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  • 1
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    HIV-1 nomenclature proposal (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-04-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Robertson, D L -- Anderson, J P -- Bradac, J A -- Carr, J K -- Foley, B -- Funkhouser, R K -- Gao, F -- Hahn, B H -- Kalish, M L -- Kuiken, C -- Learn, G H -- Leitner, T -- McCutchan, F -- Osmanov, S -- Peeters, M -- Pieniazek, D -- Salminen, M -- Sharp, P M -- Wolinsky, S -- Korber, B -- New York, N.Y. -- Science. 2000 Apr 7;288(5463):55-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10766634" target="_blank"〉PubMed〈/a〉
    Keywords: Databases, Factual ; Genome, Viral ; HIV Infections/*virology ; HIV-1/*classification/genetics ; Humans ; Recombination, Genetic ; *Terminology as Topic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Timing the ancestor of the HIV-1 pandemic strains (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-06-10
    Description: HIV-1 sequences were analyzed to estimate the timing of the ancestral sequence of the main group of HIV-1, the strains responsible for the AIDS pandemic. Using parallel supercomputers and assuming a constant rate of evolution, we applied maximum-likelihood phylogenetic methods to unprecedented amounts of data for this calculation. We validated our approach by correctly estimating the timing of two historically documented points. Using a comprehensive full-length envelope sequence alignment, we estimated the date of the last common ancestor of the main group of HIV-1 to be 1931 (1915-41). Analysis of a gag gene alignment, subregions of envelope including additional sequences, and a method that relaxed the assumption of a strict molecular clock also supported these results.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korber, B -- Muldoon, M -- Theiler, J -- Gao, F -- Gupta, R -- Lapedes, A -- Hahn, B H -- Wolinsky, S -- Bhattacharya, T -- N01 AI 85338/AI/NIAID NIH HHS/ -- R01 AI 44596/AI/NIAID NIH HHS/ -- R01-HD37356/HD/NICHD NIH HHS/ -- etc. -- New York, N.Y. -- Science. 2000 Jun 9;288(5472):1789-96.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Los Alamos National Laboratory, Los Alamos, NM 87545, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10846155" target="_blank"〉PubMed〈/a〉
    Keywords: Acquired Immunodeficiency Syndrome/*epidemiology/transmission/*virology ; Africa/epidemiology ; Animals ; Confidence Intervals ; Consensus Sequence ; Disease Outbreaks ; Europe/epidemiology ; *Evolution, Molecular ; Genes, env ; HIV Envelope Protein gp160/genetics ; HIV-1/classification/*genetics ; Haiti/epidemiology ; Humans ; Likelihood Functions ; Pan troglodytes ; Phylogeny ; Simian Acquired Immunodeficiency Syndrome/transmission/virology ; Simian Immunodeficiency Virus/genetics ; Time Factors ; United States/epidemiology ; Zoonoses
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Diversity considerations in HIV-1 vaccine selection (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-06-29
    Description: Globally, human immunodeficiency virus-type 1 (HIV-1) is extraordinarily variable, and this diversity poses a major obstacle to AIDS vaccine development. Currently, candidate vaccines are derived from isolates, with the hope that they will be sufficiently cross-reactive to protect against circulating viruses. This may be overly optimistic, however, given that HIV-1 envelope proteins can differ in more than 30% of their amino acids. To contend with the diversity, country-specific vaccines are being considered, but evolutionary relationships may be more useful than regional considerations. Consensus or ancestor sequences could be used in vaccine design to minimize the genetic differences between vaccine strains and contemporary isolates, effectively reducing the extent of diversity by half.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gaschen, Brian -- Taylor, Jesse -- Yusim, Karina -- Foley, Brian -- Gao, Feng -- Lang, Dorothy -- Novitsky, Vladimir -- Haynes, Barton -- Hahn, Beatrice H -- Bhattacharya, Tanmoy -- Korber, Bette -- N01 AI 85338/AI/NIAID NIH HHS/ -- P20 AI 27767/AI/NIAID NIH HHS/ -- R01 AI 05397/AI/NIAID NIH HHS/ -- R01 AI 35351/AI/NIAID NIH HHS/ -- R01 AI 40951/AI/NIAID NIH HHS/ -- YI AI 1500-01/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2002 Jun 28;296(5577):2354-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Los Alamos National Laboratory, Los Alamos, NM 87545, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12089434" target="_blank"〉PubMed〈/a〉
    Keywords: *AIDS Vaccines/immunology ; Base Sequence ; Consensus Sequence ; Cross Reactions ; Evolution, Molecular ; Gene Products, env/chemistry/genetics/immunology ; *Genetic Variation ; Genome, Viral ; HIV Antibodies/biosynthesis/immunology ; HIV Antigens/genetics/immunology ; HIV Infections/epidemiology/prevention & control/virology ; HIV-1/classification/*genetics/*immunology ; Humans ; Likelihood Functions ; *Phylogeny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Limitations of a molecular clock applied to considerations of the origin of HIV-1 (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-07-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korber, B -- Theiler, J -- Wolinsky, S -- 3-Y01-AI-70001-13/AI/NIAID NIH HHS/ -- R01-HD-31756/HD/NICHD NIH HHS/ -- Y1-A1-4058-03/PHS HHS/ -- etc. -- New York, N.Y. -- Science. 1998 Jun 19;280(5371):1868-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9669945" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Disease Progression ; *Evolution, Molecular ; Gene Products, env/chemistry/genetics ; Genetic Variation ; Genome, Viral ; HIV Envelope Protein gp120/chemistry/genetics ; HIV Infections/*virology ; HIV-1/chemistry/classification/*genetics ; Humans ; Mutation ; Peptide Fragments/chemistry/genetics ; *Phylogeny ; Recombination, Genetic ; Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Founder effects in the assessment of HIV polymorphisms and HLA allele associations (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-17
    Description: Escape from T cell-mediated immune responses affects the ongoing evolution of rapidly evolving viruses such as HIV. By applying statistical approaches that account for phylogenetic relationships among viral sequences, we show that viral lineage effects rather than immune escape often explain apparent human leukocyte antigen (HLA)-mediated immune-escape mutations defined by older analysis methods. Phylogenetically informed methods identified immune-susceptible locations with greatly improved accuracy, and the associations we identified with these methods were experimentally validated. This approach has practical implications for understanding the impact of host immunity on pathogen evolution and for defining relevant variants for inclusion in vaccine antigens.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhattacharya, Tanmoy -- Daniels, Marcus -- Heckerman, David -- Foley, Brian -- Frahm, Nicole -- Kadie, Carl -- Carlson, Jonathan -- Yusim, Karina -- McMahon, Ben -- Gaschen, Brian -- Mallal, Simon -- Mullins, James I -- Nickle, David C -- Herbeck, Joshua -- Rousseau, Christine -- Learn, Gerald H -- Miura, Toshiyuki -- Brander, Christian -- Walker, Bruce -- Korber, Bette -- AI27757/AI/NIAID NIH HHS/ -- AI57005/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2007 Mar 16;315(5818):1583-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Los Alamos National Laboratory, Los Alamos, NM 87545, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17363674" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Antigen Presentation ; Epitopes ; Evolution, Molecular ; *Founder Effect ; Genes, MHC Class I ; Genes, Viral ; HIV Infections/immunology/*virology ; HIV-1/classification/*genetics/*immunology ; HLA Antigens/*genetics/immunology ; HLA-C Antigens/genetics ; Humans ; Immune Tolerance ; Likelihood Functions ; Mutation ; Phenotype ; Phylogeny ; *Polymorphism, Genetic ; T-Lymphocytes, Cytotoxic/immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    AIDS/HIV. Converging on an HIV vaccine (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-09-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korber, Bette -- Gnanakaran, S -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1589-90. doi: 10.1126/science.1211919.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Theoretical Biology and Biophysics, T6, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. btk@lanl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21921189" target="_blank"〉PubMed〈/a〉
    Keywords: *AIDS Vaccines ; Antibodies, Neutralizing/chemistry/*immunology/metabolism ; Antibody Affinity ; Antigens, CD4/chemistry/immunology/metabolism ; Binding Sites ; Binding Sites, Antibody ; Complementarity Determining Regions/genetics ; Crystallography, X-Ray ; Epitopes ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/chemistry/*immunology/metabolism ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; Humans ; Models, Molecular ; Molecular Mimicry ; Protein Conformation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Structure of a V3-containing HIV-1 gp120 core (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-11-15
    Description: The third variable region (V3) of the HIV-1 gp120 envelope glycoprotein is immunodominant and contains features essential for coreceptor binding. We determined the structure of V3 in the context of an HIV-1 gp120 core complexed to the CD4 receptor and to the X5 antibody at 3.5 angstrom resolution. Binding of gp120 to cell-surface CD4 would position V3 so that its coreceptor-binding tip protrudes 30 angstroms from the core toward the target cell membrane. The extended nature and antibody accessibility of V3 explain its immunodominance. Together, the results provide a structural rationale for the role of V3 in HIV entry and neutralization.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408531/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408531/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Chih-chin -- Tang, Min -- Zhang, Mei-Yun -- Majeed, Shahzad -- Montabana, Elizabeth -- Stanfield, Robyn L -- Dimitrov, Dimiter S -- Korber, Bette -- Sodroski, Joseph -- Wilson, Ian A -- Wyatt, Richard -- Kwong, Peter D -- AI24755/AI/NIAID NIH HHS/ -- AI31783/AI/NIAID NIH HHS/ -- AI39429/AI/NIAID NIH HHS/ -- AI40895/AI/NIAID NIH HHS/ -- GM46192/GM/NIGMS NIH HHS/ -- Z99 AI999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2005 Nov 11;310(5750):1025-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16284180" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antigens, CD4/chemistry/*metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; HIV Antibodies/immunology ; HIV Envelope Protein gp120/*chemistry/immunology/metabolism ; HIV-1/*chemistry/immunology/metabolism ; Humans ; Hydrogen Bonding ; Immunodominant Epitopes ; Models, Molecular ; Molecular Sequence Data ; Peptide Fragments/*chemistry/immunology/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, CCR5/chemistry/metabolism ; Receptors, CXCR4/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Public health. A sound rationale needed for phase III HIV-1 vaccine trials (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burton, Dennis R -- Desrosiers, Ronald C -- Doms, Robert W -- Feinberg, Mark B -- Gallo, Robert C -- Hahn, Beatrice -- Hoxie, James A -- Hunter, Eric -- Korber, Bette -- Landay, Alan -- Lederman, Michael M -- Lieberman, Judy -- McCune, Joseph M -- Moore, John P -- Nathanson, Neal -- Picker, Louis -- Richman, Douglas -- Rinaldo, Charles -- Stevenson, Mario -- Watkins, David I -- Wolinsky, Steven M -- Zack, Jerome A -- New York, N.Y. -- Science. 2004 Jan 16;303(5656):316.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Scripps Research Institute, La Jolla, California, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14726576" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/*immunology ; *Clinical Trials, Phase III as Topic/economics ; Costs and Cost Analysis ; HIV Envelope Protein gp120/*immunology ; HIV Infections/*immunology/prevention & control/therapy ; HIV-1/*immunology ; Humans ; Immunization Schedule ; Immunization, Secondary ; T-Lymphocytes, Cytotoxic/immunology ; T-Lymphocytes, Helper-Inducer/immunology ; Thailand ; United States ; Vaccines, Synthetic/immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Genetic evaluation of suspected cases of transient HIV-1 infection of infants (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-06-06
    Description: Detection of human immunodeficiency virus-type 1 (HIV-1) on only one or a few occasions in infants born to infected mothers has been interpreted to indicate that infection may be transient rather than persistent. Forty-two cases of suspected transient HIV-1 viremia among 1562 perinatally exposed seroreverting infants and one mother were reanalyzed. HIV-1 env sequences were not found in specimens from 20; in specimens from 6, somatic genetic analysis revealed that specimens were mistakenly attributed to an infant; and in specimens from 17, phylogenetic analysis failed to demonstrate the expected linkage between the infant's and the mother's virus. These findings argue that transient HIV-1 infection, if it exists, will only rarely be satisfactorily documented.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frenkel, L M -- Mullins, J I -- Learn, G H -- Manns-Arcuino, L -- Herring, B L -- Kalish, M L -- Steketee, R W -- Thea, D M -- Nichols, J E -- Liu, S L -- Harmache, A -- He, X -- Muthui, D -- Madan, A -- Hood, L -- Haase, A T -- Zupancic, M -- Staskus, K -- Wolinsky, S -- Krogstad, P -- Zhao, J -- Chen, I -- Koup, R -- Ho, D -- Korber, B -- Apple, R J -- Coombs, R W -- Pahwa, S -- Roberts, N J Jr -- AI27757/AI/NIAID NIH HHS/ -- AI32910/AI/NIAID NIH HHS/ -- UO1-27658/PHS HHS/ -- etc. -- New York, N.Y. -- Science. 1998 May 15;280(5366):1073-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pediatrics, University of Rochester, Rochester, NY 14642, USA. lfrenkel@u.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9582120" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Viral/analysis/genetics ; Diagnostic Errors ; Equipment Contamination ; Female ; Genes, env ; HIV Infections/immunology/transmission/*virology ; HIV-1/*genetics/*isolation & purification ; Humans ; Infant ; Infant, Newborn ; Infectious Disease Transmission, Vertical ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Viral/analysis ; *Specimen Handling ; T-Lymphocytes, Cytotoxic/immunology ; Viremia/virology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    A plea for justice for jailed medical workers (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-10-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ahuja, Sunil K -- Aiuti, Fernando -- Berkhout, Ben -- Biberfeld, Peter -- Burton, Dennis R -- Colizzi, Vittorio -- Deeks, Steven G -- Desrosiers, Ronald C -- Dierich, Manfred P -- Doms, Robert W -- Emerman, Michael -- Gallo, Robert C -- Girard, Marc -- Greene, Warner C -- Hoxie, James A -- Hunter, Eric -- Klein, George -- Korber, Bette -- Kuritzkes, Daniel R -- Lederman, Michael M -- Malim, Michael H -- Marx, Preston A -- McCune, Joseph M -- McMichael, Andrew -- Miller, Christopher -- Miller, Veronica -- Montagnier, Luc -- Montefiori, David C -- Moore, John P -- Nixon, Douglas F -- Overbaugh, Julie -- Pauza, C David -- Richman, Douglas D -- Saag, Michael S -- Sattentau, Quentin -- Schooley, Robert T -- Shattock, Robin -- Shaw, George M -- Stevenson, Mario -- Trkola, Alexandra -- Wainberg, Mark A -- Weiss, Robin A -- Wolinsky, Steven -- Zack, Jerome A -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):924-5. Epub 2006 Oct 24.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17062652" target="_blank"〉PubMed〈/a〉
    Keywords: Child ; *Disease Outbreaks ; HIV Infections/*epidemiology/transmission ; Hiv-1 ; Health Personnel/*legislation & jurisprudence ; Humans ; Jurisprudence ; Libya/epidemiology ; *Prisoners ; *Social Justice
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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