S C Ray

Summary

Affiliation: Johns Hopkins University
Country: USA

Publications

  1. pmc Evolution of the HIV-1 nef gene in HLA-B*57 positive elite suppressors
    Maria Salgado
    Department of Medicine, Johns Hopkins University School of Medicine, 733 N, Broadway, Baltimore, MD 21205, USA
    Retrovirology 7:94. 2010
  2. pmc The transhepatic endotoxin gradient is present despite liver cirrhosis and is attenuated after transjugular portosystemic shunt (TIPS)
    Daniel Benten
    Department of Gastroenterology and Hepatology, University Hospital Hamburg Eppendorf, Martinistrasse 52, Hamburg, Germany
    BMC Gastroenterol 11:107. 2011
  3. pmc Hypervariable region 1 sequence stability during hepatitis C virus replication in chimpanzees
    S C Ray
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    J Virol 74:3058-66. 2000
  4. pmc Divergent and convergent evolution after a common-source outbreak of hepatitis C virus
    Stuart C Ray
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
    J Exp Med 201:1753-9. 2005
  5. pmc Analyses of HIV-1 drug-resistance profiles among infected adolescents experiencing delayed antiretroviral treatment switch after initial nonsuppressive highly active antiretroviral therapy
    Allison Agwu
    Department of Pediatrics, Division of Infectious Diseases, Johns Hopkins Medical Institution, Baltimore, Maryland, USA
    AIDS Patient Care STDS 22:545-52. 2008
  6. ncbi request reprint Genotypic analysis of HIV-1 drug resistance at the limit of detection: virus production without evolution in treated adults with undetectable HIV loads
    Tara L Kieffer
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21025, USA
    J Infect Dis 189:1452-65. 2004
  7. pmc Persistence of wild-type virus and lack of temporal structure in the latent reservoir for human immunodeficiency virus type 1 in pediatric patients with extensive antiretroviral exposure
    Christian T Ruff
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    J Virol 76:9481-92. 2002
  8. ncbi request reprint Needlestick transmission of hepatitis C
    Mark S Sulkowski
    Johns Hopkins School of Medicine, 424 N Bond St, Baltimore, MD 21231, USA
    JAMA 287:2406-13. 2002
  9. ncbi request reprint Slow human immunodeficiency virus type 1 evolution in viral reservoirs in infants treated with effective antiretroviral therapy
    Deborah Persaud
    Department of Pediatrics and Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    AIDS Res Hum Retroviruses 23:381-90. 2007
  10. pmc Transmission of human immunodeficiency virus type 1 from a patient who developed AIDS to an elite suppressor
    Justin R Bailey
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    J Virol 82:7395-410. 2008

Research Grants

Detail Information

Publications46

  1. pmc Evolution of the HIV-1 nef gene in HLA-B*57 positive elite suppressors
    Maria Salgado
    Department of Medicine, Johns Hopkins University School of Medicine, 733 N, Broadway, Baltimore, MD 21205, USA
    Retrovirology 7:94. 2010
    ..The results provide further evidence of ongoing viral replication in ES and suggest that the nef and gag genes in these patients respond similarly to selective pressure from the host...
  2. pmc The transhepatic endotoxin gradient is present despite liver cirrhosis and is attenuated after transjugular portosystemic shunt (TIPS)
    Daniel Benten
    Department of Gastroenterology and Hepatology, University Hospital Hamburg Eppendorf, Martinistrasse 52, Hamburg, Germany
    BMC Gastroenterol 11:107. 2011
    ..Translocation of gut-derived bacterial products such as endotoxin is a major problem in liver cirrhosis...
  3. pmc Hypervariable region 1 sequence stability during hepatitis C virus replication in chimpanzees
    S C Ray
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    J Virol 74:3058-66. 2000
    ..These findings demonstrate that nonsynonymous mutations indicate selection pressure rather than being an incidental result of HCV replication...
  4. pmc Divergent and convergent evolution after a common-source outbreak of hepatitis C virus
    Stuart C Ray
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
    J Exp Med 201:1753-9. 2005
    ..These data suggest that vaccines for genetically diverse viruses may be more effective if they represent consensus sequence, rather than a human isolate...
  5. pmc Analyses of HIV-1 drug-resistance profiles among infected adolescents experiencing delayed antiretroviral treatment switch after initial nonsuppressive highly active antiretroviral therapy
    Allison Agwu
    Department of Pediatrics, Division of Infectious Diseases, Johns Hopkins Medical Institution, Baltimore, Maryland, USA
    AIDS Patient Care STDS 22:545-52. 2008
    ..This finding may have implications for initial treatment regimens and transmission risk in HIV-infected youth, a group with rising infection rates...
  6. ncbi request reprint Genotypic analysis of HIV-1 drug resistance at the limit of detection: virus production without evolution in treated adults with undetectable HIV loads
    Tara L Kieffer
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21025, USA
    J Infect Dis 189:1452-65. 2004
    ..Thus, in some patients, HAART suppresses replication to a level that does not allow the evolution of drug resistance over a time frame of years...
  7. pmc Persistence of wild-type virus and lack of temporal structure in the latent reservoir for human immunodeficiency virus type 1 in pediatric patients with extensive antiretroviral exposure
    Christian T Ruff
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    J Virol 76:9481-92. 2002
    ....
  8. ncbi request reprint Needlestick transmission of hepatitis C
    Mark S Sulkowski
    Johns Hopkins School of Medicine, 424 N Bond St, Baltimore, MD 21231, USA
    JAMA 287:2406-13. 2002
    ..These data underscore the importance of identifying persons with acute HCV infection and promptly referring them to experienced clinicians who can provide updated counseling and treatment...
  9. ncbi request reprint Slow human immunodeficiency virus type 1 evolution in viral reservoirs in infants treated with effective antiretroviral therapy
    Deborah Persaud
    Department of Pediatrics and Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    AIDS Res Hum Retroviruses 23:381-90. 2007
    ..The effect of early therapy on HIV-1 evolution may have implications for long-term pharmacologic control of HIV-1...
  10. pmc Transmission of human immunodeficiency virus type 1 from a patient who developed AIDS to an elite suppressor
    Justin R Bailey
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    J Virol 82:7395-410. 2008
    ..The results strongly suggest that through direct and indirect mechanisms, CD8(+) T cells in some ES control HIV-1 isolates are capable of causing profound immunosuppression...
  11. pmc Control of HIV-1 in elite suppressors despite ongoing replication and evolution in plasma virus
    Karen A O'Connell
    Broadway Research Bldg, Rm 880, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA
    J Virol 84:7018-28. 2010
    ..Interestingly, there was little continual evolution in CTL epitopes, and we detected de novo CTL responses to autologous viral mutants. Thus, some ES control viremia despite ongoing replication and evolution...
  12. pmc Acceleration of hepatitis C virus envelope evolution in humans is consistent with progressive humoral immune selection during the transition from acute to chronic infection
    Lin Liu
    Division of Infectious Diseases, Department of Medicine, Johns Hopkins University, 855 N Wolfe St, Suite 530, Baltimore, MD 21205, USA
    J Virol 84:5067-77. 2010
    ..These data provide the first systematic estimates of HCV evolutionary rates in multiple genes during early infection in vivo and provide additional evidence for deterministic, rather than random, evolution of HCV...
  13. pmc Identification of nevirapine-resistant HIV-1 in the latent reservoir after single-dose nevirapine to prevent mother-to-child transmission of HIV-1
    Megan Wind-Rotolo
    Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
    J Infect Dis 199:1301-9. 2009
    ..Although resistant viruses fade to undetectable levels in plasma, they may persist as stably integrated proviruses within the latent reservoir in resting CD4(+) T cells, potentially complicating future treatment...
  14. pmc High-programmed death-1 levels on hepatitis C virus-specific T cells during acute infection are associated with viral persistence and require preservation of cognate antigen during chronic infection
    Alleluiah Rutebemberwa
    Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
    J Immunol 181:8215-25. 2008
    ..These results support the idea that PD-1 expression on T cells specific for nonescaped epitopes contributes to viral persistence and suggest that PD-1 blockade may alter the outcome of HCV infection...
  15. pmc Residual human immunodeficiency virus type 1 viremia in some patients on antiretroviral therapy is dominated by a small number of invariant clones rarely found in circulating CD4+ T cells
    Justin R Bailey
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    J Virol 80:6441-57. 2006
    ..The sequences have been deposited in GenBank. The accession numbers are DQ 391282 to DQ 391351 (for env) and DQ 391352 to DQ 392955 (for RT)...
  16. pmc HIV-1 evolution following transmission to an HLA-B*5801-positive patient
    Karen A O'Connell
    Department of Medicine, School of Medicine, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
    J Infect Dis 200:1820-4. 2009
    ..Thus, relative control of viral replication can be maintained in spite of the rapid development of multiple escape mutations within cytotoxic T lymphocyte epitopes...
  17. pmc Genetic divergence of hepatitis C virus: the role of HIV-related immunosuppression
    Dale M Netski
    Department of Medicine, Johns Hopkins Medical Institutions, 855 N Wolfe Street, Baltimore, MD 21205, USA
    J Acquir Immune Defic Syndr 49:136-41. 2008
    ..If this increase is dependent on decreased immune selective pressure, then a reduced rate of nucleotide changes resulting in amino acid replacements (nonsynonymous changes, dN) would be expected...
  18. pmc Spontaneous control of primary hepatitis C virus infection and immunity against persistent reinfection
    William O Osburn
    Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
    Gastroenterology 138:315-24. 2010
    ..We followed patients with ongoing hepatitis C virus (HCV) exposure following control of an initial HCV infection to determine whether primary control conferred protection against future persistent infections...
  19. pmc A novel assay allows genotyping of the latent reservoir for human immunodeficiency virus type 1 in the resting CD4+ T cells of viremic patients
    Daphne Monie
    Johns Hopkins University School of Medicine, Broadway Research Building, Room 879, 733 North Broadway St, Baltimore, MD 21205, USA
    J Virol 79:5185-202. 2005
    ..The ability to analyze archival species in viremic patients may have clinical utility in detecting drug-resistant variants not present in the plasma...
  20. ncbi request reprint Dynamics of SEN virus infection among injection drug users
    L E Wilson
    Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD 21231 1001, USA
    J Infect Dis 184:1315-9. 2001
    ..Among Baltimore IDUs, SENV-D and SENV-H infections are common and dynamic, including both viral clearance and reinfection. The clinical significance of SENV infection in this setting remains unknown...
  21. pmc Cellular immune selection with hepatitis C virus persistence in humans
    Andrea L Cox
    Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
    J Exp Med 201:1741-52. 2005
    ..015). These findings reveal two distinct mechanisms of sequence evolution involved in HCV persistence: viral escape from CD8+ T cell responses and optimization of replicative capacity...
  22. pmc Continued production of drug-sensitive human immunodeficiency virus type 1 in children on combination antiretroviral therapy who have undetectable viral loads
    Deborah Persaud
    Department of Pediatrics, Johns Hopkins University School of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21205, USA
    J Virol 78:968-79. 2004
    ..Thus, in most children on HAART with clinically undetectable viremia, there is continued virus production without evolution of resistance in the protease gene...
  23. pmc Identification of ongoing human immunodeficiency virus type 1 (HIV-1) replication in residual viremia during recombinant HIV-1 poxvirus immunizations in patients with clinically undetectable viral loads on durable suppressive highly active antiretroviral
    Carlum Shiu
    Johns Hopkins University, Baltimore, MD 21287, USA
    J Virol 83:9731-42. 2009
    ..001). These findings suggest that ongoing virus replication contributes to low-level viremia in patients on HAART and that this ongoing replication is subject to CD8(+) T-cell selective pressures...
  24. pmc Selection pressure from neutralizing antibodies drives sequence evolution during acute infection with hepatitis C virus
    Kimberly A Dowd
    Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
    Gastroenterology 136:2377-86. 2009
    ....
  25. ncbi request reprint Early archiving and predominance of nonnucleoside reverse transcriptase inhibitor-resistant HIV-1 among recently infected infants born in the United States
    Deborah Persaud
    Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
    J Infect Dis 195:1402-10. 2007
    ....
  26. ncbi request reprint Humoral immune response in acute hepatitis C virus infection
    Dale M Netski
    Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
    Clin Infect Dis 41:667-75. 2005
    ..We investigated the specificity, titer, and neutralizing potential of antibody responses to acute infection by examining 12 injection drug users before, during, and after infection...
  27. ncbi request reprint Prospective evaluation of community-acquired acute-phase hepatitis C virus infection
    Andrea L Cox
    Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
    Clin Infect Dis 40:951-8. 2005
    ....
  28. pmc Neutralizing antibodies do not mediate suppression of human immunodeficiency virus type 1 in elite suppressors or selection of plasma virus variants in patients on highly active antiretroviral therapy
    Justin R Bailey
    Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    J Virol 80:4758-70. 2006
    ..Both drug-mediated and natural suppression of HIV-1 replication to levels below 50 copies/ml may limit the stimulation and maintenance of effective NAb responses...
  29. pmc Human immunodeficiency virus seroconversion and evolution of the hepatitis C virus quasispecies
    Q Mao
    Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
    J Virol 75:3259-67. 2001
    ..These results are consistent with the hypothesis that HIV infection alters the HCV quasispecies, but the number of subjects and observation time may be too low to characterize the full effect...
  30. pmc Maternal neutralizing antibody and transmission of hepatitis C virus to infants
    Kimberly A Dowd
    Department of Medicine, Johns Hopkins Medical Institutions, Johns Hopkins University School of Medicine, 855 N Wolfe Street, Baltimore, MD 21205, USA
    J Infect Dis 198:1651-5. 2008
    ..1:100; P = .23). In the setting of HIV/HCV coinfection, we found no evidence that HCV nAbs are associated with the prevention of MTCT of HCV...
  31. pmc G-->A hypermutation in protease and reverse transcriptase regions of human immunodeficiency virus type 1 residing in resting CD4+ T cells in vivo
    Tara L Kieffer
    Department of Medicine, Johns Hopkins University School of Medicine, 879 Broadway Research Bldg, 733 N Broadway, Baltimore, MD 21205, USA
    J Virol 79:1975-80. 2005
    ..Mutations occurred in predicted contexts, with notable hotspots. Thus, defects in Vif function in vivo give rise to hypermutated viral genomes that can be integrated but do not produce progeny viruses...
  32. ncbi request reprint A sensitive genotyping assay for detection of drug resistance mutations in reverse transcriptase of HIV-1 subtypes B and C in samples stored as dried blood spots or frozen RNA extracts
    Carrie Ziemniak
    Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
    J Virol Methods 136:238-47. 2006
    ..This sensitive and reproducible genotypic assay is feasible for detection of antiretroviral resistance in resource-constrained settings...
  33. pmc CD4+ T cell depletion in an untreated HIV type 1-infected human leukocyte antigen-B*5801-positive patient with an undetectable viral load
    Adriana Andrade
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Clin Infect Dis 46:e78-82. 2008
    ..Our data suggest that immune activation can cause CD4(+) T cell depletion even when HIV-1 replication appears to be controlled by host factors...
  34. ncbi request reprint HIV-1 drug resistance profiles in children and adults with viral load of <50 copies/ml receiving combination therapy
    M Hermankova
    Department of Pediatrics, Johns Hopkins University School of Medicine, 600 N Wolfe St, 256 Park Bldg, Baltimore, MD 21287, USA
    JAMA 286:196-207. 2001
    ....
  35. pmc Progression of fibrosis during chronic hepatitis C is associated with rapid virus evolution
    Xiao Hong Wang
    Viral Hepatitis Center, Div of Inf Dis, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E Jefferson Street, Suite 114, Baltimore, MD 21231, USA, and Southwest Hospital, Chongqing, People s Republic of China
    J Virol 81:6513-22. 2007
    ..Thus, in a small but carefully matched cohort we found evidence for rapid neutral evolution of HCV in persons with rapid progression of hepatic fibrosis, suggesting higher turnover of infected cells...
  36. pmc Comprehensive analyses of CD8+ T cell responses during longitudinal study of acute human hepatitis C
    Andrea L Cox
    Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
    Hepatology 42:104-12. 2005
    ..Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)...
  37. ncbi request reprint Reorganization of genera in the families Rickettsiaceae and Anaplasmataceae in the order Rickettsiales: unification of some species of Ehrlichia with Anaplasma, Cowdria with Ehrlichia and Ehrlichia with Neorickettsia, descriptions of six new species combi
    J S Dumler
    Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
    Int J Syst Evol Microbiol 51:2145-65. 2001
    ..nov. and the genus Neorickettsia should be emended to include Neorickettsia (Ehrlichia) risticii comb. nov. and Neorickettsia (Ehrlichia) sennetsu comb. nov...
  38. ncbi request reprint Severe pruritus after completing pegylated interferon for hepatitis C
    Chistopher J Hoffman
    Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
    AIDS Read 18:562-5. 2008
    ..We report a case of porphyria cutanea tarda presenting primarily as severe pruritus in an HIV/HCV-coinfected person after completion of therapy for hepatitis C...
  39. pmc Human immunodeficiency virus-related microbial translocation and progression of hepatitis C
    Ashwin Balagopal
    Division of Infectious Diseases, Viral Hepatitis Center, Department of Medicine, The Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
    Gastroenterology 135:226-33. 2008
    ..We hypothesized that HIV promotes liver disease by enhancing microbial translocation...
  40. pmc Comprehensive genetic and epigenetic analysis of occult hepatitis B from liver tissue samples
    Perumal Vivekanandan
    Department of Pathology, The Johns Hopkins School of Medicine, Baltimore, Maryland 21231, USA
    Clin Infect Dis 46:1227-36. 2008
    ..Recently, it has been shown that HBV has CpG islands that are methylated, raising the possibility that epigenetic changes may also be important...
  41. pmc Analysis of HIV diversity using a high-resolution melting assay
    William I Towler
    Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    AIDS Res Hum Retroviruses 26:913-8. 2010
    ..111). The HRM assay provides a novel, rapid method for assessing HIV diversity without sequencing. This assay could be applied to any region of the HIV genome or to other genetic systems that exhibit DNA diversity...
  42. pmc Accurate representation of the hepatitis C virus quasispecies in 5.2-kilobase amplicons
    Zhi Liu
    Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
    J Clin Microbiol 42:4223-9. 2004
    ..Therefore, the HCV quasispecies is highly complex even during acute infection and is accurately represented in amplicons representing more than half of the viral genome...
  43. ncbi request reprint Characterization of novel recombinant HIV-1 genomes using the branching index
    Karin Wilbe
    Department of Virology, Swedish Institute for Infectious Disease Control, SE 171 82, Solna, Sweden
    Virology 316:116-25. 2003
    ....
  44. pmc Cross-genotype immunity to hepatitis C virus
    Robert E Lanford
    Department of Virology and Immunology, Southwest National Primate Research Center, Southwest Foundation for Biomedical Research, San Antonio, Texas 78227, USA
    J Virol 78:1575-81. 2004
    ..These studies are the first to show that cross-genotype immunity can be induced to HCV, demonstrating the feasibility of developing a vaccine protective against all HCV strains...
  45. ncbi request reprint Molecular epidemiology of HIV-1 subtypes in southern China
    Oliver Laeyendecker
    Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
    J Acquir Immune Defic Syndr 38:356-62. 2005
    ....
  46. pmc Immune evasion by hepatitis C virus NS3/4A protease-mediated cleavage of the Toll-like receptor 3 adaptor protein TRIF
    Kui Li
    Department of Microbiology and Immunology and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555 1019, USA
    Proc Natl Acad Sci U S A 102:2992-7. 2005
    ..This uniquely broad mechanism of immune evasion potentially limits expression of multiple host defense genes, thereby promoting persistent infections with this medically important virus...

Research Grants10

  1. Mechanisms of Hepatitis C Virus Evolution
    Stuart Ray; Fiscal Year: 2009
    ..Therefore, we anticipate success in these unique studies of positive and negative selection acting on an infectious agent during human infection. ..
  2. Mechanisms of Hepatitis C Virus Evolution
    Stuart Ray; Fiscal Year: 2007
    ..Therefore, we anticipate success in these unique studies of positive and negative selection acting on an infectious agent during human infection. ..
  3. Hepatitis C Recombination Incidence and Prevalence
    Stuart Ray; Fiscal Year: 2004
    ..Because the impact of HCV recombination has not yet been determined, R21 funding will provide adequate preliminary data to establish the importance and proper conduct of more extensive investigations. ..
  4. SEQUENCE SELECTION AND PERSISTENCE OF HEPATITIS C
    Stuart Ray; Fiscal Year: 2003
    ..This application is efficient and has a high likelihood of success because it makes use of a well-characterized cohort, for which years of clinical and virologic data have already been assembled. ..
  5. Mechanisms of Hepatitis C Virus Evolution
    Stuart C Ray; Fiscal Year: 2010
    ..Therefore, we anticipate success in these unique studies of positive and negative selection acting on an infectious agent during human infection. ..