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For: Mani I, Gilbert P, Sankalé JL, Eisen G, Mboup S, Kanki PJ. Intrapatient diversity and its correlation with viral setpoint in human immunodeficiency virus type 1 CRF02_A/G-IbNG infection. J Virol 2002;76:10745-55. [PMID: 12368317 PMCID: PMC136616 DOI: 10.1128/jvi.76.21.10745-10755.2002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
Number Cited by Other Article(s)
1
Griffiths ME, Broos A, Bergner LM, Meza DK, Suarez NM, da Silva Filipe A, Tello C, Becker DJ, Streicker DG. Longitudinal deep sequencing informs vector selection and future deployment strategies for transmissible vaccines. PLoS Biol 2022;20:e3001580. [PMID: 35439242 PMCID: PMC9017877 DOI: 10.1371/journal.pbio.3001580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 02/21/2022] [Indexed: 12/04/2022]  Open
2
Rife Magalis B, Autissier P, Williams KC, Chen X, Browne C, Salemi M. Predator-Prey Dynamics of Intra-Host Simian Immunodeficiency Virus Evolution Within the Untreated Host. Front Immunol 2021;12:709962. [PMID: 34691023 PMCID: PMC8527182 DOI: 10.3389/fimmu.2021.709962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/21/2021] [Indexed: 01/18/2023]  Open
3
Banin AN, Tuen M, Bimela JS, Tongo M, Zappile P, Khodadadi‐Jamayran A, Nanfack AJ, Okonko IO, Meli J, Wang X, Mbanya D, Ngogang J, Gorny MK, Heguy A, Fokunang C, Duerr R. Near full genome characterization of HIV-1 unique recombinant forms in Cameroon reveals dominant CRF02_AG and F2 recombination patterns. J Int AIDS Soc 2019;22:e25362. [PMID: 31353798 PMCID: PMC6661401 DOI: 10.1002/jia2.25362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/04/2019] [Indexed: 02/06/2023]  Open
4
Rojas Sánchez P, Cobos A, Navaro M, Ramos JT, Pagán I, Holguín Á. Impact of Clinical Parameters in the Intrahost Evolution of HIV-1 Subtype B in Pediatric Patients: A Machine Learning Approach. Genome Biol Evol 2018;9:2715-2726. [PMID: 29044435 PMCID: PMC5647794 DOI: 10.1093/gbe/evx193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2017] [Indexed: 12/24/2022]  Open
5
Domínguez-Rodríguez S, Rojas P, Fernández McPhee C, Pagán I, Navarro ML, Ramos JT, Holguín Á. Effect of HIV/HCV Co-Infection on the Protease Evolution of HIV-1B: A Pilot Study in a Pediatric Population. Sci Rep 2018;8:2347. [PMID: 29403002 PMCID: PMC5799169 DOI: 10.1038/s41598-018-19312-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/29/2017] [Indexed: 12/28/2022]  Open
6
Palumbo PJ, Wilson EA, Piwowar-Manning E, McCauley M, Gamble T, Kumwenda N, Makhema J, Kumarasamy N, Chariyalertsak S, Hakim JG, Hosseinipour MC, Melo MG, Godbole SV, Pilotto JH, Grinsztejn B, Panchia R, Chen YQ, Cohen MS, Eshleman SH, Fogel JM. Association of HIV diversity and virologic outcomes in early antiretroviral treatment: HPTN 052. PLoS One 2017;12:e0177281. [PMID: 28481902 PMCID: PMC5421787 DOI: 10.1371/journal.pone.0177281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/24/2017] [Indexed: 11/19/2022]  Open
7
DeLeon O, Hodis H, O’Malley Y, Johnson J, Salimi H, Zhai Y, Winter E, Remec C, Eichelberger N, Van Cleave B, Puliadi R, Harrington RD, Stapleton JT, Haim H. Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model. PLoS Biol 2017;15:e2001549. [PMID: 28384158 PMCID: PMC5383018 DOI: 10.1371/journal.pbio.2001549] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 01/08/2023]  Open
8
Analysis of HIV Diversity in HIV-Infected Black Men Who Have Sex with Men (HPTN 061). PLoS One 2016;11:e0167629. [PMID: 27936098 PMCID: PMC5147928 DOI: 10.1371/journal.pone.0167629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/17/2016] [Indexed: 01/01/2023]  Open
9
Pagán I, Rojas P, Ramos JT, Holguín Á. Clinical Determinants of HIV-1B Between-Host Evolution and their Association with Drug Resistance in Pediatric Patients. PLoS One 2016;11:e0167383. [PMID: 27907076 PMCID: PMC5132210 DOI: 10.1371/journal.pone.0167383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 11/14/2016] [Indexed: 01/10/2023]  Open
10
High frequency of transmitted HIV-1 Gag HLA class I-driven immune escape variants but minimal immune selection over the first year of clade C infection. PLoS One 2015;10:e0119886. [PMID: 25781986 PMCID: PMC4363590 DOI: 10.1371/journal.pone.0119886] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/03/2015] [Indexed: 11/19/2022]  Open
11
Tsai L, Tasovski I, Leda AR, Chin MPS, Cheng-Mayer C. The number and genetic relatedness of transmitted/founder virus impact clinical outcome in vaginal R5 SHIVSF162P3N infection. Retrovirology 2014;11:22. [PMID: 24612462 PMCID: PMC3975242 DOI: 10.1186/1742-4690-11-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/23/2014] [Indexed: 12/31/2022]  Open
12
Comparison of a high-resolution melting assay to next-generation sequencing for analysis of HIV diversity. J Clin Microbiol 2012;50:3054-9. [PMID: 22785188 DOI: 10.1128/jcm.01460-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
13
Rossenkhan R, Novitsky V, Sebunya TK, Musonda R, Gashe BA, Essex M. Viral diversity and diversification of major non-structural genes vif, vpr, vpu, tat exon 1 and rev exon 1 during primary HIV-1 subtype C infection. PLoS One 2012;7:e35491. [PMID: 22590503 PMCID: PMC3348911 DOI: 10.1371/journal.pone.0035491] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/16/2012] [Indexed: 01/12/2023]  Open
14
James MM, Wang L, Musoke P, Donnell D, Fogel J, Towler WI, Khaki L, Nakabiito C, Jackson JB, Eshleman SH. Association of HIV diversity and survival in HIV-infected Ugandan infants. PLoS One 2011;6:e18642. [PMID: 21533179 PMCID: PMC3077388 DOI: 10.1371/journal.pone.0018642] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 03/13/2011] [Indexed: 11/18/2022]  Open
15
Chamberland A, Sylla M, Boulassel MR, Baril JG, Côté P, Thomas R, Trottier B, Rouleau D, Routy JP, Tremblay C. Effect of antiretroviral therapy on HIV-1 genetic evolution during acute infection. Int J STD AIDS 2011;22:146-50. [DOI: 10.1258/ijsa.2010.010292] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
16
Archary D, Gordon ML, Green TN, Coovadia HM, Goulder PJR, Ndung'u T. HIV-1 subtype C envelope characteristics associated with divergent rates of chronic disease progression. Retrovirology 2010;7:92. [PMID: 21050445 PMCID: PMC2992043 DOI: 10.1186/1742-4690-7-92] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 11/04/2010] [Indexed: 11/10/2022]  Open
17
Biru T, Lennemann T, Stürmer M, Stephan C, Nisius G, Cinatl J, Staszewski S, Gürtler LG. Human immunodeficiency virus type-1 group M quasispecies evolution: diversity and divergence in patients co-infected with active tuberculosis. Med Microbiol Immunol 2010;199:323-32. [PMID: 20697741 DOI: 10.1007/s00430-010-0167-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Indexed: 10/19/2022]
18
Blood and seminal plasma HIV-1 RNA levels among HIV-1-infected injecting drug users participating in the AIDSVAX B/E efficacy trial in Bangkok, Thailand. J Acquir Immune Defic Syndr 2009;51:601-8. [PMID: 19430307 DOI: 10.1097/qai.0b013e3181a44700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
19
Piantadosi A, Chohan B, Panteleeff D, Baeten JM, Mandaliya K, Ndinya-Achola JO, Overbaugh J. HIV-1 evolution in gag and env is highly correlated but exhibits different relationships with viral load and the immune response. AIDS 2009;23:579-87. [PMID: 19516110 PMCID: PMC2727980 DOI: 10.1097/qad.0b013e328328f76e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
20
Valenzuela CY. Non-random pre-transcriptional evolution in HIV-1. A refutation of the foundational conditions for neutral evolution. Genet Mol Biol 2009;32:159-69. [PMID: 21637663 PMCID: PMC3032973 DOI: 10.1590/s1415-47572009005000025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 06/03/2008] [Indexed: 12/02/2022]  Open
21
Chalmet K, Van Wanzeele F, Demecheleer E, Dauwe K, Pelgrom J, Van Der Gucht B, Vogelaers D, Plum J, Stuyver L, Vandekerckhove L, Verhofstede C. Impact of Delta 32-CCR5 heterozygosity on HIV-1 genetic evolution and variability--a study of 4 individuals infected with closely related HIV-1 strains. Virology 2008;379:213-22. [PMID: 18692212 DOI: 10.1016/j.virol.2008.06.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2008] [Revised: 04/08/2008] [Accepted: 06/30/2008] [Indexed: 11/29/2022]
22
Gottlieb GS, Heath L, Nickle DC, Wong KG, Leach SE, Jacobs B, Gezahegne S, van 't Wout AB, Jacobson LP, Margolick JB, Mullins JI. HIV-1 variation before seroconversion in men who have sex with men: analysis of acute/early HIV infection in the multicenter AIDS cohort study. J Infect Dis 2008;197:1011-5. [PMID: 18419538 PMCID: PMC3419593 DOI: 10.1086/529206] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]  Open
23
Bello G, Casado C, Sandonis V, Alvaro-Cifuentes T, dos Santos CAR, García S, Rodríguez C, del Romero J, Pilotto JH, Grinsztejn B, Veloso VG, Morgado MG, López-Galíndez C. Plasma viral load threshold for sustaining intrahost HIV type 1 evolution. AIDS Res Hum Retroviruses 2007;23:1242-50. [PMID: 17961111 DOI: 10.1089/aid.2007.0074] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
24
Bello G, Casado C, García S, Rodríguez C, del Romero J, Carvajal-Rodriguez A, Posada D, López-Galíndez C. Lack of temporal structure in the short term HIV-1 evolution within asymptomatic naïve patients. Virology 2007;362:294-303. [PMID: 17275055 DOI: 10.1016/j.virol.2006.11.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 10/28/2006] [Accepted: 11/22/2006] [Indexed: 12/31/2022]
25
Shriner D, Liu Y, Nickle DC, Mullins JI. EVOLUTION OF INTRAHOST HIV - 1 GENETIC DIVERSITY DURING CHRONIC INFECTION. Evolution 2006. [DOI: 10.1111/j.0014-3820.2006.tb01195.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
26
Shriner D, Liu Y, Nickle DC, Mullins JI. EVOLUTION OF INTRAHOST HIV-1 GENETIC DIVERSITY DURING CHRONIC INFECTION. Evolution 2006. [DOI: 10.1554/05-473.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
27
Joos B, Trkola A, Fischer M, Kuster H, Rusert P, Leemann C, Böni J, Oxenius A, Price DA, Phillips RE, Wong JK, Hirschel B, Weber R, Günthard HF. Low human immunodeficiency virus envelope diversity correlates with low in vitro replication capacity and predicts spontaneous control of plasma viremia after treatment interruptions. J Virol 2005;79:9026-37. [PMID: 15994796 PMCID: PMC1168724 DOI: 10.1128/jvi.79.14.9026-9037.2005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
28
Bello G, Casado C, Sandonis V, Alonso-Nieto M, Vicario JL, García S, Hernando V, Rodríguez C, Romero JD, López-Galíndez C. A subset of human immunodeficiency virus type 1 long-term non-progressors is characterized by the unique presence of ancestral sequences in the viral population. J Gen Virol 2005;86:355-364. [PMID: 15659755 DOI: 10.1099/vir.0.80410-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
29
Greenier JL, Van Rompay KKA, Montefiori D, Earl P, Moss B, Marthas ML. Simian immunodeficiency virus (SIV) envelope quasispecies transmission and evolution in infant rhesus macaques after oral challenge with uncloned SIVmac251: increased diversity is associated with neutralizing antibodies and improved survival in previously immunized animals. Virol J 2005;2:11. [PMID: 15710048 PMCID: PMC552328 DOI: 10.1186/1743-422x-2-11] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2004] [Accepted: 02/14/2005] [Indexed: 01/03/2023]  Open
30
Sagar M, Lavreys L, Baeten JM, Richardson BA, Mandaliya K, Chohan BH, Kreiss JK, Overbaugh J. Infection with multiple human immunodeficiency virus type 1 variants is associated with faster disease progression. J Virol 2004;77:12921-6. [PMID: 14610215 PMCID: PMC262567 DOI: 10.1128/jvi.77.23.12921-12926.2003] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
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