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Morrissey College of Arts and Sciences

Welkin Johnson

professor & chair of biology

Dr. Welkin Johnson


Ph.D., Tufts University, School of Medicine, Boston, Mass.

Phone: 617.552.4223

Welkin Johnson Lab homepage

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 the laboratory 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 that act 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 within individuals, particularly in response to shifting selective pressures imposed by virus-specific polyclonal antibody responses.

Representative Publications

Byrareddy SN, Ayash-Rashkovsky M, Kramer VG, Lee SJ, Correll M, Novembre FJ, Villinger F, Johnson WE, von Gegerfelt A, Felber BK, Ruprecht RM. Live Attenuated Rev-Independent Nef- SIV Enhances Acquisition of Heterologous SIVsmE660 in Acutely Vaccinated Rhesus Macaques. PLoS One 2013 Sep 30;8(9):e75556. PMID:24098702.

Krupp, A., McCarthy, K.R., Ooms, M., Letko, M., Morgan, J.S., Simon, V., Johnson, W.E. 2013. Apobec3G Polymorphism as a Selective Barrier to Cross-species Transmission and Emergence of Pathogenic SIV and AIDS in a Primate Host. PLOS Pathogens 2013 Oct 3; 9(10):e1003641. doi:10.1371/journal.ppat.1003641. PMID: 24098115.

Wu, F., Kirmaier, A., Goeken, R., Ourmanov, I., Hall, L., Morgan, J.S., Matsuda, K., Buckler-White, A., Tomioka, K., Plishka, R., Whitted, S., Johnson, W., and Hirsch, V.M. Trim5 alpha Drives SIVsmm Evolution in Rhesus Macaques. PLoS Pathogens 2013 Aug 22; 9(8): e1003577. doi:10.1371/journal.ppat.1003577. PMID: 23990789.

Henzy, J.E. and Johnson, W.E.2013. Pushing the Endogenous Envelope. Philosophical Trans. Of the Royal Society B. 368(1626):20120506.

Patel et al. DNA and virus particle vaccination protects against acquisition and confers control of viremia upon heterologous simian immunodeficiency virus challenge. Proc Natl Acad Sci U S A. 2013 Feb 19; 110(8):2975-80. PMID: 23359688.

McCarthy KR, Schmidt AG, Kirmaier A, Wyand AL, Newman RM, and Johnson WE. Gain-of-Sensitivity Mutations in a TRIM5-Resistant Primary Isolate of Pathogenic SIV Identify Two Independent Conserved Determinants of TRIM5α Specificity. PLOS Pathogens. 2013 May;9(5):e1003352. PMID: 23675300.

Diehl WE, Johnson WE, Hunter E. Elevated Rate of Endogenous Retroviral Elements in Haplorhini TRIM5 and TRIM22 Genomic Sequences: Impact on Transcriptional Regulation. PLos One. 8(3):e58532. PMID:23516500.

Butler K, Morgan JS, Hanson DL, Adams DR, Garcia-Lerma G, Heneine PW, Ellenberger D, Hendry RM, McNicholl JM, Johnson W, Kersh EN. Susceptibility to repeated, low-dose, rectal SHIVSF162P3 challenge is independent of TRIM5 genotype in rhesus macaques. AIDS Res Hum Retroviruses. 2013 Mar 5. PMID:23461569.

Rathinakumar R, Dutta M, Zhu P, Johnson WE, Roux KH. 2012. Binding of anti-membrane-proximal gp41 monoclonal antibodies to CD4-liganded and -unliganded human immunodeficiency virus type 1 and simian immunodeficiency virus virions. J Virol. 86(3):1820-31.

Telenti A and Johnson WE.2012. Host Genes Important to HIV Replication and Evolution. Cold Spring Harbor Perspectives in Medicine. 2(4):a007203.

Lai L., Kwa, S.F., Kozlowski, P.A., Montefiori, D.C., Nolen, T.L., Hudgens, M.G., Johnson, W.E., Ferrari, G., Hirsch, V.M., Felber, B.K., Pavlakis, G.N., Earl, P.L., Moss, B., Amara, R.R., Robinson, H.L. 2012. SIVmac239 MVA vaccine with and without a DNA prime, similar prevention of infection by a repeated dose SIVsmE660 challenge despite different immune responses. Vaccine. 30(9):1737-45. Epub 2011 Dec 15.

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. 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. GenomeBiology 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. PLoSBiology 8(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 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 Genetics 17:1127-1136.

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.