Comparison of a high-resolution melting assay to next-generation sequencing for analysis of HIV diversity

Journal of Clinical Microbiology

Volumn 50, Issue 9, 2012, Pages 3054-3059

  Cousins, Matthew M ^a   Ou, San San ^b   Wawer, Maria J ^c   Munshaw, Supriya ^a   Swan, David ^b   Magaret, Craig A ^b   Mullis, Caroline E ^a   Serwadda, David ^d,e   Porcella, Stephen F ^f   Gray, Ronald H ^c   Quinn, Thomas C ^a,g   Donnell, Deborah ^b   Eshleman, Susan H ^a   Redd, Andrew D ^g  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

^c JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^d RAKAI HEALTH SCIENCES PROGRAM   (Uganda)

^e MAKERERE UNIVERSITY   (Uganda)

^f NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^g NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS DNA; VIRUS RNA;

ADULT; AMPLICON; ARTICLE; CONTROLLED STUDY; ENTROPY; ENVELOPE GENE; GENETIC PROCEDURES; GROUP SPECIFIC ANTIGEN GENE; HIGH RESOLUTION MELTING ANALYSIS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INTERMETHOD COMPARISON; MAJOR CLINICAL STUDY; MICROBIAL DIVERSITY; NEXT GENERATION SEQUENCING; NONHUMAN; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SCORING SYSTEM; VIRUS EXAMINATION; VIRUS GENE; VIRUS GENOME; VIRUS STRAIN;

ADULT; DNA, VIRAL; ENV GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; GAG GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HIV; HIV INFECTIONS; HUMANS; MOLECULAR BIOLOGY; NUCLEIC ACID DENATURATION; TRANSITION TEMPERATURE; UGANDA; VIROLOGY;

EID: 84865176080     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.01460-12     Document Type: Article

References (35)

1. Buzon MJ, et al. 2011. Deep molecular characterization of HIV-1 dynamics under suppressive HAART. PLoS Pathog. 7:e1002314. doi:10.1371/joural.ppat. 1002314.
2. Cousins MM, et al. 2011. Use of a high resolution melting (HRM) assay to compare gag, pol, and env diversity in adults with different stages of HIV infection. PLoS One 6:e27211. doi:10.1371/journal.pone.0027211.
3. Delwart EL, et al. 1997. Slower evolution of human immunodeficiency virus type 1 quasispecies during progression to AIDS. J. Virol. 71:7498-7508. (Pubitemid 27391690)
4. Reference deleted.
5. Eshleman SH, et al. 2011. Analysis of genetic linkage of HIV from couples enrolled in the HIV Prevention Trials Network 052 trial. J. Infect. Dis. 204:1918-1926.
6. Fischer W, et al. 2010. Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. PLoS One 5:e12303. doi:10.1371/journal.pone.0012303.
7. Frahm N, Brander C. 2007. HIV viral diversity and escape from cellular immunity. Curr. Infect. Dis. Rep. 9:161-166. (Pubitemid 46416058)
8. + children and the association of HIV diversity with age and impact of non-suppressive ART: Uganda, abstr 998. 19th Conf. Retroviruses Opportunistic Infect, CROI, Alexandria, VA.
9. James MM, et al. 2011. Association of HIV diversity and survival in HIV-infected Ugandan infants. PLoS One 6:e18642. doi:10.1371/ journal.pone.0018642.
10. Keele BF. 2010. Identifying and characterizing recently transmitted viruses. Curr. Opin. HIV AIDS 5:327-334.
11. Kinde I, Wu J, Papadopoulos N, Kinzler KW, Vogelstein B. 2011. Detection and quantification of rare mutations with massively parallel sequencing. Proc. Natl. Acad. Sci. U. S. A. 108:9530-9535.
12. Knoepfel SA, Di Giallonardo F, Daumer M, Thielen A, Metzner KJ. 2011. In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing. J. Virol. Methods 171:329-338.
13. Kouyos RD, et al. 2011. Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection. Clin. Infect. Dis. 52:532-539.
14. Reference deleted.
15. Liang B, et al. 2011. A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1. PLoS One 6:e26745. doi:10.1371/journal.pone.0026745.
16. Liu S, et al. 2008. Dynamic analysis of genetic diversity of gag and env regions of HIV-1 CRF07-BC recombinant in intravenous drug users in Xinjiang Uvghur Autonomous Region, China. Arch. Virol. 153:1233-1240.
17. Mani I, et al. 2002. Intrapatient diversity and its correlation with viral setpoint in human immunodeficiency virus type 1 CRF02-A/G-IbNG infection. J. Virol. 76:10745-10755. (Pubitemid 35176191)
18. Markham RB, et al. 1998. Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc. Natl. Acad. Sci. U. S. A. 95: 12568-12573. (Pubitemid 28483805)
19. Mild M, Hedskog C, Jernberg J, Albert J. 2011. Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation. PLoS One 6:e22741. doi:10.1371/journal.pone.0022741.
20. Pacold M, et al. 2010. Comparison of methods to detect HIV dual infection. AIDS Res. Hum. Retroviruses 26:1291-1298.
21. Piantadosi A, et al. 2009. HIV-1 evolution in gag and env is highly correlated but exhibits different relationships with viral load and the immune response. AIDS 23:579-587.
22. Redd AD, et al. 2011. Identification of HIV superinfection in seroconcordant couples in Rakai, Uganda, by use of next-generation deep sequencing. J. Clin. Microbiol. 49:2859-2867.
23. Redd AD, et al. 2012. The rates of HIV superinfection and primary HIV incidence in a general population in Rakai, Uganda. J. Infect. Dis. 206: 267-274.
24. Reed GH, Wittwer CT. 2004. Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin. Chem. 50:1748-1754. (Pubitemid 39298003)
25. Richman DD, et al. 2004. HIV evolution and escape. Trans Am. Clin. Climatol. Assoc. 115:289-303.
26. Sanders-Buell E, Salminen MO, McCutchan FE. 1995. Sequencing primers for HIV-1, p 15-21. In Korber B et al (ed), The Human Retroviruses and AIDS 1995 Compendium. Los Alamos National Laboratory, Los Alamos, NM.
27. Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nat. Biotechnol. 26:1135-1145.
28. Tebit DM, Nankya I, Arts EJ, Gao Y. 2007. HIV diversity, recombination and disease progression: how does fitness "fit" into the puzzle? AIDS Rev. 9:75-87. (Pubitemid 47162247)
29. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680. (Pubitemid 24354800)
30. Towler WI, et al. 2010. Analysis of HIV diversity using a high-resolution melting assay. AIDS Res. Hum. Retroviruses 26:913-918.
31. Tsibris AM, et al. 2009. Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. PLoS One 4:e5683. doi:10.1371/journal.pone.0005683.
32. Wawer MJ, et al. 1998. A randomized, community trial of intensive sexually transmitted disease control for AIDS prevention, Rakai, Uganda. AIDS 12:1211-1225. (Pubitemid 28302424)
33. Wolinsky SM, et al. 1996. Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 272: 537-542. (Pubitemid 26138195)
34. Zagordi O, Klein R, Daumer M, Beerenwinkel N. 2010. Error correction of next-generation sequencing data and reliable estimation of HIV quasi-species. Nucleic Acids Res. 38:7400-7409.
35. Zhang J, Chiodini R, Badr A, Zhang G. 2011. The impact of next-generation sequencing on genomics. J. Genet. Genomics 38:95-109.