Researchers Take Virus-Tracking Software Worldwide
Associate professor Daniel Janies, PhD, an expert in computational genomics at the Wexner Medical Center at The Ohio State University (OSU), is working with software engineers at the Ohio Supercomputer Center (OSC) to expand the reach of SUPRAMAP (supramap.org), a web-based application that synthesizes large, diverse datasets so that researchers can better understand the spread of infectious diseases across hosts and geography. By separating SUPRAMAP's client application from the underlying server software, the goal is to reconfigure the server in a way that researchers and public safety officials can develop other front-end applications that draw on the logic and computing resources of SUPRAMAP. Janies and his colleagues at Ohio State, the American Museum of Natural History (AMNH) and OSC developed SUPRAMAP in 2007 to track the spread and evolution of pandemic (H1N1) and avian influenza (H5N1). Using SUPRAMAP, we initially developed maps that illustrated the spread of drug-resistant influenza and host shifts in H1N1 and H5N1 influenza and in coronaviruses, such as SARS, says Janies. SUPRAMAP allows the user to track strains carrying key mutations in a geospatial browser such as Google EarthTM. Our software allows public health scientists to update and view maps on the evolution and spread of pathogens. The original implementation of SUPRAMAP was built with a single client that was tightly coupled to the server software. We now have decoupled the server from the original client to provide a modular web service for POY, (poyws.org) an open-source, freely available phylogenetic analysis program developed at AMNH. The web service can be used by other researchers with new ideas, data, and clients to create novel applications, says Ward Wheeler, PhD, curator-in-charge of scientific computing at AMNH and a coauthor with Janies and others on a recent article about the project in the journal Cladistics. To demonstrate the POY web service, we have produced a new client software application, GEOGENES (www.geogenes.org), says Wheeler. Unlike in SUPRAMAP, in which the user is required to create and upload data files, in GEOGENES the user works from a graphical interface to query a curated dataset, thus freeing the user from managing files. Currently this service is hosted on large shared systems at OSC, the centers flagship HP Intel Xeon Oakley Cluster, their IBM Opteron Glenn Cluster and on a smaller dedicated cluster at Ohio States Wexner Medical Center. Decoupling the client from the server provides another advantage in that the implementation of the server can change to take advantage of advances in computing technology, notes Thomas Bitterman, a senior software engineer at OSC and co-author of the journal article. For example, the recent addition of the Oakley Cluster at OSC has made available a large set of GPUs that could result in performance improvements. To give their new software implementation a proper road test, the researchers examined groups of key mutations in a pathogen they hadnt tracked before the H7 avian influenza virus. Infection of humans by the H7 virus is rare, but it has occurred among people who have direct contact with infected poultry. H7 influenza, like H5N1 is largely an avian virus, but infects humans periodically, and therefore we wanted to see how it evolves, says Janies. We have shown that pathogenicity of the H7 influenza is highly labile on a molecular evolutionary level and has occurred independently in many places around the world. Now that the H5N1 papers detailing transmission among mammals have been published, we can next pinpoint the natural geographic distribution of key sets of mutations that could lead to human-to-human transmission. Our maps will allow scientists to better deploy public health resources to protect citizens and forces in the field. Grant funding through the U.S. Army Research Laboratory and Office supports this Innovation Group on Global Infectious Disease Research (gidr.osu.edu) project. Support for the computational requirements of the project comes from AMNH and OSC. Ohio States Wexner Medical Center, Department of Biomedical Informatics and offices of Academic Affairs and Research provide additional support.
The Next Frontier in Infection Control: AI-Driven Operating Rooms
Published: July 15th 2025 | Updated: July 15th 2025Discover how AI-powered sensors, smart surveillance, and advanced analytics are revolutionizing infection prevention in the OR. Herman DeBoard, PhD, discusses how these technologies safeguard sterile fields, reduce SSIs, and help hospitals balance operational efficiency with patient safety.
Targeting Uncertainty: Why Pregnancy May Be the Best Time to Build Vaccine Confidence
July 15th 2025New national survey data reveal high uncertainty among pregnant individuals—especially first-time parents—about vaccinating their future children, underscoring the value of proactive engagement to strengthen infection prevention.
CDC Urges Vigilance: New Recommendations for Monitoring and Testing H5N1 Exposures
July 11th 2025With avian influenza A(H5N1) infections surfacing in both animals and humans, the CDC has issued updated guidance calling for aggressive monitoring and targeted testing to contain the virus and protect public health.
IP LifeLine: Layoffs and the Evolving Job Market Landscape for Infection Preventionists
July 11th 2025Infection preventionists, once hailed as indispensable during the pandemic, now face a sobering reality: budget pressures, hiring freezes, and layoffs are reshaping the field, leaving many IPs worried about their future and questioning their value within health care organizations.
