Public health laboratories and APHL serve as vital partners in national virologic surveillance for respiratory diseases. APHL supports the respiratory disease work of public health laboratories with communications, trainings, communities of practice and more.
Contact the Infectious Diseases team: [email protected]
For technical guidance on submission, interpretation or other technical sequencing related questions for SARS-CoV-2, please contact [email protected].
Model Practices for Verification of an Alternate Enzyme for Influenza RT-PCR Diagnostic Panel
MIRA is a bioinformatics pipeline that assembles influenza genomes, SARS-CoV-2 genomes, the SARS-CoV-2 spike-gene and RSV genomes when given the raw fastq files and a samplesheet. MIRA can assemble reads from both Illumina and OxFord Nanopore sequencing machines. Laboratory Protocols are also available (see Lab Protocols in Page Header).
MIRA Pipeline Documentation on GithubAPHL and CDC developed the  Influenza Virologic Surveillance Right Size Roadmap to systematically define the rationale, vital capabilities, and optimal "right size" for influenza virologic surveillance. The Roadmap can help states determine the optimal amount of laboratory testing to meet national surveillance goals with confidence that the data provides an accurate picture of what is really happening within the US.
In 2013, the first edition Right Size Roadmap was released. It consolidated requirements for virologic surveillance into one document and provided statistical tools to determine desired and acceptable levels of surveillance. The landscape of surveillance and data sharing capabilities has since evolved significantly, but the original document provides a historical perspective and the statistical foundation for surveillance goals.
View the original Right Size Roadmap and the related resource for alternative data:
HOW TO GET STARTED WITH THE RIGHT SIZE ROADMAP
These resources have been developed and reviewed by APHL members and peers in the public health field, and are provided as example practices.
Resources, guidance and call summaries from the HPAI A H5N1Outbreaks beginning March 2025. As human cases decreased, updates to these documents have also slowed.
These training materials were designed to facilitate a multi-sectoral discussion when there is detection of influenza virus of pandemic potential in poultry and human populations. The training was developed for an international audience but much of the material could be helpful for domestic preparedness as well. The materials consist of didactic lectures, group exercises and a case study-they can also be used in a modular manner for specific epidemiology, veterinary, laboratory or medical audiences. 
