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Sackler School of Graduate Biomedical Sciences

Recent Publications from the Coffin Lab

Shao W, Shan J, Hu WS, Halvas EK, Mellors JW, Coffin JM, Kearney M. 2019. HIV proviral sequence database (PSD): A new public database for near full-length HIV proviral sequences and their meta-analyses. AIDS Res Hum Retroviruses doi: 10.1089/AID.2019.0214. Abstract

Ferris AL, Wells DW, Guo S, Del Prete GQ, Swanstrom AE, Coffin JM, Wu X, Lifson JD, Hughes SH. 2019. Clonal expansion of SIV-infected cells in macaques on antiretroviral therapy is similar to that of HIV-infected cells in humans. PLoS Pathog. 15: e1007869. Abstract

Coffin JM, Wells DW, Zerbato JM, Kuruc JD, Guo S, Luke BT, Eron JJ, Bale M, Spindler J, Simonetti FR, Hill S, Kearney MF, Maldarelli F, Wu X, Mellors JW, Hughes SH. 2019. Clones of infected cells arise early in HIV-infected individuals. JCI Insight 4(12). pii: 128432. Abstract

Holloway JR, Williams ZH, Freeman MM, Bulow U, Coffin JM. 2019. Gorillas have been infected with the HERV-K (HML-2) endogenous retrovirus much more recently than humans and chimpanzees. Proc Natl Acad Sci USA. 116: 1337-1346. Abstract

Gifford RJ, Blomberg J, Coffin JM, Fan H, Heidmann T, Mayer J, Stoye J, Tristem M, Johnson WE. 2018. Nomenclature for endogenous retrovirus (ERV) loci. Retrovirology 15: 59. Abstract

Montesion M, Williams ZH, Subramanian RP, Kuperwasser C, Coffin JM. 2018. Promoter expression of HERV-K (HML-2) provirus-derived sequences is related to LTR sequence variation and polymorphic transcription factor binding sites. Retrovirology 15: 57. Abstract

Krupovic M, Blomberg J, Coffin JM, Dasgupta I, Fan H, Geering AD, Gifford R, Harrach B, Hull R, Johnson W, Kreuze JF, Lindemann D, Llorens C, Lockhart B, Mayer J, Muller E, Olszewski N, Pappu HR, Pooggin M, Richert-Pöggeler KR, Sabanadzovic S, Sanfaçon H, Schoelz JE, Seal S, Stavolone L, Stoye JP, Teycheney PY, Tristem M, Koonin EV, Kuhn JH. 2018. Ortervirales: A new viral order unifying five families of reverse-transcribing viruses. J Virol. 92(12). pii: e00515-18. Abstract

Kearney MF, Spindler J, Wiegand A, Shao W, Haubrich R, Riddler S, Lalama CM, Hughes MD, Coffin JM, Mellors JW. 2018. Lower pre-ART intra-participant HIV-1 pol diversity may not be associated with virologic failure in adults. PLoS One 13: e0190438. Abstract

Kearney MF, Wiegand A, Shao W, McManus WR, Bale MJ, Luke B, Maldarelli F, Mellors JW, Coffin JM. 2017. Ongoing HIV replication during ART reconsidered. Open Forum Infect Dis. 43 :ofx173. doi: 10.1093/ofid/ofx173. Abstract

Van Zyl GU, Katusiime MG, Wiegand A, McManus WR, Bale MJ, Halvas EK, Luke B, Boltz VF, Spindler J, Laughton B, Engelbrecht S, Coffin JM, Cotton MF, Shao W, Mellors JW, Kearney MF. 2017. No evidence of HIV replication in children on antiretroviral therapy. J Clin Invest. Abstract

Montesion M, Bhardwaj N, Williams ZH, Kuperwasser C, Coffin JM. 2017. Mechanisms of HERV-K (HML-2) transcription during human mammary epithelial cell transformation. J Virol. 92(1). pii: e01258-17.  Abstract

Wiegand A, Spindler J, Hong FF, Shao W, Cyktor JC, Cillo AR, Halvas EK, Coffin JM, Mellors JW, Kearney MF 2017. Proc Natl Acad Sci USA 114: E3659-E3668.  Abstract

Gay CL, Bosch RJ, Ritz J, Hataye JM, Aga E, Tressler RL, Mason SW, Hwang CK, Grasela DM, Ray N, Cyktor JC, Coffin JM, Acosta EP, Koup RA, Mellors JW, Eron JJ; AIDS Clinical Trials 5326 Study Team. 2017. Clinical trial of the anti-PD-L1 antibody BMS-936559 in HIV-1 infected participants on suppressive antiretroviral therapy. J Infect Dis. 34: 111-122. Abstract

Wildschutte JH, Coffin JM. 2017. Pushing the envelope.  Elife 6. pii: e26397.  Abstract

Bui JK, Sobolewski MD, Keele BF, Spindler J, Musick A, Wiegand A, Luke BT, Shao W, Hughes SH, Coffin JM, Kearney MF, Mellors JW. 2017. Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir. PLoS Pathog. 13: e1006283.  Abstract

Boltz VF, Rausch J, Shao W, Hattori J, Luke B, Maldarelli F, Mellors JW, Kearney MF, Coffin JM. 2016. Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA. Retrovirology 13: 87. Abstract

Coffin JM, Fan H. 2016. The discovery of reverse transcriptase. Annu Rev Virol. 3: 29-51 Abstract

Shao W, Shan J, Kearney MF, Wu X, Maldarelli F, Mellors JW, Luke B, Coffin JM, Hughes SH. 2016. Retrovirus integration database (RID): A public database for retroviral insertion sites into host genomes. Retrovirology 13: 47. Abstract

Hughes SH, Coffin JM. 2016. What integration sites tell us about HIV persistence. Cell Host Microbe 19: 588-598. Abstract

Wildschutte JH*, Williams ZH*, Montesion M, Subramanian RP, Kidd JM, Coffin JM. 2016. Discovery of unfixed endogenous retrovirus insertions in diverse human populations. Proc Natl Acad Sci USA 113: E2326-2334. (* equal contribution) Abstract

Simonetti FR, Sobolewski MD, Fyne E, Shao W, Spindler J, Hattori J, Anderson EM, Watters SA, Hill S, Wu X, Wells D, Su L, Luke BT, Halvas EK, Besson G, Penrose KJ, Yang Z, Kwan RW, Van Waes C, Uldrick T, Citrin DE, Kovacs J, Polis MA, Rehm CA, Gorelick R, Piatak M, Keele BF, Kearney MF, Coffin JM, Hughes SH, Mellors JW, Maldarelli F. 2016. Clonally expanded CD4+ T cells can produce infectious HIV-1 in vivo. Proc Natl Acad Sci USA 113: 1883-1888. Abstract

Coffin JM. 2015. The discovery of HTLV-1, the first pathogenic human retrovirus. Proc Natl Acad Sci USA 112: 15525-5529. Abstract

Kearney MF, Wiegand A, Shao W, Coffin JM, Mellors JW, Lederman M, Gandhi RT, Keele BF, Li JZ. 2015. Origin of rebound plasma HIV includes cells with identical proviruses that are transcriptionally active before stopping antiretroviral therapy. J Virol. 909: 1369-1376. Abstract

Kearney MF, Anderson EM, Coomer C, Smith L, Shao W, Johnson N, Kline C, Spindler J, Mellors JW, Coffin JM, Ambrose Z. 2015. Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy. Retrovirology 12: 93. Abstract

Bhardwaj N, Montesion M, Roy F, Coffin JM. 2015. Differential expression of HERV-K (HML-2) proviruses in cells and virions of the teratocarcinoma cell line Tera-1. Viruses 7: 939-968. Abstract

Sheng-Fowler L, Tu W, Fu H, Murata H, Lanning L, Foseh G, Macauley J, Blair D, Hughes SH, Coffin JM, Lewis AM Jr, Peden K. 2014. A mouse strain defective in both T cells and NK cells has enhanced sensitivity to tumor induction by plasmid DNA expressing both activated H-Ras and c-Myc. PLoS One 9: e108926. Abstract

Wildschutte JH, Ram D, Subramanian R, Stevens VL, Coffin JM. 2014. The distribution of insertionally polymorphic endogenous retroviruses in breast cancer patients and cancer-free controls. Retrovirology 12: 62. Abstract

Cillo AR, Vagratian D, Bedison M, Anderson E, Kearney MF, Fyne E, Koontz D, Coffin JM, Piatak M, Mellors JW. 2014. Improved single copy assays for quantification of persistent HIV-1 viremia in patients on suppressive antiretroviral therapy. J Clin Microbiol. 52: 3944-3951. Abstract

Bhardwaj N, Maldarelli F, Mellors J, Coffin JM. 2014. HIV-1 infection leads to increased transcription of HERV-K (HML-2) proviruses in vivo but not to increased virion production. J Virol. 7: 939-968. Abstract

Maldarelli F, Wu X, Su L, Simonetti FR, Shao W, Hill S, Spindler J, Ferris AL, Mellors JW, Kearney MF, Coffin JM, Hughes SH. 2014. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells. Science 345: 179-183. Abstract

Henzy JE, Gifford RJ, Johnson WE, Coffin JM. 2014. A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses. J Virol. 88: 2398-2405. Abstract

Shao W, Kearney MF, Boltz VF, Spindler JE, Mellors JW, Maldarelli F, Coffin JM. 2014. PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data. J Virol Methods 203: 73-80. Abstract

De Ravin SS, Gray JT, Throm RE, Spindler J, Kearney M, Wu X, Coffin JM, Hughes SH, Malderelli F, Sorrentino BP, Malech HL. 2014. False-positive HIV PCR test following ex vivo lentiviral gene transfer treatment of X-linked severe combined immunodeficiency vector. Mol Ther. 22: 244-255. Abstract

Boltz VF, Bao Y, Lockman S, Halvas EK, Kearney MF, McIntyre JA, Schooley RT, Hughes MD, Coffin JM, Mellors JW; for the OCTANE/A5208 Team. 2014. Low-Frequency Nevirapine (NVP)-resistant HIV-1 variants are not associated with failure of antiretroviral therapy in women without prior exposure to single-dose NVP. J Infect Dis. 209: 703-710. Abstract