Genomics Systems
APHL works with public health laboratories to improve quality laboratory practices by utilizing next generation sequencing technology and bioinformatics for infectious diseases, such as influenza.
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National Influenza Reference Centers and CLAW
Each year, APHL contracts with National Influenza Reference Centers (NIRCs) to provide influenza testing for the US Centers for Disease Control and Prevention (CDC). This testing provides efficiency to CDC by performing the initial steps of the virus identification protocols used to support the influenza surveillance programs. The influenza samples are received by a NIRC, which completes the initial steps of the process and then forwards samples of the material to CDC for further characterization.
To support this flow of information, we developed a web portal hosted on the AIMS platform for the NIRCs—known as the Contract Laboratory Accessioning Webportal (CLAW)—to accession the NIRC laboratory influenza samples. CLAW records sample-level data, provides multiple reports and sample metadata tools, and monitors sample status. CLAW also maintains traceability by processing sample parent-child relationships, which conforms to CDC’s sample management policy for sample identification. The system then produces a data payload containing the relevant sample and testing information in a format that could be easily consumed by FluLIMS at CDC.
Influenza Sequencing Centers
APHL sponsors five Influenza Reference Centers (ISCs) to build sequencing capacity for influenza. Establishing influenza next generation sequencing at these ISCs has provided increased capacity to aid CDC in vaccine virus selection.
Specifically, we onboard and monitor the data messaging used for transferring data and results from the ISCs to CDC utilizing the AIMS platform. Additionally, updates to testing variables and instrumentation require changes in data messaging, so we handle onboarding of new changes to systems between the ISCs and CDC.
MIRA
The CDC Influenza Division has developed MIRA as a solution for laboratories to download and use on a local machine to assemble and curate influenza and SARS-CoV-2 sequencing data, as well as creating metadata and config files for gene assembly. The tool is solely intended for laboratories to use for their own sequencing purposes and then upload data to national sequencing databases, like NCBI.
To support the public health response to the outbreak of influenza H5, CDC funded APHL to host MIRA on the AIMS platform. We developed an environment to host the MIRA tool on AIMS and made it securely available to domestic public health laboratories—expanding sequencing capabilities for laboratories and improving our capacity to respond to outbreaks of respiratory diseases.