30,000 and
subject to Council approval.
The $36,179.00 is budgeted in the City's FY 2001 -02 Capital Improvement
Program (CIP #7251- C5100596). Since very few entities in the nation have the
ability to conduct these tests -and since Dr. Jiang is familiar with Newport Bay -
the Regional Board and the City
have selected her to conduct this work.
THIS AGENDA This Agenda Item authorizes the Mayor to execute a contract with the Regents of
ITEM: the University
of California to perform baywide bacterial and viral sampling.
The contract cost is $36,179.00. The sampling program is complete as of the date
of this staff report, but the report - writing and data analysis may not be complete
until October 2001.
ATTACHMENT: Attachment A - Contract with the Regents of the University of Cali
fornia
Location: Six locations in Bay and tributaries — similar sites as sampled in Summer /Fall 2000
Discussion: This effort would attempt to keep continuity with 2000's enteric virus /phage/bacti studies
in
that found the presence of virus particles in one (SA Delhi Channel) of the six sites tested.
Dr. Sunny Jiang will lest for phage plus viruses
(using RT -PCR) and then save the concentrates for
infectivity analysis to be completed later. OCHCA will take a split sample and lest for
the three
bacteriological indicators.
Sampling Sites: a3rtl Street
SNVelhl- SXVelhl -Uni SDCreek—
Mesa
SDCmek—
Miebelson
Dunes East
August 16.22,
August 16, M. August 15. M. August 15. M.
August 15. M.
August 16, 22,
Dates: an 9
29 i
and 29 and and 29
and 29
an 9
Time of Day: Morning
Morning Momirp Momirp
Momirg
Morning
Liter)
Liter) r
er
r
Types of Samples Taken: I (31 Liter)
t (Y4 Dter) t fi-a Liter) 1 (Y4 Uler)
t fi-a WeQ
t (N Liter)
Testing for: FC/fC
FCIfC FCIfC FCIfC
FCIfC
FCIfC
Ent
Ertl Ent Ent
Ent
EM
Enteric Vims
EMetk VUUS Enterk Virus Erdeec Virus
Enteric Virus
Enteric Vims
InfeNvitY
Iltieptiviry Infectiviy Infectivity
IntectvitY
Infativily
Cpieent2le
Concem2te Concentrate Concent2le
Concentrate
Concentrate
Bacd Tesa/Day:
ColiPhage Teiu,Vay:
Samples Collected by: Sunny Jiang, Mike Fennessey, Coa5tKeeper (2)
Total # of Samples Collected:
36
Tests done by: Viral (RT -PCR), Inf xtkrty Conc.(hozen). Phage— Sunny Jiang
cacti (MTF)— OC HCA Estimated Cost.
A study design team oversees all four of the Summer 2001 studies -this team
includes staff from OC HCA, the Regional Board, and Newport Beach resident
Dr. Jack Skinner, and me. When the results are compiled by Dr. Jiang and
reviewed by the Study team, the data shall
become publicly available.
The total cost of the Baywide Bacti /Virus Sampling is $36,179.00. This amount
includes UCI's mandatory 50% charge for overhead. We did not anticipate this
overhead charge when the Sampling protocol was originally envisioned, since
we were told that it can be waived for certain contracts. UCI, however, denied
this waiver for the City. As such, the contract once envisioned to be less than
$30,000 and able to be authorized by the City
Manager is now over $30,000 and
subject to Council approval.
The $36,179.00 is budgeted in the City's FY 2001 -02 Capital Improvement
Program (CIP #7251- C5100596). Since very few entities in the nation have the
ability to conduct these tests -and since Dr. Jiang is familiar with Newport Bay -
the Regional Board and the City
have selected her to conduct this work.
THIS AGENDA This Agenda Item authorizes the Mayor to execute a contract with the Regents of
ITEM: the University
of California to perform baywide bacterial and viral sampling.
The contract cost is $36,179.00. The sampling program is complete as of the date
of this staff report, but the report - writing and data analysis may not be complete
until October 2001.
ATTACHMENT: Attachment A - Contract with the Regents of the University of Cali
fornia
Cdiphage C
Cdiphage C
Cdipbape �
Cdiphage C
Cdiphage
18 V
Viral TesWDay�
��Cdiphage C
6 V
become publicly available.
The total cost of the Baywide Bacti /Virus Sampling is $36,179.00. This amount
includes UCI's mandatory 50% charge for overhead. We did not anticipate this
overhead charge when the Sampling protocol was originally envisioned, since
we were told that it can be waived for certain contracts. UCI, however, denied
this waiver for the City. As such, the contract once envisioned to be less than
$30,000 and able to be authorized by the City
Manager is now over $30,000 and
subject to Council approval.
The $36,179.00 is budgeted in the City's FY 2001 -02 Capital Improvement
Program (CIP #7251- C5100596). Since very few entities in the nation have the
ability to conduct these tests -and since Dr. Jiang is familiar with Newport Bay -
the Regional Board and the City
have selected her to conduct this work.
THIS AGENDA This Agenda Item authorizes the Mayor to execute a contract with the Regents of
ITEM: the University
of California to perform baywide bacterial and viral sampling.
The contract cost is $36,179.00. The sampling program is complete as of the date
of this staff report, but the report - writing and data analysis may not be complete
until October 2001.
ATTACHMENT: Attachment A - Contract with the Regents of the University of Cali
fornia
PROFESSIONAL SERVICES AGREEMENT
THIS AGREEMENT, entered into this 15`" day of August, 2001, by and between CITY
OF NEWPORT BEACH, a Municipal Corporation (hereinafter referred to as "City "), and
The Regents of the University of California, on behalf of its Irvine campus
(hereinafter referred to as "Consultant "), is made with reference to the following:
RECITALS
A. City is a municipal corporation duly organized and validly existing under
the laws of the State of California with the power to carry on its business
as it is now being conducted under the statutes of the State of California
and the Charter of City.
B. City desires to engage Consultant to provide staff services for
BacterialNiral Source Tracking of Tributaries and Storm Drains
Discharging into Newport Bay ( "Research Project ").
C. The principal investigator of Consultant is, for purpose of this Research
Project, Dr. Sunny Jiang ( "Principal Investigator").
D. City has reviewed the previous experience and evaluated the expertise of
Consultant and desires to contract with Consultant under the terms and
conditions provided in this Agreement.
NOW, THEREFORE, it is mutually agreed by and between the undersigned
Parties as follows:
1. TERM
The term of this Agreement shall commence on the 15`" day of August 2001, and
shall terminate on the 14`" day of August 2002, unless terminated earlier as set forth
herein.
2. SERVICES TO BE PERFORMED
Consultant shall diligently perform all the duties set forth in the Scope of
Services, attached as Exhibit "A" and incorporated herein by reference.
1
3. COMPENSATION TO CONSULTANT
City shall pay Consultant for the services in accordance with the provisions of
this Section and the Research Project budget, attached as Exhibit "B" and incorporated
herein by reference. No budget changes shall be made during the term of this
Agreement without prior written approval of City. Consultant's compensation for all
work performed in accordance with this Agreement shall not exceed the total contract
price of Thirty -six thousand, one hundred seventy -nine dollars ($36,179).
3.1 Consultant shall maintain accounting records of its billings which includes
the name of the employee, type of work performed, times and dates of all work which is
billed on an hourly basis and all approved incidental expenses including testing
supplies.
3.2 Consultant shall submit monthly invoices to City payable by City within
thirty (30) days of receipt of invoice subject to the approval of City.
3.3 Consultant shall not receive any compensation for extra work without prior
written authorization of City.
3.4 City shall reimburse Consultant only for those costs or expenses which
have been specifically approved in this Agreement, or specifically approved in advance
by City. Such cost shall be limited and shall include nothing more than the following
costs incurred by Consultant:
A. The actual costs of subconsultants for performance of any of the services
which Consultant agrees to render pursuant to this Agreement which have
been approved in advance by City and awarded in accordance with the
terms and conditions of this Agreement.
B. Approved computer data processing and reproduction charges.
C. Actual costs and /or other costs and /or payments specifically authorized in
advance in writing and incurred by Consultant in the performance of this
Agreement.
3.5 Notwithstanding any other paragraph or provision of this Agreement,
beginning on the effective date of this Agreement, City may withhold payment of ten
percent (10 %) of each approved payment as approved retention until all services under
this Agreement have been substantially completed.
4. STANDARD OF CARE
4.1 All of the services shall be performed by Consultant or under Consultant's
supervision. Consultant represents that it possesses the professional and technical
2
personnel required to perform the services required by this Agreement, and that it will
perform all services in a manner commensurate with the university's professional
standards. All services shall be performed by qualified and experienced personnel who
are not employed by City nor have any contractual relationship with City. Consultant
represents and warrants to City that it has or shall obtain all licenses, permits,
qualifications and approvals required of its profession. Consultant further represents
and warrants that it shall keep in effect all such licenses, permits and other approvals
during the term of this Agreement.
4.2 Consultant shall not be responsible for delay, nor shall Consultant be
responsible for damages or be in default or deemed to be in default by reason of strikes,
lockouts, accidents, or acts of God, or the failure of City to furnish timely information or
to approve or disapprove Consultant's work promptly, or delay or faulty performance by
City, contractors, or governmental agencies, or any other delays beyond Consultant's
control or without Consultant's fault.
5. INDEPENDENT PARTIES
City retains Consultant on an independent contractor basis and Consultant is not
an employee of City. The manner and means of conducting the work are under the
control of Consultant, except to the extent they are limited by statute, rule or regulation
and the expressed terms of this Agreement. Nothing in this Agreement shall be
deemed to constitute Consultant or any of Consultant's employees or agents, to be the
agents or employees of City. Consultant shall have the responsibility for and control
over the details in means of performing the work provided that Consultant is in
compliance with the terms of this Agreement. Anything in this Agreement which may
appear to give City the right to direct Consultant as to the details of the performance of
the services or to exercise a measure of control over Consultant shall mean that
Consultant shall follow the desires of City only with respect to the results of the services.
6. COOPERATION
Consultant agrees to work closely and cooperate fully with Dave Kiff, Assistant
City Manager, the City's designated Research Project administrator ( "Project
Administrator'), and any other agencies which may have jurisdiction or interest in the
work to be performed. City agrees to cooperate with the Consultant on the Research
Project.
7. PROJECT MANAGER
Consultant shall assign responsibility for the Research Project to a Principal
Investigator, who shall coordinate all phases of Consultant's efforts on the Research
Project. The Principal Investigator shall be available to City at all reasonable times
during the Research Project term. Consultant has designated Dr. Sunny Jiang to be its
3
Principal Investigator. Consultant shall not bill any personnel to the Research Project
other than those personnel identified in Exhibit "B ", whether or not considered to be key
personnel, without City's prior written approval by name and specific salary rate.
Consultant shall not remove or reassign the Principal Investigator designated in this
Section or assign any new or replacement Principal Investigator to the Research Project
without the prior written consent of City. City's approval shall not be unreasonably
withheld with respect to replacement of the Principal Investigator.
Consultant warrants that it will continuously furnish the necessary personnel to
complete the Research Project on a timely basis as contemplated by this Agreement.
8. TIME OF PERFORMANCE
Time is of the essence in the performance of the services under this Agreement
and the services shall be performed by Consultant in accordance with Exhibit A. The
failure by Consultant to strictly adhere to the schedule may result in termination of this
Agreement by City. Notwithstanding the foregoing, Consultant shall not be responsible
for delays which are due to causes beyond Consultant's reasonable control. However,
in the case of any such delay in the services to be provided for the Research Project,
each party hereby agrees to provide notice to the other party so that all delays can be
addressed.
8.1 Consultant shall submit all requests for extensions of time for performance
in writing to the Project Administrator not later than ten (10) calendar days after the start
of the condition which purportedly causes a delay, and not later than the date upon
which performance is due. The Project Administrator shall review all such requests and
may grant reasonable time extensions for unforeseeable delays, which are beyond
Consultant's control.
8.2 For all time periods not specifically set forth herein, Consultant shall
respond in the most expedient and appropriate manner under the circumstances, by
either telephone, fax, e-mail, hand delivery or mail.
9. CITY POLICY
Consultant will discuss and review all matters relating to policy and project
direction with the Project Administrator in advance of all critical decision points in order
to ensure that the Research Project proceeds in a manner consistent with City goals
and policies.
0
10. CONFORMANCE TO APPLICABLE REQUIREMENT
All work prepared by Consultant shall conform to applicable city, county, state
and federal law, regulations and permit requirements and be subject to approval of the
Project Administrator and City.
11. PROGRESS
Consultant is responsible to keep the Project Administrator and /or his /her duly
authorized designee informed on a regular basis regarding the status and progress of
the work, activities performed and planned, and any meetings that have been scheduled
or are desired.
12. HOLD HARMLESS
Consultant shall indemnify, defend, save and hold harmless City, its City Council,
boards and commissions, officers and employees from and against any and all loss,
damages, liability, claims, allegations of liability, suits, costs and expenses for damages
of any nature whatsoever, including, but not limited to, bodily injury, death, personal
injury, property damages, or any other claims arising from any and all acts or omissions
of Consultant, its employees, agents or subcontractors in the performance of services or
work conducted or performed pursuant to this Agreement, but only in proportion to and to
the extent such loss, damages, liability, claims, allegations of liability, suits, costs and
expenses for damages are caused by or result from the negligent or intentional acts or
omissions of Consultant, its officers, agents, or employees.
City shall indemnify, defend, save and hold harmless Consultant, its trustees,
boards and commissions, officers and employees from and against any and all loss,
damages, liability, claims, allegations of liability, suits, costs and expenses for damages
of any nature whatsoever, including, but not limited to, bodily injury, death, personal
injury, property damages, or any other claims arising from any and all acts or omissions
of City, its employees, agents or subcontractors in the performance of services or work
conducted or performed pursuant to this Agreement, but only in proportion to and to the
extent such loss, damages, liability, claims, allegations of liability, suits, costs and
expenses for damages are caused by or result from the negligent or intentional acts or
omissions of City, its officers, agents, or employees.
Nothing in this indemnity shall be construed as authorizing, any award of attorneys' fees
in any action on or to enforce the terms of this Agreement.
s
13. INSURANCE
Without limiting consultant's indemnification of City, and prior to commencement
of work, Consultant shall obtain and provide and maintain at its own expense during the
term of this Agreement self- insurance or policy or policies of liability insurance of the
type and amounts described below and satisfactory to City. Certification of all required
policies shall be signed by a person authorized by that insurer to bind coverage on its
behalf and must be filed with City prior to exercising any right or performing any work
pursuant to this Agreement. Except workers compensation, all insurance policies shall
add City, its elected officials, officers, agents, representatives and employees as
additional insured for all liability arising from Consultant's services as described herein.
All insurance policies shall be issued by an insurance company currently
authorized by the Insurance Commissioner to transact business of insurance in the
State of California, with an assigned policyholders' Rating of A (or higher) and Financial
Size Category Class VII (or larger) in accordance with the latest edition of Bests Key
Rating Guide: unless otherwise approved by the City Risk Manager.
A. Worker's compensation insurance covering all employees and principals
of Consultant, per the laws of the State of California.
B. Commercial general liability insurance covering third party liability risks,
including without limitation, contractual liability, in a minimum amount of $1
million combined single limit per occurrence for bodily injury, personal
injury and property damage. If commercial general liability insurance or
other form with a general aggregate is used, either the general aggregate
shall apply separately to this Research Project, or the general aggregate
limit shall be twice the occurrence limit.
C. Commercial auto liability and property insurance covering any owned and
rented vehicles of Consultant in a minimum amount of $1 million combined
single limit per accident for bodily injury and property damage.
Said policy or policies shall be endorsed to state that coverage shall not be
canceled by either party, except after thirty (30) days' prior notice has been given in
writing to City. Consultant shall give City prompt and timely notice of claim made or suit
instituted arising out of Consultant's operation hereunder. Consultant shall also procure
and maintain, at its own cost and expense, any additional kinds of insurance, which in
its own judgment may be necessary for its proper protection and prosecution of the
work.
Consultant agrees that, in the event of loss due to any of the perils for which it
has agreed to provide comprehensive general and automotive liability insurance,
Consultant shall look solely to its insurance for recovery. Consultant hereby grants to
City, on behalf of any insurer providing comprehensive general and automotive liability
insurance to either Consultant or City with respect to the services of Consultant herein,
R
a waiver of any right of subrogation which any such insurer of said Consultant may
acquire against City by virtue of the payment of any loss under such insurance.
14. PROHIBITION AGAINST TRANSFERS
Consultant shall not assign, sublease, hypothecate or transfer this Agreement or
any for the services to be performed under this Agreement, directly or indirectly, by
operation of law or otherwise without prior written consent of City. Any attempt to do so
without consent of City shall be null and void.
15. OWNERSHIP OF DOCUMENTS
Each and every report, draft, work product, map, record and other document
reproduced, prepared or caused to be prepared by Consultant pursuant to or in
connection with this Agreement and delivered to City shall be the exclusive property of
City.
Documents, including drawings and specifications, prepared by Consultant
pursuant to this Agreement are not intended or represented to be suitable for reuse by
City or others on any other project. Any use of completed documents for other projects
and any use of incomplete documents without specific written authorization from
Consultant will be at City's sole risk and without liability to Consultant. Further, any and
all liability arising out of changes made to Consultant's deliverables under this
Agreement by City or persons other than Consultant is waived against Consultant and
City assumes full responsibility for such changes unless City has given Consultant prior
notice and has received from Consultant written consent for such changes.
Consultant shall, at such time and in such form as City may require, furnish
reports concerning the status of services required under this Agreement.
16. CONFIDENTIALITY
Because the City deems the Scope of Services outlined in Attachment A to be of
benefit to a wide variety of constituencies, the City and its Consultant apply no specific
confidentiality limitations on any information which results from the services in this
Agreement. Both parties reserve the right to retain any information as confidential if
agreed to by both parties.
17. ADMINISTRATION
This Agreement will be administered by the City Manager's Department. Dave
Kiff, Assistant City Manager, shall be considered the Project Administrator and shall
have the authority to act for City under this Agreement. The Assistant City Manager or
his authorized representative shall represent City in all matters pertaining to the
services to be rendered pursuant to this Agreement.
18. RECORDS
Consultant shall keep records and invoices in connection with the work to be
performed under this Agreement. Consultant shall maintain complete and accurate
records with respect to the costs incurred under this Agreement. All such records shall
be clearly identifiable. Consultant shall allow a representative of City to examine, audit
and make transcripts or copies of such records during normal business hours.
Consultant shall allow inspection of all work, data, documents, proceedings and
activities related to the Agreement for a period of three (3) years from the date of final
payment under this Agreement.
19. WITHHOLDINGS
City may withhold payment of any disputed sums until satisfaction of the dispute
with respect to such payment. Such withholding shall not be deemed to constitute a
failure to pay according to the terms of this Agreement. Consultant shall not discontinue
work as a result of such withholding. Consultant shall have an immediate right to
appeal to the City Manager or his designee with respect to such disputed sums.
Consultant shall be entitled to receive interest on any withheld sums at the rate of seven
percent (7 %) per annum from the date of withholding of any amounts found to have
been improperly withheld.
20. CITY'S RIGHT TO EMPLOY OTHER CONSULTANTS
City reserves the right to employ other consultants in connection with the
Research Project.
21. CONFLICTS OF INTEREST
A. The Consultant or its employees may be subject to the provisions of the
California Political Reform Act of 1974 (the "Act "), which (1) requires such
persons to disclose financial interest that may foreseeably be materially
affected by the work performed under this Agreement, and (2) prohibits
such persons from making, or participating in making decisions that will
foreseeably financially affect such interest.
B. If subject to the Act, Consultant shall conform to all requirements of the
Act. Failure to do so constitutes a material breach and is grounds for
termination of this Agreement by City. Consultant shall indemnify and
n
hold harmless City for any and all claims for damages resulting from
Consultant's violation of this Section.
22. SUBCONSULTANT AND ASSIGNMENT
Except as specifically authorized under this Agreement, the services included in
this Agreement shall not be assigned, transferred, contracted or subcontracted without
prior written approval of City.
23. NOTICES
All notices, demands, requests or approvals to be given under this Agreement
shall be given in writing and conclusively shall be deemed served when delivered
personally or on the third business day after the deposit thereof in the United States
mail, postage prepaid, first class mail, addressed as hereinafter provided.
All notices, demands, requests or approvals from Consultant to City shall be
addressed to City at:
City of Newport Beach
City Manager's Office
3300 Newport Boulevard
P. O. Box 1768
Newport Beach, CA, 92658 -8915
949/644- 3002(phone)
949/644 -3020 (fax)
All notices, demands, requests or approvals from City to Consultant shall be
addressed to Consultant at:
Attention: Doug Bickham
Contracts Officer
Sponsored Projects Administration
University of California, Irvine
160 Administration Building
Irvine, CA 92697- 1875
(949) 824- 2644 (phone)
(949) 824- 2094 (fax)
24. TERMINATION
In the event either party hereto fails or refuses to perform any of the provisions
hereof at the time and in the manner required hereunder, that party shall be deemed in
9
default in the performance of this Agreement. If such default is not cured within a period
of two (2) days, or if more than two (2) days are reasonably required to cure the default
and the defaulting party fails to give adequate assurance of due performance within two
(2) days after receipt of written notice of default, specifying the nature of such default
and the steps necessary to cure such default, the nondefaulting party may terminate the
Agreement forthwith by giving to the defaulting party written notice thereof.
City or Consultant shall have the option, at its sole discretion and without cause,
of terminating this Agreement by giving seven (7) days' prior written notice to the other
party as provided herein. Upon termination of this Agreement, City shall pay to the
Consultant that portion of compensation specified in this Agreement that is earned and
unpaid prior to the effective date of termination.
25. COMPLIANCES
Consultant shall comply with all laws, state or federal and all ordinances, rules
and regulations enacted or issued by City.
26. WAIVER
A waiver by either party of any breach, of any term, covenant or condition
contained herein shall not be deemed to be a waiver of any subsequent breach of the
same or any other term, covenant or condition contained herein, whether of the same or
a different character.
27. INTEGRATED CONTRACT
This Agreement represents the full and complete understanding of every kind or
nature whatsoever between the Parties hereto, and all preliminary negotiations and
agreements of whatsoever kind or nature are merged herein. No verbal agreement or
implied covenant shall be held to vary the provisions herein. Any modification of this
Agreement will be effective only by written execution signed by both City and
Consultant.
IN WITNESS WHEREOF, the Parties have caused this Agreement to be
executed on the day and year first written above.
Im
APPROVED AS TO FORM:
0
Robert Burnham
City Attorney
for the City of Newport Beach
ATTEST:
By:
LaVonne Harkless
City Clerk
CITY OF NEWPORT BEACH
A Municipal Corporation
In
Garold B. Adams
Mayor
for the City of Newport Beach
CONSULTANT
M
The Regents of the University of
California
11
EXHIBIT A
Scope of Work
and Study Description
Determining the Relationship Between Fecal Indicators and
Human Pathogenic Viruses in Newport Bay Watershed
- What do Indicators Indicate?
Phase
Background and Objectives:
The microbial quality of water is a prime public health concern in today's world. It
is estimated that the risk of becoming ill as a result of microbial contamination of food
and water is 100,000 times greater than the risk from pesticide contamination (WHO
1993). To protect public health, the World Health Organization and the U.S.
Environmental Protection Agency have established microbial pollution indicator
standards and recommended routine monitoring of water for fecal bacterial indicators
(Dufour, 1984, U.S. EPA 1986,1994, WHO 1993).
Coastal recreational water quality standards in California, and throughout most of
the world, are based on the concentration of total coliform, fecal coliform, and
enterococcus groups of indicator bacteria (Bartram and Rees 2000). However, the
adequacy of current water quality standards to indicate the presence or absence of human
pathogens is still questionable. For example, human viruses are more resistant to sewage
treatment processes and environmental conditions than bacterial indicators and therefore
may pose a substantial threat. It is now recognized that the absence, or a low
concentration, of indicator organisms in water may not adequately reflect the absence of
human viruses. In our previous study of southern California coastal waters, we found over
30% of coastal waters tested contained human viruses, and the presence of these viruses
did not correlate with an elevated level of bacterial indicators (Jiang et al. 2000).
Waterbome infectious viruses are suspected to be more important than current knowledge
suggests because viral diseases are hard to identify by current diagnostic techniques.
While the causative agent of nearly 50% of all acute gastrointestinal illnesses cannot be
identified (Center for Disease Control, 1988, 1990, 1991, 1993) most of these illnesses are
suspected to be caused by viruses. Therefore, viral quality of recreational coastal water is
of particular importance and a rising public health concern.
Newport Bay, California is an important estuarine system in Southern California.
Tourists worldwide visit this area for boating, kayaking, sailing, swimming and other
water recreational activities. To protect public health and the beneficial use of this
valuable resource, the State Water Quality Control Board requires strategies to be
developed and stepwise implemented to improve Newport Bay water quality to meet
recreational standards (REC -1) by the year 2014. With the goal of understanding the
relationship between fecal indicator bacterial concentrations and human pathogenic
viral loads in this watershed, the specific objectives of this study are the following:
12
1. To determine the presence and distribution of human enteric viruses in various
locations in Newport Bay and its tributaries using polymerase chain reaction
(PCR) analysis;
2. To determine the abundance and distribution of F- specific coliphage in order to
evaluate its adequacy as an alternative indicator of human viruses in the Newport
Bay watershed.
3. To investigate the infectivity of human viruses present in the Watershed by
combining PCR with tissue culture analysis.
4. To statistically determine the relationship between human viruses and fecal
indicators in the Watershed.
Project Approach:
Results from the phase I & II Newport Bay water quality investigation conducted
during the summer of 2000 indicated that the occurrence and distribution of human
enteroviruses did not correlate with the abundance of total coliform, fecal coliform and
enterococcus. However, only a few locations around the Bay were sampled repetitively
to produce a statistically valid analysis of the relationship between human viruses and
indicators. This proposed study will expand sampling locations and frequencies for
human viral testing, guided by a desired statistical sensitivity and power. In addition, two
more viruses will also be included in our detection effort because the presence of viral
contamination in the watershed may shift with the human disease load and the
populations harboring the disease (either symptomatic or asympotomatic) in a local
community. Additional viruses that will be tested in this research are adenoviruses and
hepatitis A viruses. Adenoviruses are widespread in coastal waters of Southern
California according to a recent study (Jiang et al. 2000). Seasonal outbreaks of
hepatitis A virus in Southern California are also documented by the Los Angeles Health
Care Agency. The addition of these two viruses to the testing panel will increase the
sensitivity and resolution of detection of human viral pathogens in the Newport Bay
watershed.
Sampling Plans
This project will be conducted over a two -year period. The first year, the phase I
part of the study, will primarily focus on a large -scale sampling effort from multiple
locations in Newport Bay. The primary sampling locations will include 5 of the 6 sites
collected in the previous year (Figure 1). The Backbay drain location will not be sampled
this year due to the divergence of the flow. An additional location at Newport Dunes
swimming lagoon will be added as the 6"' site due to high usage of this location by
bathers. Samples will be collected from each location on a weekly basis starting on
August 15"' for three consecutive weeks. Sampling times on each day will be
determined based on the tidal chart to ensure all samples are collected during the ebb -
tide period. This design will maximize the possibility of capturing urban runoff without
being diluted with intruding seawater during the flood -tide period. The sampling
frequencies at each site will be determined by statistical tests to achieve the desired
resolution.
13
Ten to twenty liter water samples will be collected from each site and split for
detection of fecal bacterial indicators, human viruses and coliphage. Table 1. shows the
proposed sampling schedule and parameters that will be determined at each location.
Simultaneously, the temperature and salinity of the water will also be measured in situ
to provide background information on basic environmental conditions. All data collected
will be logged into a database on the same day of the sample collection.
14
Location: Six locations in Bay and tributaries — similar sites as sampled in Summer /Fall 2000
Discussion: This effort would attempt to keep continuity with 2000's enteric virus /phage /bacfi studies in
that found the presence of virus particles in
one (SA Delhi Channel) of
the six sites tested.
ing
Dr. Sunny Jiang will lest for phage plus viruses (using RT -PCR) and then save the concentrates for
Infectivity analysis to be completed later. CICHCA will take a split sample and test for the three
bacteriological indicators.
Sampling Sites: 43rd Street
SA/Delhi -
SA/Delhi -Univ
SD Creek — SD Creek —
Dunes East
Mesa
Campus Michelson
August 15, 22,
August 15, 22, August 15. 22.
August 15, 22. August 15. 22,
August 15, 22,
Dates: an 29
an 29 and 29
and 29 an 29
and 29
Time of Day: Morning
Morning Morning
Maming Morn
Liter)
ter ter
ter Liter)
ter
Types of Samples Taken: 1 (3-4 Liter)
1 (3� Liter) 1 (3� Liter)
1 (34 Liter) 1 (34 Liter)
1 (34 Liter)
Testing for: FC/TC
FC/TC FC/TC
FC/TC
C/TC
Ent
Ent Ent
Ent
Ent
Enteric Virus
Enteric Virus Enteric Virus
Enteric Virus =VimsEnte6c
eric Virus
Infectivity
Infectivity Infectivity
Infectiv ity
fectivity
Concentrate
Concentrate Concentrate
Concentrate
ncentrate
Coliphage
Coliphage Coliphage
Coliphage
liphage
Bacti Tests/Day 18
Viral Tests /Day:
6
Coliphage Tests /Day 6
Viral Infect Conc/Day:
6
14
ing
Maming
14
De An.. H
ceataa'aya
Nenno
(
Ar s Drain Planned
3 4.
CH Bride,
hine h
a nos she
ud
38t1, 3 St. Island
S. YBe
19th t each
5 t. -Beac
Balboa Peninam°
Nav,.rt Nor Bay
Sant Ana- elhi Channel
\.Jamboree Road
Main Dike B
rel
i ne
it I Bann
upper bl
Th. Nam
Middle Is
thstar I
It Basin
Launch
Canyon Wash
u i�Ji
y Dr. Pipe
is tI—
I^ ,
15 er +\Lj
bland
,.--, Alvarado
A. Isle
eas e,ln °• P`° N St.
mrs
Pacific Ocean
Harbor Patrol Beach
Corona Del Mar Drain
` Rocky Pt. Beach
Figure 1:Map of Newport Bay watershed, California. • indicates OCHCA Sampling
Stations and 4-indicates sampling locations of this study.
Detection of Human Adeno -, Entero- and Hepatitis A Viruses
A minimum of ten liters of water from each site will be concentrated using an
ultrafiltration system as previously described (Jiang et al. 2000). The final concentrates
will be split for determination of coliphage by plaque assay and human viruses by PCR.
For human virus detection, the concentrates will either be used immediately for viral
assay or frozen after concentration for analysis until the completion of the intensive
sampling effort.
is
Viral nucleic acid extraction and purification will follow the method originally
developed by Boom et al. (1990) with minor modifications. This method uses
guanidinium thiocyanate (GuSCN) with Triton X -100 to lyse viral particles and silica
beads to absorb nucleic acid, allowing effective purification of DNA and RNA at the
same time. In brief, 50 pl of viral concentrate are lysed by 900 µl of GuSCN lysis buffer
at room temperature for 10 min. Then 40 pl of silica particles are added and nucleic
acids absorbed at room temperature for 10 min with gentle shaking. Silica beads are
pelleted, washed and dried. The nucleic acid will then eluted from the beads using 50 µl
TE buffer at a temperature of 56 °C. The purified nucleic acid will be used for detection
of human viruses by PCR or RT -PCR as described below. This method has been
shown to be effective at purification of viral nucleic acid from seawater concentrates and
sewage effluent. I do not expect a great deal of difficulty in purification of viral nucleic
acids from Newport Bay waters.
Primers specific for human enterovirus, hepatitis A virus and adenovirus will be
used for amplification of the respective viral genomes (Table 1). The procedure for RT-
PCR of enterovirus and hepatitis A virus will follow the protocol developed by Tsai et al.
(1993) with a modification of the total reaction volume. Amplification products will be
further confirmed by probing with internal oligonucleotide probes in a dot - blotting format.
Probing will also increase the detection limit of the PCR amplification product. For
adenovirus detection, a nested PCR protocol will be used as previously described by
Pina et al. (1998). This procedure has been successfully used in my laboratory for
detection of viruses in coastal waters.
Table 1. PCR primers and Drobes for human virus detection
Target
viruses
Primer and probe sequences
Amplicon and
target
Pan-
Upstream, 5'- CCTCCGGCCCTGAATG -3'
197 -bp highly
enteroviru
Downstream, 5'- ACCGGATGGCCAATC -3'
conserved 5'
s
Probe, 5'- TACTTTGGGTGTCCGTGTTTC -3'
untranslated
region.
Hepatitis
Upstream, 5'- CAGCACATCAGAAAGGTGAG -3'
192 -bp VP 1
A virus
Downstream, 5'- CTCCAGAATCATCTCCAAC -3'
and VP 2
Probe, 5'- TGCTCCTCTTTATCATGCTATG -3'
capside
protein
interphase.
Adenoviru
First upstream, 5'-
301 -bp Hexon
s
GCCGCAGTGGTCTTACATGCACATC -3'
First downstream, 5'-
CAGCACGCCGCGGATGTCAAAGT-3'
143 -bp Hexon
Nested upstream,5'-
GCCACCGAGACGTACTTCAGCCTG-3'
Nested downstream 5'-
TTGTACGAGTACGCGGTATCCTCGCGGTC-3'
16
Quantification of F- specific Coliphage by Plaque Assay
The presence of F- specific coliphage will be quantified in each sample by a top
agar overlay method using either freshly concentrated or unconcentrated water samples.
One milliliter and 0.1 ml of sample are mixed with one ml of exponential E. coli HS
(pFamp)R host in 1% soft agar, then overiayed over bottom nutrient agar containing 15
pg /ml of each ampicillin and streptomycin to prevent background growth of indigenous
bacteria. E. coli HS (pFamp)R contains a plasmid coding for both ampicillin and
streptomycin resistance and is a specific host for F- specific RNA coliphage. Plaques will
be enumerated after 12 hours of incubation at 37 °C.
Quantification of F- specific Coliphage by Culture enrichment
In addition to direct plaque assay using concentrated viral samples, 1 -liter water
samples from each site will be enriched with 50 ml sterile 11x TSB medium, 10 ml late
log phase E. coli host and a final concentration of 15 mg /L of ampicillin and
streptomycin. The enrichment method is expected to encourage the recovery of injured
phage. Since this method was used in our previous study, enrichment will also be
performed this year to provide consistency in sampling method. Five -tube enrichment
will be used to determine the most probable number (MPN) of the phage. For MPN
determination, five 100 -ml water samples from each site were amended with 5 ml sterile
11 x TSB medium, 1 ml E. coli host and antibiotics. Negative controls will contain five
tubes of 100 -ml sterile DI water amended with nutrient medium, E. coli host and
antibiotic as in regular sample assay. The enrichment cultures will be incubated at 37 °C
for 24 hours before spot testing for the presence of F- specific coliphage.
For replicate spot testing, 1 ml of log phase E. coli host will be mixed with top
agar and overlaid onto TSB agar plates containing antibiotics to form an even bacterial
lawn. Two microliters of each enrichment culture was spotted onto the freshly prepared
bacterial lawn. Plates are incubated at 37 °C for 8 to16 hours. Clearing spots are scored
and the MPN calculated using Thomas' formula (Clesceri et al. 1998).
Determine the Infectivity of Human Viruses by Integrated Cell Culture PCR
For samples that test positive for human viruses by PCR assay, the frozen
concentrate will be analyzed to determine the infectivity of these viruses by integrated
cell culture PCR as described by Ballaster et al. (2000). This portion of the study will be
conducted during the second year of the project once initial PCR screening have been
completed. Due to the intensity of labor and time requirements for integrated cell culture
PCR, analyses will focus on samples that are initially PCR positive for human viruses. A
random selection of PCR negative samples will also be tested to ensure the correlation
between the PCR results and infectivity analysis. The integrated cell culture PCR assay
will be conducted by subcontracting with the Metropolitan Water District of southern
California. Final results from these analyses will be compared with the results on
presence of human viruses by direct PCR, standard fecal indicators, coliphage and
basic environmental parameters.
17
Statistical Analysis to Determine the Relationship Between Human Viruses and
Fecal Indicators
Statistical analysis of the entire data set will be performed during the second project
year when all tests for all samples are completed. Both linear regression analysis and
multiple regression analysis will be conducted using the data set. The concentration of
fecal indicators, human viruses and coliphage may be natural log transformed to achieve
normal distribution. Human viruses will be used as the dependent variable and all other
measured factors will be used as independent variables in the linear regression analysis.
The relationship between independent variables will be examined by analysis of variance
(ANOVA) to ruleout of the possibility of covariance. Other statistical analysis may also be
used if considered necessary when data becomes available. All statistical analyses will be
performed using the SAS or SPSS software packages (SPSS Inc. Chicago, IL).
M
EXHIBIT B
RESEARCH PROJECT BUDGET
Budget Period: 8/15/01 — 08/14/02
TOTAL
A. PERSONNEL SERVICES - SALARIES AND WAGES
Name: Position Title: Salary /hrlv rate
% or hrs
S. Jiang Prin Investigator $5711 (summer)
0.5
$2,856
TBN Lab Asst III 2535x1.5mo; 2586x4.5mo
50% 6 mo.
$7,720
Total Salaries And Wages
$ 10,576
Staff Fringe Benefits:
Sunny Jiang PI 12.7 %fb x $2856 sal
$363
TBN Lab Asst III 23% fb x $7720 sal
1.776
Total Fringe Benefits
$ 2,139
Total Personnel Cost
$12,715
B. OPERATING EXPENSES
Supplies: sample bottles, plastic petridishes, pippets, flasks, and
microbiological media
Sample Preservation
Expenses per sample for coliphage analysis @ $3008 samples
$540
Expenses per sample for enteric virus analysis @ $60008 samples
$10,800
Total Operating Expenses
$11,340
Total Direct Costs
$24,055
C. UNIVERSITY ADMINISTRATIVE OVERHEAD @ 50.4%
$12,124
D. TOTAL COSTS
13-6,179
Breakdown of Costs per Sample:
Direct Indirect
Collphage $ 100 $
50
Human Viruses $ 1,236 $
623
(Include entero-, hepatitus A- and adenovlrus)
19
F- SPECIFIC COLIPHAGE ANALYSIS AT UC IRVINE P.I. - S. JIANG
CITY OF NEWPORT BEACH, CA
BUDGET JUSTIFICATION
PERSONNEL
Principal Investigator: Sunny Jiang, Ph.D. will be in charge of the study design, data
analysis for F- specific coliphage results. She will also train the research assistant for
conducting the research, assist with sample collection, and sample analysis. Dr, Jiang
will take compensation in the form of summer salary calculated at approximately 42% of
one summer salary month for Phase I and Phase II of the study.
Laboratory Research Assistant: Ms. Waxia Fu will be in charge of conducting the
experiments and collection of the samples for F- specific coliphage analysis using the
multi -tube enrichment method. She will conduct experiment for plaque assay and spot
test to confirm the presence of coliphage. She will devote 5.5 hours per sample at the
rate of $11.40 /hour.
Fringe Benefits:
Benefits for academic and staff personnel have been calculated at the University -
established benefit rate of 9.2% for summer for academic personnel and 5.2% for
casual staff.
OPERATING EXPENSES
Materials and supplies for this project are estimated to cost $30 per sample. These
supplies include sample bottles, plastic petridishes, pippets, flasks, and microbiological
media. Estimation is based on historical costs and listed catalog pricing.
ADMINISTRATIVE OVERHEAD
University Overhead (Facilities and Administrative costs) were estimated in accordance
with UCI's current indirect cost rate agreement. UCI's indirect cost rate agreement was
approved by DHHS, the Federal Cognizant Audit Agency for UCI on 4/10/97 and
remains valid through June 30, 2001.
20