Pilot of Global Hepatitis Outbreak and Surveillance Technology (GHOST) for Molecular Surveillance of HCV Infection
APHL seeks to select up to 4 public health laboratories that will perform next generation sequencing (NGS) for hepatitis C virus (HCV) and utilize GHOST for tracking HCV transmission during outbreak investigation and molecular surveillance in different epidemiological settings.
The HCV GHOST Pilot sites will perform next generation sequencing using the Illumina MiSeq and utilize on online web portal to access GHOST to test the functionality of using this platform for tracking HCV transmission during outbreak investigations and for molecular surveillance.
Proposals will be evaluated based on the laboratory's existing capability and facilities and applicants must have:
- Established capacity for isolating high quality viral RNA and
- Established and demonstrated capacity for sequencing using Illumina MiSeq
- Sufficient equipment, laboratory space and workforce capacity for the proposed workload
|July 27, 2016||- RFP Issued|
August 8, 2016||
- Letter of Intent due to APH (see RFP)|
September 9, 2016||
- RFP Response Due|
|September 19, 2016||- Proposal review completed|
|September 20-21, 2016|| - If needed, follow-up interviews and updated proposals due|
|September 22, 2016||- Final review completed and awardees selected|
|September 30, 2016||- Draft contracts submitted to APHL Legal Dept. for final internal review|
Any modification to this anticipated schedule will be posted here (www.aphl.org/rfp) and via an email blast to the public health laboratories (PHLs).
Request for Proposal Materials
Pilot of Global Hepatitis Outbreak and Surveillance Technology (GHOST) for Molecular Surveillance of HCV Infection RFP provides details on how to complete this RFP. The RFP contains a copy of the scoring criteria that will be used for evaluation of proposals in Appendix C. The details for sample processing are contained in Appendix A and D.
Questions And Answers
Can this project be done using sequencing platforms besides Illumina?
A: This RFP is only for the Illumina system due to the way that the GHOST analysis pipelines must be created/modified for each sequencing system. If you are interested in working on HCV sequencing with other platforms please let us know so that we can work with CDC’s DVH on potential future projects.
Will APHL/CDC supply the primers for this project?
A: APHL/CDC will provide an initial starter package including aliquots of the primers and a panel of specimens to ensure everyone can get started on the project and to attempt to minimize differences between the selected laboratories.
It appears that this RFP is weighted heavily towards labs with experience specifically with HCV and general NGS experience is not sufficient, is that true?
A: Yes, the goal of this RFP is to optimize and troubleshoot the use of GHOST and therefore the selected laboratories must have sufficient experience sequencing HCV to minimize challenges associated with sequencing from high quality RNA. However, experience with other RNA projects including RNA viruses will also be considered as relevant experience. .
The project calls for 7-8 sequencing runs during the project period. Can you confirm that it is acceptable to include the HCV NGS samples in mixed runs with other types of samples?
A: The current protocol recommended in the RFP is laid out for sequencing of 8 HCV samples. CDC also has protocols in place for more samples ranging from 24 to 96 samples/library. However, for the RFP we would like the states to test the 8 sample library protocol. Of the 7-8 sequencing runs during the project period, at the very least 50% of the libraries are to be dedicated to HCV samples only to validate our GHOST SOP. Further details will be discussed on the initial kick-off call.
I don’t see any mention of IRB status of the protocol. Is CDC submitting for a non-research determination?
A: CDC is currently conducting their HCV NGS activities under an IRB exempt protocol. The RFP is purely technical, and only for protocol validation where patient info or other associated information will not be needed. When outbreak samples are to be included as part of the test samples, it is a public health emergency testing, so no IRB is required.
Will the contract be set up to provide reimbursement at a set price per sequence?
A: No, the contract payments will be based on deliverables and not fee based.