HIV drug resistance testing by high-multiplex "wide" sequencing on the MiSeq instrument.
作者： H. R. Lapointe , W. Dong , G. Q. Lee , D. R. Bangsberg , J. N. Martin
DOI: 10.1128/AAC.01490-15
关键词:
摘要: Limited access to HIV drug resistance testing in low- and middle-income countries impedes clinical decision-making at the individual patient level. An efficient protocol address this issue must be established minimize negative therapeutic outcomes for HIV-1-infected individuals such settings. This is an observational study ascertain potential of newer genomic sequencing platforms, as Illumina MiSeq instrument, provide accurate genotypes hundreds samples simultaneously. Plasma were collected from Canadian patients during routine (n = 759) a Ugandan cohort 349). Amplicons spanning reverse transcriptase codons 90 234 sequenced with both conventional Sanger methods. Sequences evaluated nucleotide concordance between methods, using coverage mixture parameters quality control. Consensus sequences also analyzed disparities identification mutations. was successful 881 (80%) 892 (81%), respectively, 832 having results Most failures viral loads <3.0 log10 RNA copies/ml. Overall, 99.3% methods observed. achieved 97.4% sensitivity specificity detecting mutations identified by sequencing. Findings suggest that platform can yield high-quality data high-multiplex "wide" approach. strategy used multiple subtypes, demonstrating widespread annual population surveillance resource-limited
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D Katzenstein, A Zolopa, V DeGruttola, R Harrigan, S Hammer, A Phillips, J Baxter, M Miller, V Miller, M Para, D Holder, S Castillo, L Dix, J Murray, P Clevenbergh, L Pedneault, S Yerly, A Patick, R Lanier, R D'Aquila, J Mellors, M Ait-Khaled, The relation between baseline HIV drug resistance and response to antiretroviral therapy: re-analysis of retrospective and prospective studies using a standardized data analysis plan Antiviral Therapy. ,vol. 5, pp. 41- 48 ,(2000)
Annemarie M Wensing, Huldrych F Gunthard, Douglas D Richman, Victoria A Johnson, Robert W Shafer, Roger Paredes, Deenan Pillay, Vincent Calvez, Update of the drug resistance mutations in HIV-1: March 2013. Topics in antiviral medicine. ,vol. 21, pp. 6- 14 ,(2013)
Richard Pilon, Silvia Bertagnolio, P Richard Harrigan, Paul Sandstrom, Luis Fuentes, Theresa Mo, Monica Viveros, Roberto Rodriguez, Don Sutherland, Luis Soto-Ramirez, HIV-1 drug resistance surveillance using dried whole blood spots. Antiviral Therapy. ,vol. 12, pp. 107- 113 ,(2007)
Guinevere Q Lee, David R Bangsberg, Conrad Muzoora, Yap Boum, Jessica H Oyugi, Nneka Emenyonu, John Bennett, Peter W Hunt, David Knapp, Chanson J Brumme, P Richard Harrigan, Jeffrey N Martin, None, Prevalence and virologic consequences of transmitted HIV-1 drug resistance in Uganda AIDS Research and Human Retroviruses. ,vol. 30, pp. 896- 906 ,(2014) , 10.1089/AID.2014.0043
Richard M W Hoetelmans, Vanitha Sekar, David Back, Darunavir: pharmacokinetics and drug interactions. Antiviral Therapy. ,vol. 13, pp. 1- 13 ,(2008)
Birgitte B. Simen, Jan Fredrik Simons, Katherine Huppler Hullsiek, Richard M. Novak, Rodger D. MacArthur, John D. Baxter, Chunli Huang, Christine Lubeski, Gregory S. Turenchalk, Michael S. Braverman, Brian Desany, Jonathan M. Rothberg, Michael Egholm, Michael J. Kozal, , Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. The Journal of Infectious Diseases. ,vol. 199, pp. 693- 701 ,(2009) , 10.1086/596736
Jessica D. Church, Dana Jones, Tamara Flys, Donald Hoover, Natalia Marlowe, Shu Chen, Chanjuan Shi, James R. Eshleman, Laura A. Guay, J. Brooks Jackson, Newton Kumwenda, Taha E. Taha, Susan H. Eshleman, Sensitivity of the ViroSeq HIV-1 genotyping system for detection of the K103N resistance mutation in HIV-1 subtypes A, C, and D. The Journal of Molecular Diagnostics. ,vol. 8, pp. 430- 432 ,(2006) , 10.2353/JMOLDX.2006.050148
Allison K. DeLong, Mingham Wu, Diane Bennett, Neil Parkin, Zhijin Wu, Joseph W. Hogan, Rami Kantor, Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase. AIDS Research and Human Retroviruses. ,vol. 28, pp. 894- 901 ,(2012) , 10.1089/AID.2011.0120
Daniela Ram, Dena Leshkowitz, Dimitri Gonzalez, Relly Forer, Itzchak Levy, Michal Chowers, Margalit Lorber, Musa Hindiyeh, Ella Mendelson, Orna Mor, Evaluation of GS Junior and MiSeq next-generation sequencing technologies as an alternative to Trugene population sequencing in the clinical HIV laboratory Journal of Virological Methods. ,vol. 212, pp. 12- 16 ,(2015) , 10.1016/J.JVIROMET.2014.11.003
Soo-Yon Rhee, Jose Luis Blanco, Michael R. Jordan, Jonathan Taylor, Philippe Lemey, Vici Varghese, Raph L. Hamers, Silvia Bertagnolio, Tobias F. Rinke de Wit, Avelin F. Aghokeng, Jan Albert, Radko Avi, Santiago Avila-Rios, Pascal O. Bessong, James I. Brooks, Charles A. B. Boucher, Zabrina L. Brumme, Michael P. Busch, Hermann Bussmann, Marie-Laure Chaix, Bum Sik Chin, Toni T. D’Aquin, Cillian F. De Gascun, Anne Derache, Diane Descamps, Alaka K. Deshpande, Cyrille F. Djoko, Susan H. Eshleman, Herve Fleury, Pierre Frange, Seiichiro Fujisaki, P. Richard Harrigan, Junko Hattori, Africa Holguin, Gillian M. Hunt, Hiroshi Ichimura, Pontiano Kaleebu, David Katzenstein, Sasisopin Kiertiburanakul, Jerome H. Kim, Sung Soon Kim, Yanpeng Li, Irja Lutsar, Lynn Morris, Nicaise Ndembi, Kee Peng NG, Ramesh S. Paranjape, Martine Peeters, Mario Poljak, Matt A. Price, Manon L. Ragonnet-Cronin, Gustavo Reyes-Terán, Morgane Rolland, Sunee Sirivichayakul, Davey M. Smith, Marcelo A. Soares, Vincent V. Soriano, Deogratius Ssemwanga, Maja Stanojevic, Mariane A. Stefani, Wataru Sugiura, Somnuek Sungkanuparph, Amilcar Tanuri, Kok Keng Tee, Hong-Ha M. Truong, David A. M. C. van de Vijver, Nicole Vidal, Chunfu Yang, Rongge Yang, Gonzalo Yebra, John P. A. Ioannidis, Anne-Mieke Vandamme, Robert W. Shafer, Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis PLOS Medicine. ,vol. 12, pp. e1001810- ,(2015) , 10.1371/JOURNAL.PMED.1001810