TY - JOUR AU - Schim van der Loeff, M. F. AU - Sarge-Njie, R. AU - Ceesay, S. AU - Awasana, A. A. AU - Jaye, P. AU - Sam, O. AU - Jaiteh, K. O. AU - Cubitt, D. AU - Milligan, P. AU - Whittle, H. C. PY - 2003 DA - 2003// TI - Regional differences in HIV trends in The Gambia: results from sentinel surveillance among pregnant women JO - Aids VL - 17 UR - https://doi.org/10.1097/00002030-200308150-00014 DO - 10.1097/00002030-200308150-00014 ID - Schim van der Loeff2003 ER - TY - JOUR AU - van der Loeff, M. F. AU - Awasana, A. A. AU - Sarge-Njie, R. AU - van der Sande, M. AU - Jaye, A. AU - Sabally, S. AU - Corrah, T. AU - McConkey, S. J. AU - Whittle, H. C. PY - 2006 DA - 2006// TI - Sixteen years of HIV surveillance in a West African research clinic reveals divergent epidemic trends of HIV-1 and HIV-2 JO - Int J Epidemiol VL - 35 UR - https://doi.org/10.1093/ije/dyl037 DO - 10.1093/ije/dyl037 ID - van der Loeff2006 ER - TY - STD TI - Los Alamos HIV Database. [http://www.hiv.lanl.gov/] UR - http://www.hiv.lanl.gov/ ID - ref3 ER - TY - STD TI - Barouch DH, O'Brien KL, Simmons NL, King SL, Abbink P, Maxfield LF, Sun YH, La Porte A, Riggs AM, Lynch DM, et al: Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys. Nat Med. 16: 319-323. 10.1038/nm.2089. ID - ref4 ER - TY - STD TI - Santra S, Liao HX, Zhang R, Muldoon M, Watson S, Fischer W, Theiler J, Szinger J, Balachandran H, Buzby A, et al: Mosaic vaccines elicit CD8+ T lymphocyte responses that confer enhanced immune coverage of diverse HIV strains in monkeys. Nat Med. 16: 324-328. 10.1038/nm.2108. ID - ref5 ER - TY - JOUR AU - Salazar-Gonzalez, J. F. AU - Bailes, E. AU - Pham, K. T. AU - Salazar, M. G. AU - Guffey, M. B. AU - Keele, B. F. AU - Derdeyn, C. A. AU - Farmer, P. AU - Hunter, E. AU - Allen, S. PY - 2008 DA - 2008// TI - Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing JO - J Virol VL - 82 UR - https://doi.org/10.1128/JVI.02660-07 DO - 10.1128/JVI.02660-07 ID - Salazar-Gonzalez2008 ER - TY - STD TI - Metabion. [http://www.metabion.com/] UR - http://www.metabion.com/ ID - ref7 ER - TY - STD TI - Macrogen. [http://www.macrogen.com/] UR - http://www.macrogen.com/ ID - ref8 ER - TY - JOUR AU - Hall, T. A. PY - 1999 DA - 1999// TI - BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT JO - Nucleic Acids Symposium Series VL - 41 ID - Hall1999 ER - TY - STD TI - BioEdit. [http://www.mbio.ncsu.edu/bioedit/bioedit.html] UR - http://www.mbio.ncsu.edu/bioedit/bioedit.html ID - ref10 ER - TY - JOUR AU - Stothard, P. PY - 2000 DA - 2000// TI - The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences JO - Biotechniques VL - 28 ID - Stothard2000 ER - TY - STD TI - Sequence Manipulation Suite. [http://www.bioinformatics.org/sms2/orf_find.html] UR - http://www.bioinformatics.org/sms2/orf_find.html ID - ref12 ER - TY - JOUR AU - Meloni, S. T. AU - Kim, B. AU - Sankale, J. L. AU - Hamel, D. J. AU - Tovanabutra, S. AU - Mboup, S. AU - McCutchan, F. E. AU - Kanki, P. J. PY - 2004 DA - 2004// TI - Distinct human immunodeficiency virus type 1 subtype A virus circulating in West Africa: sub-subtype A3 JO - J Virol VL - 78 UR - https://doi.org/10.1128/JVI.78.22.12438-12445.2004 DO - 10.1128/JVI.78.22.12438-12445.2004 ID - Meloni2004 ER - TY - JOUR AU - Meloni, S. T. AU - Sankale, J. L. AU - Hamel, D. J. AU - Eisen, G. AU - Gueye-Ndiaye, A. AU - Mboup, S. AU - Kanki, P. J. PY - 2004 DA - 2004// TI - Molecular epidemiology of human immunodeficiency virus type 1 sub-subtype A3 in Senegal from 1988 to 2001 JO - J Virol VL - 78 UR - https://doi.org/10.1128/JVI.78.22.12455-12461.2004 DO - 10.1128/JVI.78.22.12455-12461.2004 ID - Meloni2004 ER - TY - JOUR AU - Larkin, M. A. AU - Blackshields, G. AU - Brown, N. P. AU - Chenna, R. AU - McGettigan, P. A. AU - McWilliam, H. AU - Valentin, F. AU - Wallace, I. M. AU - Wilm, A. AU - Lopez, R. PY - 2007 DA - 2007// TI - Clustal W and Clustal × version 2.0 JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm404 DO - 10.1093/bioinformatics/btm404 ID - Larkin2007 ER - TY - STD TI - EBI ClustalW2. [http://www.ebi.ac.uk/Tools/clustalw2/index.html] UR - http://www.ebi.ac.uk/Tools/clustalw2/index.html ID - ref16 ER - TY - STD TI - Phylogenetic analysis using parsimony and other methods. Version 4.0b10. [http://paup.csit.fsu.edu/paupfaq/faq.html] UR - http://paup.csit.fsu.edu/paupfaq/faq.html ID - ref17 ER - TY - JOUR AU - Felsenstein, J. PY - 1973 DA - 1973// TI - Maximum-likelihood estimation of evolutionary trees from continuous characters JO - Am J Hum Genet VL - 25 ID - Felsenstein1973 ER - TY - JOUR AU - Yang, Z. PY - 1994 DA - 1994// TI - Estimating the pattern of nucleotide substitution JO - J Mol Evol VL - 39 ID - Yang1994 ER - TY - STD TI - Inkscape. [http://www.inkscape.org/] UR - http://www.inkscape.org/ ID - ref20 ER - TY - JOUR AU - Huelsenbeck, J. P. AU - Ronquist, F. PY - 2001 DA - 2001// TI - MRBAYES: Bayesian inference of phylogenetic trees JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.8.754 DO - 10.1093/bioinformatics/17.8.754 ID - Huelsenbeck2001 ER - TY - JOUR AU - Lole, K. S. AU - Bollinger, R. C. AU - Paranjape, R. S. AU - Gadkari, D. AU - Kulkarni, S. S. AU - Novak, N. G. AU - Ingersoll, R. AU - Sheppard, H. W. AU - Ray, S. C. PY - 1999 DA - 1999// TI - Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination JO - J Virol VL - 73 ID - Lole1999 ER - TY - STD TI - Gambian 2003 Census Data. [https://www.cia.gov/library/publications/the-world-factbook/fields/2075.html] UR - https://www.cia.gov/library/publications/the-world-factbook/fields/2075.html ID - ref23 ER - TY - JOUR AU - Carr, J. K. AU - Salminen, M. O. AU - Albert, J. AU - Sanders-Buell, E. AU - Gotte, D. AU - Birx, D. L. AU - McCutchan, F. E. PY - 1998 DA - 1998// TI - Full genome sequences of human immunodeficiency virus type 1 subtypes G and A/G intersubtype recombinants JO - Virology VL - 247 UR - https://doi.org/10.1006/viro.1998.9211 DO - 10.1006/viro.1998.9211 ID - Carr1998 ER - TY - JOUR AU - Abecasis, A. B. AU - Lemey, P. AU - Vidal, N. AU - de Oliveira, T. AU - Peeters, M. AU - Camacho, R. AU - Shapiro, B. AU - Rambaut, A. AU - Vandamme, A. M. PY - 2007 DA - 2007// TI - Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form JO - J Virol VL - 81 UR - https://doi.org/10.1128/JVI.00463-07 DO - 10.1128/JVI.00463-07 ID - Abecasis2007 ER - TY - STD TI - Zhang M, Foley B, Schultz AK, Macke JP, Bulla I, Stanke M, Morgenstern B, Korber B, Leitner T: The role of recombination in the emergence of a complex and dynamic HIV epidemic. Retrovirology. 7: 25-10.1186/1742-4690-7-25. ID - ref26 ER - TY - JOUR AU - Bobkov, A. AU - Cheingsong-Popov, R. AU - Salminen, M. AU - McCutchan, F. AU - Louwagie, J. AU - Ariyoshi, K. AU - Whittle, H. AU - Weber, J. PY - 1996 DA - 1996// TI - Complex mosaic structure of the partial envelope sequence from a Gambian HIV type 1 isolate JO - AIDS Res Hum Retroviruses VL - 12 UR - https://doi.org/10.1089/aid.1996.12.169 DO - 10.1089/aid.1996.12.169 ID - Bobkov1996 ER - TY - JOUR AU - Cham, F. AU - Heyndrickx, L. AU - Janssens, W. AU - Van der Auwera, G. AU - Vereecken, K. AU - De Houwer, K. AU - Coppens, S. AU - Whittle, H. AU - van der Groen, G. PY - 2000 DA - 2000// TI - Study of HIV type 1 gag/env variability in The Gambia, using a multiplex DNA polymerase chain reaction JO - AIDS Res Hum Retroviruses VL - 16 UR - https://doi.org/10.1089/08892220050195874 DO - 10.1089/08892220050195874 ID - Cham2000 ER - TY - JOUR AU - Binley, J. M. AU - Wrin, T. AU - Korber, B. AU - Zwick, M. B. AU - Wang, M. AU - Chappey, C. AU - Stiegler, G. AU - Kunert, R. AU - Zolla-Pazner, S. AU - Katinger, H. PY - 2004 DA - 2004// TI - Comprehensive cross-clade neutralization analysis of a panel of anti-human immunodeficiency virus type 1 monoclonal antibodies JO - J Virol VL - 78 UR - https://doi.org/10.1128/JVI.78.23.13232-13252.2004 DO - 10.1128/JVI.78.23.13232-13252.2004 ID - Binley2004 ER - TY - JOUR AU - Novitsky, V. A. AU - Gaolekwe, S. AU - McLane, M. F. AU - Ndung'u, T. P. AU - Foley, B. T. AU - Vannberg, F. AU - Marlink, R. AU - Essex, M. PY - 2000 DA - 2000// TI - HIV type 1 A/J recombinant with a pronounced pol gene mosaicism JO - AIDS Res Hum Retroviruses VL - 16 UR - https://doi.org/10.1089/08892220050058434 DO - 10.1089/08892220050058434 ID - Novitsky2000 ER - TY - JOUR AU - Vidal, N. AU - Peeters, M. AU - Mulanga-Kabeya, C. AU - Nzilambi, N. AU - Robertson, D. AU - Ilunga, W. AU - Sema, H. AU - Tshimanga, K. AU - Bongo, B. AU - Delaporte, E. PY - 2000 DA - 2000// TI - Unprecedented degree of human immunodeficiency virus type 1 (HIV-1) group M genetic diversity in the Democratic Republic of Congo suggests that the HIV-1 pandemic originated in Central Africa JO - J Virol VL - 74 UR - https://doi.org/10.1128/JVI.74.22.10498-10507.2000 DO - 10.1128/JVI.74.22.10498-10507.2000 ID - Vidal2000 ER - TY - CHAP AU - Ndiaye, H. D. AU - Kane, C. T. AU - Vidal, N. AU - Niama, F. R. AU - Niang-Diallo, P. A. AU - Dieye, T. AU - Gaye-Diallo, A. AU - Wade, A. S. AU - Peeters, M. AU - Mboup, S. PY - 2009 DA - 2009// TI - Surprisingly High Prevalence of Subtype C and Specific HIV-1 Subtype/CRF Distribution in Men Having Sex With Men in Senegal BT - J Acquir Immune Defic Syndr ID - Ndiaye2009 ER - TY - JOUR AU - Hamel, D. J. AU - Sankale, J. L. AU - Eisen, G. AU - Meloni, S. T. AU - Mullins, C. AU - Gueye-Ndiaye, A. AU - Mboup, S. AU - Kanki, P. J. PY - 2007 DA - 2007// TI - Twenty years of prospective molecular epidemiology in Senegal: changes in HIV diversity JO - AIDS Res Hum Retroviruses VL - 23 UR - https://doi.org/10.1089/aid.2007.0037 DO - 10.1089/aid.2007.0037 ID - Hamel2007 ER - TY - STD TI - Abecasis AB, Wang Y, Libin P, Imbrechts S, de Oliveira T, Camacho RJ, Vandamme AM: Comparative performance of the REGA subtyping tool version 2 versus version 1. Infect Genet Evol. 10: 380-385. 10.1016/j.meegid.2009.09.020. ID - ref34 ER - TY - JOUR AU - Njai, H. F. AU - Gali, Y. AU - Vanham, G. AU - Clybergh, C. AU - Jennes, W. AU - Vidal, N. AU - Butel, C. AU - Mpoudi-Ngolle, E. AU - Peeters, M. AU - Arien, K. K. PY - 2006 DA - 2006// TI - The predominance of Human Immunodeficiency Virus type 1 (HIV-1) circulating recombinant form 02 (CRF02_AG) in West Central Africa may be related to its replicative fitness JO - Retrovirology VL - 3 UR - https://doi.org/10.1186/1742-4690-3-40 DO - 10.1186/1742-4690-3-40 ID - Njai2006 ER - TY - JOUR AU - Abraha, A. AU - Nankya, I. L. AU - Gibson, R. AU - Demers, K. AU - Tebit, D. M. AU - Johnston, E. AU - Katzenstein, D. AU - Siddiqui, A. AU - Herrera, C. AU - Fischetti, L. PY - 2009 DA - 2009// TI - CCR5- and CXCR4-tropic subtype C human immunodeficiency virus type 1 isolates have a lower level of pathogenic fitness than other dominant group M subtypes: implications for the epidemic JO - J Virol VL - 83 UR - https://doi.org/10.1128/JVI.02051-08 DO - 10.1128/JVI.02051-08 ID - Abraha2009 ER - TY - JOUR AU - Tscherning, C. AU - Alaeus, A. AU - Fredriksson, R. AU - Bjorndal, A. AU - Deng, H. AU - Littman, D. R. AU - Fenyo, E. M. AU - Albert, J. PY - 1998 DA - 1998// TI - Differences in chemokine coreceptor usage between genetic subtypes of HIV-1 JO - Virology VL - 241 UR - https://doi.org/10.1006/viro.1997.8980 DO - 10.1006/viro.1997.8980 ID - Tscherning1998 ER - TY - JOUR AU - Ping, L. H. AU - Nelson, J. A. AU - Hoffman, I. F. AU - Schock, J. AU - Lamers, S. L. AU - Goodman, M. AU - Vernazza, P. AU - Kazembe, P. AU - Maida, M. AU - Zimba, D. PY - 1999 DA - 1999// TI - Characterization of V3 sequence heterogeneity in subtype C human immunodeficiency virus type 1 isolates from Malawi: underrepresentation of X4 variants JO - J Virol VL - 73 ID - Ping1999 ER - TY - JOUR AU - Kaleebu, P. AU - French, N. AU - Mahe, C. AU - Yirrell, D. AU - Watera, C. AU - Lyagoba, F. AU - Nakiyingi, J. AU - Rutebemberwa, A. AU - Morgan, D. AU - Weber, J. PY - 2002 DA - 2002// TI - Effect of human immunodeficiency virus (HIV) type 1 envelope subtypes A and D on disease progression in a large cohort of HIV-1-positive persons in Uganda JO - J Infect Dis VL - 185 UR - https://doi.org/10.1086/340130 DO - 10.1086/340130 ID - Kaleebu2002 ER - TY - JOUR AU - Kiwanuka, N. AU - Laeyendecker, O. AU - Robb, M. AU - Kigozi, G. AU - Arroyo, M. AU - McCutchan, F. AU - Eller, L. A. AU - Eller, M. AU - Makumbi, F. AU - Birx, D. PY - 2008 DA - 2008// TI - Effect of human immunodeficiency virus Type 1 (HIV-1) subtype on disease progression in persons from Rakai, Uganda, with incident HIV-1 infection JO - J Infect Dis VL - 197 UR - https://doi.org/10.1086/527416 DO - 10.1086/527416 ID - Kiwanuka2008 ER - TY - JOUR AU - Baeten, J. M. AU - Chohan, B. AU - Lavreys, L. AU - Chohan, V. AU - McClelland, R. S. AU - Certain, L. AU - Mandaliya, K. AU - Jaoko, W. AU - Overbaugh, J. PY - 2007 DA - 2007// TI - HIV-1 subtype D infection is associated with faster disease progression than subtype A in spite of similar plasma HIV-1 loads JO - J Infect Dis VL - 195 UR - https://doi.org/10.1086/512682 DO - 10.1086/512682 ID - Baeten2007 ER - TY - JOUR AU - Kanki, P. J. AU - Hamel, D. J. AU - Sankale, J. L. AU - Hsieh, C. AU - Thior, I. AU - Barin, F. AU - Woodcock, S. A. AU - Gueye-Ndiaye, A. AU - Zhang, E. AU - Montano, M. PY - 1999 DA - 1999// TI - Human immunodeficiency virus type 1 subtypes differ in disease progression JO - J Infect Dis VL - 179 UR - https://doi.org/10.1086/314557 DO - 10.1086/314557 ID - Kanki1999 ER - TY - JOUR AU - Laurent, C. AU - Bourgeois, A. AU - Faye, M. A. AU - Mougnutou, R. AU - Seydi, M. AU - Gueye, M. AU - Liegeois, F. AU - Kane, C. T. AU - Butel, C. AU - Mbuagbaw, J. PY - 2002 DA - 2002// TI - No difference in clinical progression between patients infected with the predominant human immunodeficiency virus type 1 circulating recombinant form (CRF) 02_AG strain and patients not infected with CRF02_AG, in Western and West-Central Africa: a four-year prospective multicenter study JO - J Infect Dis VL - 186 UR - https://doi.org/10.1086/341833 DO - 10.1086/341833 ID - Laurent2002 ER - TY - JOUR AU - Invernizzi, C. F. AU - Coutsinos, D. AU - Oliveira, M. AU - Moisi, D. AU - Brenner, B. G. AU - Wainberg, M. A. PY - 2009 DA - 2009// TI - Signature nucleotide polymorphisms at positions 64 and 65 in reverse transcriptase favor the selection of the K65R resistance mutation in HIV-1 subtype C JO - J Infect Dis VL - 200 UR - https://doi.org/10.1086/605894 DO - 10.1086/605894 ID - Invernizzi2009 ER - TY - JOUR AU - Martinez-Cajas, J. L. AU - Pai, N. P. AU - Klein, M. B. AU - Wainberg, M. A. PY - 2009 DA - 2009// TI - Differences in resistance mutations among HIV-1 non-subtype B infections: a systematic review of evidence (1996-2008) JO - J Int AIDS Soc VL - 12 UR - https://doi.org/10.1186/1758-2652-12-11 DO - 10.1186/1758-2652-12-11 ID - Martinez-Cajas2009 ER -