I study how viruses and bacteria evolve using experimental and computational methods. I am currently a James S. McDonnell Foundation postdoctoral fellow at Stanford University, where I study microbiome evolution in the labs of David Relman and Dmitri Petrov. In my PhD, I studied how influenza viruses evolve within hosts in Jesse Bloom’s lab at the University of Washington and Fred Hutchinson Cancer Research Center.

Evolution in the human microbiome

How do adaptation and dispersal shape the human microbiome?

The trillions of microbes that live in and on the human body play crucial roles in human health and disease. As a postdoctoral fellow, I am working with Dmitri Petrov and David Relman to understand how these microbial communities change over time through both mutation and strain migration.

I am currently studying how household transmission shapes the human microbiome. For more, see our study website here. This work is funded by a postdoctoral fellowship from the James S. McDonnell Foundation.

Evolution of influenza viruses

Image credit: Kim Carney

How do influenza viruses evolve within hosts?

Influenza viruses evolve rapidly from year to year across the globe, with immense consequences for human health. This rapid global evolution begins with mutations that arise as viruses replicate within infected individuals. In my PhD work in Jesse Bloom’s lab, I used deep sequencing to determine how and why influenza viruses evolve within hosts.

My work has shown that influenza viruses can cooperate in cell culture (Xue et al., eLife 2016); influenza viruses can evolve similarly in chronic infections and on a global scale (Xue et al., eLife 2017); and influenza’s genetic diversity within hosts is dominated by transient, deleterious mutations (Xue et al., Virus Evolution 2020).

For this work, I was a finalist for the Walter M. Fitch Award (2017), and I received the James F. Crow Early Career Researcher Award (2018) and the Harold M. Weintraub Graduate Student Award (2018). My research has been covered in The Atlantic, Wired, and Science News, and I have also given a public lecture on my work at Seattle Town Hall. I was funded by the NSF Graduate Research fellowship (2014-2017) and a Fannie and John Hertz Foundation fellowship (2015-2019).

Selected publications

Xue, K.S., Bloom, J.D. Linking influenza virus evolution within and between human hosts. Virus Evolution 6(1): veaa010. (2020). DOI: 10.1093/ve/veaa010

Xue, K.S., Moncla, L.H., Bedford, T., Bloom, J.D. Within-host evolution of human influenza virus. Trends in Microbiol. 26(8):781-793(2018). DOI: 10.1016/j.tim.2018.02.007

Xue, K.S., Stevens-Ayers, T., Campbell, A.P., Englund, J.A., Pergam, S.A., Boeckh, M., Bloom, J.D. Parallel evolution of influenza across multiple spatiotemporal scales. eLife 6: e26875 (2017). DOI: 10.7554/eLife.26875

Xue, K.S., Hooper, K.A., Ollodart, A.R., Dingens, A., Bloom, J.D. Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture. eLife 5: e13974 (2016). DOI: 10.7554/eLife.13974

Other publications

Xue, K.S., Bloom, J.D. Reconciling disparate estimates of viral genetic diversity during human influenza infections. Nature Genetics 51:1298-1301(2019). DOI: 10.1038/s41588-019-0349-3

Davis, A.K.F., McCormick, K., Gumina, M.E., Petrie, J.G., Martin, E.T., Xue, K.S., Bloom, J.D., Monto, A.S., Bushman, F.D., Hensley, S.E. Sera from individuals with narrowly focused influenza virus antibodies rapidly select viral escape mutations in ovo. J. Virol.:00859-18 (2018). DOI: 10.1128/JVI.00859-18

Xue, K.S., Greninger, A.L., Pérez-Osorio, A., Bloom, J.D. Cooperating H3N2 influenza virus variants are not detectable in primary clinical samples. mSphere 3: e00552-17 (2017). DOI: 10.1128/mSphereDirect.00552-17