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For: Kapoor A, Jones M, Shafer RW, Rhee SY, Kazanjian P, Delwart EL. Sequencing-based detection of low-frequency human immunodeficiency virus type 1 drug-resistant mutants by an RNA/DNA heteroduplex generator-tracking assay. J Virol 2004;78:7112-23. [PMID: 15194787 PMCID: PMC421662 DOI: 10.1128/jvi.78.13.7112-7123.2004] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
Number Cited by Other Article(s)
1
Parkin N, Harrigan PR, Inzaule S, Bertagnolio S. Need assessment for HIV drug resistance testing and landscape of current and future technologies in low- and middle-income countries. PLOS GLOBAL PUBLIC HEALTH 2023;3:e0001948. [PMID: 37851634 PMCID: PMC10584185 DOI: 10.1371/journal.pgph.0001948] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
2
Next generation sequencing technologies. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014;2:255-60. [PMID: 24981944 DOI: 10.1016/j.ddtec.2005.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
3
Xiaobai Z, Xi C, Tian H, Williams AB, Wang H, He J, Zhen J, Chiarella J, Blake LA, Turenchalk G, Kozal MJ. Prevalence of WHO transmitted drug resistance mutations by deep sequencing in antiretroviral-naïve subjects in Hunan Province, China. PLoS One 2014;9:e98740. [PMID: 24896087 PMCID: PMC4045886 DOI: 10.1371/journal.pone.0098740] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 05/07/2014] [Indexed: 11/18/2022]  Open
4
Shankarappa R, Mullins JI. Inferring viral population structures using heteroduplex mobility and DNA sequence analyses. J Virol Methods 2013;194:169-77. [PMID: 23994080 DOI: 10.1016/j.jviromet.2013.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 08/08/2013] [Accepted: 08/09/2013] [Indexed: 11/19/2022]
5
Next-generation sequencing reveals cryptic mtDNA diversity of Plasmodium relictum in the Hawaiian Islands. Parasitology 2013;140:1741-50. [PMID: 23953131 DOI: 10.1017/s0031182013000905] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
6
Morabito K, Kantor R, Tai W, Schreier L, Tripathi A. Detection of HIV-1 minority variants containing the K103N drug-resistance mutation using a simple method to amplify RNA targets (SMART). J Mol Diagn 2013;15:401-12. [PMID: 23541840 DOI: 10.1016/j.jmoldx.2013.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 01/30/2013] [Accepted: 02/12/2013] [Indexed: 11/26/2022]  Open
7
Armitage AE, Deforche K, Chang CH, Wee E, Kramer B, Welch JJ, Gerstoft J, Fugger L, McMichael A, Rambaut A, Iversen AKN. APOBEC3G-induced hypermutation of human immunodeficiency virus type-1 is typically a discrete "all or nothing" phenomenon. PLoS Genet 2012;8:e1002550. [PMID: 22457633 PMCID: PMC3310730 DOI: 10.1371/journal.pgen.1002550] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 01/07/2012] [Indexed: 11/18/2022]  Open
8
Parboosing R, Naidoo A, Gordon M, Taylor M, Vella V. Resistance to antiretroviral drugs in newly diagnosed, young treatment-naïve HIV-positive pregnant women in the province of KwaZulu-Natal, South Africa. J Med Virol 2012;83:1508-13. [PMID: 21739439 DOI: 10.1002/jmv.22143] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
9
D'Aquila RT, Geretti AM, Horton JH, Rouse E, Kheshti A, Raffanti S, Oie K, Pappa K, Ross LL. Tenofovir (TDF)-selected or abacavir (ABC)-selected low-frequency HIV type 1 subpopulations during failure with persistent viremia as detected by ultradeep pyrosequencing. AIDS Res Hum Retroviruses 2011;27:201-9. [PMID: 20929395 DOI: 10.1089/aid.2010.0077] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
10
Gianella S, Richman DD. Minority variants of drug-resistant HIV. J Infect Dis 2010;202:657-66. [PMID: 20649427 PMCID: PMC2916955 DOI: 10.1086/655397] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
11
Paredes R, Clotet B. Clinical management of HIV-1 resistance. Antiviral Res 2009;85:245-65. [PMID: 19808056 DOI: 10.1016/j.antiviral.2009.09.015] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2009] [Revised: 09/28/2009] [Accepted: 09/30/2009] [Indexed: 11/18/2022]
12
Juliano JJ, Ariey F, Sem R, Tangpukdee N, Krudsood S, Olson C, Looareesuwan S, Rogers WO, Wongsrichanalai C, Meshnick SR. Misclassification of drug failure in Plasmodium falciparum clinical trials in southeast Asia. J Infect Dis 2009;200:624-8. [PMID: 19591576 PMCID: PMC2761972 DOI: 10.1086/600892] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]  Open
13
Passage of dengue virus type 4 vaccine candidates in fetal rhesus lung cells selects heparin-sensitive variants that result in loss of infectivity and immunogenicity in rhesus macaques. J Virol 2009;83:10384-94. [PMID: 19656873 DOI: 10.1128/jvi.01083-09] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
14
Le T, Chiarella J, Simen BB, Hanczaruk B, Egholm M, Landry ML, Dieckhaus K, Rosen MI, Kozal MJ. Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use. PLoS One 2009;4:e6079. [PMID: 19562031 PMCID: PMC2698118 DOI: 10.1371/journal.pone.0006079] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 06/05/2009] [Indexed: 02/07/2023]  Open
15
Compartmentalized human immunodeficiency virus type 1 originates from long-lived cells in some subjects with HIV-1-associated dementia. PLoS Pathog 2009;5:e1000395. [PMID: 19390619 PMCID: PMC2668697 DOI: 10.1371/journal.ppat.1000395] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Accepted: 03/25/2009] [Indexed: 11/22/2022]  Open
16
Shafer RW. Low-abundance drug-resistant HIV-1 variants: finding significance in an era of abundant diagnostic and therapeutic options. J Infect Dis 2009;199:610-2. [PMID: 19210160 PMCID: PMC4764065 DOI: 10.1086/596737] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]  Open
17
Metzner KJ, Giulieri SG, Knoepfel SA, Rauch P, Burgisser P, Yerly S, Günthard HF, Cavassini M. Minority quasispecies of drug-resistant HIV-1 that lead to early therapy failure in treatment-naive and -adherent patients. Clin Infect Dis 2009;48:239-47. [PMID: 19086910 DOI: 10.1086/595703] [Citation(s) in RCA: 166] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]  Open
18
Schnell G, Ince WL, Swanstrom R. Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes. Nucleic Acids Res 2008;36:e146. [PMID: 18948297 PMCID: PMC2602764 DOI: 10.1093/nar/gkn713] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
19
Vandenbroucke I, Eygen VV, Rondelez E, Vermeiren H, Baelen KV, Stuyver LJ. Minor Variant Detection at Different Template Concentrations in HIV-1 Phenotypic and Genotypic Tropism Testing. Open Virol J 2008;2:8-14. [PMID: 19440459 PMCID: PMC2678814 DOI: 10.2174/1874357900802010008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Revised: 02/21/2008] [Accepted: 02/25/2008] [Indexed: 11/22/2022]  Open
20
Dash PK, Siddappa NB, Mangaiarkarasi A, Mahendarkar AV, Roshan P, Anand KK, Mahadevan A, Satishchandra P, Shankar SK, Prasad VR, Ranga U. Exceptional molecular and coreceptor-requirement properties of molecular clones isolated from an Human Immunodeficiency Virus Type-1 subtype C infection. Retrovirology 2008;5:25. [PMID: 18328091 PMCID: PMC2292743 DOI: 10.1186/1742-4690-5-25] [Citation(s) in RCA: 21] [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: 10/11/2007] [Accepted: 03/07/2008] [Indexed: 11/10/2022]  Open
21
García-Arriaza J, Domingo E, Briones C. Characterization of minority subpopulations in the mutant spectrum of HIV-1 quasispecies by successive specific amplifications. Virus Res 2007;129:123-34. [PMID: 17706828 DOI: 10.1016/j.virusres.2007.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 06/29/2007] [Accepted: 07/02/2007] [Indexed: 01/06/2023]
22
Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW. Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res 2007;17:1195-201. [PMID: 17600086 PMCID: PMC1933516 DOI: 10.1101/gr.6468307] [Citation(s) in RCA: 321] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Accepted: 04/27/2007] [Indexed: 12/13/2022]
23
Juliano JJ, Kwiek JJ, Cappell K, Mwapasa V, Meshnick SR. Minority-variant pfcrt K76T mutations and chloroquine resistance, Malawi. Emerg Infect Dis 2007;13:872-7. [PMID: 17553226 DOI: 10.3201/eid1306.061182] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
24
Lalonde MS, Troyer RM, Syed AR, Bulime S, Demers K, Bajunirwe F, Arts EJ. Sensitive oligonucleotide ligation assay for low-level detection of nevirapine resistance mutations in human immunodeficiency virus type 1 quasispecies. J Clin Microbiol 2007;45:2604-15. [PMID: 17567789 PMCID: PMC1951259 DOI: 10.1128/jcm.00431-07] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
25
Gao F. More sensitive assays for better drug resistance prediction? Pharmacogenomics 2007;8:533-6. [PMID: 17559341 DOI: 10.2217/14622416.8.6.533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
26
Gao F, Wang D. Minor-drug-resistant HIV populations and treatment failure. Future Virol 2007. [DOI: 10.2217/17460794.2.3.293] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
27
Friedrich A, Hoheisel JD, Marmé N, Knemeyer JP. DNA-probes for the highly sensitive identification of single nucleotide polymorphism using single-molecule spectroscopy. FEBS Lett 2007;581:1644-8. [PMID: 17399707 DOI: 10.1016/j.febslet.2007.03.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Revised: 03/09/2007] [Accepted: 03/12/2007] [Indexed: 10/23/2022]
28
Fernàndez G, Clotet B, Martínez MA. Fitness landscape of human immunodeficiency virus type 1 protease quasispecies. J Virol 2007;81:2485-96. [PMID: 17151104 PMCID: PMC1865935 DOI: 10.1128/jvi.01594-06] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Accepted: 11/29/2006] [Indexed: 11/20/2022]  Open
29
Jacobs GB, de Beer C, Fincham JE, Adams V, Dhansay MA, van Rensburg EJ, Engelbrecht S. Serotyping and genotyping of HIV-1 infection in residents of Khayelitsha, Cape Town, South Africa. J Med Virol 2007;78:1529-36. [PMID: 17063507 DOI: 10.1002/jmv.20735] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
30
Georgopapadakou N. Discontinued drugs in 2005: anti-infectives. Expert Opin Investig Drugs 2007;16:1-10. [PMID: 17155849 DOI: 10.1517/13543784.16.1.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
31
Chapter 5 The 454 Life Sciences Picoliter Sequencing System. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/s1871-0069(06)02005-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
32
Ziebolz B, Droege M. Toward a new era in sequencing. ACTA ACUST UNITED AC 2007;13:1-26. [PMID: 17875471 DOI: 10.1016/s1387-2656(07)13001-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
33
Metzner KJ, Rauch P, Walter H, Boesecke C, Zöllner B, Jessen H, Schewe K, Fenske S, Gellermann H, Stellbrink HJ. Detection of minor populations of drug-resistant HIV-1 in acute seroconverters. AIDS 2005;19:1819-25. [PMID: 16227789 DOI: 10.1097/01.aids.0000189878.97480.ed] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
34
Senescau A, Berry A, Benoit-Vical F, Landt O, Fabre R, Lelièvre J, Cassaing S, Magnaval JF. Use of a locked-nucleic-acid oligomer in the clamped-probe assay for detection of a minority Pfcrt K76T mutant population of Plasmodium falciparum. J Clin Microbiol 2005;43:3304-8. [PMID: 16000452 PMCID: PMC1169138 DOI: 10.1128/jcm.43.7.3304-3308.2005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
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