Public health laboratories perform testing for the detection and routine surveillance for respiratory pathogens, as well as novel influenza virus detection. Surveillance testing informs local, national and international surveillance systems by providing valuable data to guide vaccine development.
Contact the Infectious Diseases team: [email protected]
APHL builds public health laboratory capability to detect, identify and respond to respiratory diseases. We work with the US Centers for Disease Control and Prevention (CDC) to support domestic and international respiratory pathogen surveillance through training, guidance, technical assistance and project management. We also coordinate evaluations of new assays and surveillance approaches for respiratory infections to make the public health response to these pathogens as robust and efficient as possible.
APHL promotes the role of state and local public health laboratories in the detection and surveillance of respiratory viruses. To aid in that process, guidance documents, specimen submission information, protocols and other relevant documents are shared for member use. Be sure to check regularly as guidance is updated at least annually.
Through routine monitoring of viruses in their jurisdiction public health laboratories help to determine what viruses are circulating, where they are circulating and if they are changing in ways that could lead to reduced vaccine efficacy or antiviral resistance.
Public health laboratories and APHL serve as vital partners in national virologic surveillance for respiratory diseases. For guidance and additional resources, such as national teleconferences and follow-up communications, visit the Respiratory Guidance page.
Middle East respiratory syndrome (MERS) is a zoonotic disease caused by Middle East respiratory syndrome coronavirus (MERS-CoV) that was first identified in Saudi Arabia in 2012.
Most state public health laboratories in the US are approved to test for MERS-CoV using CDC's rRT-PCR assay. This test is conducted under the authority of EUA because there are no FDA-cleared/approved tests available for diagnostic purposes in the US.
Current testing and sequencing guidance and resources for MERS-CoV are available on the Respiratory Guidance page.
For information about the 2014 MERS-Cov public health response, visit the APHL Public Health Response Coordination page.
SARS-CoV-2 is commonly referred to by the disease it causes: Coronavirus Disease (COVID-19). APHL works domestically and internationally to develop or clarify SARS-CoV-2 testing guidance, implement training and provide necessary support for laboratories to perform safe, high quality and effective testing to meet the diagnostic and surveillance needs of their jurisdiction.
Public health laboratories continue to perform diagnostic and surveillance testing for SARS-CoV-2 as part of their larger respiratory diseases testing portfolio. Current testing and sequencing guidance and resources are available on the Respiratory Guidance Page.
Testing wastewater for SARS-CoV-2 is a tool that public health officials can use to better understand community COVID-19 infection trends. Because SARS-CoV-2 can be shed in the feces of infected symptomatic and asymptomatic individuals, wastewater can be tested for SARS-CoV-2 RNA to provide early estimates of increasing and decreasing infection trends of the people living or working in a wastewater collection area, or "sewershed.” If you are interested in learning more about SARS-CoV-2 testing in wastewater check out our Wastewater Surveillance page or the CDC Dashboard.
For information about the 2020-2022 worldwide COVID-19 pandemic and APHL’s role in the public health response, visit the APHL Public Health Response Coordination page.
Report of survey results on testing needs of APHL's member laboratories during the first 59 weeks of the COVID-19 pandemic.
Results from 2024 survey of US public health laboratories on their capacity for SARS-CoV-2 sequencing. Findings about testing and resources will guide a national SARS-CoV-2 surveillance strategy.
Enteroviruses (EV) are respiratory viruses that are associated with acute respiratory illness. Increasingly, non-polio enteroviruses have been tied to outbreaks of acute flaccid myelitis (AFM) and both community and institutional outbreaks of meningitis, encephalitis, and neonatal sepsis-like illness, primarily in children. To better characterize circulation patterns, CDC and APHL have initiated a program to support surveillance efforts through testing of specimens at two of the established Vaccine Preventable Disease Reference Centers. Data from the project will be submitted to the National Enterovirus Surveillance System. In establishing the EV surveillance project, APHL and CDC hope to better characterize EV circulation patterns to prepare for potential future outbreaks.
Public health laboratories perform three critical influenza-related functions: diagnostic testing for influenza virus, routine/seasonal surveillance and novel influenza virus detection. Public health laboratories are actively engaged in national influenza surveillance; they contribute specimens to the National Influenza Reference Centers (NIRCs) to meet Right Size goals (see Right Size Resources on Respiratory Guidance Page) and their data is included in CDC's weekly FluView publication. In support of these roles, APHL provides timely updates and informational resources to support influenza testing in public health laboratories.
APHL supports six Influenza Sequencing Centers (ISCs) including contracts, project management and ensuring data messaging and transfer to CDC. The ISCs are public health laboratories that contribute to national surveillance goals by sequencing additional influenza viruses from their jurisdiction each year. The ISCs are strategically placed across the US to ensure the greatest variety of viruses possible (e.g., in high-travel or metropolitan areas that are geographically diverse):
In collaboration with CDC, APHL established the NIRCs in 2009 to expand national influenza sequencing capacity, support national vaccine strain selection efforts and monitor influenza antiviral resistance. NIRCs meet these goals through next generation sequencing (NGS) and virus isolation from specimens submitted from state and territorial public health laboratories nationwide. Sequencing at the NIRCs provides close to real-time NGS data for national surveillance due to a continuous integration between the NIRCS and CDC, utilizing several systems developed and deployed on the APHL Informatics Messaging Services (AIMS) cloud-based environment for data transfer and analysis.
State and territorial public health laboratories regularly submit influenza positive specimens—every two weeks during the influenza season—to their designated NIRC, in accordance with national influenza surveillance guidance to meet Influenza Right Size goals.
For questions about submission to the NIRCs, contact [email protected].
The most common novel influenza virus detection in the US has been highly pathogenic avian influenza (HPAI) viruses. They are highly contagious and frequently cause fatal disease, primarily affecting poultry. They may also be referred to as bird or avian flu. Since late March 2024, outbreaks of HPAI A(H5N1) in dairy cows have been occurring in the US and they have impacted humans, animals (wild birds, domestic poultry, livestock [particularly dairy cows], other wild mammals and pets) and food products. Monitoring for additional cases and human impact is ongoing.
To learn more about APHL’s role in the H5N1 public health response, visit our Public Health Response Coordination page.
For Testing resources, call summaries and response communications, visit the Respiratory Guidance page.
Legionella bacteria naturally occur in fresh water but can multiply to harmful levels in manmade water systems that are not properly maintained. Infection with Legionella bacteria (Legionellosis) varies in severity from a mild illness (Pontiac fever) to severe pneumonia (Legionnaires' disease). The most common route of exposure is inhalation of aerosolized water contaminated with Legionella bacteria. Legionella pneumophila serogroup 1 is the predominant species and serogroup associated with Legionnaires' disease. Public health laboratories may perform clinical and/or environmental testing for Legionellosis case detection, outbreak response and surveillance. Laboratory testing for investigation of suspected Legionellosis outbreaks can be complex, as Legionella bacteria are notoriously difficult to culture and linking human cases to environmental sources is very challenging
APHL and CDC launched the Legionella Reference Center (LRC) in 2023 to expand access to clinical and environmental testing for case detection and outbreak responses. The current LRC is the State Hygienic Laboratory at the University of Iowa.
All US state, local and territorial public health and environmental laboratories are eligible for enrollment in the LRC.
Eligible laboratories must submit an enrollment application and receive approval prior to using the reference center. In order to access the enrollment application, you will need to log into your APHL account (Create a free APHL account if you don't already have one). CDC testing services remain available as described in the CDC testing directory.
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections among young children. RSV is classified into two subtypes, A and B, which circulate widely in the US; however, circulating viruses are not well characterized and there is a dearth of RSV genetic sequence information. To improve the understanding of the molecular epidemiology of actively circulating RSV viruses and the potential impact of virus diversity on intervention or treatment efforts, APHL and CDC are supporting a program for ongoing virologic surveillance for RSV in the US.
For the most recent submission guidance and GFAT Form, visit the Respiratory Guidance Page.
Visit the Respiratory Virus Roundup page to read previous issues and subscribe for updates on workshops, training, diagnostic methods and guidance to support ongoing surveillance for influenza, RSV, SARS-CoV-2 and other viral respiratory pathogens.
Visit the APHL Respiratory Diseases Testing Guidance for more resources and training information.
Visit the APHL Training Hub to search our training materials, access courses through the APHL Learning Center, and find upcoming webinars via the Event Calendar.
