Development of Assays for Characterizing Influenza Viruses
Added: May 14, 2015 10:59 am The Centers for Disease Control and Prevention (CDC) intends to issue a full and open competition Request for Proposal (RFP) to support National Center for Immunizations and Respiratory Diseases (NCIRD) /Influenza Division. This will be a follow-on requirement to a previous Interagency Agreement. It is anticipated that the resultant contract will be cost plus fixed fee and will have a period of performance of sixty (60) months. The applicable NAICS code is 541712. The RFP will be posted on FedBizOpps and is expected to be released on or about June 15, 2015. Interested parties are responsible for checking the website regularly for release of the RFP and for other procurement-related documents. TELEPHONE CALLS WILL NOT BE ACCEPTED. The information provided in this pre-solicitation is for information purposes only. If there are any differences in the information provided here and the actual solicitation when released, the information provided in the actual solicitation shall govern.The NCIRD Influenza Division at the Centers for Disease Control and Prevention (CDC) is responsible for the detection and characterization of influenza viruses for the purposes of disease surveillance and vaccine strain selection. Tests that measure immunity to influenza and characterize the antigenicity of the virus are critical for detecting influenza infection, understanding the mode of transmission, and selecting viruses to be included in the annual vaccine. New, High toughput and automated assays are necessary to keep up the pace with the testing demands of global influenza surveillance. Development of new assays to support surveillance was initiated several years ago, but updates are required to ensure that the assays can detect newly emerging influenza viruses and to keep up with new technologies.The test most often used to evaluate immunity and antigenicity related to influenza is the hemagglutination inhibition (HI) assay. This assay has been used for over 60 years because it is easy to perform. Data obtained from the assay is essential for World Health Organization (WHO) and Food and Drug Administration (FDA) to make influenza vaccine recommendations. However, this assay is difficult to make mobile, standardize, and automate because it relies on the use of red blood cells, antisera dilutions and humans to read the test results. The purpose of this activity in the contract is to develop new technologies to improve upon the traditional HI assay to make the assay mobile, high-toughput, standardized, and automated.The Influenza Division is also responsible for influenza outbreak investigations, seasonal vaccine strain selections, and vaccine effectiveness studies. There are often situations where the influenza laboratories are not capable of completing research projects due to a significant outbreak or emergence of a new virus subtype thus requiring a shift of testing priorities. In these cases, HI assays, microneutralization (MN) assays, Sanger gene sequencing, Reverse Transcription Polymerase Chain Reaction (RT-PCR) testing for vaccine strain selection and effectiveness studies need to be outsourced to publish study results in a timely manner. Activities supporting vaccine effectiveness and vaccine development, such as avidity antibody assays, Antibody-dependent cell-mediated cytotoxicity (ADCC) and related assays, and B-cell sequencing activities are necessary to support the vaccine development and efficacy determination activities of the entire influenza surveillance process. These activities in the contract will also serve as a vehicle for influenza surge testing when CDC laboratories are overwhelmed with other testing demands.Influenza pandemics occur when a new strain of influenza virus is easily transmitted to humans. Since 1918 there have been four influenza pandemics, each with different characteristics. The death tolls associated with these pandemics have ranged from ~18,000 to over 50 million. Given the continuous emergence of novel strains, it remains important for pandemic risk assessment purposes to characterize more precisely the frequency of serum cross-reactive antibody to these novel viruses in all age groups in the United States, and to identify past exposure to human influenza viruses that may contribute to differences in the levels of antibodies detected. This information could further be used to assess and better understand the potential for these novel viruses to spread among humans in the United States. It will also serve as a benchmark for incidences of infection in the United States population in the event these novel viruses become more widespread among humans. The purpose of this activity in the contract is to acquire left over sera from various diagnostic laboratories across the United States to establish seroprevalences against emerging novel influenza viruses.Lastly, as part of the USG pandemic preparedness and response, it is important to evaluate/assess influenza vaccine potency and efficacy with the goals of supporting the development, approval, and production of influenza vaccines. The purpose of this activity in this activity is the development of an enzyme-linked immunoassay (or equivalent assay) to assess influenza vaccine potency and efficacy.Purpose and Objectives. The primary purpose of this contract is to study, analyze, advice, research, and develop deliverables to advance CDC's related scientific and technical information (STI) tough the application of knowledge and resources in achieving the CDC's mission requirements defined herein. The focus of this contract includes the development of serological and diagnostic assays (for influenza and other infectious disease agents) including a Field Influenza Immunity Test and a High-Toughput Influenza Laboratory Immunity Test. The contract is also focused on the improvement of current serological assays used at CDC (i.e. HI) including the development of a Synthetic HI assay as well as the development of HI automation system. Lastly, this contract will also focus on the development of an enzyme-linked immunoassay (or equivalent assay) to assess influenza vaccine potency and efficacy. To accomplish these tasks, the contractor shall procure left over sera from various diagnostic laboratories across the United States. These sera will also allow for the establishment of seroprevalences against emerging novel pathogens including influenza viruses. As part of the Government pandemic preparedness and response, to the contractor shall test patient specimens via HI, MN, and Sanger sequencing. The contractor will also evaluate/assess influenza vaccine potency and efficacy with the goals of supporting the development, approval, and production of influenza vaccines. Activities supporting vaccine effectiveness and vaccine development, such as avidity antibody assays, Antibody-dependent cell-mediated cytotoxicity (ADCC) and related assays, and B-cell sequencing activities are necessary to support the vaccine development and efficacy determination activities of the entire influenza surveillance process. These activities in the contract will also serve as a vehicle for influenza surge testing when CDC laboratories are overwhelmed with other testing demands.The contractor shall perform the following tasks:A. Core Requirements1. Project Management. The contractor will be responsible for planning, organizing, coordinating, and managing all tasks funded during each base or option year. The contractor will work with each program area that a set of tasks fall under to develop general task, project and activity plans, progress monitoring plans, issue resolution and risk mitigation plans, and user acceptability of completed products, services or deliverables. Contractor shall be responsible for ensuring the technical proficiency and productivity of staff and the quality of the task deliverables. Contractor shall provide status reports and deliverables as directed with allowances for special out of cycle reporting as needed to effectively communicate critical issues or special achievements. Some travel, both domestic and international, may be required to support certain subtasks. 2. Field Influenza Immunity Test (FIIT) Development Studies - CURRENT PLATFORM VALIDATION ONLY. Serological detection of influenza H2, H5, H7, and H9 infection in the field is important for conducting influenza surveillance for novel or emerging influenza viruses. The current version of the CDC FIIT test was developed under a previous Government contract employing the Dual Path Platform technology from ChemBio Diagnostics Systems Incorporated (Medford, NY). The first assay prototype utilized full-length recombinant influenza H1, H3, and H5 proteins to detect influenza subtype-specific responses in the blood (Li, et al., in preparation). The most recent assay prototype utilizes recombinant hemagglutinin (HA)1 subunit antigens and full length HA bound to latex beads. The H1, H2, H3, H5, H7, and H9 recombinant HA1 subunit proteins are used in place of full-length antigens to remove cross-reactive stalk epitopes from the assay. To remove cross-reactive antibody against seasonal influenza prior to addition to the test cassette, patient antisera is treated with full length H1 and H3 recombinant HA protein bound to latex beads (unpublished).3. High-Toughput Influenza Laboratory Immunity Test (HTILIT) Development Studies - CURRENT PLATFORM VALIDATION ONLY. The goal of this task is to design, produce, and deliver a High-Toughput Influenza Laboratory Immunity Test (HTILIT) that detects influenza subtype-specific antibody in patient specimens. High-toughput serology testing of patient specimens is important for conducting influenza surveillance for novel or emerging influenza viruses. The current version of the CDC HTILIT test employs the xMAP technology (Luminex Corporation, Austin, TX). The first assay prototype utilized full-length recombinant influenza H1, H3, and H5 proteins to detect influenza subtype-specific responses in the blood (Li, et al., in preparation). The most recent prototype utilizes recombinant HA1 subunit antigens and full length HA bound to latex beads. The H1, H2, H3, H5, H7, and H9 recombinant HA1 subunit proteins are used in place of full-length antigens to remove cross-reactive stalk epitopes from the assay. To deplete cross-reactive antibody against seasonal influenza, patient antisera is first treated with full length H1 and H3 recombinant HA proteins bound to latex beads (unpublished).B. Optional Projects4. Field Influenza Immunity Test (FIIT) Development Studies - NEW PLATFORM DEVELOPMENT. The optional project consists on the development of an alternative commercial platform to the FIIT that can yield improvements over the current platform (Core Requirements CLIN 2.1). Significant improvements would include increased sensitivity and specificity as well as reduction of cross-reactivity. The new platform should also show a cost benefit over current platform. The primary goal of this optional project will be the creation of a field test that meets the technical requirements outlined under Core Requirements C.4.A.2.1.c - C.4.A.2.1.s. Initiation of this task requires CO approval.5. High-Toughput Influenza Laboratory Immunity Test (HTILIT) Development Studies - NEW PLATFORM DEVELOPMENT. The optional project consists on the development of an alternative commercial platform to the HTILIT that can yield improvements over the current platform (Core Requirements CLIN 3.1). Significant improvements would include increased sensitivity and specificity as well as reduction of cross-reactivity. The new platform should also show a cost benefit over current platform. The primary goal of this optional project will be the creation of a laboratory test that meets the technical requirements outlined under Core Requirements C.4.A.3.1.c - C.4.A.3.1.r. Initiation of this task requires CO approval.6. Develop Quantitative ELISAs for Vaccine Potency Testing. As part of the Government pandemic preparedness and response, it is important to evaluate/assess influenza vaccine potency and efficacy with the goals of supporting the development, approval, and production of influenza vaccines. The purpose of this task is the development of an enzyme-linked immunoassay (or equivalent assay) to assess influenza vaccine potency and efficacy including those developed with chimeric influenza HAs. 7. Synthetic Hemagglutination Inhibition Assay. The goal of this task is to design and deliver a high-toughput influenza binding assay that detects influenza subtype-specific antibody for antigenic characterization. This assay shall also characterize viruses within a subtype as either normal reactors (0 to 4-fold lower than reference virus or vaccine strain) or low-reactors (8-fold or more-lower than reference virus or vaccine strain). High-toughput serology testing of ferret antisera is important for the generation of influenza surveillance data, which yield critical indicators for the implementation of pandemic counter strategies and selection of influenza vaccine strains. The current version of the CDC tests to detect and characterize influenza viruses include HI, RT-PCR, enzyme-linked immunosorbent assay (ELISA), ELISA-based MN, and lateral flow immunoassays. However, these platforms, in their current form, are not suitable for high-toughput testing. 8. Automation of the Hemagglutination Inhibition (HI) Assay. The objective of this task is to implement a more automated HI assay platform in the Influenza Division at the Centers for Disease Control and Prevention in Atlanta. The current HI assay consists of 6 major steps outlined as follows: 1) Standardization of test viruses to 4 HA units in 25-50 uL by diluting the test viruses in PBS. 2) Verify standardized viruses by back titration and make necessary adjustment by adding additional virus (if <4HA U) or PBS (If > 4HA U) followed by a final back titration. 3) Serial dilution of antiserum panel in a 96 well plate format; 4) Addition of 25-50 uL (4HA units) of test virus sample to each well of the microplates with diluted serum panel; mix well then incubate the plates at room temperature for 15 mins. 5) Addition of 50uL of 0.5-0.75% red blood cells; mix well and incubate for 30-60 mins. and 6) Scoring of each well for agglutination. See link for full CDC protocol: http://whqlibdoc.who.int/publications/2011/9789241548090_eng.pdf9. Biannual Acquisition of Left Over Sera for Seroprevalence Estimations. The objective of this task is to provide a biannual source of sera from healthy individuals across the United States to characterize more precisely the frequency of serum cross-reactive antibody to emerging novel viruses including influenza viruses, for pandemic preparedness purposes. These sera will also aid in the development and validation of both subtype specific and broadly neutralizing detection antibody assays. Initiation of this task requires CO approval. C. Optional Surge Projects10. Conduct Sanger Sequencing Testing of Patient Specimens. The Influenza Division at the CDC sequences the HA and NA genes of influenza virus, isolates for vaccine strain selection and research purposes. During periods where test volume is high, the testing of research specimens can be delayed, which interrupts multicenter research projects and negatively affects the performance of associated grants and contracts. In this situation, it becomes most effective and efficient to outsource the sequencing of influenza isolates. This task order is an option to be exercised during periods when CDC laboratories have reached maximum capacity and are unable to test additional samples. The testing of patient samples will be done in batches and is dependent upon completion of studies or outbreak investigations, thus potentially resulting in periods of no performance. There may be instances where the base level of samples (100 virus isolate per month) and additional levels of testing samples (200 and 400 virus isolates per month) are running concurrently due to overlapping priorities/studies. Initiation of this task requires CO approval.11. Conduct Serological Testing of Patient Specimens by HI. One of the Influenza Division's responsibilities is to investigate outbreaks and other emerging infectious diseases and to provide immediate and accurate information for vaccine strain selection and vaccine effectiveness studies. At times, the influenza laboratories are unable to complete research projects due to large number of outbreaks or emergence of new virus subtypes thus requiring a shift in testing priorities. The objective of this task is to provide CDC laboratories with surge capacities at times when CDC laboratories are overwhelmed. This task is an option to be exercised during periods when CDC laboratories have reached maximum capacity and are unable to test additional samples. The testing of patient samples will be done in batches and is dependent upon completion of studies or outbreak investigations, thus potentially resulting in periods of no performance. There may be instances where the base level of samples (800 samples per month) and additional levels of serum samples (1000, 1200, 1400, and 1600 samples per month) are running concurrently due to overlapping priorities/studies.12. Conduct Serological Testing of Patient Specimens by MN. One of the Influenza Division's responsibilities is to investigate outbreaks and other emerging infectious diseases and to provide immediate and accurate information for vaccine strain selection and vaccine effectiveness studies. At times, the influenza laboratories are unable to complete research projects due to large number of outbreaks or emergence of new virus subtypes thus requiring a shift in testing priorities. The objective of this task is to provide CDC laboratories with surge capacities at times when CDC laboratories are overwhelmed. This task is an option to be exercised during periods when CDC laboratories have reached maximum capacity and are unable to test additional samples. The testing of patient samples will be done in batches and is dependent upon completion of studies or outbreak investigations, thus potentially resulting in periods of no performance. There may be instances where the base level of samples (400 samples per month) and additional levels of serum samples (500, 600, 700, and 800 samples per month) are running concurrently due to overlapping priorities/studies.13. Conduct Diagnostic and Serological Testing of Patient Specimens by Assay as Defined by Infectious Pathogen. The contractor shall conduct research and public health evaluation activities to develop and assess new diagnostic methods and improve existing diagnostic assays to allow for rapid response to influenza outbreaks or other emerging infectious diseases. The contractor shall perform an analysis of human specimens including serum, and document the results to the CDC. The contractor shall test no more than 200 samples per month against the newly emerging infectious antigen, upon completion of seroepidemiological studies and/or outbreak investigations. In the event that the NCIRD must respond to a novel influenza or other respiratory disease event or pandemic, contractor will be required to perform additional level of effort (300 and 400 samples per month) requirements of ongoing activity. Prior to initiation of task, two contractor staff will receive 1-week training at the CDC for pathogens not classified as Select Agents. Initiation of this task requires CO approval.14. Conduct RT-PCR Testing of Patient Specimens. The Influenza Division at the CDC tests patient respiratory specimens by RT-PCT to detect the presence of the influenza virus and to determine the subtype and lineage of influenza viruses in positive specimens. During periods where test volume is high, the testing of research specimens can be delayed, which interrupts multicenter research projects and negatively affects the performance of associated grants and contracts. In this situation, it becomes most effective and efficient to outsource the RT-PCR testing of patient specimens. This option will be exercised during periods when CDC laboratories have reached maximum capacity and are unable to test additional samples. The testing of patient samples will be done in batches and is dependent upon completion of studies or outbreak investigations, thus potentially resulting in periods of no performance. The contractor shall perform RT-PCR for each patient specimen using a CDC provided protocol or protocols deemed acceptable by the CDC. Initiation of this task requires CO approval.15. Conduct Sequencing of Ig heavy and light V (D) J Regions in mouse B cells by Sanger Sequencing or Next-generation Sequencing. One of the Influenza Division's responsibilities is to analyze the immunological response to influenza vaccination and infection, both to determine the protective response induced by seasonal vaccines and to assess the potential efficacy of novel vaccines. Standard approaches to measuring immunogenicity involve screening the patient antibody response by hemagglutination inhibition and virus neutralization assays. A more detailed understanding of the response to influenza may be obtained by correlating the repertoire of antibody genes expressed by B cells specific for influenza with function. This approach involves sequencing of large numbers of antibodies, often during times when the Influenza Sequencing Unit is fully involved in mission-critical activities, such as sequencing viral isolates. The objective of this task is to provide CDC laboratories with additional sequencing capacity so that the Influenza Sequencing Unit can focus on sequencing viral genomes. This task is an option to be exercised during periods when sequencing at the Influenza Sequencing Unit, or at CDC collaborator's labs, would disrupt viral genome sequencing activity. Antibody sequencing will be done in batches and is dependent upon completion of studies and availability of samples, thus potentially resulting in periods of no performance. Initiation of this task requires CO approval.16. Cell-mediated immune assessment. The determination of Vaccine Effectiveness (VE) is critical during the influenza season. A suboptimal response to the vaccine may negatively affect the health care systems during the cold and flu season. Cell based assays targeting populations at risk can provide critical information to other data collection mechanisms already in place to complement CDC's existing Vaccine Effectiveness program. The contractor shall assess cell-mediated immune responses consisting of T and B cell responses in a subset of participants prior to vaccination (day 0) and at 1 week, 1 month and 6 months post-vaccination. The actual time points for PBMC collection will be finalized in consultation with the COR, Project Officer and CO. Prior to initiation of the task, two contractor staff will receive 1-2 week training. Initiation of this task requires CO approval. 17. Antibody binding avidity studies. Determination of the antibody avidity post influenza vaccination can help assess the vaccines efficacy to drifted seasonal or pandemic viruses. The contractor shall assess antibody binding to recombinant hemagglutinin (recHA) by bio-layer interferometry on an Octet Red instrument (Fortebio, Inc.) or a similar technology using the recombinant HA from vaccine strains and additional strains (maximum = 2) from the circulating strains especially when the circulating strains are antigenically distinct from the strains included in the vaccine. Prior to initiation of the task, two contractor staff will receive 1-2 week training in antibody binding avidity assays at the CDC. Initiation of this task requires CO approval. 18. Studies to characterize neuraminidase antibody response and Antibody Dependent Cellular Cytotoxicity (ADCC) response post influenza: vaccination. Antibodies to the Neuraminidase can prevent the release and spread of the influenza viruses. Influenza vaccines can generate varying amounts of antibodies to the neuraminidase depending on the host and the vaccine. Thus vaccines that can generate more antibodies to neuraminidase are preferred. Antibody-dependent cell-mediated cytotoxicity (ADCC) and Complement-mediated cytotoxicity are other mechanisms of cell-mediated immunity to influenza. Influenza-specific antibodies when bound to the influenza virus can prepare the virus for destruction by other immune cells. Assessment of these cell-mediated mechanisms can help determine the effectiveness of the vaccine against vaccine viruses and circulating seasonal and pandemic viruses. The contractor will assess the ADCC, Complement-mediated cytotoxicity and Neuraminidase antibody levels on sera provided by CDC. CDC will provide 1 week training as needed for ADCC, Complement-mediated cytotoxicity and neuraminidase antibody assays at CDC. Initiation of this task requires CO approval.
2015-N-17131 Department of Health and Human Services Centers for Disease Control and Prevention Office of Acquisition Services
5/14/15, 10:59 AM