A collaborative partnership of researchers at the University of New Mexico, Los Alamos National Laboratory, New Mexico State University, University of Kansas, Gorgas Memorial Institute in Panama, and the Center for Research on Health in Latin America in Quito, Ecuador, are developing a new model for predicting pandemics thanks to a $1 million planning grant from the National Science Foundation’s Predictive Intelligence for Pandemic Prevention Phase I program

Currently in the planning phase, the goal of the Pathogen Informatics Center for Analysis, Networking, Translation & Education, or PICANTE! is to move from a purely reactive approach to pandemics to an approach that is both predictive and proactive. One of the large challenges of understanding the risk of zoonotic pathogens that spillover from animals to humans such as SARS-CoV-2 and hantavirus here in New Mexico is knowing how diseases are evolving and spreading in animal populations.

The PICANTE effort represents partnerships among individuals in the fields of engineering, computer sciences, social sciences, pathobiology, epidemiology and virology. PICANTE will take aim at shedding light on the evolution and spread of pathogens before they spill over into human populations by studying and using the extensive frozen animal tissue biorepositories housed at the UNM Museum of Southwestern Biology (MSB). This foundation will be utilized to determine the social, environmental, and biological features contributing to pandemic risk.

UNM has the world’s largest collection of cryopreserved mammalian tissues coupled to an extensive network of international biorepositories, while Los Alamos National Laboratory (LANL) has decades-long experience developing methodology to model the evolution, epidemiology, and control of pathogens and the computational power to implement those methods. LANL’s team, which includes Ethan Romero-Severson and Emma Goldberg, will develop methods for studying the evolutionary relationships among hosts and pathogens by utilizing pathogen sequence data coming from these biorepositories to document the history of pathogens such as hantavirus jumping between different rodent hosts.

New Mexico State University adds expertise in fungal pathogens and the University of Kansas has expertise in mammalian genetics, biorepository, and spatial (GIS) analyses. Collaborating institutions in Panama and Ecuador are at the frontlines of pathogen emergence and human/wildlife interfaces. If scientists can understand what allows or inhibits pathogens to move between different animal species, scientists can better understand the risk animal pathogens serve to human health and global security.

Using tissues from the UNM Museum of Southwestern Biology’s mammal collection and from other collaborating biorepositories, scientists in PICANTE will develop screening and genetic sequencing methods to isolate pathogens that can be adopted by natural history museums across the globe. Because the data have been curated and vouchsafed by museums such as MSB over a period of decades, scientists have access to datasets spanning both space and time that otherwise would be impossible to collect.

“Ever since the devastating emergence of hantavirus in the Four Corners region, UNM has maintained a leadership role in zoonotic pathogen research and mitigation efforts in the Southwest and internationally,” said UNM Distinguished Professor of Biology and Principal Investigator Joseph Cook. “UNM’s multidisciplinary approach has been facilitated by close collaborative ties that span the Health Sciences Center, international partners, and diverse scientists who leverage the vast biodiversity collections and associated informatics resources of the Museum of Southwestern Biology and other natural history biorepositories.”

By examining the dynamic environmental interfaces between wildlife and semi-urban and rural communities, the team will strategically monitor the pathways for prediction, detection, and mitigation of zoonotic pathogens at the nexus of emerging infectious disease. This work could shed light on how pathogens jump between species and what conditions lead to increased risk of spillover into human populations.

By using state-of-the-art genomic sequencing, bioinformatic workflows, geovisualization empowered interactive web tools, mathematical modeling, and machine learning approaches, researchers will be able to interpret, analyze and communicate data from vast biorepositories to predict the next pandemic.

“Our understanding of pathogens with high spill-over potential is limited by our preference for sampling human cases after a spill-over has already happened,” said Romero-Severson, a Los Alamos co-lead on the project. “This type of reactive data collection limits our ability to see the clues to what was going on in the animal populations before the spill-over occurred.”

SARS-CoV-2 demonstrated that pandemics pose a global challenge in desperate need for new international, collaborative solutions. With researchers spanning the fields of engineering, computer sciences, social sciences, pathobiology, epidemiology, virology, wildlife managers, and museum collection managers, PICANTE addresses this need.

“The planning phase allows us to expand efforts in new ways, with new initiatives in engineering to more efficiently detect and screen new pathogens from museum collections, in social sciences to work more closely and productively with rural communities, and in computer sciences to model human-pathogen-environment dynamics,” said Cook.

“PICANTE offers a new way for Los Alamos and UNM scientists to collaborate on some of the most pressing questions that will dominate the intersection of public health and global security in the coming decades,” added Romero-Severson.

The next phase of this effort will be a full proposal for an NSF PIPP Center due in early 2024.