Pursuit: unveiling microbial eukaryotic melting-pots: virus emergence via RNA-DNA gene transfer

The National Science Foundation Division of Environmental Biology awarded Portland State University $1,020,345 on September 1, 2026, to discover and characterize cruciviruses—hybrid viruses exhibiting both RNA and DNA genetic features—and their eukaryotic host microorganisms in environmental samples, advancing understanding of virus evolution and horizontal gene transfer mechanisms.

The project develops biotechnological and artificial intelligence tools to detect cruciviruses in soil, freshwater, seawater, and hot spring samples, and isolates the protist microbes they infect. Work proceeds through three research aims: establishing an ecological framework for DNA-RNA gene exchange using novel molecular enrichment techniques; identifying crucivirus-infected protists via fluorescence-activated cell sorting to isolate host-crucivirus pairs and explore in vivo mechanisms of RNA-DNA gene transfer; and determining crucivirus origin and evolutionary pathways through sequence analysis. The research strengthens the biotechnology workforce through training and informs public understanding through outreach events. Potential applications extend to detection and prediction of future viral pandemics.

Performance occurs at Portland State University in Portland, Oregon, with a period of performance from September 1, 2026, through August 31, 2029. The award is funded under NSF's Biological Sciences program (CFDA 47.074), which supports basic research to advance the biological sciences and enhance understanding of major national problems.

Abstract

The origin of viruses and how they evolve is poorly understood. DNA viruses, like herpesviruses, were thought to evolve completely separately from RNA viruses, like flu. Recently discovered cruciviruses that appear to have evolved from both RNA and DNA viruses challenge that thought. This project seeks to understand the evolution of cruciviruses by developing biotechnological and artificial intelligence (AI) tools to 1) discover cruciviruses in environmental samples, and 2) isolate the microbes that they infect. Beyond advancing the understanding of virus evolution, this work serves the national interest by creating technologies with potential broader applications including detection and prediction of future viral pandemics. Furthermore, this research will strengthen our future biotechnology workforce through training, and inform the general public through outreach events. This project is focused on the targeted discovery of cruciviruses and related RNA-viruses, and their eukaryotic host microorganisms in environmental samples to assess patterns of horizontal gene transfer in virus evolution. This will be done by pursuing three research aims. First, IT will establish an ecological framework for DNA/RNA gene exchange. Novel molecular enrichment techniques will preferentially amplify cruciviruses and related RNA-viruses, DNA-viruses and plasmids in soil, fresh- and sea water, and hot spring samples. Second, the project will identify crucivirus-infected protists from environmental samples. Fluorescence-activated cell sorting on samples will be used to detect associations of cruciviruses with host organisms. The isolation of a host-crucivirus pair will allow exploration of the molecular mechanisms and in vivo analysis of RNA-DNA gene transfer and identify new protists and their viruses. Finally, the project will determine the origin and evolution of cruciviruses using sequence analysis. Multipartite network analysis and machine learning (AI) trained for virus-type recognition will be used to model the evolutionary history of cruciviruses. This will allow an examination of their possible role in DE novo virus emergence. These three aims will enhance our understanding the origin of ubiquitous, poorly understood circular single-stranded DNA viruses, and the evolution and mechanisms of gene transfer between RNA and DNA viruses. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the foundation's intellectual merit and broader impacts review criteria.- subawards are not planned for this award.