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medRxivFeb 2025 DOI:
10.1101/2025.02.12.25321810

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

Adams, Gordon; Devlin, J; Klontz, Erik H.; Laing, R; Branda, John A.; Chowdhury, Navid; Kwon, Soonil; Sabeti, Pardis C.; Stachler, Elyse; Thiriveedhi, Vamsi; Shenoy, Erica S.; Lemieux, Jacob E.; Turbett, Sarah E.
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Abstract
Background: Highly 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. Objective: To evaluate an H5 testing algorithm in subjects with respiratory symptoms presenting for routine care during low influenza A virus circulation. Design: Observational study using clinical- and research-developed nucleic acid amplification tests (NAATs) and pooled screening methods. Setting: Academic medical center in Boston, MA. Participants: 5,400 symptomatic individuals contributing 6,935 respiratory specimens from June 23 to August 28, 2024. Measurements: Specimens 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. Results: Influenza 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. Limitations: Single center design, convenience sampling, absence of ocular specimens, and minimal sampling in high-risk areas may limit generalizability. Conclusion: Expanded 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.
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