Combing the haystacks: The search for highly pathogenic avian influenza virus using a combined clinical and research-developed testing strategy

BackgroundHighly pathogenic H5 avian influenza A has caused sporadic human infections, increasing the risk for potential human-to-human spread. In 2024, the U.S. experienced outbreaks among poultry and cattle, prompting enhanced surveillance. ObjectiveTo evaluate an H5 testing algorithm in subjects with respiratory symptoms presenting for routine care during low influenza A virus circulation. DesignObservational study using clinical- and research-developed nucleic acid amplification tests (NAATs) and pooled screening methods. SettingAcademic medical center in Boston, MA. Participants5,400 symptomatic individuals contributing 6,935 respiratory specimens from June 23 to August 28, 2024. MeasurementsSpecimens underwent initial respiratory pathogen testing per clinical protocols, which did not routinely include influenza due to low summer-month prevalence. Influenza A-positive specimens were subtyped using a clinical assay for H5 assessment. SARS-CoV-2-negative specimens not tested for influenza were screened in pooled batches. Positive pools were deconvoluted to individual specimens and screened for H5 using quantitative polymerase chain reaction. ResultsInfluenza A was detected in 40 of 6,935 specimens (0.6%), comprising 35 of 5,400 unique subjects (0.7%). No H5 infections were identified. Of the 35 influenza-positive individuals, 10 cases (29%) were found through research-specific screening of SARS-CoV-2-negative specimens. No deaths attributed to influenza were recorded. LimitationsSingle center design, convenience sampling, absence of ocular specimens, and minimal sampling in high-risk areas may limit generalizability. ConclusionExpanded influenza testing using pooled NAATs successfully identified low-prevalence influenza A and ruled out H5 in this cohort. These data support targeted influenza screening to enhance surveillance for emerging subtypes rather than a broad-based clinical testing strategy for influenza A testing. Primary Funding SourceSupported by institutional resources and Center for Disease Control and Prevention contracts.