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Jeffrey Houpt Distinguished Investigator
Professor and Chair
6012 Marsico Hall


Viral Genome Replication

Our laboratory is contributing to pandemic preparedness by elucidating the details of genome replication using the most tractable models for several families of RNA viruses.

Viral infection poses a never-ending threat to human health. It is nearly impossible to predict the next viral outbreak of concern because of the ever-evolving nature of viruses and the potential for new human pathogens to originate in non-human members of the animal kingdom. Readiness for a viral epidemic of unknown etiology requires broad-spectrum, antiviral therapeutics and universal strategies for viral attenuation, for example strategies based on attenuating changes to the activity of a conserved viral enzyme. Our laboratory has had a longstanding interest in discovering fundamental biological knowledge relevant to the treatment and/or prevention of viral infection.

The era of biology on the single-cell level is well underway, and we have become a standard-bearer for “single-cell virology.” Currently, most studies emphasize the between-cell variability of populations in terms of gene expression. Even those studies with viral infection as the focus emphasize end-point differences in yield of virus or viral nucleic acid. No doubt there is much to learn from these studies. However, there is also much to be learned by evaluating viral infection dynamics on the single-cell level.

We have developed a microfluidics-based, cell-culturing, imaging, and data-analysis platform that enables high-throughput, kinetic analysis of single, isolated cells infected with a viral population harboring fluorescent reporters. We have observed unprecedented between-cell variation in the onset, speed, and yield of replication, as well as variation in lysis, both if and when lysis occurs. Our studies demonstrate that analysis of viral infection dynamics on the single-cell level yields knowledge about virus-host interactions and the response of the host to viral infection eluded by population methods.

Selected Preprints and Publications

  • Chinthapatla, R., Sotoudegan, M., Srivastava, P., Anderson, T.K., Moustafa, I.M., Passow, K.T., Kennelly, S.A., Moorthy, R., Dulin, D., Feng, J.Y., Harki, D.A., Kirchdoerfer, R.N., Cameron, C.E., and Arnold, J.J. Interfering with nucleotide excision by the coronavirus 3′-to-5′ exoribonuclease. (2023). Nucleic Acids Res 51, 315-336
  • Kim, H., Aponte-Diaz, D., Sotoudegan, M.S., Shengjuler, D., Arnold, J.J., and Cameron, C.E. The enterovirus genome can be translated in an IRES-independent manner that requires the initiation factors eIF2A/eIF2D. (2023). PLoS Biol 21, 315-336.
  • Yeager, C., Carter, G., Gohara, D.W., Yennawar, N.H., Enemark, E.J., Arnold, J.J., and Cameron, C.E. (2022). Enteroviral 2C protein is an RNA-stimulated ATPase and uses a two-step mechanism for binding to RNA and ATP. Nucleic Acids Res 50, 11775-11798.
  • Li, Y., Misumi, I., Shiota, T., Sun, L., Lenarcic, E.M., Kim, H., Shirasaki, T., Hertel-Wulff, A., Tibbs, T., Mitchell, J.E., McKnight, K.L., Cameron, C.E., Moorman, N.J., McGivern, D.R., Cullen, J.M., Whitmire, J.K., and Lemon S.M. (2022). The ZCCHC14/TENT4 complex is required for hepatitis A virus RNA synthesis. Proc Natl Acad Sci U S A 119, e2204511119.
  • Jiang, Y., Hoenisch, R.C., Chang, Y., Bao, X., Cameron, C.E., and Lian, X.L. (2022). Robust genome and RNA editing via CRISPR nucleases in PiggyBac systems. Bioact Mater 14, 313-320.
  • Janissen, R., Woodman, A., Shengjuler, D., Vallet, T., Lee, K.M., Kuijpers, L., Moustafa, I.M., Fitzgerald, F., Huang, P.N., Perkins, A.L., Harki, D.A., Arnold, J.J., Solano, B., Shih, S.R., Vignuzzi, M., Cameron, C.E., and Dekker, N.H. (2021). Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses. Mol Cell 81, 4467-4480.
  • Passow, K.T., Caldwell, H.S., Ngo, K.A., Arnold, J.J., Antczak, N.M., Narayanan, A., Jose, J., Sturla, S.J., Cameron, C.E., Ciota, A.T., and Harki, D.A. (2021). A Chemical Strategy for Intracellular Arming of an Endogenous Broad-Spectrum Antiviral Nucleotide. J Med Chem 64, 15429-15439.
  • Seifert, M., Bera, S.C., van Nies, P., Kirchdoerfer, R.N., Shannon, A., Le, T.T., Meng, X., Xia, H., Wood, J.M., Harris, L.D., Papini, F.S., Arnold, J.J., Almo, S., Grove, T.L., Shi, P.Y., Xiang, Y., Canard, B., Depken, M., Cameron, C.E., and Dulin, D. (2021). Inhibition of SARS-CoV-2 polymerase by nucleotide analogs from a single-molecule perspective. Elife 10, e70968.
  • Bera, S.C., Seifert, M., Kirchdoerfer, R.N., van Nies, P., Wubulikasimu, Y., Quack, S., Papini, F.S., Arnold, J.J., Canard, B., Cameron, C.E., Depken, M., and Dulin, D. (2021). The nucleotide addition cycle of the SARS-CoV-2 polymerase. Cell Rep 36, 109650.
  • Stern-Ginossar, N., Kanneganti, T.D., Cameron, C.E., Lou, Z., Cherry, S., Abraham, J., and Martin-Sancho, L. (2021). Rising to the challenge of COVID-19: Working on SARS-CoV-2 during the pandemic. Mol Cell 81, 2261-2265.

Link to My Bibliography