Implementation of the US Department of Health and Human Services Zika Specimen Repository and Its Effect on Zika Diagnostic Test Development, 2016

Abstract

This study describes the efforts and outcomes associated with the establishment of a clinical sample repository during the 2016 Zika virus epidemic. To overcome the challenge of limited access to clinical samples to support diagnostic test development, multiple US Department of Health and Human Services (HHS) agencies formed a partnership to create the HHS Zika Specimen Repository. In 2016-2017, the Biomedical Advanced Research and Development Authority and the Centers for Disease Control and Prevention collected patient specimens (4420 convalescent sera aliquots from 100 donors and 7171 plasma aliquots from 239 donors), confirmed Zika virus test results, assembled 1 panel for molecular testing (n = 25 sets) and 7 panels for serologic testing (n = 92), and distributed the panels to test developers. We manufactured 8 test panels and distributed 74 sets of panels to 32 commercial companies, public health partners, and research institutions. Manufacturers used these panels to generate data that supported 14 US Food and Drug Administration (FDA) emergency use authorizations and 1 FDA approval. To develop a repository that can respond immediately to future disease outbreaks, we recommend that organizations pre-position procedures, resources, and partnerships to optimize each partner’s contribution.

On February 1, 2016, the World Health Organization declared a public health emergency of international concern because of clusters of fetal microcephaly and other neurologic disorders in geographic areas affected by Zika virus.¹ At the beginning of the Zika outbreak, the existing Clinical Laboratory Improvement Amendments (CLIA)–compliant laboratory-developed tests, which were developed by the Centers for Disease Control and Prevention (CDC) in its Ft. Collins, Colorado, laboratory to diagnose Zika virus infection, were not approved for distribution.² The US Food and Drug Administration (FDA) issued emergency use authorizations (EUAs) for the CDC molecular assay that detects Zika virus RNA and the CDC serologic assay that detects antibodies to Zika virus. An EUA allows unapproved medical products or unapproved applications of approved medical products to be used in an emergency to diagnose, treat, or prevent serious or life-threatening diseases or conditions, to facilitate the availability of medical countermeasures during an emergency.³ These assays were then distributed to state and local public health laboratories to support the testing of persons suspected to have recent infection with Zika virus.

Before 2016, diagnostic testing for Zika virus was offered only through CDC and select research laboratories in the United States.⁴ However, the growing number of persons potentially exposed to the virus and increased demand for diagnostic testing resulted in a critical need for additional diagnostic tests that could be performed in clinical laboratories (eg, hospitals and commercial laboratories) under EUA.

Early on in the response, the tests used by public health laboratories could not be made available to clinical laboratories because CDC’s capacity for manufacturing and distributing Zika diagnostic kits and training of users, was limited. Demand also increased for assays that could be used to screen blood donors for Zika virus to prevent transmission via transfusion. Expanded availability of tests would also support CDC’s mission to control the spread and severity of the disease by increasing access to testing and reducing the time to receive test results, especially for pregnant women at risk for fetal complications.^5,6

Commercial diagnostic development companies rapidly began to develop Zika assays in response to rising demand for testing; however, lack of access to sufficient numbers of positive Zika virus specimens and inadequate sample volumes of convalescent serum samples limited their ability to validate the performance of their tests. No existing repositories of Zika samples were readily accessible to assay developers. Obtaining acute Zika virus samples is difficult because most persons infected with the virus are asymptomatic and do not seek medical care.⁷ In addition, because the period of Zika virus viremia (when the virus is circulating in the bloodstream) is brief, by the time symptoms develop, there is only a short time for collecting acute infection specimens.⁴ Serologic tests to detect immunoglobulin M against Zika virus are needed to confirm recent infection in asymptomatic pregnant women when the time of exposure and viremia are unknown.⁸

Convalescent samples used to develop a test to detect immunoglobulin M against Zika virus must be collected from patients who test positive for Zika virus 1-12 weeks postinfection, the window during which immunoglobulin M is typically detected.⁷ Before local transmission of Zika virus occurred in the continental United States, HHS attempted to acquire samples from other countries. However, establishing cross-border partnerships, developing study protocols, and obtaining institutional review board approvals proved complicated and resource intensive. This effort was further confounded by individual country export laws, national sample sharing policies, intricate US import regulations, and complex transport logistics. Finally, samples used to develop new tests had to first be confirmed by the CDC-authorized assay, which was not widely available. Altogether, these obstacles created a formidable barrier to developing new diagnostic tests essential for the medical and public health response to the Zika virus outbreak.

The aforementioned challenges compelled the Biomedical Advanced Research and Development Authority (BARDA), a governmental organization that supports the advancement, development, and research of medical countermeasures, to partner with CDC to create the HHS Zika Sample Repository. The repository provided standardized panels of Zika-positive specimens to commercial test developers to assess test performance directly and independently, thereby expediting FDA EUA. In addition, because we provided the samples at no charge, the overall cost of diagnostic test development was reduced, helping to increase the number of commercial companies developing tests. We report the coordinated efforts to establish the HHS Zika Sample Repository, the outcomes of these efforts, lessons learned, areas for improvement, and the benefits of this model in developing diagnostics in response to an infectious disease public health emergency. To our knowledge, no similar studies on the implementation of a Zika biospecimen collection have been published in the literature. Such a study would be invaluable for improving preparedness for future infection outbreaks.

Methods

Because of the urgent need for convalescent serum samples, BARDA established a contract with a member of its Medical Countermeasures Clinical Studies Network,⁹ a network of 5 private-sector clinical research organizations that design, conduct, and report clinical trials for medical countermeasures. The contract directed the clinical research organization to collect convalescent serum samples from patients who were aged ≥18 and had received a laboratory-confirmed Zika diagnosis in the 12 weeks before collection. Participants were recruited by a clinical study site in Puerto Rico, state and local public health agencies, print advertisements, and social media. Recruitment efforts targeted populations in Puerto Rico, Texas, Florida, and New York City. Most participants were recruited in Puerto Rico, where Zika was endemic, and in New York State, where the New York State Department of Health and New York City Department of Health and Mental Hygiene agreed to enlist participants from among the many Zika-infected travelers returning home from endemic areas.¹⁰ The clinical research organization was also responsible for determining participant eligibility, working with the local public health department to confirm Zika virus infection status based on results of CDC molecular or serologic tests performed in accordance with CDC recommendations for diagnosing Zika infection, and ensuring that all patient information was de-linked from the sample. CDC, BARDA, the clinical research organization, and the New York State Department of Health collaborated to develop human study protocols required for each recruitment area, create consent forms, and obtain human subjects institutional review board approval. The clinical research organization subcontracted with clinical and commercial laboratories to perform phlebotomy, process and prepare 0.5-mL aliquots of the collected serum samples, and ship them to CDC. The number of aliquots received per donor varied based on the amount of blood obtained during the blood draw; the average number of aliquots was 43 (range, 17-80). Each donor represented a distinct sample. On arrival at CDC, the serum samples were accessioned by the Specimen Tracking and Triage Team and stored at –80°C. A total of 4420 convalescent serum aliquots from 100 donors (72 women, 28 men) were added to the HHS Zika Sample Repository as a result of this collaboration.

One aliquot from each serum donor was distributed to CDC laboratories for confirmatory testing by using the Zika immunoglobulin M antibody capture enzyme-linked immunosorbent assay and plaque reduction neutralization tests. The Specimen Tracking and Triage Team compiled all test results and forwarded them to BARDA for panel design.

Because of difficulties in identifying and recruiting viremic donors, Zika virus RNA-positive samples were obtained as part of a BARDA contract to support development of Zika blood screening nucleic acid amplification tests to ensure the safety of the blood supply. Plasma samples from blood units that tested positive by the contractor’s proprietary nucleic acid amplification test were dispensed into 1-mL aliquots and shipped to CDC, where the Specimen Tracking and Triage Team accessioned and stored them. A total of 7171 plasma aliquots from 239 unique positive donors were added to the HHS Zika Sample Repository.

Based on immunoglobulin M confirmatory test results at CDC or nucleic acid amplification test blood screening results, BARDA designed sample panels to support development of both Zika virus immunoglobulin M detection assays and molecular tests for viral RNA. The validation panels consisted of positive samples, with varying degrees of reactivity, from 10-15 donors, along with 2 commercially procured negative control samples. The serologic and molecular validation panels were assembled at CDC under established standard operating procedures and stored at –80°C until shipment.

BARDA provided CDC with a list of recipients that were approved to receive validation panels. Because of the limited number of samples available in 2016, we initially distributed samples only to companies in advanced stages of development (ie, seeking an EUA from the FDA). As more samples became available, panels were made available to researchers and vaccine developers in early stages of development. All recipients were also required to sign a simple letter of agreement for the transfer of Zika serum panels to document recipients’ understanding of the allowable research uses for the samples. Recipients received test samples within 3 or 4 days of their requests, and the expected results were shared with developers only after their testing data were submitted to BARDA. Manufacturers’ results were also shared with CDC and FDA so that they could make an independent assessment of test performance. BARDA and CDC tracked the utility and effectiveness of the repository over time by monitoring the number of companies and researchers that requested panels, the number of companies and researchers that returned results, the accuracy of results from developers, and FDA EUA status.

Outcomes

In 2016-2017, BARDA and CDC manufactured 25 sets of a single molecular validation panel and 92 sets of 7 distinct types of serologic validation panels (Figure) to fulfill requests from developers and researchers.

Figure.

Status of the unique Zika assay validation panels developed by the Biomedical Advanced Research and Development Authority and manufactured by the Centers for Disease Control and Prevention during 2016-2017 (N = 117). Molecular panels were used to detect Zika virus RNA and serologic panels to detect immunoglobulin M against Zika virus. Stored panels remain in the repository and are available for future use. Shipped panels were distributed to approved recipients. This effort focused on making samples available for commercial companies and research institutions.

In 2016 and 2017, we distributed 15 molecular and 59 serology panels to 32 recipients (26 commercial companies and 6 educational, research, and government institutions) for Zika virus research and development. Of the 26 commercial companies that received panels, 10 received FDA EUAs to distribute Zika virus diagnostic tests, including 4 immunoassays and 6 reverse-transcriptase polymerase chain reaction assays, and 1 commercial company received approval for a blood screening assay.^3,4,11

Lessons Learned

The Zika virus outbreak revealed the need for rapid development of diagnostics for effective response, which required the timely collection, processing, storage, and distribution of patient samples to support test development and FDA EUA. The success of this program, as measured by the 32 fulfilled panel requests and EUAs received by 9 participants, was the result of multiple factors. The BARDA–CDC partnership, with collaboration from the FDA, combined the capabilities of each agency to respond successfully to this unmet need. BARDA’s ability to establish a contract with a clinical research organization quickly and the assistance of state and local health departments, especially the New York State Department of Health and New York City Department of Health and Mental Hygiene, were essential in recruiting participants. Leveraging existing capabilities at CDC for storing and shipping infectious material and using established protocols for panel manufacturing expedited the availability of positive samples for developers. We also identified multiple areas for improvement, including specimen handling and recruitment processes.

In an emerging disease scenario, the many unknowns make it difficult to set firm contract requirements and recruitment plans. The repository team established specimen collection contracts, recruited patients, collected samples, and shipped samples to CDC within 3 months. The use of social media and advertising in local media generated only a few potential donors. Partnering with state and local health departments that were willing to help recruit from the pool of Zika-positive persons in their jurisdictions was critical to achieving the required number of sample donors. However, each jurisdiction had its own policies and institutional review board requirements. Developing and implementing contracts, study protocols, and agreements consumed several weeks, delaying specimen collection. To prepare for diagnostic development needs in future outbreaks, we propose drafting contracts, developing and pre-positioning agreements, and creating study protocols that can be quickly updated and implemented. Although each new disease may require unique recruiting and specimen collection procedures, generic contracts could be negotiated and implemented in advance that require only minor event-specific modifications. These generic contracts would reduce the time needed to begin specimen collection during an outbreak. Advance planning and cost negotiations might also reduce costs associated with contracting in an emergency. Although BARDA was able to contract for sample collection, the agency does not have laboratories or infectious sample storage. Therefore, the partnership with CDC allowed for specimens to be processed, qualified, and stored and for standardized panels to be created under a rigorous quality management system. The usefulness of the serum panels was substantially enhanced because CDC validated the samples with the authorized CDC Zika immunoglobulin M antibody capture enzyme-linked immunosorbent assay and plaque reduction neutralization tests, and manufacturers could use the results as a standardized comparator for their new test evaluations.

Several elements of specimen handling could be improved. The specimen collection contracts required that aliquots be made from serum and plasma at the time of collection to reduce the workload at CDC. However, this requirement resulted in an additional freeze–thaw phase during assembly to ensure uniformity and anonymity of vials in a single panel. In the future, aliquots will not have to be made at collection. Instead, samples will be shipped immediately after collection at 4°C and processed within 24 hours. During the initial stages of manufacturing, validation panels were assembled to fill orders in real time. As demand grew, CDC manufactured panel lots that could be stored for future requests. Having stored panels greatly reduced the amount of time between a product request and fulfillment.

When new diseases emerge, diagnostic companies need access to clinical samples from infected persons to develop and validate new assays. The rapid acquisition of clinical samples during a novel disease outbreak is challenging because of the cost and complexity of acquiring samples that may contain infectious agents, especially for new diseases with few cases. Governmental and research laboratories may have small numbers of samples acquired during previous or new outbreaks but not under institutional review board–approved protocols that allow distribution to commercial product developers. The HHS Zika Sample Repository was the first attempt by collaborating US government agencies to address this unmet need in real time during a public health emergency. One commercial company that provides biospecimens to support product development also collected Zika samples. The company’s protocol supported serial collection of specimens during acute and convalescent stages of infection and included samples from pregnant women. These samples allowed diagnostic developers to validate their tests’ ability to detect Zika immunoglobulin M for multiple weeks postinfection among pregnant and non-pregnant populations, an FDA requirement. However, because of the high cost of these specimens, developers generally limited their use to producing final validation data for EUA submission. Although the HHS Zika Sample Repository protocol was a one-time collection, samples were available rapidly and at no cost to the developers. These samples were especially useful to support early stage assay design and optimization. In addition, the samples were provided to developers without results (blinded), and test results were provided to FDA, allowing for an unbiased assessment of performance.

Overall, implementation of the HHS Zika Sample Repository was viewed as a successful example of public–private and cross-agency partnerships because it accelerated the development of Zika tests and, subsequently, the FDA authorized 10 virus diagnostics.⁴ From 2016 to 2017, the availability of a commercial serologic test for Zika virus expanded the capacity for testing.¹² Data quantifying the use and public health impact of new EUA-approved tests were not available for this article. Although expanded testing capacity to meet patient demand is a clear public health benefit, future studies measuring the time to result, impact on patient management decisions, and the effect on public health response measures would be helpful when prioritizing response activities, especially in environments with limited resources. Collecting these data could be a component of use agreements when feasible or part of a distinct public health study should funds be available. To build on the success of this program and decrease the time for diagnostic development in future emerging infectious disease outbreaks, we recommend that specimen repositories be a mainstay of public–private public health response and that elements such as contracts for specimen acquisition, sample sharing agreements, and infrastructure for specimen repositories that are necessary to support these repositories are pre-positioned where possible and resourced for sustainability.