Using ultradeep pyrosequencing to study HIV-1 coreceptor usage in primary and dual infection

Journal of Infectious Diseases

Volumn 208, Issue 2, 2013, Pages 271-274

  Wagner, Gabriel A ^a   Pacold, Mary E ^b   Vigil, Edgar ^a   Caballero, Gemma ^c   Morris, Sheldon R ^a   Kosakovsky Pond, Sergei L ^a   Little, Susan J ^a   Richman, Douglas D ^a,c   Gianella, Sara ^a   Smith, Davey M ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Life Technologies Corporation   (United States)

^c VA SAN DIEGO HEALTHCARE SYSTEM   (United States)

Author keywords

coreceptor tropism; coreceptor usage; genotypic coreceptor usage prediction; genotypic tropism prediction; HIV 1 coinfection; HIV 1 dual infection; HIV 1 superinfection; next generation sequencing; ultradeep pyrosequencing

Indexed keywords

CHEMOKINE RECEPTOR CXCR4; COMPLEMENTARY DNA;

ADULT; ARTICLE; BLOOD SAMPLING; CD4 LYMPHOCYTE COUNT; CONTROLLED STUDY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; HUMAN IMMUNODEFICIENCY VIRUS INFECTED PATIENT; INFECTION RISK; INFECTIONS ASSOCIATED WITH OTHER INFECTIONS OR CONDITIONS; MAJOR CLINICAL STUDY; MALE; MEN WHO HAVE SEX WITH MEN; MIXED INFECTION; MONOINFECTION; PHYLOGENY; PRIMARY INFECTION; PRIORITY JOURNAL; PYROSEQUENCING; RISK ASSESSMENT; RISK FACTOR; SUPERINFECTION; VIRUS STRAIN;

CORECEPTOR TROPISM; CORECEPTOR USAGE; GENOTYPIC CORECEPTOR USAGE PREDICTION; GENOTYPIC TROPISM PREDICTION; HIV-1 COINFECTION; HIV-1 DUAL INFECTION; HIV-1 SUPERINFECTION; NEXT-GENERATION SEQUENCING; ULTRADEEP PYROSEQUENCING;

ADULT; HIV INFECTIONS; HIV-1; HUMANS; MALE; RECEPTORS, CXCR4; SEQUENCE ANALYSIS, DNA;

EID: 84879391764     PISSN: 00221899     EISSN: None     Source Type: Journal    
DOI: 10.1093/infdis/jit168     Document Type: Article

References (13)

1. Smith DM, Richman DD, Little SJ. HIV superinfection. J Infect Dis 2005; 192:438-44 (Pubitemid 41023122)
2. Pacold ME, Pond SL, Wagner GA, et al. Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men. AIDS 2012; 26:157-65
3. Chalmet K, Dauwe K, Foquet L, et al. Presence of CXCR4-using HIV-1 in patients with recently diagnosed infection: correlates and evidence for transmission. J Infect Dis 2012; 205:174-84
4. Richman DD, Bozzette SA. The impact of the syncytium-inducing phenotype of human immunodeficiency virus on disease progression. J Infect Dis 1994; 169:968-74 (Pubitemid 24303213)
5. Bozzette SA, McCutchan JA, Spector SA, Wright B, Richman DD. A cross-sectional comparison of persons with syncytium- and nonsyncytium- inducing human immunodeficiency virus. J Infect Dis 1993; 168:1374-9 (Pubitemid 23344894)
6. Thielen A, Lengauer T. Geno2pheno[454]: a Web server for the prediction of HIV-1 coreceptor usage from next-generation sequencing data. Intervirology 2012; 55:113-7
7. Little SJ, Frost SD,Wong JK, et al. Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection. J Virol 2008; 82:5510-8 (Pubitemid 351705258)
8. Gianella S, Delport W, Pacold ME, et al. Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants. J Virol 2011; 85:8359-67
9. Mild M, Hedskog C, Jernberg J, Albert J. Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation. PLoS One 2011; 6:e22741
10. Swenson LC, Moores A, Low AJ, et al. Improved detection of CXCR4- using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA. J Acquir Immune Defic Syndr 2010; 54:506-10
11. Daumer M, Kaiser R, Klein R, Lengauer T, Thiele B, Thielen A. Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis. BMC Med Inform Decis Mak 2011; 11:30
12. Swenson LC, Mo T, Dong WW, et al. Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients. J Infect Dis 2011; 203:237-45
13. Hughes JP, Totten P. Estimating the accuracy of polymerase chain reactionbased tests using endpoint dilution. Biometrics 2003; 59:505-11. (Pubitemid 37093389)