.g.m.
UNIVERSITY OF SOUTH FLORIDA
PURCHASING AND FINANCIAL SERVICES
4202 E. FOWLER AVENUE, ADM 185
TAMPA, FLORIDA 33620-5900
(813) 974-2481
Fax-On-Demand No.: (813) 974-3536
Web Address: usfweb.usf.edu/purchasing/purch2.htm
October 17, 2006
__________________________________________________________________________
INVITATION TO BID NO. 7-3-G
TITLE: Rotavirus Laboratory
OPENING DATE: October 31, 2006
__________________________________________________________________________
ADDENDUM NO.1
The following are answers to questions posed
1,
Section I, paragraph 5 of Section I, (third full paragraph on page 15).
A. "This QC protocol will be employed in all sites which process blood, serum, plasma or
stool samples in open tubes:
Questions. "This QC protocol will be employed"? What QC protocol is referred to? Will a QC
stool processing protocol for all sites need to be developed by personnel at the Rotavirus
Laboratory submitting an RFP? – No, the lab will not be developing the QC protocol. The
Infectious Agents QC protocol for TEDDY has already been established and is in place. The
RFP is for a lab to analyze the samples related to this established QC protocol. TEDDY’s QC
protocol consists of 2 parts – 1) The TEDDY clinical centers will aliquot PBS samples in the
same location where they process study blood and stool samples on a monthly basis and then
ship to the repository for storage. The Rotavirus lab that is chosen will be sent a portion
of these PBS samples on a quarterly basis to analyze for the presence of rotavirus. The
purpose is to ensure that cross-contamination of samples is not occurring in the aliquoting
process 2) Rotavirus lab will obtain rotavirus positive stool samples from non-TEDDY subjects
and make 100 aliquots. Initially lab will measure 2 samples for the level of rotavirus and
ship the remainder to the repository for long-term storage. Samples will be pulled on a
scheduled basis and sent to the rotavirus lab to measure the virus level. The point is to
make sure that the level of virus in the sample is not deteriorating as it is being stored
for a long period of time since TEDDY is storing large amounts of samples from study
participants for many years prior to analysis.
B. Page 15, same paragraph as above, "Risk of cross-contamination will be monitored
regularly by each of the clinical centers processing sterile PBS on a monthly basis."
Questions. Do the clinical centers monitor for rotavirus contamination? If so, how will they
monitor contamination? Does the rotavirus lab provide a protocol for monitoring rotavirus
contamination? Does the Rotavirus Laboratory monitor for all possible rotavirus
contamination?
- No, the clinical centers will not monitor for contamination, the chosen
lab will.
The lab won’t provide a protocol – TEDDY already has an established QC protocol.
C. Page 15, same paragraph as above, "It is estimated that the Rotavirus Lab will receive a
total of 360 PBS samples per year."
Questions. Are these 360 PBS samples all rotavirus positives? Will the samples for years 2,
3, 4 and 5 be from different (rotavirus positive?) patients than tested in year 1 samples, or
will samples in years 2, 3, 4 and 5 all be from the same patients as tested in year 1? Will
PBS samples, if rotavirus positive, need to be identified by viral sequencing? If yes, how
many are anticipated to be sequenced? – The PBS samples should all be rotavirus negative,
otherwise a positive result indicates contamination at the clinical center. If a PBS sample
is found to be positive our TEDDY Infectious Agents committee will work with the site. The
samples you refer to for the different years will be the stool samples I describe in my first
1
paragraph which is part of the second part
from the same batch aliquoted in the first
will be stored at repository until time of
will be requested, but I will check w/ Dr.
D.
."
of the QC protocol. These samples will all be
year (stool samples analyzed in years 2, 3 etc
analysis). I do not believe that viral sequencing
Hyoty to be sure.
Page 15, paragraph 5, "The preservation of viruses in clinical samples is monitored . . .
Questions. How many clinical samples will be monitored for viral and nucleic acid stability
at -70 degree C and -150 degrees C?
Who provides the clinical rotavirus samples for
stability studies? - Please see description in my first paragraph. The rotavirus lab will
provide the stool samples for this part of the protocol.
E. Page 15, paragraph 5 - Cryovials are to be used for storage of stool suspensions and
later shipped on dry ice.
Question. Would glass sealed ampules be acceptable in place of cryovials? Cryovials may not
seal tight enough to keep out CO2 gas that is liberated from the dry ice which could alter
the pH of the suspensions and alter sample integrity. Also, cryovials can leak liquid
nitrogen and contaminate the sample. Dr. Hyoty indicated that this was a good point and that
we will discuss our options with the repository that will be storing these samples.
2. Page 15, paragraph 6. "Identity of virus in the initial aliquot will also be validated
by sequencing."
Questions. At what level (by sequencing) is viral identity expected? In other words,
identity as just being a rotavirus, or identity to subgroup, serotype, genotype and
subtypes? Will the entire sequence for the genes that encode VP4 and VP7 be required? Will
the complete sequence for other genes be required? Dr. Hyoty’s response: “THE AIM IS TO
CONFIRM THAT THE VIRUS IS ROTAVIRUS (SUBGROUP OR SEROTYPE IS ENOUGH)”
3. Also, on page 15, second full paragraph, "The clinics will work together with the
Rotavirus Laboratory to maintain the quality of the data."
Questions. For the TEDDY study is there also a enterovirus laboratory? Also, are there
other specific virus laboratories, if so what are they? Will there be a rhinovirus
laboratory as part of the TEDDY study? – For the Infectious Agents QC process we do have an
enterovirus lab in Finland. No other labs will be established for TEDDY’s Infectious Agents
protocol.
4. Page 16, section b. "Prepare 100 aliquots of stool samples from individuals infected
with rotavirus."
Questions. What are the sources of infected stool samples? How many different samples from
individuals infected with rotaviruses are required during the five years of the study?
Is
the source of the rotavirus samples from clinical sites (worldwide) or does the Rotavirus Lab
collect its own clinical samples for testing and aliquoting, etc.? – Please see my
explanation in my first paragraph
Failure to return any and all addenda shall result in disqualification of that Proposer’s Invitation
to Bid or Request for Proposal.
Note:
Please note receipt of this addendum by signing and returning with your bid response.
__________________________________________
Authorized Signature
__________________________________________
Company Name
__________________________________________
Date
BG/hh
2