Our projects on viral metagenomics have reconstructed the natural history of ectromelia virus isolates causing mousepox outbreaks in animal house facilities around the world and provided the first genomic sequence from a natural isolate. Studies on herpesviruses showed that herpes simplex virus 1 (HSV-1) and HSV-2 generate greater diversity than expected for DNA viruses. HSV-2, infecting genital mucosa, generates more variants than HSV-1, infecting oronasal mucosa, and this may have contributed to the evolutionary divergence of these viruses adapting to different anatomical niches. We are extending our environmental viral metagenomic projects to the identification of new viruses in Antarctic Dry Valleys, Antarctic and Arctic lake sediments, and water samples from Alpine ecosystems in the Ordesa and Monte Perdido National Park in the Pyrenees. These studies may identify common properties of viruses that inhabit polar and alpine regions, similar extreme ecosystem separated geographically.

The COVID19 pandemic has illustrated the importance of airborne virus transmission and the need to improve the microbiological quality of the air. During the COVID19 pandemic we optimized a filtration technology to capture airborne viruses and have used it to monitor the presence of SARS-CoV-2 in the air of hospitals and to sequence complete genomes of viruses present in air samples. We are extending these studies to other human respiratory viruses. Using this technology, we demonstrated the presence of mpox (monkeypox) virus in air samples during the recent 2022 international mpox outbreak, suggesting that airborne transmission may play a role in future outbreaks of mpox. In collaboration with technologists, we are developing new methods to sample airborne viruses and to inactivate viruses in the air.