FIELDS OF INTEREST

Retroviruses; Primate lentiviruses (HIV and SIV); Co-evolution of viruses and their hosts

 

ACADEMIC PROFILE

Work in our laboratory combines traditional, molecular virology with evolutionary genetics, in order to study how viruses adapt to their hosts. Our goal is to understand how virus evolution is influenced by genetic variation both within host populations(polymorphism) and between host species (divergence). Current projects in thelaboratory focus on retroviruses, specifically the lentiviruses of  humans and their primate relatives (the human and simian immunodeficiency viruses – HIV and SIV). Among other things, we are interested in the interactions between these viruses and host genes thatact as genetic barriers to cross-species transmission (also known as restriction factors), and in understanding how viruses adapt to new genetic environments once a species barrier has been breeched. We are also interested in how lentiviruses adapt withinindividuals, particularly in response to shifting selective pressures imposed by virus-specific, polyclonal antibody responses.

REPRESENTATIVE PUBLICATIONS

Fofana IB, Colantonio AD, Reeves RK, Connole MA, Gillis JM, Hall LR, Sato S, Audin CR, Evans DT, Shida H, Johnson RP, Johnson WE. 2011. Flow cytometry based identification of simian immunodeficiency virus Env-specific B lymphocytes. J ImmunolMethods. 370(1-2):75-85

Gokcumen, O.O., Babb, P.L., Iskow, R., Zhu, Q., Shi, X. Mills, R.E., Ionita-Laza, I., Vallender, E.J., Clark, A.G., Johnson, W.E., Lee, C. 2011. Refinement of primate CNV hotspots identifies candidate genomic regions evolving under positive selection. Genome Biology.12(5):R52

Johnson, W.E. 2010. Endless Forms Most Viral. PLoS Genetics 6(11): e1001210.

Kirmaier, A., Wu, F., Newman, R.M., Hall, L.R., Morgan, J.S., O’Connor, S., Marx, P.A.,Meythaler, M., Goldstein, S., Buckler-White, A., Kaur, A., Hirsch, V., Johnson, W.E.2010.TRIM5 Suppresses Cross-Species Transmission of a Primate Immunodeficiency Virus and Selects for Emergence of Resistant Variants in the New Species. PLoS Biology8(8):e1000462

Jia, B., Serra-Moreno, R., Neidermyer, W., Rahmberg, A., Mackey, J., Fofana, I., Johnson, W.E., Westmoreland, S., Evans, D.T. 2009. Species-specific Activity of SIV Nef and HIV-1 Vpu in Overcoming Restriction by Tetherin/BST2.  PLoS Pathogens 5:e1000429.PMCID:PMC2673686

Kirmaier, A., Diehl, W. and Johnson, W.E. 2009. Acquisition and processing of nonhuman primate samples for genetic and phylogenetic analyses. Methods 49:5-10.PMID: 19508893

McNatt, M.W., Zang, T., Hatziioannou, T., Bartlett, M., Fofana, I.B., Johnson, W.E., Neil, S.J.D., Bieniasz, P.D. 2009. Species-specific activity of HIV-1 Vpu resulting from positive selection of Tetherin variants. PLoS Pathogens (5) e1000300.

Johnson, W.E. and Sawyer, S.L. 2009. Evolution of the antiretroviral TRIM5 gene.Immunogenetics 61:63-76

 

Johnson, W.E. 2008. A Proviral Puzzle with a Prosimian Twist. Proceedings of the National Academy of Sciences 105:20051-20052.

Sato, S., Yuste, E., Lauer, W.A., Chang, E-H., Morgan, J.S., Bixby, J.G., Lifson, J.D., Desrosiers,R.C., and Johnson, W.E. 2008. Potent antibody mediated neutralization and evolution of antigenic escape variants of simian immunodeficiency virus strain SIVmac239 in vivo. Journal of Virology 82:9739-52.

Vallender, E. and Johnson, W.E. 2008. Balancing Selection in Human Evolution. In The Encyclopedia of Life Sciences (publisher- John Wiley & Sons).

Lee, A.S., Gutierrez-Arcelus, M., Perry, G.H., Vallender, E.J., Johnson, W.E., Miller, G.M.,Korbel, J.O., Lee, C. 2008. Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies. Human Molecular Genetics17:1127-1136.

Johnson, W.E. Endogenous Retroviruses. 2008. In The Encyclopedia of Virology, 3rd Ed.(publisher- Elsevier)

Newman, R.M., Hall, L., Kirmaier, A., Pozzi, L., Pery, E., Farzan, M., O’Neil, S.P., Johnson, W.E. 2008. Evolution of a TRIM5-CypA Splice Isoform in Old World Monkeys. PLoSPathogens 4(2):e1000003.

Johnson, W.E. Host Genetic Variation and Susceptibility to Primate Lentiviruses. 2007. Future HIV Medicine 1(4):399-413.

Newman, R.N. and Johnson, W.E. A Brief History of TRIM5. 2007. AIDS Reviews 9:114-125

Sato, S. and Johnson, W.E. Antibody-mediated Neutralization and Simian Immunodeficiency Virus Models of HIV/AIDS. 2007. Current HIV Research 5:594-607. 

Johnson, W.E. 2007. Assisted Suicide for Retroviruses. Nature Biotechnology 25:643-644.

Newman, R.M., Hall, L.R., Connole, M., Chen, G-L, Yuste, E., Diehl, W., Hunter, E., Kaur, A., Miller, G., Johnson, W.E.2006. Balancing Selection and Functional Polymorphism in Old World Monkey TRIM5. Proceedings of the National Academy of Sciences 103(50)19134-19139

Yuste, E., Sanford, H.B., Carmody, J., Bixby, J., Little, S., Zwick, M., Greenough, T., Burton, D.R., Richman, D.D., Desrosiers, R.C., Johnson, W.E. 2006. Simian Immunodeficiency Virus Engrafted with HIV-1 Specific Epitopes: Replication, Neutralization, and Survey of HIV-1-Positive Plasma. Journal of Virology 80:3030-3041