A highly pathogenic bird flu variant circulated undetected across wild bird populations for months before it was identified, and then spread rapidly across the continental United States in a stepwise pattern that surveillance systems only partially captured. The finding, detailed in a new phylodynamic analysis of H5N1 genotype D1.1, exposes a blind spot in how quickly emerging variants can establish and disseminate before routine detection systems recognize them—and underscores the risk that future variants might follow the same pattern without detection until clusters of human illness appear.
The D1.1 genotype of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b became the dominant bird flu strain circulating in North America by late 2024, replacing earlier variants that had circulated since the virus first arrived in 2021. Researchers combining Arizona wildlife surveillance with phylodynamic analysis of publicly available genetic sequences reconstructed the timing and geographic spread of D1.1 across the four major flyway regions of North America. The analysis reveals that the variant likely diverged from earlier lineages in late 2023 but did not begin its major expansion until mid-2024—a period of undetected circulation of several months during which the virus spread without being identified. Once detected in the Pacific Flyway around September 2024, D1.1 then disseminated in a predominantly west-to-east pattern through adjacent flyway regions over the following months.
An Invisible Expansion Window
The most striking finding is the timing mismatch: genetic analysis places D1.1’s emergence around late June to July 2024, but the variant was not detected until September 2024—a three-month gap during which the virus was actively transmitting, reassorting, and evolving in wild bird populations. That period of undetected spread is consistent with patterns observed in earlier H5N1 lineages, suggesting it is not anomalous but rather endemic to how novel variants establish themselves before entering routine surveillance networks.
During these months, D1.1 was likely spreading across multiple states and flyways without triggering alerts. Only when it reached sufficient prevalence in late September to be captured by existing surveillance systems—primarily through testing of sick or dead birds—did its presence become apparent. By that point, the variant had already achieved regional establishment and was positioned to spread further.
Stepwise Geographic Dissemination
Once detected, D1.1 expanded in a geographically predictable pattern: from the Pacific Flyway (early source), through the Central Flyway (secondary hub for further spread), then to the Mississippi and Atlantic flyways later in fall 2024. The Pacific Flyway functioned as the primary source region early in the season, exporting virus to adjacent regions. The Central Flyway transitioned from receiving introductions to becoming a secondary transmission hub, while the Atlantic Flyway primarily acted as a sink, receiving lineages but contributing less to onward geographic spread.
Importantly, transitions between flyways occurred mainly between adjacent regions, not as long-distance jumps from coast to coast. This stepwise dissemination pattern suggests that if surveillance had detected D1.1 earlier in the Pacific region, targeted monitoring and response in the Central Flyway could have potentially slowed or tracked its subsequent expansion eastward.
Closing the Detection Gap Before the Risk Materializes
The D1.1 genotype has demonstrated substantial zoonotic potential. By early 2025, confirmed human infections had occurred, including a fatal case in Louisiana. The new analysis found no immediate genetic markers in the Arizona isolates examined—such as the Q226L substitution that alters receptor binding to favor human cells—predicting imminent human transmissibility. However, the absence of such a marker does not mean the risk is absent. It underscores a larger problem: emerging avian influenza variants may routinely circulate for weeks or months before detection systems identify them, establishing themselves across multiple regions before alert systems activate.
That detection gap carries direct preparedness implications. If surveillance depends on detecting illness clusters or waiting for variants to reach high prevalence, early detection windows are lost, and the opportunity to track mutations in real time vanishes. The authors argue that coordinated genomic surveillance across adjacent flyways—particularly during pre-migration seasons—could compress that lag. Standardized sequencing, validated bioinformatics pipelines, rapid data sharing among states, and integration of wildlife and poultry surveillance within a One Health framework could all accelerate identification of novel variants and flag emerging genetic changes before they spread.
Sources and further reading:
Scotch M, Faleye T, Urquidez-Negrete A, et al. Rapid Expansion of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Genotype D1.1 Virus across Flyway Regions, North America, Fall 2024. Emerging Infectious Diseases, July 13, 2026.
This article was researched and sourced by Global Biodefense editors and reported with Claude AI assistance for drafting and editing.