Virus Evolution

Virus evolution, transmission, and pathogenesis in populations at risk

We study the evolution of respiratory viruses of prominent public health concern. During the course of infection, viruses adapt to the host environment. These adaptations may impact virus transmission and disease severity. Our goal is to characterize virus diversity and quantify the impact of host factors on diversity, transmission, and pathogenesis. We can also use genomic epidemiology to track the emergence of novel variants and identify transmission clusters.

We are investigating the dynamic landscape of virus evolution to yield insights into pathogenesis, transmission, and novel virus emergence.

Katherine Johnson

Computational Biologist

Stephanie Banakis

Laboratory Manager

Tung Nguyen

PhD Student, OxCam Program

Shruti Sathish

Postbaccalaureate Fellow

Jack Fiore

Postbaccalaureate Fellow

RyeAnne Ricker

PhD Student

Yin-Ting Yeh

Visiting Researcher

Selected Publications

Veronique Nussenblatt, Allison E. Roder, Sanchita Das, Emmie de Wit, Jung-Ho Youn, Stephanie Banakis, Alexandra Mushegian, Christopher Mederos, Wei Wang, Matthew Chung, Lizzette Perez-Perez, Tara Palmore, Jennifer N. Brudno, James N. Kochenderfer, Elodie Ghedin. Yearlong COVID-19 Infection Reveals Within-Host Evolution of SARS-CoV-2 in a Patient with B-Cell Depletion. J Infect Dis, 2022. PMID: 34940844

Jiarong Ye, Yin-Ting Yeh, Yuan Due, Ziyang Wang, Na Zhang, He Liu, Kunyan Zhang, RyeAnne Rocker, Zhuohang Yu, Allison Roder, Nestor Perea Lopez, Lindsey Organtini, Wallace Greene, Susan Hafenstein, Huaguang Lu, Elodie Ghedin, Mauricio Terrones, Shengxi-Huang, Sharon Xiaolei Huang. Accurate virus identification with interpretable Raman signatures by machine learning. Proc Natl Acad Sci, 2022. PMID: 35653572

Chang Wang, Rebekah Once, Mirella Salvatore, Daniela Chow, Davide Randazzo, Jianjun Yang, Nicholas M Twells, Lara K Mahal, Stacey Schultz-Cherry, Elodie Ghedin. Influenza Defective Interfering Virus Promotes Multiciliated Cell Differentiation and Reduces the Inflammatory Response in Mice. J Virol, 2023. PMID: 37255439

 

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