Recent Publications from the Coffin Lab

 

Research Publications Genetics Immunology Microbiology

 

 

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 Epub ahead of print.  books

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. Epub ahead of print. books

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

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.  books

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. books

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

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. books

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

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) books

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. books

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

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. books

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. books

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. books

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. books

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. books

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. books

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. books

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. books

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. books

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. books

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. books

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. books

Delviks-Frankenberry K, Paprotka T, Cingöz O, Wildt S, Hu WS, Coffin JM, Pathak VK. 2013. Generation of multiple replication competent retroviruses through recombination between PreXMRV-1 and PreXMRV-2. J Virol. 87: 11525-11537. books

Josefsson L, Palmer S, Faria NR, Lemey P, Casazza J, Ambrozak D, Kearney M, Shao W, Kottilil S, Sneller M, Mellors J, Coffin JM, Maldarelli F. 2013. Single cell analysis of lymph node tissue from HIV-1 infected patients reveals that the majority of CD4+ T-cells contain one HIV-1 DNA molecule. PLoS Pathog. 9: e1003432. books

Coffin, JM. 2013. Virions at the gates: receptors and the host-virus arms race. PLoS Biol. 11: e1001574. books

Maldarelli F, Kearney M, Palmer S, Stephens R, Mican J, Polis MA, Davey RT, Kovacs J, Shao W, Rock-Kress D, Metcalf JA, Rehm C, Greer SE, Lucey DL, Danley K, Alter H, Mellors JW, Coffin JM. 2013. HIV populations are large and accumulate high genetic diversity in a nonlinear fashion. J Virol. 87: 10313-10323. books

Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, Stewart C, Volfovsky N, Levitsky A, Stephens RM, Coffin JM. 2013. Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA. Retrovirology 10: 18. books

Coffin J, Swanstrom R. 2013. HIV pathogenesis: dynamics and genetics of viral populations and infected cells. Cold Spring Harb Perspect Med. 3: a012526. books

Coffin, JM. 2013. Virions at the gates: receptors and the host-virus arms race. PLoS Biol. 11: e1001574. books

Henzy JE, Coffin JM. 2013. Betaretroviral envelope subunits are noncovalently associated and restricted to the mammalian class. J Virol. 87: 1937-1946. books

Boltz VF, Ambrose Z, Kearney MF, Shao W, Kewalramani VN, Maldarelli F, Mellors JW, Coffin JM. 2012. Ultrasensitive allele-specific PCR reveals rare preexisting drug-resistant variants and a large replicating virus population in macaques infected with a simian immunodeficiency virus containing human immunodeficiency virus reverse transcriptase. J Virol. 86: 12525-12530. books

Archin NM, Liberty AL, Kashuba AD, Choudhary SK, Kuruc JD, Crooks AM, Parker DC, Anderson EM, Kearney MF, Strain MC, Richman DD, Hudgens MG, Bosch RJ, Coffin JM, Eron JJ, Hazuda DJ, Margolis DM. 2012. Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy. Nature 487: 482-485. books

Delviks-Frankenberry K, Cingöz O, Coffin JM, Pathak VK. 2012. Recombinant origin, contamination, and de-discovery of XMRV. Curr Opin Viorl. 2: 499-507. books

Sanchez-Martinez S, Aloia AL, Harvin D, Mirro J, Gorelick RJ, Jern P, Coffin JM, Rein A. 2012. Studies on the restriction of murine leukemia viruses by mouse APOBEC3. PLoS One 7: e38190. books

Archin NM, Vaidya NK, Kuruc JD, Liberty AL, Wiegand A, Kearney MF, Cohen MS, Coffin JM, Bosch RJ, Gay CL, Eron JJ, Margolis DM, Perelson AS. 2012. Immediate antiviral therapy appears to restrict resting CD4+ cell HIV-1 infection without accelerating the decay of latent infection. Proc natl Acad Sci USA 109: 9523-9528. books

Tipper CH, Cingöz O, Coffin JM. 2012. Mus spicilegus endogenous retrovirus HEMV uses murine sodium-dependent myo-inositol transporter 1 as a receptor. J Virol. 86: 6341-6344. books

Kearney MF, Spindler J, Wiegand A, Shao W, Anderson EM, Maldarelli F, Ruscetti FW, Mellors JW, Hughes SH, Le Grice SF, Coffin JM. 2012. Multiple sources of contamination in samples from patients reported to have XMRV infection. PLoS One 7: e30889. books

Cingöz O, Paprotka T, Delviks-Frankenberry KA, Wildt S, Hu WS, Pathak VK, Coffin JM. 2012. Characterization, mapping, and distribution of the two XMRV parental proviruses. J Virol. 86: 328-338. books

Batorsky R, Kearney MF, Palmer SE, Maldarelli F, Rouzine IM, Coffin JM. 2011. Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection. Proc Natl Acad Sci U S A 108: 5661-5666. books

Jordan MR, Kearney M, Palmer S, Shao W, Maldarelli F, Coakley EP, Chappey C, Wanke C, Coffin JM. 2010. Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations.  J Virol Methods 168: 114-120. books

Rouzine IM, Coffin JM. 2010. Multi-site adaptation in the presence of infrequent recombination. Theor Popul Biol. 77: 189-204. books

Sergeev RA, Batorsky RE, Coffin JM, Rouzine IM. 2009. Interpreting the effect of vaccination on steady state infection in animals challenged with Simian Immunodeficiency Virus. J Theor Biol. 263: 285-292.  books

Boltz VF, Maldarelli F, Martinson N, Morris L, McIntyre JA, Gray G, Hopley MJ, Kimura T, Mayers DL, Robinson P, Mellors JW, Coffin JM, Palmer SE. 2009. Optimization of allele-specific PCR using patient-specific HIV consensus sequences for primer design. J Virol Methods 164: 122-126. books

Shao W, Kearney M, Maldarelli F, Mellors JW, Stephens RM, Lifson JD, KewalRamani VN, Ambrose Z, Coffin JM, Palmer SE. 2009. RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapy. Retrovirology 6: 101. books

Coffin JM, Stoye JP. 2009. Virology. A new virus for old diseases? Science 326: 530-531. books

Pereyra F, Palmer S, Miura T, Block BL, Wiegand A, Rothchild AC, Baker B, Rosenberg R, Cutrell E, Seaman MS, Coffin JM, Walker BD. 2009. Persistent low-level viremia in HIV-1 elite controllers and relationship to immunologic parameters. Infect Immun. 200: 984-990. books

Chen J, Nikolaitchik O, Singh J, Wright A, Bencsics CE, Coffin JM, Ni N, Lockett S, Pathak VK, Hu WS. 2009. High efficiency of HIV-1 genomic RNA packaging and heterozygote formation revealed by single virion analysis. Proc Natl Acad Sci USA 106: 13535-13540. books

Dinoso JB, Kim SY, Wiegand AM, Palmer SE, Gange SJ, Cranmer L, O'Shea A, Callender M, Spivak A, Brennan T, Kearney MF, Proschan MA, Mican JM, Rehm CA, Coffin JM, Mellors JW, Siliciano RF, Maldarelli F. 2009. Treatment intensification does not reduce residual HIV-1 viremia in patients on highly active antiretroviral therapy. Proc Natl Acad Sci USA 106: 9403-9408. books

Jern P, Russell RA, Pathak VK, Coffin JM. 2009. Likely role of APOBEC3G-mediated G-to-A mutations in HIV-1 evolution and drug resistance. PLoS Pathog. 5: e1000367. books

Wilkin TJ, McKinnon JE, DiRienzo AG, Mollan K, Fletcher CV, Margolis DM, Bastow B, Thal G, Woodward W, Godfrey C, Wiegand A, Maldarelli F, Palmer S, Coffin JM, Mellors JW, Swindells S. 2009. Regimen simplification to atazanavir-ritonavir alone as maintenance antiretroviral therapy: final 48-week clinical and virologic outcomes. J Infect Dis. 199: 866-871. books

Kearney M, Maldarelli F, Shao W, Margolick JB, Daar ES, Mellors JW, Rao V, Coffin JM, Palmer S. 2009. Human immunodeficiency virus type 1 population genetics and adaptation in newly infected individuals. J Virol. 83: 2715-2727. books

Migueles SA, Osborne CM, Royce C, Compton AA, Joshi RP, Weeks KA, Rood JE, Berkley AM, Sacha JB, Cogliano-Shutta NA, Lloyd M, Roby G, Kwan R, McLaughlin M, Stallings S, Rehm C, O'Shea MA, Mican J, Packard BZ, Komoriya A, Palmer S, Wiegand AP, Maldarelli F, Coffin JM, Mellors JW, Hallahan CW, Follman DA, Connors M. 2008. Lytic granule loading of CD8+ T cells is required for HIV-infected cell elimination associated with immune control. Immunity 29: 1009-1021. books

Coffin JM. 2008. Attenutation by a thousand cuts. N Eng J Med. 359: 2283-2285. books

Jern P, Coffin JM. 2008. Host-retrovirus arms race: trimming the budget. Cell Host Microbe 4: 196-197. books

Jern P, Coffin JM. 2008. Effects of retroviruses on host gene function. Annu Rev Genet. 42: 709-732. books

Delviks-Frankenberry KA, Nikolenko GN, Boyer PL, Hughes SH, Coffin JM, Jere A, Pathak VK. 2008. HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision. Proc Natl Acad Sci USA 105: 10943-10948. books

Archin NM, Eron JJ, Palmer S, Hartmann-Duff A, Martinson JA, Wiegand A, Bandarenko N, Schmitz JL, Bosch RJ, Landay AL, Coffin JM, Margolis DM. 2008. Valproic acid without intensified antiviral therapy has limited impact on persistent HIV infection of resting CD4+ T cells. AIDS 22: 1131-1135. books

Rulli SJ Jr, Mirro J, Hill SA, Lloyd P, Gorelick RJ, Coffin JM, Derse D, Rein A. 2008. Interactions of murine APOBEC3 and human APOBEC3G with murine leukemia viruses. J Virol. 82: 6666-6675. books

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