Complete Bibliography

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Relevant Publications

Clinical Trial Simulation

Esmaeili S, Owens K, Wagoner J, Polyak SJ, White JM, Schiffer JT. A unifying model to explain frequent SARS-CoV-2 rebound after nirmatrelvir treatment and limited prophylactic efficacy. Nat Commun. 2024 Jun 28; 15(1):5478. PMID: 38942778, PMCID: PMC11213957

Reeves DB, Mayer BT, deCamp AC, Huang Y, Zhang B, Carpp LN, Magaret CA, Juraska M, Gilbert PB, Montefiori DC, Bar KJ, Cardozo-Ojeda EF, Schiffer JT, Rossenkhan R, Edlefsen P, Morris L, Mkhize NN, Williamson C, Mullins JI, Seaton KE, Tomaras GD, Andrew P, Mgodi N, Ledgerwood JE, Cohen MS, Corey L, Naidoo L, Orrell C, Goepfert PA, Casapia M, Sobieszczyk ME, Karuna ST, Edupuganti S. High monocolonal neutralization titers reduced breakthrough HIV-1 viral loads in the Antibody Mediated Prevention trials. Nat Commun. 2023 Dec 14; 14(1):8299. PMID: 38097552, PMCID: PMC10721814. 

Goyal A, Duke ER, Cardozo-Ojeda EF, Schiffer JT. Modeling explains prolonged SARS-CoV-2 nasal shedding relative to lung shedding in remdesivir-treated rhesus macaques. iScience. 2022 Jun 17; 25(6):104448. PMID: 35634576, PMCID: PMC9130309. 

Gottlieb RL, Vaca CE, Paredes R, Mera J, Webb BJ, Perez G, Oguchi G, Ryan P, Nielsen BU, Brown M, Hidalgo A, Sachdeva Y, Mittal S, Osiyemi O, Skarbinski J, Juneja K, Hyland RH, Osinusi A, Chen S, Camus G, Abdelghany M, Davies S, Behenna-Renton N, Duff F, Marty FM, Katz MJ, Ginde AA, Brown SM, Schiffer JT, Hill JA; GS-US-540-9012 (PINETREE) Investigators. Early Remdesivir to Prevent Progression to Severe Covid-19 in Outpatients. N Engl J Med. 2022 Jan 27; 386(4):305-315. PMID: 34937145, PMCID: PMC8757570.

Finch CL, Dyall J, Xu S, Nelson EA, Postnikova E, Liang JY, Zhou H, DeWald LE, Thomas CJ, Wang A, Xu X, Hughes E, Morris PJ, Mirsalis JC, Nguyen LH, Arolfo MP, Koci B, Holbrook MR, Hensley LE, Jahrling PB, Schmaljohn C, Johansen LM, Olinger GG, Schiffer JT, White JM. Formulation, Stability, Pharmacokinetic, and Modeling Studies for Tests of Synergistic Combinations of Orally Available Approved Drugs against Ebola Virus In Vivo. Microorganisms. 2021 Mar 10; 9(3):566. PMID: 33801811, PMCID: PMC7998926.

Goyal A, Cardozo-Ojeda EF, Schiffer JT. Potency and timing of antiviral therapy as determinants of duration of SARS-CoV-2 shedding and intensity of inflammatory response. Sci Adv. 2020 Nov 20; 6(47):eabc7112. PMID: 33097472, PMCID: PMC7679107.

Reeves DB, Huang Y, Duke ER, Mayer BT, Cardozo-Ojeda EF, Boshier FA, Swan DA, Rolland M, Robb ML, Mascola JR, Cohen MS, Corey L, Gilbert PB, Schiffer JT. Mathematical modeling to reveal breakthrough mechanisms in the HIV Antibody Mediated Prevention (AMP) trials. PLoS Comput Biol. 2020 Feb 21; 16(2):e1007626. PMID: 32084132, PMCID: PMC7055956.

Schiffer JT, Swan DA, Magaret A, Corey L, Wald A, Ossig J, Ruebsamen-Schaeff H, Stoelben S, Timmler B, Zimmerman H, Melhem MR, Van Wart SA, Rubino CM, Birkmann A. Mathematical modeling of herpes simplex virus-2 suppression with pritelivir predicts trial outcomes. Sci Transl Med. 2016; 8(324):324ra15. PMID: 26843190, PMCID: PMC4880060.

Schiffer JT, Swan DA, Corey L, Wald A. Rapid viral expansion and short drug half-life explain the incomplete effectiveness of current herpes simplex virus-2 directed antiviral agents. Antimicrob Agents Chemother. 2013; 57(12):5820-9. PMID: 24018260, PMCID: PMC3837890.

HIV Cure

Salgado M, Gálvez C, Nijhuis M, Kwon M, Cardozo-Ojeda EF, Badiola J, Gorman MJ, Huyveneers LEP, Urrea V, Bandera A, Jensen BO, Vandekerckhove L, Jurado M, Raj K, Schulze Zur Wiesch J, Bailén R, Eberhard JM, Nabergoj M, Hütter G, Saldaña-Moreno R, Oldford S, Barrett L, Ramirez MLM, Garba S, Gupta RK, Revollo B, Ferra-Coll C, Kuball J, Alter G, Sáez-Cirión A, Diez-Martin JL, Duke ER, Schiffer JT, Wensing A, Martinez-Picado J; IciStem Consortium. Dynamics of virological and immunological markers of HIV persistence after allogeneic haematopoietic stem-cell transplantation in the IciStem cohort: a prospective observational cohort study. Lancet HIV. 2024 Jun; 11(6):e389-e405. PMID: 38816141, PMCID: PMC11417461.

Reeves DB, Bacchus-Souffan C, Fitch M, Abdel-Mohsen M, Hoh R, Ahn H, Stone M, Hecht F, Martin J, Deeks SG, Hellerstein MK, McCune JM, Schiffer JT, Hunt PW. Estimating the contribution of CD4 T cell subset proliferation and differentiation to HIV persistence. Nat Commun. 2023 Oct 2; 14(1):6145. PMID: 37783718, PMCID: PMC10545742.

Reeves DB, Gaebler C, Oliveira TY, Peluso MJ, Schiffer JT, Cohn LB, Deeks SG, Nussenzweig MC. Impact of misclassified defective proviruses on HIV reservoir measurements. Nat Commun. 2023 Jul 13; 14(1):4186. PMID: 37443365, PMCID: PMC10345136.

Tettamanti Boshier FA, Reeves DB, Duke ER, Swan DA, Prlic M, Cardozo-Ojeda EF, Schiffer JT. Substantial uneven proliferation of CD4+ T cells during recovery from acute HIV infection is sufficient to explain the observed expanded clones in the HIV reservoir. J Virus Erad. 2022 Nov 30; 8(4):100091. PMID: 36582473, PMCID: PMC9792356.

Schiffer JT, Levy C, Hughes SM, Pandey U, Padullo M, Jerome KR, Zhu H, Puckett K, Helgeson E, Harrington RD, Hladik F. Stable HIV Reservoir Despite Prolonged Low-Dose Mycophenolate to Limit CD4+ T-cell Proliferation. Open Forum Infect Dis. 2022 Nov 19;9(12):ofac620. PMID: 36519118, PMCID: PMC9745781.

Goyal A, Gardner M, Mayer BT, Jerome KR, Farzan M, Schiffer JT, Cardozo-Ojeda EF. Estimation of the in vivo neutralization potency of eCD4Ig and conditions for AAV-mediated production for SHIV long-term remission. Sci Adv. 2022 Jan 14; 8(2):eabj5666. doi: 10.1126/sciadv.abj5666. Epub 2022 Jan 12. PMID: 35020436, PMCID: PMC8754410.

Cardozo-Ojeda EF, Duke ER, Peterson CW, Reeves DB, Mayer BT, Kiem HP, Schiffer JT. Thresholds for post-rebound SHIV control after CCR5 gene-edited autologous hematopoietic cell transplantation. Elife. 2021 Jan 12; 10:e57646. PMID: 33432929, PMCID: PMC7803377.

Pankau MD, Reeves DB, Harkins E, Ronen K, Jaoko W, Mandaliya K, Graham SM, McClelland RS, Matsen Iv FA, Schiffer JT, Overbaugh J, Lehman DA. Dynamics of HIV DNA reservoir seeding in a cohort of superinfected Kenyan women. PLoS Pathog. 2020 Feb 5; 16(2):e1008286. PMID: 32023326, PMCID: PMC7028291.

Reeves DB, Duke ER, Wagner TA, Palmer SE, Spivak AM, Schiffer JT. A majority of HIV persistence during antiretroviral therapy is due to infected cell proliferation. Nature Communications. 2018; 9(1):4811. PMID: 30446650, PMCID:PMC6240116.

Reeves DB, Duke ER, Hughes SM, Prlic M, Hladik F, Schiffer JT. Anti-proliferative therapy for HIV cure: a compound interest approach. Sci Rep. 2017; 7(1):4011. PMID: 28638104, PMCID: PMC5479830.

SARS-CoV-2 Immune Responses

Byrne C, Schiffer JT. Ensemble modeling of SARS-CoV-2 immune dynamics in immunologically naïve rhesus macaques predicts that potent, early innate immune responses drive viral elimination. Front Immunol. 2024 Nov 7; 15:1426016. PMID: 39575237, PMCID: PMC11578959.

Owens K, Esmaeili S, Schiffer JT. Heterogeneous SARS-CoV-2 kinetics due to variable timing and intensity of immune responses. JCI Insight. 2024 Apr 4; 9(9):e176286. PMID: 38573774, PMCID: PMC11141931.

Lim FY, Kim SY, Kulkarni KN, Blazevic RL, Kimball LE, Lea HG, Haack AJ, Gower MS, Stevens-Ayers T, Starita LM, Boeckh M, Hyrien O, Schiffer JT, Theberge AB, Waghmare A. High-frequency home self-collection of capillary blood correlates IFI27 expression kinetics with SARS-CoV-2 viral clearance. J Clin Invest. 2023 Dec 1; 133(23):e173715. PMID: 38038134, PMCID: PMC10688975.

Yang S, Jerome KR, Greninger AL, Schiffer JT, Goyal A. Endogenously Produced SARS-CoV-2 Specific IgG Antibodies May Have a Limited Impact on Clearing Nasal Shedding of Virus during Primary Infection in Humans. Viruses. 2021 Mar 20; 13(3):516. PMID: 33804667, PMCID: PMC8003723.

Waghmare A, Krantz EM, Baral S, Vasquez E, Loeffelholz T, Chung EL, Pandey U, Kuypers J, Duke ER, Jerome KR, Greninger AL, Reeves DB, Hladik F, Cardozo-Ojeda EF, Boeckh M, Schiffer JT. Reliability of Self-Sampling for Accurate Assessment of Respiratory Virus Viral and Immunologic Kinetics. J Infect Dis. 2022 Aug 24; 226(2):278-286. PMID: 32710762, PMCID: PMC7454707.

HSV-2 Infection Micro-Environments

Davé V, Richert-Spuhler LE, Arkatkar T, Warrier L, Pholsena T, Johnston C, Schiffer JT, Prlic M, Lund JM. Recurrent infection transiently expands human tissue T cells while maintaining long-term homeostasis. J Exp Med. 2023 Sep 4; 220(9):e20210692. PMID: 37314481, PMCID: PMC10267593.

Arkatkar T, Davé V, Cruz Talavera I, Graham JB, Swarts JL, Hughes SM, Bell TA, Hock P, Farrington J, Shaw GD, Kirby A, Fialkow M, Huang ML, Jerome KR, Ferris MT, Hladik F, Schiffer JT, Prlic M, Lund JM. Memory T cells possess an innate-like function in local protection from mucosal infection. J Clin Invest. 2023 May 15; 133(10):e162800. PMID: 36951943, PMCID: PMC10178838.

Davé VA, Cardozo-Ojeda EF, Mair F, Erickson J, Woodward-Davis AS, Koehne A, Soerens A, Czartoski J, Teague C, Potchen N, Oberle S, Zehn D, Schiffer JT, Lund JM, Prlic M. Cervicovaginal Tissue Residence Confers a Distinct Differentiation Program upon Memory CD8 T Cells. J Immunol. 2021 Jun 15; 206(12):2937-2948. PMID: 34088770, PMCID: PMC8642491.

Roychoudhury P, Swan DA, Duke E, Corey L, Zhu J, Davé V, Spuhler LR, Lund JM, Prlic M, Schiffer JT. Tissue-resident T cell-derived cytokines eliminate herpes simplex virus-2-infected cells. J Clin Invest. 2020 Jun 1; 130(6):2903-2919. PMID: 32125285, PMCID: PMC7260013.

Schiffer JT, Swan DA, Roychoudhury P, Lund JM, Prlic M, Zhu J, Wald A, Corey L. A Fixed Spatial Structure of CD8+ T Cells in Tissue during Chronic HSV-2 Infection. J Immunol. 2018 Sep 1; 201(5):1522-1535. PMID: 30045971, PMCID: PMC6103892.

Schiffer JT. Mucosal HSV-2 Specific CD8+ T-Cells Represent Containment of Prior Viral Shedding Rather than a Correlate of Future Protection. Front Immunol. 2013 Jul 29; 4:209. PMID: 23908652, PMCID: PMC3725545.

Schiffer JT, Swan D, Al Sallaq R, Magaret A, Johnston C, Mark KE, Selke S, Ocbamichael N, Kuntz S, Zhu J, Robinson B, Huang ML, Jerome KR, Wald A, Corey L. Rapid localized spread and immunologic containment define Herpes simplex virus-2 reactivation in the human genital tract. Elife. 2013 Apr 16; 2:e00288. PMID: 23606943, PMCID: PMC3629793.

Schiffer JT, Abu-Raddad L, Mark KE, Zhu J, Selke S, Koelle DM, Wald A, Corey L. Mucosal host immune response predicts the severity and duration of herpes simplex virus-2 genital tract shedding episodes. Proc Natl Acad Sci U S A. 2010 Nov 2; 107(44):18973-8. PMID: 20956313, PMCID: PMC2973882.

Viral Transmission

Schiffer JT. The Continuing Puzzle of Defining Duration of Severe Acute Respiratory Syndrome Coronavirus 2 Infectivity. J Infect Dis. 2023 Jun 15; 227(12):1339-1342. PMID: 36705262.

Goyal A, Reeves DB, Schiffer JT. Multi-scale modelling reveals that early super-spreader events are a likely contributor to novel variant predominance. J R Soc Interface. 2022 Apr; 19(189):20210811. PMID: 35382576, PMCID: PMC8984334.

Swan DA, Goyal A, Bracis C, Moore M, Krantz E, Brown E, Cardozo-Ojeda F, Reeves DB, Gao F, Gilbert PB, Corey L, Cohen MS, Janes H, Dimitrov D, Schiffer JT. Mathematical Modeling of Vaccines That Prevent SARS-CoV-2 Transmission. Viruses. 2021 Sep 24; 13(10):1921. PMID: 34696352, PMCID: PMC8539635.

Swan DA, Bracis C, Janes H, Moore M, Matrajt L, Reeves DB, Burns E, Donnell D, Cohen MS, Schiffer JT, Dimitrov D. COVID-19 vaccines that reduce symptoms but do not block infection need higher coverage and faster rollout to achieve population impact. Sci Rep. 2021 Jul 30; 11(1):15531. PMID: 34330945, PMCID: PMC8324774.

Goyal A, Reeves DB, Thakkar N, Famulare M, Cardozo-Ojeda EF, Mayer BT, Schiffer JT. Slight reduction in SARS-CoV-2 exposure viral load due to masking results in a significant reduction in transmission with widespread implementation. Sci Rep. 2021 Jun 4; 11(1):11838. PMID: 34088959, PMCID: PMC8178300.

Reeves DB, Bracis C, Swan DA, Burns E, Moore M, Dimitrov D, Schiffer JT. Rapid vaccination and partial lockdown minimize 4th waves from emerging highly contagious SARS-CoV-2 variants. Med. 2021 May 14; 2(5):573-574. PMID: 33899042, PMCID: PMC8057771.

Goyal A, Reeves DB, Cardozo-Ojeda EF, Schiffer JT, Mayer BT. Viral load and contact heterogeneity predict SARS-CoV-2 transmission and super-spreading events. Elife. 2021 Feb 23; 10:e63537. PMID: 33620317, PMCID: PMC7929560.

Mayer BT, Krantz EM, Wald A, Corey L, Casper C, Gantt S, Schiffer JT. Estimating the Risk of Human Herpesvirus 6 and Cytomegalovirus Transmission to Ugandan Infants from Viral Shedding in Saliva by Household Contacts. Viruses. 2020 Feb 3; 12(2):171. PMID: 32028569, PMCID: PMC7077293.

Boucoiran I, Mayer BT, Krantz EM, Marchant A, Pati S, Boppana S, Wald A, Corey L, Casper C, Schiffer JT, Gantt S. Nonprimary Maternal Cytomegalovirus Infection After Viral Shedding in Infants. Pediatr Infect Dis J. 2018 Jul; 37(7):627-631. PMID: 29889809, PMCID: PMC6016842.

Reeves DB, Magaret AS, Greninger AL, Johnston C, Schiffer JT. Model-based estimation of superinfection prevalence from limited datasets. J R Soc Interface. 2018 Feb; 15(139):20170968. PMID: 29491180, PMCID: PMC5832741.

Mayer BT, Matrajt L, Casper C, Krantz EM, Corey L, Wald A, Gantt S, Schiffer JT. Dynamics of Persistent Oral Cytomegalovirus Shedding During Primary Infection in Ugandan Infants. J Infect Dis. 2016 Dec 1; 214(11):1735-1743. PMID: 27651417, PMCID: PMC5144733.

Schiffer JT, Mayer BT, Fong Y, Swan DA, Wald A. Herpes simplex virus-2 transmission probability estimates based on quantity of viral shedding. J R Soc Interface. 2014 Mar 26; 11(95):20140160. PMID: 24671939, PMCID: PMC4006256.

Viral Evolution

Swan DA, Rolland M, Herbeck JT, Schiffer JT, Reeves DB. Evolution during primary HIV infection does not require adaptive immune selection. Proc Natl Acad Sci U S A. 2022 Feb 15; 119(7):e2109172119. PMID: 35145025, PMCID: PMC8851487.

Viral Infection in Immunocompromised Hosts

Krantz EM, Mutyaba I, Nankoma J, Okuku F, Casper C, Orem J, Swan DA, Phipps W, Schiffer JT. Highly Heterogeneous Kaposi Sarcoma-Associated Herpesvirus Oral Shedding Kinetics Among People With and Without Kaposi Sarcoma and Human Immunodeficiency Virus Coinfection. Open Forum Infect Dis. 2024 Sep 23; 11(10):ofae548. doi: 10.1093/ofid/ofae548. PMID: 39371366, PMCID: PMC11450676.

Duke ER, Boshier FAT, Boeckh M, Schiffer JT, Cardozo-Ojeda EF. Mathematical Modeling of Within-Host, Untreated, Cytomegalovirus Infection Dynamics after Allogeneic Transplantation. Viruses. 2021 Nov 16; 13(11):2292. PMID: 34835098, PMCID: PMC8618844.

Duke ER, Williamson BD, Borate B, Golob JL, Wychera C, Stevens-Ayers T, Huang ML, Cossrow N, Wan H, Mast TC, Marks MA, Flowers ME, Jerome KR, Corey L, Gilbert PB, Schiffer JT, Boeckh M. CMV viral load kinetics as surrogate endpoints after allogeneic transplantation. J Clin Invest. 2021 Jan 4; 131(1):e133960. PMID: 32970635, PMCID: PMC7773411.

Hill JA, Mayer BT, Xie H, Leisenring WM, Huang ML, Stevens-Ayers T, Milano F, Delaney C, Jerome KR, Zerr DM, Nichols G, Boeckh M, Schiffer JT. Kinetics of Double-Stranded DNA Viremia After Allogeneic Hematopoietic Cell Transplantation. Clin Infect Dis. 2018 Jan 18; 66(3):368-375. PMID: 29020348, PMCID: PMC5850428.