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Epitranscriptomic Addition of m5C to HIV-1 Transcripts Regulates Viral Gene Expression.

Courtney DG, Tsai K, Bogerd HP, Kennedy EM, Law BA, Emery A, Swanstrom R, Holley CL, Cullen BR.

Cell Host Microbe. 2019 Aug 14;26(2):217-227.e6. doi: 10.1016/j.chom.2019.07.005.


Genome wide analysis of hnRNP binding to HIV-1 RNA reveals a key role for hnRNP H1 in alternative viral mRNA splicing.

Kutluay SB, Emery A, Penumutchu S, Townsend D, Tenneti K, Madison MK, Stukenbroeker AM, Powell C, Jannain D, Tolbert BS, Swanstrom RI, Bieniasz PD.

J Virol. 2019 Aug 14. pii: JVI.01048-19. doi: 10.1128/JVI.01048-19. [Epub ahead of print]


HIV-1 Protease Inhibitors Incorporating Stereochemically Defined P2' Ligands to Optimize Hydrogen Bonding in the Substrate Envelope.

Rusere LN, Lockbaum GJ, Lee SK, Henes M, Kosovrasti K, Spielvogel E, Nalivaika EA, Swanstrom R, Kurt Yilmaz N, Schiffer CA, Ali A.

J Med Chem. 2019 Aug 6. doi: 10.1021/acs.jmedchem.9b00838. [Epub ahead of print]


Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance.

Henes M, Lockbaum GJ, Kosovrasti K, Leidner F, Nachum GS, Nalivaika EA, Lee SK, Spielvogel E, Zhou S, Swanstrom R, Bolon DNA, Kurt Yilmaz N, Schiffer CA.

ACS Chem Biol. 2019 Aug 13. doi: 10.1021/acschembio.9b00370. [Epub ahead of print]


Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies.

Zhu C, Dukhovlinova E, Council O, Ping L, Faison EM, Prabhu SS, Potter EL, Upton SL, Yin G, Fay JM, Kincer LP, Spielvogel E, Campbell SL, Benhabbour SR, Ke H, Swanstrom R, Dokholyan NV.

Nat Commun. 2019 Feb 27;10(1):948. doi: 10.1038/s41467-019-08876-w.


Constrained Mutational Sampling of Amino Acids in HIV-1 Protease Evolution.

Boucher JI, Whitfield TW, Dauphin A, Nachum G, Hollins C, Zeldovich KB, Swanstrom R, Schiffer CA, Luban J, Bolon DNA.

Mol Biol Evol. 2019 Apr 1;36(4):798-810. doi: 10.1093/molbev/msz022.


Predicting Efavirenz Concentrations in the Brain Tissue of HIV-Infected Individuals and Exploring their Relationship to Neurocognitive Impairment.

Srinivas N, Joseph SB, Robertson K, Kincer LP, Menezes P, Adamson L, Schauer AP, Blake KH, White N, Sykes C, Luciw P, Eron JJ, Forrest A, Price RW, Spudich S, Swanstrom R, Kashuba ADM.

Clin Transl Sci. 2019 May;12(3):302-311. doi: 10.1111/cts.12620. Epub 2019 Feb 27.


HIV-1 RNA Detected in the CNS after Years of Suppressive Antiretroviral Therapy Can Originate from a Replicating CNS Reservoir or Clonally Expanded Cells.

Joseph SB, Kincer LP, Bowman NM, Evans C, Vinikoor MJ, Lippincott CK, Gisslén M, Spudich S, Menezes P, Robertson K, Archin N, Kashuba A, Eron JJ, Price RW, Swanstrom R.

Clin Infect Dis. 2018 Dec 18. doi: 10.1093/cid/ciy1066. [Epub ahead of print]


HIV-1 Protease Uses Bi-Specific S2/S2' Subsites to Optimize Cleavage of Two Classes of Target Sites.

Potempa M, Lee SK, Kurt Yilmaz N, Nalivaika EA, Rogers A, Spielvogel E, Carter CW Jr, Schiffer CA, Swanstrom R.

J Mol Biol. 2018 Dec 7;430(24):5182-5195. doi: 10.1016/j.jmb.2018.10.022. Epub 2018 Nov 7.


Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma.

Smith CC, Beckermann KE, Bortone DS, De Cubas AA, Bixby LM, Lee SJ, Panda A, Ganesan S, Bhanot G, Wallen EM, Milowsky MI, Kim WY, Rathmell WK, Swanstrom R, Parker JS, Serody JS, Selitsky SR, Vincent BG.

J Clin Invest. 2018 Nov 1;128(11):4804-4820. doi: 10.1172/JCI121476. Epub 2018 Oct 2.


Evolutionary pathways to NS5A inhibitor resistance in genotype 1 hepatitis C virus.

Zhou S, Williford SE, McGivern DR, Burch CL, Hu F, Benzine T, Ingravallo P, Asante-Appiah E, Howe AYM, Swanstrom R, Lemon SM.

Antiviral Res. 2018 Oct;158:45-51. doi: 10.1016/j.antiviral.2018.07.024. Epub 2018 Aug 3.


Using Primer-ID Deep Sequencing to Detect Recent Human Immunodeficiency Virus Type 1 Infection.

Dennis AM, Zhou S, Sellers CJ, Learner E, Potempa M, Cohen MS, Miller WC, Eron JJ, Swanstrom R.

J Infect Dis. 2018 Oct 20;218(11):1777-1782. doi: 10.1093/infdis/jiy426.


Characterization of the Transmitted Virus in an Ongoing HIV-1 Epidemic Driven by Injecting Drug Use.

Dukhovlinova E, Masharsky A, Vasileva A, Porrello A, Zhou S, Toussova O, Verevochkin S, Akulova E, Frishman D, Montefiori D, Labranche C, Hoffman I, Miller W, Cohen MS, Kozlov AP, Swanstrom R.

AIDS Res Hum Retroviruses. 2018 Oct;34(10):867-878. doi: 10.1089/AID.2017.0313. Epub 2018 Jul 30.


Editorial: The HIV/SIV Envelope Protein: From Structure To Function To Host Evasion.

Swanstrom R, Joseph SB.

Curr HIV Res. 2018;16(1):3-4. doi: 10.2174/1570162X1601180419095704. No abstract available.


The evolution of HIV-1 entry phenotypes as a guide to changing target cells.

Joseph SB, Swanstrom R.

J Leukoc Biol. 2018 Mar;103(3):421-431. doi: 10.1002/JLB.2RI0517-200R. Epub 2018 Feb 1. Review.


Global synonymous mutagenesis identifies cis-acting RNA elements that regulate HIV-1 splicing and replication.

Takata MA, Soll SJ, Emery A, Blanco-Melo D, Swanstrom R, Bieniasz PD.

PLoS Pathog. 2018 Jan 29;14(1):e1006824. doi: 10.1371/journal.ppat.1006824. eCollection 2018 Jan.


Correction: Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization.

Rademeyer C, Korber B, Seaman MS, Giorgi EE, Thebus R, Robles A, Sheward DJ, Wagh K, Garrity J, Carey BR, Gao H, Greene KM, Tang H, Bandawe GP, Marais JC, Diphoko TE, Hraber P, Tumba N, Moore PL, Gray GE, Kublin J, McElrath MJ, Vermeulen M, Middelkoop K, Bekker LG, Hoelscher M, Maboko L, Makhema J, Robb ML, Karim SA, Karim QA, Kim JH, Hahn BH, Gao F, Swanstrom R, Morris L, Montefiori DC, Williamson C.

PLoS Pathog. 2017 Sep 25;13(9):e1006641. doi: 10.1371/journal.ppat.1006641. eCollection 2017 Sep.


Elucidating the Interdependence of Drug Resistance from Combinations of Mutations.

Ragland DA, Whitfield TW, Lee SK, Swanstrom R, Zeldovich KB, Kurt-Yilmaz N, Schiffer CA.

J Chem Theory Comput. 2017 Nov 14;13(11):5671-5682. doi: 10.1021/acs.jctc.7b00601. Epub 2017 Oct 9.


Prevalence of Drug-Resistant Minority Variants in Untreated HIV-1-Infected Individuals With and Those Without Transmitted Drug Resistance Detected by Sanger Sequencing.

Clutter DS, Zhou S, Varghese V, Rhee SY, Pinsky BA, Jeffrey Fessel W, Klein DB, Spielvogel E, Holmes SP, Hurley LB, Silverberg MJ, Swanstrom R, Shafer RW.

J Infect Dis. 2017 Aug 1;216(3):387-391. doi: 10.1093/infdis/jix338.


Sequencing the Biology of Entry: The Retroviral env Gene.

Swanstrom R, Graham WD, Zhou S.

Curr Top Microbiol Immunol. 2017;407:65-82. doi: 10.1007/82_2017_35. Review.


Virion-Associated Vpr Alleviates a Postintegration Block to HIV-1 Infection of Dendritic Cells.

Miller CM, Akiyama H, Agosto LM, Emery A, Ettinger CR, Swanstrom RI, Henderson AJ, Gummuluru S.

J Virol. 2017 Jun 9;91(13). pii: e00051-17. doi: 10.1128/JVI.00051-17. Print 2017 Jul 1.


Characterizing HIV-1 Splicing by Using Next-Generation Sequencing.

Emery A, Zhou S, Pollom E, Swanstrom R.

J Virol. 2017 Feb 28;91(6). pii: e02515-16. doi: 10.1128/JVI.02515-16. Print 2017 Mar 15.


Highlights of the Global HIV-1 CSF Escape Consortium Meeting, 9 June 2016, Bethesda, MD, USA.

Joseph J, Cinque P, Colosi D, Dravid A, Ene L, Fox H, Gabuzda D, Gisslen M, Beth Joseph S, Letendre S, Mukerji SS, Nath A, Perez-Valero I, Persaud D, Price RW, Rao VR, Sacktor N, Swanstrom R, Winston A, Wojna V, Wright E, Spudich S.

J Virus Erad. 2016 Oct 5;2(4):243-250.


Quantification of the Latent HIV-1 Reservoir Using Ultra Deep Sequencing and Primer ID in a Viral Outgrowth Assay.

Lee SK, Zhou S, Baldoni PL, Spielvogel E, Archin NM, Hudgens MG, Margolis DM, Swanstrom R.

J Acquir Immune Defic Syndr. 2017 Feb 1;74(2):221-228. doi: 10.1097/QAI.0000000000001187.


Treatment as Prevention: Characterization of Partner Infections in the HIV Prevention Trials Network 052 Trial.

Eshleman SH, Hudelson SE, Redd AD, Swanstrom R, Ou SS, Zhang XC, Ping LH, Piwowar-Manning E, Porcella SF, Sievers MF, Martens CA, Bruno D, Dukhovlinova E, McCauley M, Gamble T, Fogel JM, Sabin D, Quinn TC, Gunde L, Maliwichi M, Nhando N, Akelo V, Moyo S, Panchia R, Kumarasamy N, Chotirosniramit N, Melo MG, Pilotto J, Grinsztejn B, Mayer K, Chen YQ, Hughes JP, Cohen MS.

J Acquir Immune Defic Syndr. 2017 Jan 1;74(1):112-116.


Generation and Characterization of a Bivalent HIV-1 Subtype C gp120 Protein Boost for Proof-of-Concept HIV Vaccine Efficacy Trials in Southern Africa.

Zambonelli C, Dey AK, Hilt S, Stephenson S, Go EP, Clark DF, Wininger M, Labranche C, Montefiori D, Liao HX, Swanstrom RI, Desaire H, Haynes BF, Carfi A, Barnett SW.

PLoS One. 2016 Jul 21;11(7):e0157391. doi: 10.1371/journal.pone.0157391. eCollection 2016.


Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization.

Rademeyer C, Korber B, Seaman MS, Giorgi EE, Thebus R, Robles A, Sheward DJ, Wagh K, Garrity J, Carey BR, Gao H, Greene KM, Tang H, Bandawe GP, Marais JC, Diphoko TE, Hraber P, Tumba N, Moore PL, Gray GE, Kublin J, McElrath MJ, Vermeulen M, Middelkoop K, Bekker LG, Hoelscher M, Maboko L, Makhema J, Robb ML, Abdool Karim S, Abdool Karim Q, Kim JH, Hahn BH, Gao F, Swanstrom R, Morris L, Montefiori DC, Williamson C.

PLoS Pathog. 2016 Jul 19;12(7):e1005742. doi: 10.1371/journal.ppat.1005742. eCollection 2016 Jul. Erratum in: PLoS Pathog. 2017 Sep 25;13(9):e1006641.


Cytosine deamination and the precipitous decline of spontaneous mutation during Earth's history.

Lewis CA Jr, Crayle J, Zhou S, Swanstrom R, Wolfenden R.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):8194-9. doi: 10.1073/pnas.1607580113. Epub 2016 Jul 5.


Deep Sequencing of the HIV-1 env Gene Reveals Discrete X4 Lineages and Linkage Disequilibrium between X4 and R5 Viruses in the V1/V2 and V3 Variable Regions.

Zhou S, Bednar MM, Sturdevant CB, Hauser BM, Swanstrom R.

J Virol. 2016 Jul 27;90(16):7142-58. doi: 10.1128/JVI.00441-16. Print 2016 Aug 15.


Diversity and Tropism of HIV-1 Rebound Virus Populations in Plasma Level After Treatment Discontinuation.

Bednar MM, Hauser BM, Zhou S, Jacobson JM, Eron JJ Jr, Frank I, Swanstrom R.

J Infect Dis. 2016 Aug 1;214(3):403-7. doi: 10.1093/infdis/jiw172. Epub 2016 Apr 30.


Improving Viral Protease Inhibitors to Counter Drug Resistance.

Kurt Yilmaz N, Swanstrom R, Schiffer CA.

Trends Microbiol. 2016 Jul;24(7):547-557. doi: 10.1016/j.tim.2016.03.010. Epub 2016 Apr 15. Review.


Multivariable analysis to determine if HIV-1 Tat dicysteine motif is associated with neurodevelopmental delay in HIV-infected children in Malawi.

Dara J, Dow A, Cromwell E, Sturdevant CB, Mallewa M, Swanstrom R, Van Rie A, Prasad VR.

Behav Brain Funct. 2015 Dec 17;11:38. doi: 10.1186/s12993-015-0083-7.


HIV reservoirs: what, where and how to target them.

Churchill MJ, Deeks SG, Margolis DM, Siliciano RF, Swanstrom R.

Nat Rev Microbiol. 2016 Jan;14(1):55-60. doi: 10.1038/nrmicro.2015.5. Epub 2015 Nov 30. Review.


Phenotypic Correlates of HIV-1 Macrophage Tropism.

Arrildt KT, LaBranche CC, Joseph SB, Dukhovlinova EN, Graham WD, Ping LH, Schnell G, Sturdevant CB, Kincer LP, Mallewa M, Heyderman RS, Rie AV, Cohen MS, Spudich S, Price RW, Montefiori DC, Swanstrom R.

J Virol. 2015 Nov;89(22):11294-311. doi: 10.1128/JVI.00946-15. Epub 2015 Sep 2.


R5 Macrophage-Tropic HIV-1 in the Male Genital Tract.

Bednar MM, Hauser BM, Ping LH, Dukhovlinova E, Zhou S, Arrildt KT, Hoffman IF, Eron JJ, Cohen MS, Swanstrom R.

J Virol. 2015 Oct;89(20):10688-92. doi: 10.1128/JVI.01842-15. Epub 2015 Jul 29.


Bottlenecks in HIV-1 transmission: insights from the study of founder viruses.

Joseph SB, Swanstrom R, Kashuba AD, Cohen MS.

Nat Rev Microbiol. 2015 Jul;13(7):414-25. doi: 10.1038/nrmicro3471. Epub 2015 Jun 8. Review.


Ongoing HIV Transmission and the HIV Care Continuum in North Carolina.

Cope AB, Powers KA, Kuruc JD, Leone PA, Anderson JA, Ping LH, Kincer LP, Swanstrom R, Mobley VL, Foust E, Gay CL, Eron JJ, Cohen MS, Miller WC.

PLoS One. 2015 Jun 4;10(6):e0127950. doi: 10.1371/journal.pone.0127950. eCollection 2015.


Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations.

Zhou S, Jones C, Mieczkowski P, Swanstrom R.

J Virol. 2015 Aug;89(16):8540-55. doi: 10.1128/JVI.00522-15. Epub 2015 Jun 3.


A Direct Interaction with RNA Dramatically Enhances the Catalytic Activity of the HIV-1 Protease In Vitro.

Potempa M, Nalivaika E, Ragland D, Lee SK, Schiffer CA, Swanstrom R.

J Mol Biol. 2015 Jul 17;427(14):2360-78. doi: 10.1016/j.jmb.2015.05.007. Epub 2015 May 15.


Compartmentalization, Viral Evolution, and Viral Latency of HIV in the CNS.

Bednar MM, Sturdevant CB, Tompkins LA, Arrildt KT, Dukhovlinova E, Kincer LP, Swanstrom R.

Curr HIV/AIDS Rep. 2015 Jun;12(2):262-71. doi: 10.1007/s11904-015-0265-9. Review.


Compartmentalized replication of R5 T cell-tropic HIV-1 in the central nervous system early in the course of infection.

Sturdevant CB, Joseph SB, Schnell G, Price RW, Swanstrom R, Spudich S.

PLoS Pathog. 2015 Mar 26;11(3):e1004720. doi: 10.1371/journal.ppat.1004720. eCollection 2015 Mar.


The triple threat of HIV-1 protease inhibitors.

Potempa M, Lee SK, Wolfenden R, Swanstrom R.

Curr Top Microbiol Immunol. 2015;389:203-41. doi: 10.1007/82_2015_438. Review.


HIV-1 replication capacity: Setting the pace of disease.

Williamson C, Swanstrom R.

Proc Natl Acad Sci U S A. 2015 Mar 24;112(12):3591-2. doi: 10.1073/pnas.1502208112. Epub 2015 Mar 16. No abstract available.


Primer ID Informs Next-Generation Sequencing Platforms and Reveals Preexisting Drug Resistance Mutations in the HIV-1 Reverse Transcriptase Coding Domain.

Keys JR, Zhou S, Anderson JA, Eron JJ Jr, Rackoff LA, Jabara C, Swanstrom R.

AIDS Res Hum Retroviruses. 2015 Jun;31(6):658-68. doi: 10.1089/AID.2014.0031. Epub 2015 Apr 2.


HIV-1 target cells in the CNS.

Joseph SB, Arrildt KT, Sturdevant CB, Swanstrom R.

J Neurovirol. 2015 Jun;21(3):276-89. doi: 10.1007/s13365-014-0287-x. Epub 2014 Sep 19. Review.


Impact of clade, geography, and age of the epidemic on HIV-1 neutralization by antibodies.

Hraber P, Korber BT, Lapedes AS, Bailer RT, Seaman MS, Gao H, Greene KM, McCutchan F, Williamson C, Kim JH, Tovanabutra S, Hahn BH, Swanstrom R, Thomson MM, Gao F, Harris L, Giorgi E, Hengartner N, Bhattacharya T, Mascola JR, Montefiori DC.

J Virol. 2014 Nov;88(21):12623-43. doi: 10.1128/JVI.01705-14. Epub 2014 Aug 20.


Hepatitis C Virus (HCV) NS3 sequence diversity and antiviral resistance-associated variant frequency in HCV/HIV coinfection.

Jabara CB, Hu F, Mollan KR, Williford SE, Menezes P, Yang Y, Eron JJ, Fried MW, Hudgens MG, Jones CD, Swanstrom R, Lemon SM.

Antimicrob Agents Chemother. 2014 Oct;58(10):6079-92. doi: 10.1128/AAC.03466-14. Epub 2014 Aug 4.


Affinofile Assay for Identifying Macrophage-Tropic HIV-1.

Joseph SB, Lee B, Swanstrom R.

Bio Protoc. 2014 Jul 20;4(14). pii: e1184. doi: 10.21769/BioProtoc.1184.


HIV/AIDS. A fitness bottleneck in HIV-1 transmission.

Joseph SB, Swanstrom R.

Science. 2014 Jul 11;345(6193):136-7. doi: 10.1126/science.1257425. No abstract available.


Evolving character of chronic central nervous system HIV infection.

Price RW, Spudich SS, Peterson J, Joseph S, Fuchs D, Zetterberg H, Gisslén M, Swanstrom R.

Semin Neurol. 2014 Feb;34(1):7-13. doi: 10.1055/s-0034-1372337. Epub 2014 Apr 8. Review.

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