Predicting pandemics through museum animal collections

Coalition studies UNM museum samples to explore pathogens

February 13, 2023

A preserved vampire bat, part of the UNM Museum of Southwest Biology collection, is held by Jonathan L. Dunnum, Ph.D., Senior Collection Manager, Division of Mammals, Museum of Southwestern Biology. Items from the museum's collection will be sampled by Los Alamos and UNM scientists to explore how pathogens travel from one species to another.

Zoonotic pathogens, those that spill over from animals to humans such as SARS-CoV-2 and hantavirus, present a challenge for scientists in terms of how the diseases evolve and spread in animal populations. Now, a broad coalition of institutions, including Los Alamos National Laboratory and the University of New Mexico, seeks to shed light on the evolution and spread of these pathogens before they make the jump into human populations.

“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 Ethan Romero-Severson, a Los Alamos co-lead on the project. “This type of reactive data collection limits our ability to see the clues as to what was going on in the animal populations before the spill-over occurred.”

The central innovation behind the coalition — called the Pathogen Informatics Center for Analysis, Networking, Translation & Education (PICANTE) — directly addresses this deficiency by using the extensive frozen animal-tissue biorepositories housed at natural history museums around the globe. In fact, the most extensive collection of cryopreserved mammalian tissue known to date is housed at UNM’s Museum of Southwestern Biology (MSB).

PICANTE is currently funded through a Phase 1 Predictive Intelligence for Pandemic Preparedness (PIPP) grant from the National Science Foundation.

Premier datasets allow scientists to study host-pathogen relationships

Using the preserved tissues at MSB and those from collaborating biorepositories, scientists in PICANTE can develop screening and genetic sequencing methods to isolate pathogens from these extensive collections. Because the data has been curated and vouchsafed by museums such as MSB over a period of decades, scientists have access to datasets spanning both space and time, resources that would be impossible to collect without the foresight of the collaborators at MSB.

The Los Alamos team includes Romero-Severson and Emma Goldberg, whose role in PICANTE is to develop methods for studying the evolutionary relationships among hosts and pathogens. They will also use pathogen sequence data coming from these biorepositories to document the history of pathogens such as hantavirus jumping between different rodent species.

“If we can understand what allows or inhibits pathogens to move between different animal species, we can better understand the risk animal pathogens pose to human health and global security,” said Romero-Severson. “Despite being a small state, we have a golden opportunity here in New Mexico: UNM has the world’s largest collection of cryopreserved mammalian tissues coupled to an extensive network of international biorepositories, and Los Alamos has decades-long experience developing the methodology to model the evolution, epidemiology and control of pathogens and the computational power to actually implement those methods.”

Romero-Severson added, “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.”

Broad spectrum of expertise and tools

PICANTE represents partnerships among individuals in the fields of engineering, computer sciences, social sciences, pathobiology, epidemiology and virology. In addition, other professionals participate, such as wildlife managers and museum collection managers who will use state-of-the-art genomic sequencing, bioinformatic workflows, geovisualization tools, mathematical modeling and machine-learning approaches to provide pathways for prediction, detection and mitigation of zoonotic pathogens.

“The planning phase allows us to expand efforts in new ways. For example, we can explore 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 Joseph Cook, principal investigator and Distinguished Professor of Biology at UNM.

The partnership includes 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 (CISeAL) in Quito, Ecuador.