The Association of Public Health Laboratories (APHL), in cooperation with the US Centers for Disease Control and Prevention's (CDC) Influenza Division (ID), is seeking to identify up to five (5) state or local public health laboratories (PHLs) to serve as Influenza Sequencing Centers (ISCs) in support of national influenza surveillance initiatives. The sequencing centers will perform influenza virus genomic sequencing on specimens from their jurisdictions using next generation sequencing (NGS) based methods and a data assembly pipeline approved by APHL and CDC. 


Eligible laboratories include all US public health laboratories with the following capabilities, resources and facilities in place. Specific expectations regarding the methodologies to be used by the reference center are outlined in Appendix A: Expectations for Influenza Sequencing Center. All applicants are required to agree to the following minimum requirements (as outlined in Appendix B: Minimum Requirements for Influenza Sequencing Center):

  1. Surveillance networks are in place to receive specimens required to sequence 500 specimens per year;

  2. Sufficient equipment, laboratory space and workforce capacity for the proposed work;

  3. Established capacity to perform influenza NGS while meeting expected quality metrics;

  4. Willingness to alter or amend existing sequencing protocols;

  5. Willingness to increase frequency of performing certain methods (if required) to meet expected turnaround times;

  6. Ability to collect all required metadata;

  7. Willingness to share copies of QA or biosafety documentation associated with relevant procedures to APHL and CDC upon request;

  8. Informatics capabilities to stream NGS read-level data to APHL Informatics Messaging Services (AIMS) cloud-based environment in near real-time using the Amazon Simple Storage Service (S3) Utility synchronization tools with IT support;

  9. Ability to upload consensus genomic data to public database with prescribed naming convention and required metadata;

  10. Ability to retain residual clinical specimens (properly stored, not inactivated) for up to 12 months post-selection for sequencing and provide CDC with specimens, upon request, for additional characterization/use at CDC;

  11. Ability to contract with APHL have an existing relationship with a third party that can contract directly with APHL on behalf of the laboratory.

Anticipated RFP Schedule

November 11, 2022                      –            RFP Issued

November 29, 2022                      –            Informational teleconference (optional)

December 2, 2022                         –            Letter of Intent Due to APHL (see below)

December 12, 2022                      –            RFP Responses Due

January 6, 2023                             –            Proposal review completed

January 11, 2022                           –            As needed, follow-up interviews/proposals due

January 12, 2022                           –            Final review completed and awardees selected

January - June 2023                      –            Contract year one (training and proficiency testing)

APHL will communicate any modification to this anticipated schedule on APHL's procurement website ( and via an email blast to public health laboratories (PHLs).

Response Submittal

Confirmation of Intent to Respond

APHL requires that prospective applicants submit a brief email statement indicating an intent to submit a proposal. APHL must receive this email by no later than 5:00 pm EST on Friday, December 2, 2022. To allow for appropriate review process planning, a letter of intent is required for consideration.


Final Response

APHL must receive complete responses by 5:00 pm EST on Monday, December 12, 2022. Please see Proposal-Required Submissions section for items that must be included in the completed proposal. Applicants may send proposals via email to

 APHL will send an email acknowledging the receipt of your application; if you do not receive an acknowledgement within 2 business days, please email the RFP point of contact above to confirm receipt.


The official RFP document will provide detailed information in regards to this request, please read it in its entirety.

Questions and Answers

Is there an expected turnaround time for influenza sequencing results to be shared with the CDC analysis pipelines?

What is the weekly or monthly testing expectation for funded sites?

Does CDC have a pre-screening PCR assay and Ct value cutoff for positive samples to determine whether they are appropriate for sequencing?

Are there specific extraction platforms that are required for the amplicon sequencing method that will be shared by the CDC? If so, what are the required platforms?

Can the CDC share their sequencing procedures and quality assessment steps with labs prior to the RFP response due date?

Please share the metadata elements that need to be submitted to Clarity LIMS.

What types of data will be transmitted through the APHL AIMS S3 bucket?

Are you looking for long or short read sequences?

Would Google Cloud Platform (GCP) be able to be used instead of Amazon Web Services (AWS)?

Can you provide more information about Clarity LIMS? Does the lab need to have Clarity LIMS or will Clarity LIMS be hosted on the AIMS platform for us to use?

Can we access a cloud-based version of Clarity hosted by APHL/CDC rather than purchasing and maintaining our own copy of Clarity?

Will there be a standardized analysis workflow such as using IRMA?

Will there be a training session such as clarity LIMS or analysis for the sites selected?

Is the estimate of 500 for total samples tested or sequenced?

Is there a focus on solely sequencing the most common influenza type or are all types expected to be sequenced?

Could you expand upon the multi-segment RT-PCR enrichment step?

If we are a participatory site, is submission of samples to the NIRC still needed?

What needs to be included in the letter of intent?

Can we submit NextSeq data which delivers 8 files per sample instead of 2?

Can older specimens (collected in 11/2022 or 12/2022) be included?

We created a budget for our department of sponsored programs this morning and realized there will be no revenue until invoicing for sequence generated, however we will spend months possibly the whole six months without any revenue, which is problematic because the DSP sets this contract up as a grant. Is there any possibility to request upfront development funds prior to sequence generation? Or would we be able to sequence frozen specimens collected during this season when we get test live to generate revenue before the end of the 6 month period?

To confirm, this would be for samples in our own jurisdiction only, correct?

Would CDC be submitting sequence data to GISAID/NCBI or would the ISC be responsible for data submission to public repository? It sounds like CDC will be assembly the raw read data.

What is the CDC's target turnaround time from the collection date to submission?

To streamline, we could bypass normal test development and validation and just run the CDC proficiency panel and go live?

Will APHL/CDC send us 500 flu samples to sequence or would you expect samples to come from our lab?

We have approval for a few different ways to share Influenza reads with the AIMS S3 bucket. I see there is a guidance doc for sharing via the AIMS AWS S3 bucket option on APHL from 2015, is this the most up to date guidance for preferred sharing and if not would you be able to send us updated specifics?

Would AIMs be ok with transfer from our GCP bucket storage?

Would AIMs be ok with transfer from our GCP bucket storage?

Is there architecture of the solution in AWS cloud?

Is there any Personal Identifiable Information (PII) in the dataset being exchanged with AIMS?

We currently have an FTP-based interface with AIMS for eCR transactions, and our lab is using this same interface to transmit/test ARLN lab results with APHL. Can this same interface be used for the influenza data, or must CrossFTP be installed per the attached PDF to connect to Amazon S3?

My understanding is that after the primary selection, APHL ISC committee will bring the PH laboratories and their respective IT personnel to set up the AIMS S3 hosted by APHL. Will there be any formal training or instruction for this?

Our IT’s major concern is that they do not have any prior experience in AWS cloud network service though we know that most of this cloud-based data transmission pipeline will be operated by our sequencing team. Would you suggest anything that we can explain them to ease their concern.

Will funding be provided for our IT Department as well to assist with the projects to whatever extent they would need should we be approved to become an Influenza Sequencing Center?

Is indirect an allowable use of funds?

Is there an "east" Amazon S3 that labs in that region would connect, or does everyone use the "west" web address?