Biology subjects

Runstadler, J.

Publications and source records attributed to Runstadler, J..

4 recordsLinked to original sources

bioRxiv2026

H5N5 virus transmission is driven by repeated cross-Atlantic introductions and transmission among high latitude seabirds

In November 2025, the first global H5N5 infection was reported in a person in Washington State. Previously, these viruses had only been detected in seabirds and shorebirds near the Atlantic Ocean, suggesting potentially distinct ecology from dominant H5N1 strains. Using 354 global H5N5 genomes, we show that H5N5 viruses have been carried by high latitude seabirds and shorebirds across the Atlantic at least 9 times, with introductions more frequent in the fall and spring. We reconstruct a plausible path of cross-continental movement via Arctic or sub-Arctic regions, followed by a year of cryptic circulation prior to human spillover. These data show that H5N5 viruses have undergone far more intercontinental movements than previously recognized, and exhibit host and geographic patterns that are fundamentally distinct from dominant H5N1 lineages. The distinct host ecology, geography, and movement, paired with the capacity to infect a person, suggest that enhanced surveillance may be warranted.

evolutionary biology↗

bioRxiv2024

Unbiased, Cell-free Profiling of Single Influenza Genomes at High-throughput

The segmented structure of the Influenza A virus (IAV) genome facilitates reassortment, segment exchange during co-infection. When divergent strains mix across human, agricultural, and wildlife reservoirs novel strains are generated, which has been the source of pandemics. Due to the limited throughput and infection-based assays, IAV reassortment studies has been limited to permissive reassortment. We have developed DE-flowSVP to achieve extremely high throughput, direct profiling of as many as 105 IAV particles in a single-day experiment and enabled quantitative profiling of reassortment propensity between divergent strains for the first time. By profiling reassortants between two naturally circulating low-pathogenicity avian IAVs, we confirmed that molecular incompatibility yields strong preference toward within-strain mixing. Surprisingly, we revealed that two-to-three particle aggregation contributed primarily to genome mixing (75-99%), suggesting that aggregation mediated by sialic acid binding by viral surface proteins provides a secondary pathway to genome mixing while avoiding the co-packaging fitness cost. We showed that genome mixing is sensitively dependent on co-infection timing, relative segment abundances, and viral surface-protein background. DE-flowSVP enables large-scale survey of reassortment potential among the broad diversity of IAV strains informing pandemic strain emergence.

molecular biology↗

bioRxiv2017

Bacterial lipopolysaccharide reduces the stability of avian and human influenza viruses

Commensal bacteria can promote or reduce the severity of viral infection and disease progression in their hosts depending on the specific viral pathogen1. Influenza A virus (IAV) has a broad host-range, comprises many subtypes, and utilizes different routes of transmission including the fecal-oral route in wild birds2. It has been previously demonstrated that commensal bacteria can interact with the hosts immune system to protect against IAV pathogenesis3,4. However, it is unclear whether bacteria and their products may be interacting directly with IAV to impact virion stability. Herein we show that gastrointestinal (GI) tract bacterial isolates in an in vitro system significantly reduce the thermal stability of IAV. Moreover, bacterial lipopolysaccharide (LPS), found on the exterior surfaces of bacteria, was sufficient to significantly decrease the stability of both human and avian viral strains at the physiological temperatures of their respective hosts, as well as in the aquatic environment. Subtype and host-origin of the viruses were shown to affect the extent to which IAV was susceptible to LPS. Furthermore, using a receptor-binding assay and transmission electron microscopy, we observed that LPS binds to and affects the morphology of influenza virions.

microbiology↗

bioRxiv2016

Bayesian Analysis of High Throughput Data

Duplicate or triplicate experimental replicates are commonplace in the high throughput literature. However, it has not been tested whether this is statistically defensible or not. To address this issue, we use probabilistic programming to develop a simple hierarchical model for analyzing high throughput measurement data. With the model and simulated data, we show that a small increase in replicate experiments can quantitatively improve accuracy in measurement. We also provide posterior densities for statistical parameters used in the evaluation of HT data. Finally, we provide an extensible open source implementation that ingests data structured in a simple format and produces posterior densities of estimated measurement and assay evaluation parameters.

Scientific Communication and Education↗