Sinha A and Johnson WE. Retroviruses of the RDR superinfection interference group: ancient origins and broad host distribution of a promiscuous Env gene. Current Opinion in Virology 25:105-112, 2017. p://

Henzy JE, Gifford RJ, Kenaley CP, Johnson WE. An Intact Retroviral Gene Conserved in Spiny-Rayed Fishes for over 100 My. Mol Biol Evol. 2016 Dec 30. pii: msw262.

Wu F, Kirmaier A, White E, Ourmanov I, Whitted S, Matsuda K, Riddick N, Hall LR, Morgan JS, Plishka RJ, Buckler-White A, Johnson WE, Hirsch VM. 2016. TRIM5α resistance escape mutations in the capsid are transferable between simian immunodeficiency virus strains. J Virol 90:11087–11095. doi:10.1128/JVI.01620-16.

Kevin R. McCarthy, Welkin E. Johnson, and Andrea Kirmaier. (2016) Phylogeny and History of the Lost SIV from Crab-Eating Macaques: SIVmfa. PLOS ONE. 2016 July 14.

Jamie E. Henzy and Welkin E. Johnson. (2016) Host-virus interactions: Phylogenetic sleuthing reveals pair of paralogous genes. Elife. 2016 May 31.

Diehl WE, Patel N, Halm K, Johnson WE. (2016) Tracking interspecies transmission and long-term evolution of an ancient retrovirus using the genomes of modern mammals.  Elife. 2016 Mar 8;5. pii: e12704. doi: 10.7554/eLife.12704. PMID:26952212

Johnson WE. (2015) Endogenous Retroviruses in the Genomics Era. Annu Rev Virol. 2015 Nov;2(1):135-59. doi: 10.1146/annurev-virology-100114-054945. Epub 2015 Aug 28. PMID:26958910

Land AM, Wang J, Law EK, Aberle R, Kirmaier A, Krupp A, Johnson WE, Harris RS. (2015) Degradation of the cancer genomic DNA deaminase APOBEC3B by SIV Vif. Oncotarget. 2015 Nov 24;6(37):39969-79. doi: 10.18632/oncotarget.5483. PMID:26544511

McCarthy KR, Kirmaier A, Autissier P, Johnson WE. (2015) Evolutionary and Functional Analysis of Old World Primate TRIM5 Reveals the Ancient Emergence of Primate Lentiviruses and Convergent Evolution Targeting a Conserved Capsid Interface. PLoS Pathogens. DOI: 10.1371/journal.ppat.1005085

Kirmaier A, Krupp A, Johnson WE. (2014) Understanding restriction factors and intrinsic immunity: lessons and insights from the primate lentiviruses. Future Virology 9(5), 483-497

McCarthy KR, Johnson WE (2014) Plastic Proteins and Monkey Blocks: How Lentiviruses Evolved to Replicate in the Presence of Primate Restriction Factors. PLoS Pathog 10(4): e1004017. doi:10.1371/journal.ppat.1004017

Henzy JE, Gifford RJ, Johnson WE, Coffin JM. 2013 A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses.  J. Virol. 88(5).

Sholukh et al. Passive Immunization of Macaques with Poly-clonal anti-SHIV IgG Against a Heterologous Tier 2 SHIV: Outcome Depends on IgG Dose. Retrovirology 2014. 11:8

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, I.B., Colantonio, A.D., Reeves, R.K., Connole, M.A., Gillis, J.M., Hall, L.R., Sato, S., Audin, C.R., Evans, D.T., Shida, H., Johnson, R.P., Johnson, W.E. 2011. Flow cytometry based identification of simian immunodeficiency virus Env-specific B lymphocytes. Journal of Immunological Methods.370(1-2):75-85.

Lakhashe, S.K., Velu, V., Sciaranghella, G., Siddappa, N.B., Dipasquale, J.M., Hemashettar, G., Yoon, J.K., Rasmussen, R.A., Yang, F., Lee, S.J., Montefiori, D.C., Novembre, F.J., Villinger, F., Amara, R.R., Kahn, M., Hu, S.L., Li, S., Li, Z., Frankel, F.R., Robert-Guroff, M., Johnson, W.E., Lieberman, J., Ruprecht, R.M. 2011. Prime-boost vaccination with heterologous live vectors encoding SIV gag and multimeric HIV-1 gp160 protein: Efficacy against repeated mucosal R5 clade C SHIV challenges.Vaccine. 29(34):5611-22. Epub 2011 Jul 14

Schell, J.B., Rose, N.F., Bahl, K., Diller, K., Buonocore, L., Hunter, M., Marx, P.A., Gambhira, R., Tang, H., Montefiori, D.C., Johnson, W.E., Rose, J.K. 2011. Significant Protection against High-Dose Simian Immunodeficiency Virus Challenge Conferred by a New Prime-Boost Vaccine Regimen. Journal of Virology. Jun; 85(12):5764-72. Epub 2011 Apr 13.

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 * co-corresponding authors

Lai, L., Kwa, S., Kozlowski, P.A., Montefiori, D.C., Ferrari, G., Johnson, W.E., Hirsch, V., Villinger, F., Chennareddi, L., Earl, P.L., Moss, B., Amara, R.R., Robinson, H.L. 2011. Prevention of Infection by a Granulocyte-Macrophage Colony-Stimulating Factor Co-Expressing DNA/Modified Vaccinia Ankara Simian Immunodeficiency Virus Vaccine. Journal of Infectious Diseases. 204(1):164-73.

Johnson, W.E. Endless Forms Most Viral.2010. 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 Biology 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 and HIV-1 Vpu in Overcoming Restriction by Tetherin/BST2. PLoS Pathogens 5:e1000429.

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.

Yuste, E., Bixby, J., Lifson, J., Sato, S., Johnson, W.E., and Desrosiers, R. 2008. Glycosylation of gp41 of simian immunodeficiency virus shields epitopes that can be targets for neutralizing antibodies. Journal of Virology 82: 12472-12486.

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. PLoS Pathogens 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 TRIM5α. 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.

Dhillon, A. K., Donners, H., Pantophlet, R., Johnson, W. E., Decker, J. M., Shaw, G. M., Lee, F-H., Richman, D. D., Doms, R. W., Vanham, G., Burton, D. R. 2007. Dissecting the neutralizing antibody specificities of broadly neutralizing sera from HIV-1 infected donors. Journal of Virology 81(12):6548-6562.

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 TRIM5a. 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.

Yuste E, Johnson W, Pavlakis GN, Desrosiers RC.2005. Virion envelope content, infectivity, and neutralization sensitivity of simian immunodeficiency virus. Journal of Virology 79:12455-63

Johnson, W.E., Lifson, J.D., Lang, S.M., Johnson, R.P. and Desrosiers, R.C. 2003. The Importance of B-Cell Responses for Immunological Control of Variant Strains of Simian Immunodeficiency Virus. Journal of Virology 77; 375-381.

Johnson, W.E., Sanford, H., Schwall, L., Burton, D.R., Parren, P.W.H.I., Robinson, J.E., and Desrosiers, R.C. 2003. Assorted mutations in the envelope gene of simian immunodeficiency virus isolate SIVmac239 lead to loss of neutralization resistance against antibodies representing a broad spectrum of specificities. Journal of Virology 77: 9993-10003.

Johnson, W.E., Sauvron, J.M., Reitter, J., Czajak, S., Puffer, B., Robinson, J.E., Doms, R. and Desrosiers, R.C. 2002. A Replication Competent, Neutralization-sensitive Variant of SIVmac239 Lacking 100 Amino Acids of Envelope. Journal of Virology 76:2075-2086.

Johnson, W. E., Desrosiers, R. C. 2002. Viral persistance: HIV’s strategies of immune system evasion. Annual Review of Medicine 53: 499-518.

Johnson, W.E., Sauvron, J.M., and Desrosiers, R.C. 2001.The conserved N-linked Carbohydrates of HIV-1 gp41 are Largely Dispensable for Viral Replication. Journal of Virology 75: 11426-11436.

Auerbach, M.R., Czajak, S.C., Johnson, W.E., Desrosiers, R.C., Alexander, L. 2000. Species specificity of macaque rhadinovirus glycoprotein B sequences. Journal of Virology 74:584-590.

Johnson, W.E. and Coffin, J.M. 1999. Constructing Primate Phylogenies from Endogenous Retrovirus Sequences. Proceedings of the National Academy of Sciences 96(18):10254-60.

LaVail, J.H., Johnson, W.E., Spencer, L.C. 1993. Immunohistochemical identification of trigeminal ganglion neurons that innervate the mouse cornea: relevance to intercellular spread of herpes simplex virus. Journal of Comparative Neurology 327(1):133-40.


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