Research Topics
Genomes and GenesSpecies | F E McCutchanSummaryAffiliation: Division of Retrovirology Country: USA Publications
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Detail Information
Publications
Variable contexts and levels of hypermutation in HIV-1 proviral genomes recovered from primary peripheral blood mononuclear cellsGustavo H Kijak
Henry M Jackson Foundation for the Advancement of Military Medicine US Military HIV Research Program, 1600 East Gude Drive, Rockville, Maryland 20850, USA
Virology 376:101-11. 2008..These data suggest considerable complexity in the interplay of host restriction and viral defense during HIV-1 infection...
CTL epitope distribution patterns in the Gag and Nef proteins of HIV-1 from subtype A infected subjects in Kenya: use of multiple peptide sets increases the detectable breadth of the CTL responseJeffrey R Currier
The US Military HIV Research Program, Rockville, MD 20850, USA
BMC Immunol 7:8. 2006..While considerable effort has been focused upon mapping and defining immunodominant CTL epitopes in HIV-1 subtype B and subtype C infections, few epitope mapping studies have focused upon subtype A...- In-depth analysis of a heterosexually acquired human immunodeficiency virus type 1 superinfection: evolution, temporal fluctuation, and intercompartment dynamics from the seronegative window period through 30 months postinfectionF E McCutchan
US Military HIV Research Program, 1600 E Gude Drive, Rockville, MD 20850, USA
J Virol 79:11693-704. 2005.... 
Precise mapping of recombination breakpoints suggests a common parent of two BC recombinant HIV type 1 strains circulating in ChinaF E McClutchan
Henry M Jackson Foundation, Rockville, Maryland 20850, USA
AIDS Res Hum Retroviruses 18:1135-40. 2002..Both CRFs are broadly distributed from north to south in western China and have maintained low interpatient diversity...- Global epidemiology of HIVFrancine E McCutchan
US Military HIV Research Program, 1600 E Gude Drive, Rockville, MD 20850, USA
J Med Virol 78:S7-S12. 2006.... - HIV type 1 circulating recombinant form CRF09_cpx from west Africa combines subtypes A, F, G, and may share ancestors with CRF02_AG and Z321Francine E McCutchan
Global Molecular Epidemiology Program, Henry M Jackson Foundation, 1600 East Gude Drive, Rockville, Maryland 20850, USA
AIDS Res Hum Retroviruses 20:819-26. 2004..Although newly identified, at least one infection with CRF09_cpx has already occurred outside of Africa... - Full genome sequences of human immunodeficiency virus type 1 subtypes G and A/G intersubtype recombinantsJ K Carr
Henry M Jackson Foundation, Rockville, Maryland, USA
Virology 247:22-31. 1998..The geographic spread of the IbNG-like strains suggests that, like the subtype E recombinants, these should be given a specific name to facilitate future identification and tracking; the name "IbNG subtype" is proposed... - Full-length sequence and mosaic structure of a human immunodeficiency virus type 1 isolate from ThailandJ K Carr
Henry M Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland 20850, USA
J Virol 70:5935-43. 1996..The mosaic structure of a CM240 virion is suggestive of phenotypic differences which might have contributed to the emergence of this variant... - Evolution and probable transmission of intersubtype recombinant human immunodeficiency virus type 1 in a Zambian coupleM O Salminen
Henry M Jackson Foundation and Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, Maryland 20850, USA
J Virol 71:2647-55. 1997..Intersubtype recombination apparently played a central role in the evolution of HIV-1 in this couple and may contribute substantially to the rapid emergence of HIV-1 variants whenever mixed-subtype HIV-1 infections occur... - Characterization of subtype A HIV-1 from Africa by full genome sequencingJ K Carr
Henry M Jackson Foundation, Rockville, MD, USA
AIDS 13:1819-26. 1999..To improve our understanding of the genetic complexity of HIV-1 subtype A by increasing the number of subtype A isolates that have been sequenced in their entirety... - Infectious molecular clones with the nonhomologous dimer initiation sequences found in different subtypes of human immunodeficiency virus type 1 can recombine and initiate a spreading infection in vitroD C St Louis
The Henry M Jackson Foundation for the Advancement of Military Medicine and Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, Maryland 20850, USA
J Virol 72:3991-8. 1998..Our studies indicate that the nonhomologous DIS sequences found in different HIV-1 subtypes are not a primary obstacle to intersubtype recombination... - HLA class I allele and haplotype diversity in Ugandans supports the presence of a major east African genetic clusterG H Kijak
Division of Retrovirology, US Military HIV Research Program Henry M Jackson Foundation, Rockville, MD 20850, USA
Tissue Antigens 73:262-9. 2009..The congruence of major alleles in different populations would permit consideration of East Africa as an integrated setting when designing and evaluating much needed malaria, tuberculosis, and AIDS vaccines... - Socio-demographic and drug use factors associated with HIV-1 recombinants and dual infections in Northern Thai drug users: associations of risk with genetic complexityG H Kijak
US Military HIV Research Program, Henry M Jackson Foundation, Rockville, MD 20850, USA
Drug Alcohol Depend 116:24-30. 2011..In this study we aim to investigate the socio demographic factors associated with an increasing level of genetic diversity among HIV strains in a population of drug-users in Northern Thailand... - Diverse BF recombinants have spread widely since the introduction of HIV-1 into South AmericaJ K Carr
Henry M Jackson Foundation, Rockville, MD 20850, USA
AIDS 15:F41-7. 2001..To describe the genetic diversity of HIV-1 in South America by full genome sequencing and analysis... - The AG recombinant IbNG and novel strains of group M HIV-1 are common in CameroonJ K Carr
Henry M Jackson Foundation, Rockville, Maryland 20850, USA
Virology 286:168-81. 2001..This suggests that there was an ancestral AG recombinant that gave rise to CRF02 AG (IbNG), the successful circulating recombinant form, and to others that were less successful and are now rare... - Development of calibrated viral load standards for group M subtypes of human immunodeficiency virus type 1 and performance of an improved AMPLICOR HIV-1 MONITOR test with isolates of diverse subtypesN L Michael
Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, Maryland 20850, USA
J Clin Microbiol 37:2557-63. 1999.... - Subtype G and multiple forms of A/G intersubtype recombinant human immunodeficiency virus type 1 in NigeriaF E McCutchan
The Henry M Jackson Foundation, 1600 East Gude Drive, Rockville, Maryland, 20850, USA
Virology 254:226-34. 1999..The remaining patient had a strain that was otherwise subtype G but shared an unclassified carboxyl-terminal gp41 segment with the CA1-like strains. Other subtypes and group O were not found... - Human immunodeficiency virus type 1 DNA sequences genetically damaged by hypermutation are often abundant in patient peripheral blood mononuclear cells and may be generated during near-simultaneous infection and activation of CD4(+) T cellsM Janini
Henry M Jackson Foundation, Rockville, Maryland 20850, USA
J Virol 75:7973-86. 2001..Near-simultaneous activation and infection of CD4(+) T cells may represent a window of susceptibility where the informational content of HIV-1 sequences is lost due to hypermutation... - A nascent HIV type 1 epidemic among injecting drug users in Kabul, Afghanistan is dominated by complex AD recombinant strain, CRF35_ADE Sanders-Buell
US Military HIV Research Program Division of Retrovirology, Walter Reed Army Institute of Research, Rockville Maryland 20850, USA
AIDS Res Hum Retroviruses 23:834-9. 2007..2% HIV-1 prevalence, are either CRF35_AD or a related recombinant. Voluntary HIV-1 screening and harm reduction programs in Afghanistan, applied now, could limit the spread of HIV-1, both in IDUs and in other social networks... - High-throughput genotyping of KIR2DL2/L3, KIR3DL1/S1, and their HLA class I ligands using real-time PCRR N Koehler
Division of Retrovirology, US Military HIV Research Program Henry M Jackson Foundation, Rockville, MD 20850, USA
Tissue Antigens 74:73-80. 2009..The application of this platform will further clarify the nature and impact of the KIR-HLA epistatic interaction on disease course in large global population-based studies... - Molecular epidemiology of HIV Type 1 in preparation for a Phase III prime-boost vaccine trial in Thailand and a new approach to HIV Type 1 genotypingVeerachai Watanaveeradej
Department of Pediatrics, Phramongkutklao Hospital School of Medicine, Bangkok, Thailand
AIDS Res Hum Retroviruses 22:801-7. 2006.... - Frequency of HIV type 1 dual infection and HIV diversity: analysis of low- and high-risk populations in Mbeya Region, TanzaniaKarl-Heinz Herbinger
Department of Infectious Diseases and Tropical Medicine, Ludwig-Maximilians-University, Munich, Germany
AIDS Res Hum Retroviruses 22:599-606. 2006..High-risk populations may play an important role in the evolution of HIV, as they can provide an opportunity for the virus to coinfect, recombine, and adapt to the host-specific genetic background... - Higher HIV-1 incidence and genetic complexity along main roads in Rakai District, UgandaMiguel A Arroyo
US Military HIV Research Program (USMHRP, Division of Retrovirology, Walter Reed Army Institute of Research, Silver Spring, MD, USA
J Acquir Immune Defic Syndr 43:440-5. 2006..4 to 47.7). CONCLUSIONS: HIV-1 incidence and genetic complexity are associated with geographic strata and population mobility in Rakai District and are important variables to be considered in planning and recruitment for vaccine trials... - Circulating and unique recombinant forms of HIV type 1 containing subsubtype A2Unchalee Visawapoka
Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
AIDS Res Hum Retroviruses 22:695-702. 2006..Monitoring of A2-containing recombinants and subtype C strains, both relatively rare in Kenya, may be informative in the course of cohort development and evaluation of candidate vaccines... - HyperPack: a software package for the study of levels, contexts, and patterns of APOBEC-mediated hypermutation in HIVGustavo H Kijak
U S Military HIV Research Program, Henry M Jackson Foundation for the Advancement of Military Medicine, 1600 East Gude Drive, Rockville, MD 20850, USA
AIDS Res Hum Retroviruses 23:554-7. 2007..HyperPack is a platform-flexible, Java stand-alone application available through http://www.hivresearch.org/hyperpack/... - Distinguishing molecular forms of HIV-1 in Asia with a high-throughput, fluorescent genotyping assay, MHAbce v.2Gustavo H Kijak
Henry M Jackson Foundation for the Advancement of Military Medicine US Military HIV Research Program, Rockville, MD 20850, USA
Virology 358:178-91. 2007..MHAbce v.2, with an area of application including China, India, Southeast Asia, and the Pacific Rim, can be used to develop a comprehensive and detailed picture of this important component of the HIV/AIDS pandemic... - Cross-clade neutralization patterns among HIV-1 strains from the six major clades of the pandemic evaluated and compared in two different modelsBruce K Brown
Henry M Jackson Foundation, Rockville, MD, USA
Virology 375:529-38. 2008..These data highlight the importance of the neutralization assay format employed and suggest that clade C envelopes merit further evaluation for the elicitation of broadly neutralizing antibodies... - The challenge of HIV-1 subtype diversityBarbara S Taylor
Department of Medicine and the Division of Infectious Diseases, Columbia University Medical Center, New York 10032, USA
N Engl J Med 358:1590-602. 2008 - Recent advances in the characterization of HIV-1 neutralization assays for standardized evaluation of the antibody response to infection and vaccinationVictoria R Polonis
Walter Reed Army Institute of Research, Washington, DC, USA
Virology 375:315-20. 2008.... - Antibodies induced by liposomal protein exhibit dual binding to protein and lipid epitopesNicos Karasavvas
Division of Retrovirology, Walter Reed Army Institute of Research, US Military HIV Research Program, Department of Vaccine Production and Delivery, 1600 East Gude Drive, Rockville, MD 20850, USA
Biochem Biophys Res Commun 366:982-7. 2008..Surface plasmon resonance studies with the former antibody showed that the liposomal cholesterol and liposomal gp140 each contributed to the overall binding energy of the antibody to liposomes containing cholesterol and protein... - Identification of CRF34_01B, a second circulating recombinant form unrelated to and more complex than CRF15_01B, among injecting drug users in northern ThailandSodsai Tovanabutra
US Military HIV Research Program, Rockville, Maryland 20850, USA
AIDS Res Hum Retroviruses 23:829-33. 2007..More comprehensive HIV-1 prevention and treatment programs in IDU can help to limit the growing complexity of HIV-1 strains in Thailand... - HIV-1 genetic diversity and compartmentalization in mother/infant pairs infected with CRF01_AESodsai Tovanabutra
Research Institute for Health Sciences, Thailand
AIDS 21:1050-3. 2007..Infant viruses were almost distinct, but phylogenetically related, to maternal viruses, mostly from the maternal PBMC compartment, reflecting the frequent transmission of HIV-1 from maternal cells rather than free viruses... - HIV-1 diversity and prevalence differ between urban and rural areas in the Mbeya region of TanzaniaMiguel A Arroyo
US Military HIV Research Program USMHRP, Walter Reed Army Institute of Research, Division of Retrovirology, 1600 East Gude Drive, Silver Spring, MD 20850, USA
AIDS 19:1517-24. 2005..To characterize HIV-1 strains in a potential vaccine trial cohort (CODE) in the Mbeya region of southwest Tanzania... - HIV-1 envelope pseudotyped viral vectors and infectious molecular clones expressing the same envelope glycoprotein have a similar neutralization phenotype, but culture in peripheral blood mononuclear cells is associated with decreased neutralization sensiMark K Louder
Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, NIH, 40 Convent Drive, Bethesda, MD 20892, USA
Virology 339:226-38. 2005..Replication competent HIV-1 and isogenic envelope pseudoviruses have similar neutralization characteristics, but passage into PBMC is associated with decreased sensitivity to neutralization... - Detection of high frequencies of HIV-1 cross-subtype reactive CD8 T lymphocytes in the peripheral blood of HIV-1-infected KenyansJeffrey R Currier
US Military HIV Research Program, Suite 200, 13 Taft Court, Rockville, MD 20850, USA
AIDS 17:2149-57. 2003..To quantitate rapidly the frequency of HIV-1 subtype-specific and broadly HIV-1 cross-subtype-reactive CD8 T cells in the peripheral blood of HIV-1-infected individuals from a geographical region of multiple subtype endemicity... - Subtype C/CRF01_AE recombinant HIV-1 found in ThailandVeerachai Watanaveeradej
AIDS 17:2138-40. 2003 - A new circulating recombinant form, CRF15_01B, reinforces the linkage between IDU and heterosexual epidemics in ThailandSodsai Tovanabutra
Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand
AIDS Res Hum Retroviruses 19:561-7. 2003..These recombinants must be considered in ongoing or projected efficacy evaluations of HIV-1 vaccines and antiviral therapies... - Heterosexually acquired CRF01_AE/B recombinant HIV type 1 found in ThailandKwanjai Viputtijul
Thai Component, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
AIDS Res Hum Retroviruses 18:1235-7. 2002..Studies are underway to determine whether either recombinant is circulating widely... - Among 46 near full length HIV type 1 genome sequences from Rakai District, Uganda, subtype D and AD recombinants predominateMatthew E Harris
Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA
AIDS Res Hum Retroviruses 18:1281-90. 2002..Subtype D comprised more than 70% of all the HIV-1 genomes in Rakai when both pure subtypes and recombinants were considered. Candidate vaccines based on HIV-1 subtype D would be appropriate for evaluation in Rakai District, Uganda... - Detection of HIV-1 subtypes, recombinants, and dual infections in east Africa by a multi-region hybridization assayMichael Hoelscher
Department of Infectious Diseases and Tropical Medicine, Ludwig-Maximilians-University, Munich, Germany
AIDS 16:2055-64. 2002.... - Forty-one near full-length HIV-1 sequences from Kenya reveal an epidemic of subtype A and A-containing recombinantsWilliam E Dowling
Walter Reed Army Institute of Research, Washington, DC, USA
AIDS 16:1809-20. 2002.... - Full-length genome analysis of HIV-1 subtype C utilizing CXCR4 and intersubtype recombinants isolated in South AfricaMaria A Papathanasopoulos
National Institute for Communicable Diseases, Sandringham, Johannesburg 2131, South Africa
AIDS Res Hum Retroviruses 18:879-86. 2002..These results establish the presence of intersubtype recombinants in South Africa, indicating that ongoing surveillance for other subtypes and recombinants is necessary... - Diverse HIV-1 subtypes and clinical, laboratory and behavioral factors in a recently infected US military cohortStephanie K Brodine
Graduate School of Public Health, San Diego State University, San Diego, California 92182, USA
AIDS 17:2521-7. 2003..Efficient diagnosis of acute primary HIV-1 infection was identified as a goal for prevention programs. Modifiable risk behaviors and target populations for intervention were identified... - A cluster of HIV type 1 subtype C sequences from Ethiopia, observed in full genome analysis, is not sustained in subgenomic regionsMatthew E Harris
Walter Reed Army Institute of Research, Washington, D C, USA
AIDS Res Hum Retroviruses 19:1125-33. 2003..Although immunological responses must be considered, from a phylogenetic perspective, there is no compelling support for use of Ethiopian subtype C sequences, compared to other subtype C, as vaccine prototype strains... - Lost in translation: implications of HIV-1 codon usage for immune escape and drug resistanceGustavo H Kijak
Henry M Jackson Foundation for the Advancement of Military Medicine, 1600 East Gude Drive, Rockville, MD 20850, USA
AIDS Rev 6:54-60. 2004..Quasi-synonymy conditions HIV-1 and, potentially, other rapidly evolving organisms in their exploration of the mutational space... - Characterization of complete HIV type 1 genomes from non-B subtype infections in U.S. military personnelSodsai Tovanabutra
US Military HIV Research Program, Henry M. Jackson Foundation, Rockville, Maryland 20850, USA
AIDS Res Hum Retroviruses 21:424-9. 2005..S. military exposure while deployed and sets the bar higher for breadth of cross-subtype protection to be afforded by an HIV-1 vaccine... - Emergence of unique primate T-lymphotropic viruses among central African bushmeat huntersNathan D Wolfe
Department of Epidemiology, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD 21205, USA
Proc Natl Acad Sci U S A 102:7994-9. 2005.... - Biologic and genetic characterization of a panel of 60 human immunodeficiency virus type 1 isolates, representing clades A, B, C, D, CRF01_AE, and CRF02_AG, for the development and assessment of candidate vaccinesBruce K Brown
The Henry M Jackson Foundation, 13 Taft Court, Suite 200, Rockville, MD 20850, USA
J Virol 79:6089-101. 2005.... - Immunodominance and cross-reactivity of B5703-restricted CD8 T lymphocytes from HIV type 1 subtype C-infected EthiopiansJeffrey R Currier
The U S Military HIV Research Program, Rockville, Maryland 20850, USA
AIDS Res Hum Retroviruses 21:239-45. 2005..Efforts to optimize the cross-reactivity of vaccine-induced CD8 T cells may need to focus on the relative immunogenicity of minor sequence variation... - Distinct human immunodeficiency virus type 1 subtype A virus circulating in West Africa: sub-subtype A3Seema Thakore Meloni
Department of Immunology and Infectious Diseases, Harvard School of Public Health, 651 Huntington Ave, Boston, MA 02115, USA
J Virol 78:12438-45. 2004..Based on phylogenetic analyses, we propose that the group of viruses found in the Dakar sex worker cohort, previously referred to as HIV-1 A subcluster 2, be referred to as HIV-1 sub-subtype A3... - HIV type 1 subtypes among blood donors in the Mbeya region of southwest TanzaniaMiguel A Arroyo
U S Military HIV Research Program USMHRP, Walter Reed Army Research Institute, Division of Retrovirology, Rockville, Maryland 20850, USA
AIDS Res Hum Retroviruses 20:895-901. 2004..Based on this work, subtype C appears to be the prevalent subtype in southwest Tanzania, followed by a high proportion of intersubtype recombinants... - Development and application of a high-throughput HIV type 1 genotyping assay to identify CRF02_AG in West/West Central AfricaGustavo H Kijak
The Henry M Jackson Foundation, Rockville, Maryland 20850, USA
AIDS Res Hum Retroviruses 20:521-30. 2004..Together with other regional genotyping assays MHAcrf02 will contribute to the development of a global picture of HIV-1 diversity and geographic distribution, providing a strong foundation for intervention, including vaccine development... - The changing molecular epidemiology of HIV type 1 among northern Thai drug users, 1999 to 2002Sodsai Tovanabutra
Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand
AIDS Res Hum Retroviruses 20:465-75. 2004..Ongoing molecular surveillance of circulating HIV-1 strains is imperative for the evaluation of HIV vaccine efficacy... - Identification of a novel clade of human immunodeficiency virus type 1 in Democratic Republic of CongoJohn L K Mokili
Henry M Jackson Foundation, Rockville, MD 20850, USA
AIDS Res Hum Retroviruses 18:817-23. 2002....