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Inherited chromosomally integrated HHV-6 demonstrates tissue-specific RNA expression in vivo that correlates with increased antibody immune response.

Peddu V, Dubuc I, Gravel A, Xie H, Huang ML, Tenenbaum D, Jerome KR, Tardif JC, Dubé MP, Flamand L, Greninger AL.

J Virol. 2019 Oct 9. pii: JVI.01418-19. doi: 10.1128/JVI.01418-19. [Epub ahead of print]


Closing the Brief Case: Inherited Chromosomally Integrated Human Herpesvirus 6 (HHV-6) in the Age of Multiplex HHV-6 Testing.

Greninger AL, Naccache SN, Pannaraj P, Jerome KR, Dien Bard J, Ruderman JW.

J Clin Microbiol. 2019 Sep 24;57(10). pii: e02018-18. doi: 10.1128/JCM.02018-18. Print 2019 Oct. No abstract available.


The Brief Case: Inherited Chromosomally Integrated Human Herpesvirus 6 (HHV-6) in the Age of Multiplex HHV-6 Testing.

Greninger AL, Naccache SN, Pannaraj P, Jerome KR, Dien Bard J, Ruderman JW.

J Clin Microbiol. 2019 Sep 24;57(10). pii: e02016-18. doi: 10.1128/JCM.02016-18. Print 2019 Oct. No abstract available.


Predictive Value of Respiratory Viral Detection in the Upper Respiratory Tract for Infection of the Lower Respiratory Tract with Hematopoietic Stem Cell Transplantation.

Boonyaratanakornkit J, Vivek M, Xie H, Pergam SA, Cheng GS, Mielcarek M, Hill JA, Jerome KR, Limaye AP, Leisenring W, Boeckh MJ, Waghmare A.

J Infect Dis. 2019 Sep 21. pii: jiz470. doi: 10.1093/infdis/jiz470. [Epub ahead of print]


Human Herpesvirus 6B and Lower Respiratory Tract Disease After Hematopoietic Cell Transplantation.

Hill JA, Vande Vusse LK, Xie H, Chung EL, Yeung CCS, Seo S, Stevens-Ayers T, Fisher CE, Huang ML, Stewart FM, Jerome KR, Zerr DM, Corey L, Leisenring WM, Boeckh M.

J Clin Oncol. 2019 Oct 10;37(29):2670-2681. doi: 10.1200/JCO.19.00908. Epub 2019 Aug 26.


Comparison of Three Adenovirus Quantitative PCR Assays with ATCC Reference Strains and Clinical Samples.

Starr K, Greninger AL, Makhsous N, Jerome KR, Cook L.

J Clin Microbiol. 2019 Aug 21. pii: JCM.00735-19. doi: 10.1128/JCM.00735-19. [Epub ahead of print]


Phylogenetic characterization of rhinoviruses from infants in Sarlahi, Nepal.

Kuypers J, Perchetti GA, Chu HY, Newman KL, Katz J, Khatry SK, LeClerq SC, Jerome KR, Tielsch JM, Englund JA.

J Med Virol. 2019 Dec;91(12):2108-2116. doi: 10.1002/jmv.25563. Epub 2019 Aug 21.


Large, stable, contemporary interspecies recombination events in circulating human herpes simplex viruses.

Casto AM, Roychoudhury P, Xie H, Selke S, Perchetti GA, Wofford H, Huang ML, Verjans GMGM, Gottlieb GS, Wald A, Jerome KR, Koelle DM, Johnston C, Greninger AL.

J Infect Dis. 2019 Apr 23. pii: jiz199. doi: 10.1093/infdis/jiz199. [Epub ahead of print]


Evaluating addition of self-collected throat swabs to nasal swabs for respiratory virus detection.

Fisher CE, Boeckh M, Jerome KR, Englund J, Kuypers J.

J Clin Virol. 2019 Jun;115:43-46. doi: 10.1016/j.jcv.2019.04.001. Epub 2019 Apr 4.


Hybrid nanocarriers incorporating mechanistically distinct drugs for lymphatic CD4+ T cell activation and HIV-1 latency reversal.

Cao S, Slack SD, Levy CN, Hughes SM, Jiang Y, Yogodzinski C, Roychoudhury P, Jerome KR, Schiffer JT, Hladik F, Woodrow KA.

Sci Adv. 2019 Mar 27;5(3):eaav6322. doi: 10.1126/sciadv.aav6322. eCollection 2019 Mar.


Human Rhinovirus Infections in Hematopoietic Cell Transplant Recipients: Risk Score for Progression to Lower Respiratory Tract Infection.

Waghmare A, Xie H, Kuypers J, Sorror ML, Jerome KR, Englund JA, Boeckh M, Leisenring WM.

Biol Blood Marrow Transplant. 2019 May;25(5):1011-1021. doi: 10.1016/j.bbmt.2018.12.005. Epub 2018 Dec 8.


RNA Sequencing of the In Vivo Human Herpesvirus 6B Transcriptome To Identify Targets for Clinical Assays Distinguishing between Latent and Active Infections.

Hill JA, Ikoma M, Zerr DM, Basom RS, Peddu V, Huang ML, Hall Sedlak R, Jerome KR, Boeckh M, Barcy S.

J Virol. 2019 Jan 17;93(3). pii: e01419-18. doi: 10.1128/JVI.01419-18. Print 2019 Feb 1.


Viral Genetics Modulate Orolabial Herpes Simplex Virus Type 1 Shedding in Humans.

Ramchandani MS, Jing L, Russell RM, Tran T, Laing KJ, Magaret AS, Selke S, Cheng A, Huang ML, Xie H, Strachan E, Greninger AL, Roychoudhury P, Jerome KR, Wald A, Koelle DM.

J Infect Dis. 2019 Mar 15;219(7):1058-1066. doi: 10.1093/infdis/jiy631.


Evidence for persistence of the SHIV reservoir early after MHC haploidentical hematopoietic stem cell transplantation.

Colonna L, Peterson CW, Schell JB, Carlson JM, Tkachev V, Brown M, Yu A, Reddy S, Obenza WM, Nelson V, Polacino PS, Mack H, Hu SL, Zeleski K, Hoffman M, Olvera J, Furlan SN, Zheng H, Taraseviciute A, Hunt DJ, Betz K, Lane JF, Vogel K, Hotchkiss CE, Moats C, Baldessari A, Murnane RD, English C, Astley CA, Wangari S, Agricola B, Ahrens J, Iwayama N, May A, Stensland L, Huang MW, Jerome KR, Kiem HP, Kean LS.

Nat Commun. 2018 Oct 25;9(1):4438. doi: 10.1038/s41467-018-06736-7.


Limited Marginal Utility of Deep Sequencing for HIV Drug Resistance Testing in the Age of Integrase Inhibitors.

Dalmat RR, Makhsous N, Pepper GG, Magaret A, Jerome KR, Wald A, Greninger AL.

J Clin Microbiol. 2018 Nov 27;56(12). pii: e01443-18. doi: 10.1128/JCM.01443-18. Print 2018 Dec.


Risk Factors for Parainfluenza Virus Lower Respiratory Tract Disease after Hematopoietic Cell Transplantation.

Seo S, Xie H, Leisenring WM, Kuypers JM, Sahoo FT, Goyal S, Kimball LE, Campbell AP, Jerome KR, Englund JA, Boeckh M.

Biol Blood Marrow Transplant. 2019 Jan;25(1):163-171. doi: 10.1016/j.bbmt.2018.08.021. Epub 2018 Aug 25.


Initial High Viral Load Is Associated with Prolonged Shedding of Human Rhinovirus in Allogeneic Hematopoietic Cell Transplant Recipients.

Ogimi C, Xie H, Leisenring WM, Kuypers JM, Jerome KR, Campbell AP, Englund JA, Boeckh M, Waghmare A.

Biol Blood Marrow Transplant. 2018 Oct;24(10):2160-2163. doi: 10.1016/j.bbmt.2018.07.006. Epub 2018 Aug 7.


Viral diversity is an obligate consideration in CRISPR/Cas9 designs for targeting the HIV reservoir.

Roychoudhury P, De Silva Feelixge H, Reeves D, Mayer BT, Stone D, Schiffer JT, Jerome KR.

BMC Biol. 2018 Jul 11;16(1):75. doi: 10.1186/s12915-018-0544-1.


Ultrasensitive Capture of Human Herpes Simplex Virus Genomes Directly from Clinical Samples Reveals Extraordinarily Limited Evolution in Cell Culture.

Greninger AL, Roychoudhury P, Xie H, Casto A, Cent A, Pepper G, Koelle DM, Huang ML, Wald A, Johnston C, Jerome KR.

mSphere. 2018 Jun 13;3(3). pii: e00283-18. doi: 10.1128/mSphereDirect.00283-18. Print 2018 Jun 27.


Antibiotic Exposure Prior to Respiratory Viral Infection Is Associated with Progression to Lower Respiratory Tract Disease in Allogeneic Hematopoietic Cell Transplant Recipients.

Ogimi C, Krantz EM, Golob JL, Waghmare A, Liu C, Leisenring WM, Woodard CR, Marquis S, Kuypers JM, Jerome KR, Pergam SA, Fredricks DN, Sorror ML, Englund JA, Boeckh M.

Biol Blood Marrow Transplant. 2018 Nov;24(11):2293-2301. doi: 10.1016/j.bbmt.2018.05.016. Epub 2018 May 16.


Differential impact of transplantation on peripheral and tissue-associated viral reservoirs: Implications for HIV gene therapy.

Peterson CW, Wang J, Deleage C, Reddy S, Kaur J, Polacino P, Reik A, Huang ML, Jerome KR, Hu SL, Holmes MC, Estes JD, Kiem HP.

PLoS Pathog. 2018 Apr 19;14(4):e1006956. doi: 10.1371/journal.ppat.1006956. eCollection 2018 Apr.


Alveolar levels of immuno-inflammatory mediators in diffuse alveolar hemorrhage after allogeneic transplant.

Vande Vusse LK, Wurfel MM, Madtes DM, Schoch HG, Harju-Baker S, Hill JA, Jerome KR, Boeckh M, Watkins TR.

Bone Marrow Transplant. 2018 Sep;53(9):1206-1209. doi: 10.1038/s41409-018-0168-7. Epub 2018 Apr 18. No abstract available.


Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6.

Greninger AL, Knudsen GM, Roychoudhury P, Hanson DJ, Sedlak RH, Xie H, Guan J, Nguyen T, Peddu V, Boeckh M, Huang ML, Cook L, Depledge DP, Zerr DM, Koelle DM, Gantt S, Yoshikawa T, Caserta M, Hill JA, Jerome KR.

BMC Genomics. 2018 Mar 20;19(1):204. doi: 10.1186/s12864-018-4604-2.


CRISPR/Cas9 and Genome Editing for Viral Disease-Is Resistance Futile?

De Silva Feelixge HS, Stone D, Roychoudhury P, Aubert M, Jerome KR.

ACS Infect Dis. 2018 Jun 8;4(6):871-880. doi: 10.1021/acsinfecdis.7b00273. Epub 2018 Mar 21. Review.


Enterovirus D-68 in children presenting for acute care in the hospital setting.

Savage TJ, Kuypers J, Chu HY, Bradford MC, Buccat AM, Qin X, Klein EJ, Jerome KR, Englund JA, Waghmare A.

Influenza Other Respir Viruses. 2018 Jul;12(4):522-528. doi: 10.1111/irv.12551. Epub 2018 Mar 23.


Copy Number Heterogeneity, Large Origin Tandem Repeats, and Interspecies Recombination in Human Herpesvirus 6A (HHV-6A) and HHV-6B Reference Strains.

Greninger AL, Roychoudhury P, Makhsous N, Hanson D, Chase J, Krueger G, Xie H, Huang ML, Saunders L, Ablashi D, Koelle DM, Cook L, Jerome KR.

J Virol. 2018 Apr 27;92(10). pii: e00135-18. doi: 10.1128/JVI.00135-18. Print 2018 May 15.


Dual-strain genital herpes simplex virus type 2 (HSV-2) infection in the US, Peru, and 8 countries in sub-Saharan Africa: A nested cross-sectional viral genotyping study.

Johnston C, Magaret A, Roychoudhury P, Greninger AL, Reeves D, Schiffer J, Jerome KR, Sather C, Diem K, Lingappa JR, Celum C, Koelle DM, Wald A.

PLoS Med. 2017 Dec 27;14(12):e1002475. doi: 10.1371/journal.pmed.1002475. eCollection 2017 Dec.


Myeloablation-associated deletion of ORF4 in a human coronavirus 229E infection.

Greninger AL, Pepper G, Shean RC, Cent A, Palileo I, Kuypers JM, Schiffer JT, Jerome KR.

NPJ Genom Med. 2017 Oct 9;2:30. doi: 10.1038/s41525-017-0033-4. eCollection 2017.


Diagnostic and Prognostic Plasma Biomarkers for Idiopathic Pneumonia Syndrome after Hematopoietic Cell Transplantation.

Seo S, Yu J, Jenkins IC, Leisenring WM, Steven-Ayers T, Kuypers JM, Huang ML, Jerome KR, Boeckh M, Paczesny S.

Biol Blood Marrow Transplant. 2018 Apr;24(4):678-686. doi: 10.1016/j.bbmt.2017.11.039. Epub 2017 Dec 6.


Comparison of Preemptive Therapy and Antiviral Prophylaxis for Prevention of Cytomegalovirus in Seropositive Liver Transplant Recipients.

Liu AW, Jutivorakool K, Fisher CE, Rakita RM, Reyes JD, Bhattacharya RB, Jerome KR, Limaye AP.

Transplantation. 2018 Apr;102(4):632-639. doi: 10.1097/TP.0000000000002029.


Kinetics of Double-Stranded DNA Viremia After Allogeneic Hematopoietic Cell Transplantation.

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.

Clin Infect Dis. 2018 Jan 18;66(3):368-375. doi: 10.1093/cid/cix804.


Performance of Commercial Enzyme-Linked Immunoassays for Diagnosis of Herpes Simplex Virus-1 and Herpes Simplex Virus-2 Infection in a Clinical Setting.

Agyemang E, Le QA, Warren T, Magaret AS, Selke S, Johnston C, Jerome KR, Wald A.

Sex Transm Dis. 2017 Dec;44(12):763-767. doi: 10.1097/OLQ.0000000000000689.


Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses.

Niyonzima N, Lambert AR, Werther R, De Silva Feelixge H, Roychoudhury P, Greninger AL, Stone D, Stoddard BL, Jerome KR.

Protein Eng Des Sel. 2017 Jul 1;30(7):503-522. doi: 10.1093/protein/gzx037.


Isolation and characterization of the fall Chinook aquareovirus.

Makhsous N, Jensen NL, Haman KH, Batts WN, Jerome KR, Winton JR, Greninger AL.

Virol J. 2017 Sep 5;14(1):170. doi: 10.1186/s12985-017-0839-9.


Prolonged Shedding of Human Coronavirus in Hematopoietic Cell Transplant Recipients: Risk Factors and Viral Genome Evolution.

Ogimi C, Greninger AL, Waghmare AA, Kuypers JM, Shean RC, Xie H, Leisenring WM, Stevens-Ayers TL, Jerome KR, Englund JA, Boeckh M.

J Infect Dis. 2017 Jul 15;216(2):203-209. doi: 10.1093/infdis/jix264.


Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 UL and US regions from genital swabs collected from 3 continents.

Johnston C, Magaret A, Roychoudhury P, Greninger AL, Cheng A, Diem K, Fitzgibbon MP, Huang ML, Selke S, Lingappa JR, Celum C, Jerome KR, Wald A, Koelle DM.

Virology. 2017 Oct;510:90-98. doi: 10.1016/j.virol.2017.06.031. Epub 2017 Jul 13.


Outcomes of hematopoietic cell transplantation using donors or recipients with inherited chromosomally integrated HHV-6.

Hill JA, Magaret AS, Hall-Sedlak R, Mikhaylova A, Huang ML, Sandmaier BM, Hansen JA, Jerome KR, Zerr DM, Boeckh M.

Blood. 2017 Aug 24;130(8):1062-1069. doi: 10.1182/blood-2017-03-775759. Epub 2017 Jun 8.


Biopsy Specimens From Allograft Liver Contain Histologic Features of Hepatitis C Virus Infection After Virus Eradication.

Whitcomb E, Choi WT, Jerome KR, Cook L, Landis C, Ahn J, Te HS, Esfeh J, Hanouneh IA, Rayhill SC, Gibson W, Plesec T, Koo J, Wang HL, Hart J, Pai RK, Westerhoff M.

Clin Gastroenterol Hepatol. 2017 Aug;15(8):1279-1285. doi: 10.1016/j.cgh.2017.04.041. Epub 2017 May 10.


Cell Culture Systems To Study Human Herpesvirus 6A/B Chromosomal Integration.

Gravel A, Dubuc I, Wallaschek N, Gilbert-Girard S, Collin V, Hall-Sedlak R, Jerome KR, Mori Y, Carbonneau J, Boivin G, Kaufer BB, Flamand L.

J Virol. 2017 Jun 26;91(14). pii: e00437-17. doi: 10.1128/JVI.00437-17. Print 2017 Jul 15.


Comparison of self-collected nasal swabs with oral washes for sequential viral load monitoring in lung transplant recipients with respiratory virus infection.

Fisher CE, Bornstein R, Kuypers J, Jerome KR, Boeckh M, Limaye AP.

J Clin Virol. 2017 Jun;91:49-51. doi: 10.1016/j.jcv.2017.04.009. Epub 2017 Apr 14. No abstract available.


Excision of Latent HIV-1 from Infected Cells In Vivo: An Important Step Forward.

De Silva Feelixge HS, Jerome KR.

Mol Ther. 2017 May 3;25(5):1062-1064. doi: 10.1016/j.ymthe.2017.04.009. Epub 2017 Apr 24. No abstract available.


In vivo dynamics of AAV-mediated gene delivery to sensory neurons of the trigeminal ganglia.

Dang CH, Aubert M, De Silva Feelixge HS, Diem K, Loprieno MA, Roychoudhury P, Stone D, Jerome KR.

Sci Rep. 2017 Apr 19;7(1):927. doi: 10.1038/s41598-017-01004-y.


Rule-Out Outbreak: 24-Hour Metagenomic Next-Generation Sequencing for Characterizing Respiratory Virus Source for Infection Prevention.

Greninger AL, Waghmare A, Adler A, Qin X, Crowley JL, Englund JA, Kuypers JM, Jerome KR, Zerr DM.

J Pediatric Infect Dis Soc. 2017 Jun 1;6(2):168-172. doi: 10.1093/jpids/pix019.


Risk Factors and Outcomes of Ganciclovir-Resistant Cytomegalovirus Infection in Solid Organ Transplant Recipients.

Fisher CE, Knudsen JL, Lease ED, Jerome KR, Rakita RM, Boeckh M, Limaye AP.

Clin Infect Dis. 2017 Jul 1;65(1):57-63. doi: 10.1093/cid/cix259.


Clinical Significance of Human Coronavirus in Bronchoalveolar Lavage Samples From Hematopoietic Cell Transplant Recipients and Patients With Hematologic Malignancies.

Ogimi C, Waghmare AA, Kuypers JM, Xie H, Yeung CC, Leisenring WM, Seo S, Choi SM, Jerome KR, Englund JA, Boeckh M.

Clin Infect Dis. 2017 Jun 1;64(11):1532-1539. doi: 10.1093/cid/cix160. Erratum in: Clin Infect Dis. 2017 Oct 15;65(8):1431-1433.


Applications of Digital PCR for Clinical Microbiology.

Kuypers J, Jerome KR.

J Clin Microbiol. 2017 Jun;55(6):1621-1628. doi: 10.1128/JCM.00211-17. Epub 2017 Mar 15. Review.


Worldwide circulation of HSV-2 × HSV-1 recombinant strains.

Koelle DM, Norberg P, Fitzgibbon MP, Russell RM, Greninger AL, Huang ML, Stensland L, Jing L, Magaret AS, Diem K, Selke S, Xie H, Celum C, Lingappa JR, Jerome KR, Wald A, Johnston C.

Sci Rep. 2017 Mar 13;7:44084. doi: 10.1038/srep44084.


Draft Genome Sequences of Six Novel Picorna-Like Viruses from Washington State Spiders.

Shean RC, Makhsous N, Crawford RL, Jerome KR, Greninger AL.

Genome Announc. 2017 Mar 2;5(9). pii: e01705-16. doi: 10.1128/genomeA.01705-16.


Loss of immune homeostasis dictates SHIV rebound after stem-cell transplantation.

Peterson CW, Benne C, Polacino P, Kaur J, McAllister CE, Filali-Mouhim A, Obenza W, Pecor TA, Huang ML, Baldessari A, Murnane RD, Woolfrey AE, Jerome KR, Hu SL, Klatt NR, DeRosa S, Sékaly RP, Kiem HP.

JCI Insight. 2017 Feb 23;2(4):e91230. doi: 10.1172/jci.insight.91230.


Genome Sequences of Three Novel Bunyaviruses, Two Novel Rhabdoviruses, and One Novel Nyamivirus from Washington State Moths.

Makhsous N, Shean RC, Droppers D, Guan J, Jerome KR, Greninger AL.

Genome Announc. 2017 Feb 16;5(7). pii: e01668-16. doi: 10.1128/genomeA.01668-16.

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