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1
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34250681614
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UNAIDS/WHO. Report on the global AIDS epidemic. May 2006. Available at: http://unaids.org. [Accessed November 2006] This website gives important information on evolving trends in the HIV-1 epidemic. It is noteworthy that non-B subtypes are not as yet discussed.
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UNAIDS/WHO. Report on the global AIDS epidemic. May 2006. Available at: http://unaids.org. [Accessed November 2006] This website gives important information on evolving trends in the HIV-1 epidemic. It is noteworthy that non-B subtypes are not as yet discussed.
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3
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34250672217
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Leitner T, Sorber B, Daniels M, et al. HIV subtype and circulating form (CRF) reference sequences. Los Alamos National Laboratory; 2005. Available at: http://hiv.lanl.gov. [Accessed November 2006] The Los Alamos reference laboratory has an updated compendium of new HIV sequences, describing the nomenclature and genomic diversity of rapidly expanding non-B subtypes and CRFs. The Recombination Identification Program (http:// hiv.lanl.gov?RIP/RIP submit.html) can be used to assign subtype or show sequence similarity to all the major CRFs.
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Leitner T, Sorber B, Daniels M, et al. HIV subtype and circulating form (CRF) reference sequences. Los Alamos National Laboratory; 2005. Available at: http://hiv.lanl.gov. [Accessed November 2006] The Los Alamos reference laboratory has an updated compendium of new HIV sequences, describing the nomenclature and genomic diversity of rapidly expanding non-B subtypes and CRFs. The Recombination Identification Program (http:// hiv.lanl.gov?RIP/RIP submit.html) can be used to assign subtype or show sequence similarity to all the major CRFs.
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4
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30944461040
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Molecular epidemiology of HIV-1 variants in the global AIDS pandemic
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The role of superinfection and 'geographical recombination hotspots' in the growing diversification of the HIV pandemic is described
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Thomson MM, Najera R. Molecular epidemiology of HIV-1 variants in the global AIDS pandemic. AIDS Rev 2005; 7:210-224. The role of superinfection and 'geographical recombination hotspots' in the growing diversification of the HIV pandemic is described.
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(2005)
AIDS Rev
, vol.7
, pp. 210-224
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Thomson, M.M.1
Najera, R.2
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5
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29744448144
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HIV subtypes: Epidemiology and significance for HIV management
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This is another recent review describing the potential clinical impact of viral subtype diversity
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Geretti AM. HIV subtypes: epidemiology and significance for HIV management. Curr Opin Infect Dis 2006; 19:1-7. This is another recent review describing the potential clinical impact of viral subtype diversity.
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(2006)
Curr Opin Infect Dis
, vol.19
, pp. 1-7
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Geretti, A.M.1
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6
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0036319711
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Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy
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Thomson MM, Perez-Alvarez L, Najera R. Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy. Lancet Infect Dis 2002; 2:461-471.
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(2002)
Lancet Infect Dis
, vol.2
, pp. 461-471
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Thomson, M.M.1
Perez-Alvarez, L.2
Najera, R.3
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7
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21244449912
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Different epidemic potentials of the HIV-1 B and C subtypes
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This molecular epidemiology study shows the rapidity of the shift to subtype C in a Western world setting
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Salemi M, de Oliveira T, Soares MA, et al. Different epidemic potentials of the HIV-1 B and C subtypes. J Mol Evol 2005; 60:598-605. This molecular epidemiology study shows the rapidity of the shift to subtype C in a Western world setting.
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(2005)
J Mol Evol
, vol.60
, pp. 598-605
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Salemi, M.1
de Oliveira, T.2
Soares, M.A.3
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8
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19344373478
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Kantor R, Katzenstein DA, Efron B, et al. Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaboration. PLoS Med 2005; 2 (e112):325-337; www. plosmedine.org. This international collaborative team has been established to compile non-B subtype sequences from different geographical regions.
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Kantor R, Katzenstein DA, Efron B, et al. Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaboration. PLoS Med 2005; 2 (e112):325-337; www. plosmedine.org. This international collaborative team has been established to compile non-B subtype sequences from different geographical regions.
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9
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33645084526
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Genotypic drug resistance interpretation algorithms display high levels of discordance when applied to non-B strains from HIV-1 naive and treated patients
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The problems arising from interpretative algorithms are discussed
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Vergne L, Snoeck J, Aghokeng A, et al. Genotypic drug resistance interpretation algorithms display high levels of discordance when applied to non-B strains from HIV-1 naive and treated patients. FEMS Immunol Med Microbiol 2006; 46:53-62. The problems arising from interpretative algorithms are discussed.
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(2006)
FEMS Immunol Med Microbiol
, vol.46
, pp. 53-62
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Vergne, L.1
Snoeck, J.2
Aghokeng, A.3
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10
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0032562985
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Public health implications of antiretroviral therapy and HIV drug resistance
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Wainberg MA, Friedland G. Public health implications of antiretroviral therapy and HIV drug resistance. JAMA 1998; 279:1977-1983.
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(1998)
JAMA
, vol.279
, pp. 1977-1983
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Wainberg, M.A.1
Friedland, G.2
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11
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33745639270
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HIV-1 subtypes and recombinants in the Republic of Congo
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Phylogenetic surveillance at the epicentre of the HIV pandemic shows the diversity of non-B subtypes and CRFs with the notable absence of subtype C
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Niama FR, Tour-Kane C, Vidal N, et al. HIV-1 subtypes and recombinants in the Republic of Congo. Infect Genet Evol 2006; 6:337-343. Phylogenetic surveillance at the epicentre of the HIV pandemic shows the diversity of non-B subtypes and CRFs with the notable absence of subtype C.
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(2006)
Infect Genet Evol
, vol.6
, pp. 337-343
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Niama, F.R.1
Tour-Kane, C.2
Vidal, N.3
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12
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33748746942
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HIV genetic diversity in cameroon: Possible public health importance
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Another study illustrating subtype diversity at a geographical 'hotspot
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Ndongmo CB, Pieniazek D, Holberg-Petersen M, et al. HIV genetic diversity in cameroon: possible public health importance. AIDS Res Hum Retroviruses 2006; 22:812-816. Another study illustrating subtype diversity at a geographical 'hotspot'.
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(2006)
AIDS Res Hum Retroviruses
, vol.22
, pp. 812-816
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Ndongmo, C.B.1
Pieniazek, D.2
Holberg-Petersen, M.3
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13
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23244453195
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Chohan B, Lavreys L, Rainwater SMJ, Overbaugh J. Evidence for frequent reinfection with human immunodeficiency virus type 1 of different subtype. J Virol 2005; 79:10701-10708. Superinfection and co-infection remain the sources for the ongoing diversification of the HIV epidemic.
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Chohan B, Lavreys L, Rainwater SMJ, Overbaugh J. Evidence for frequent reinfection with human immunodeficiency virus type 1 of different subtype. J Virol 2005; 79:10701-10708. Superinfection and co-infection remain the sources for the ongoing diversification of the HIV epidemic.
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14
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33748743293
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Molecular epidemiology of HIV type 1 in the Ukraine: Birthplace of an epidemic
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This study shows the shift in the dynamics towards non-B subtype infections in Europe and Asia
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Saad MD, Shchererbinskaya AM, Nadai Y, et al. Molecular epidemiology of HIV type 1 in the Ukraine: birthplace of an epidemic. AIDS Res Hum Retroviruses 2006; 22:709-714. This study shows the shift in the dynamics towards non-B subtype infections in Europe and Asia.
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(2006)
AIDS Res Hum Retroviruses
, vol.22
, pp. 709-714
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Saad, M.D.1
Shchererbinskaya, A.M.2
Nadai, Y.3
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15
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33748743977
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HIV type 1 molecular epidemiology in Cuba: High genetic diversity, frequent mosaicism, and recent expansion of BG intersubtype recombinant forms
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This study shows the introduction of non-B subtype diversity and CRF mosaics into the Americas
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Pérez L, Thomson MM, Bleda MJ, et al. HIV type 1 molecular epidemiology in Cuba: high genetic diversity, frequent mosaicism, and recent expansion of BG intersubtype recombinant forms. AIDS Res Hum Retroviruses 2006; 22:724-733. This study shows the introduction of non-B subtype diversity and CRF mosaics into the Americas.
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(2006)
AIDS Res Hum Retroviruses
, vol.22
, pp. 724-733
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Pérez, L.1
Thomson, M.M.2
Bleda, M.J.3
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16
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Evidence for onward transmission of HIV-1 non-B subtype strains in the United Kingdom
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The forward transmission of non-B subtypes from immigrant patient populations is documented
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Aggarwalm I, Smith M, Tatt ID, et al. Evidence for onward transmission of HIV-1 non-B subtype strains in the United Kingdom. J Acquir Immune Defic Syndr 2006; 41:201-209. The forward transmission of non-B subtypes from immigrant patient populations is documented.
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(2006)
J Acquir Immune Defic Syndr
, vol.41
, pp. 201-209
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Aggarwalm, I.1
Smith, M.2
Tatt, I.D.3
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17
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20844455114
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Sides TL, Akinsete O, Henry K, et al. HIV-1 subtype diversity in Minnesota. J Infect Dis 2005; 192:37-45. This is the first study to show the introduction of non-B subtype strains into the heartland of the United States.
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Sides TL, Akinsete O, Henry K, et al. HIV-1 subtype diversity in Minnesota. J Infect Dis 2005; 192:37-45. This is the first study to show the introduction of non-B subtype strains into the heartland of the United States.
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18
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Akoumada BS, Viel J, Charest H, et al. HIV-1 genetic diversity in antenatal cohort. Can Emerg Infect Dis 2005; 11:1230-1234. The introduction into Quebec of diverse non-B viral subtypes from francophone countries in west and central Africa shows the diversification arising at the epicentre of the HIV-1 epidemic.
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Akoumada BS, Viel J, Charest H, et al. HIV-1 genetic diversity in antenatal cohort. Can Emerg Infect Dis 2005; 11:1230-1234. The introduction into Quebec of diverse non-B viral subtypes from francophone countries in west and central Africa shows the diversification arising at the epicentre of the HIV-1 epidemic.
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19
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33745085240
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Rhee SY, Kantor R, Katzenstein DA, et al. HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes. AIDS 2006; 20:643-651. The Stanford HIV sequence database, established in 2000, is invaluable, allowing users to assess viral sequence subtype, using the HIVdb subtyping tool (RT and protease region) and the Rega subtyping tool. The database includes mutation frequency of pure viral non-B subtypes submitted to their site. Recent advances allow clinicians and researchers to explore intersubtype differences in genotype with treatment correlates.
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Rhee SY, Kantor R, Katzenstein DA, et al. HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes. AIDS 2006; 20:643-651. The Stanford HIV sequence database, established in 2000, is invaluable, allowing users to assess viral sequence subtype, using the HIVdb subtyping tool (RT and protease region) and the Rega subtyping tool. The database includes mutation frequency of pure viral non-B subtypes submitted to their site. Recent advances allow clinicians and researchers to explore intersubtype differences in genotype with treatment correlates.
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20
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33748879209
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Rationale and uses of a public HIV drug resistance database
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This paper explains to clinicians and researchers how to take advantage of the Stanford database
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Shafer RW. Rationale and uses of a public HIV drug resistance database. J Infect Dis 2006; 194:S51-S58. This paper explains to clinicians and researchers how to take advantage of the Stanford database.
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(2006)
J Infect Dis
, vol.194
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Shafer, R.W.1
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21
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85142161601
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De Oliveira T, Deforche K, Cassol S, et al. An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics 2005; 21:3797-3800. The REGA is a subtyping tool accessible in the Stanford database to designate HIV-1 subtypes and CRFs more effectively.
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De Oliveira T, Deforche K, Cassol S, et al. An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics 2005; 21:3797-3800. The REGA is a subtyping tool accessible in the Stanford database to designate HIV-1 subtypes and CRFs more effectively.
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22
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33747150776
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Algorithms for the interpretation of HIV-1 genotypic drug resistance information
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A good review that lists current interpretative algorithms
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Vercauteren J, Vandamme AM. Algorithms for the interpretation of HIV-1 genotypic drug resistance information. Antiviral Res 2006; 71:335-342. A good review that lists current interpretative algorithms.
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(2006)
Antiviral Res
, vol.71
, pp. 335-342
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Vercauteren, J.1
Vandamme, A.M.2
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23
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0037062513
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Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype
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Beerenwinkel N, Schmidt B, Walter H, et al. Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype. Proc Natl Acad Sci U S A 2002; 99:8271-8276.
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(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 8271-8276
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Beerenwinkel, N.1
Schmidt, B.2
Walter, H.3
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24
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26944487974
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Use of sequence data generated in the Bayer TruGene genotyping assay to recognize and characterize nonsubtype-B human immunodeficiency virus type 1 strains
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Hirigoyen DL, Cartwright CP. Use of sequence data generated in the Bayer TruGene genotyping assay to recognize and characterize nonsubtype-B human immunodeficiency virus type 1 strains. J Clin Microbiol 2005; 43: 5263-5271.
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(2005)
J Clin Microbiol
, vol.43
, pp. 5263-5271
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Hirigoyen, D.L.1
Cartwright, C.P.2
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33746192134
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Gifford R, de Oliveira T, Rambout A, et al. Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. AIDS 2006; 20:1521-1529. The ability of different subtyping tools in assessing subtype and CRF is discussed.
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Gifford R, de Oliveira T, Rambout A, et al. Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. AIDS 2006; 20:1521-1529. The ability of different subtyping tools in assessing subtype and CRF is discussed.
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26
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Van Laethem K, Schrooten Y, Dedecker S, et al. A genotypic assay for the amplification and sequencing of gag and protease from diverse human immunodeficiency virus type 1 group M subtypes. J Virol Methods 2006; 132:181-186. Alternative sequencing strategies for non-B subtypes are described.
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Van Laethem K, Schrooten Y, Dedecker S, et al. A genotypic assay for the amplification and sequencing of gag and protease from diverse human immunodeficiency virus type 1 group M subtypes. J Virol Methods 2006; 132:181-186. Alternative sequencing strategies for non-B subtypes are described.
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27
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22144494590
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Optimization of a genotypic assay applicable to all immunodeficiency virus type 1 protease and reverse transcriptase types
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Snoeck J, Riva C, Steegen K, et al. Optimization of a genotypic assay applicable to all immunodeficiency virus type 1 protease and reverse transcriptase types. J Virol Methods 2005; 128:47-53.
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(2005)
J Virol Methods
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Snoeck, J.1
Riva, C.2
Steegen, K.3
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28
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33745149658
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Performance evaluation of the two protease sequencing primers of the Trugene HIV-1 genotyping kit
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The divergence in the US Food and Drug Administration-approved primers and the alternative primers required for non-B subtype strains is described
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Ribas SG, Heyndrickx L, Ondoa P, et al. Performance evaluation of the two protease sequencing primers of the Trugene HIV-1 genotyping kit. J Virol Methods 2006; 135:137-142. The divergence in the US Food and Drug Administration-approved primers and the alternative primers required for non-B subtype strains is described.
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(2006)
J Virol Methods
, vol.135
, pp. 137-142
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Ribas, S.G.1
Heyndrickx, L.2
Ondoa, P.3
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29
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33645098601
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The calculated genetic barrier for antiretroviral drug resistance substitutions is largely similar for different HIV-1 subtypes
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This elegant study has assessed codon usage among different viral subtypes in an attempt to calculate genetic barrier and predict resistance in different viral subtypes
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Van de Vijver DA, Wensing AMJ, Angarano G, et al. The calculated genetic barrier for antiretroviral drug resistance substitutions is largely similar for different HIV-1 subtypes. J Acquir Immune Defic Syndr 2006; 41:352-360. This elegant study has assessed codon usage among different viral subtypes in an attempt to calculate genetic barrier and predict resistance in different viral subtypes.
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(2006)
J Acquir Immune Defic Syndr
, vol.41
, pp. 352-360
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Van de Vijver, D.A.1
Wensing, A.M.J.2
Angarano, G.3
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0038238324
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Variable prediction of antiviral treatment outcome by different systems for interpreting genotypic human immunodeficiency virus type 1 drug resistance
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De Luca A, Cingolani A, Giambennedetto SD, et al. Variable prediction of antiviral treatment outcome by different systems for interpreting genotypic human immunodeficiency virus type 1 drug resistance. J Infect Dis 2003; 187:1934-1943.
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J Infect Dis
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De Luca, A.1
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Johnson VA, Brun-Vézinet F, Clotet B, et al. Update of the drug resistance mutations in HIV-1: fall 2006. Topics HIV Med 2006; 14:125-130. The International AIDS Society - USA group of HIV-1 clinicians and specialists provides one of the most widely accepted listings of major and minor drug resistance mutations.
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Johnson VA, Brun-Vézinet F, Clotet B, et al. Update of the drug resistance mutations in HIV-1: fall 2006. Topics HIV Med 2006; 14:125-130. The International AIDS Society - USA group of HIV-1 clinicians and specialists provides one of the most widely accepted listings of major and minor drug resistance mutations.
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Antiviral drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase occur in specific RNA structural regions
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Schinazi RF, Lloyd RM, Ramanathan CS, Taylor EW. Antiviral drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase occur in specific RNA structural regions. Antimicrobial Agents Chemother 1994; 38:268-274.
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Antimicrobial Agents Chemother
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Schinazi, R.F.1
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Taylor, E.W.4
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3342894656
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Nucleotide and amino acid polymorphisms at drug resistance sites in non-B-subtype variants of human immunodeficiency virus type 1
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Turner D, Brenner B, Moisi D, et al. Nucleotide and amino acid polymorphisms at drug resistance sites in non-B-subtype variants of human immunodeficiency virus type 1. Antimicrob Agents Chemother 2004; 48: 2993-2998.
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Turner, D.1
Brenner, B.2
Moisi, D.3
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Changing patterns in the selection of viral mutations among patients receiving nucleoside and nucleotide drug combinations directed against human immunodeficiency virus type 1 reverse transcriptase
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Wainberg MA, Brenner BG, Turner D. Changing patterns in the selection of viral mutations among patients receiving nucleoside and nucleotide drug combinations directed against human immunodeficiency virus type 1 reverse transcriptase. Antimicrob Agents Chemother 2005; 49:1671-1678.
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Antimicrob Agents Chemother
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Wainberg, M.A.1
Brenner, B.G.2
Turner, D.3
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35
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33750519867
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Impact of HIV-1 pol diversity on drug resistance and its clinical implications
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This in an important overview summarizing results from clinical studies in geographical regions where multiple non-B strains circulate
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Kantor R. Impact of HIV-1 pol diversity on drug resistance and its clinical implications. Current Opin Infect Dis 2006; 19:594-606. This in an important overview summarizing results from clinical studies in geographical regions where multiple non-B strains circulate.
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(2006)
Current Opin Infect Dis
, vol.19
, pp. 594-606
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Kantor, R.1
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36
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Natural polymorphism in protease and reverse transcriptase genes and in vitro antiretroviral drug susceptibilities of non-B HIV-1 strains from treatment-naive patients
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The baseline susceptibility of non-B subtype strains from drug-naive individuals is described
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Vergne L, Stuyver L, Houtte MV, et al. Natural polymorphism in protease and reverse transcriptase genes and in vitro antiretroviral drug susceptibilities of non-B HIV-1 strains from treatment-naive patients. J Clin Virol 2006; 39:43-49. The baseline susceptibility of non-B subtype strains from drug-naive individuals is described.
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(2006)
J Clin Virol
, vol.39
, pp. 43-49
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Vergne, L.1
Stuyver, L.2
Houtte, M.V.3
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37
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Natural polymorphisms in the protease gene modulate the replicative capacity of non-B HIV-1 variants in the absence of drug pressure
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Holguin A, Sune C, Hamy F, et al. Natural polymorphisms in the protease gene modulate the replicative capacity of non-B HIV-1 variants in the absence of drug pressure. J Clin Virol 2006; 36:264-271.
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J Clin Virol
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Holguin, A.1
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Bartlett JA, Fath Mj, DeMasi R, et al. An updated systematic overview of triple combination therapy in antiretroviral-naive HIV-infected adults. AIDS 2006; 20:2051-2064. This study compiled data from 53 clinical trials showing that HAART fails to achieve viral suppression (<50 copies/ml) in 40-60% of individuals harbouring subtype B infections. Drug resistance may be facilitated in resource-poor settings where suboptimal therapies are being intrioduced.
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Bartlett JA, Fath Mj, DeMasi R, et al. An updated systematic overview of triple combination therapy in antiretroviral-naive HIV-infected adults. AIDS 2006; 20:2051-2064. This study compiled data from 53 clinical trials showing that HAART fails to achieve viral suppression (<50 copies/ml) in 40-60% of individuals harbouring subtype B infections. Drug resistance may be facilitated in resource-poor settings where suboptimal therapies are being intrioduced.
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39
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0242529051
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Insights into the reasons for discontinuation of the first highly active antiretroviral therapy (HAART) regimen in a cohort of antiretroviral naive patients
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Monforte AA, Lepri AC, Rezza G, et al. Insights into the reasons for discontinuation of the first highly active antiretroviral therapy (HAART) regimen in a cohort of antiretroviral naive patients. AIDS 2000; 14:499-507.
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AIDS
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Monforte, A.A.1
Lepri, A.C.2
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40
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Perspectives on adherence and simplicity for HIV-infected patients on antiretroviral therapy
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Stone VE, Jordan J, Tolson J, et al. Perspectives on adherence and simplicity for HIV-infected patients on antiretroviral therapy. J Acquir Immune Defic Syndr 2004; 36:808-816.
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J Acquir Immune Defic Syndr
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Stone, V.E.1
Jordan, J.2
Tolson, J.3
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Wools-Kaloustian K, Kimaiyo S, Diero L, et al. Viability and effectiveness of large-scale HIV treatment initiatives in sub-Saharan Africa: experience from western Kenya. AIDS 2006; 20:41-48. The clinical benefit of new treatment initiatives in Africa is highlighted.
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Wools-Kaloustian K, Kimaiyo S, Diero L, et al. Viability and effectiveness of large-scale HIV treatment initiatives in sub-Saharan Africa: experience from western Kenya. AIDS 2006; 20:41-48. The clinical benefit of new treatment initiatives in Africa is highlighted.
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Calmy A, Pinoge L, Szumilin E, et al. Generic fixed-dose combination antiretroviral treatment in resource-poor settings: multicentric observational cohort. AIDS 2006; 20:1163-1169. The introduction of cost-effective ART strategies is investigated.
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Calmy A, Pinoge L, Szumilin E, et al. Generic fixed-dose combination antiretroviral treatment in resource-poor settings: multicentric observational cohort. AIDS 2006; 20:1163-1169. The introduction of cost-effective ART strategies is investigated.
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Bunnell R, Wamai N, Ekwaru JP, et al. Changes in sexual behavior and risk of HIV transmission after two years of antiretroviral therapy and prevention interventions in rural Uganda. Program and abstracts of the XVIth International AIDS Conference. Toronto, Canada. 13-18 August 2006. Abstract MOAC0204.
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Bunnell R, Wamai N, Ekwaru JP, et al. Changes in sexual behavior and risk of HIV transmission after two years of antiretroviral therapy and prevention interventions in rural Uganda. Program and abstracts of the XVIth International AIDS Conference. Toronto, Canada. 13-18 August 2006. Abstract MOAC0204.
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Impact of human immunodeficiency virus type 1 subtype on first-line antiretroviral therapy effectiveness
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Bocket L, Cheret A, Deuffic-Burban S, et al. Impact of human immunodeficiency virus type 1 subtype on first-line antiretroviral therapy effectiveness. Antivir Ther 2005; 10:247-254.
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Antivir Ther
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Bocket, L.1
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Wainberg, M.A.1
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