High concordance of genotypic coreceptor prediction in plasma-viral RNA and proviral DNA of HIV-1 subtype C: Implications for use of whole blood DNA in resource-limited settings

Journal of Antimicrobial Chemotherapy

Volumn 68, Issue 9, 2013, Pages 2003-2006

  Gupta, Soham ^a   Neogi, Ujjwal ^a,b   Srinivasa, Hiresave ^a   Shet, Anita ^a,b  

^a ST JOHN'S NATIONAL ACADEMY OF HEALTH SCIENCES   (India)

^b KAROLINSKA INSTITUTE   (Sweden)

Author keywords

Geno2Pheno; Genotypic tropism testing; HIV

Indexed keywords

VIRUS DNA; VIRUS RNA;

ALGORITHM; ARTICLE; DNA RNA HYBRIDIZATION; DNA VIRUS; GENOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; MAJOR CLINICAL STUDY; PERSONAL EXPERIENCE; PROVIRUS; RNA VIRUS; TROPISM; VIRUS LOAD;

GENO2PHENO; GENOTYPIC TROPISM TESTING; HIV;

ADULT; BLOOD; CHILD; CLINICAL LABORATORY TECHNIQUES; DNA, VIRAL; FEMALE; GENOTYPE; HIV-1; HUMANS; INDIA; MALE; MIDDLE AGED; RECEPTORS, HIV; RNA, VIRAL; VIRAL TROPISM; VIROLOGY; VIRUS ATTACHMENT; YOUNG ADULT;

EID: 84882581615     PISSN: 03057453     EISSN: 14602091     Source Type: Journal    
DOI: 10.1093/jac/dkt138     Document Type: Article

References (20)

1. Verhofstede C, Nijhuis M, Vandekerckhove L. Correlation of coreceptor usage and disease progression. Curr Opin HIV AIDS 2012; 7: 432-9.
2. Vandekerckhove LP, Wensing AM, Kaiser R et al. European guidelines on the clinical management of HIV-1 tropism testing. Lancet Infect Dis 2011; 11: 394-407.
3. Obermeier MJ, Carganico S, Dupke S et al. Clinical application of genotypic co-receptor tropism testing from viral RNA and proviral DNA: week 24 analysis of the Berlin maraviroc cohort. J Int AIDS Soc 2010; 13 Suppl 4: P129.
4. Lengauer T, Sander O, Sierra S et al. Bioinformatics prediction of HIV coreceptor usage. Nat Biotechnol 2007; 25: 1407-10.
5. Prosperi MC, Bracciale L, Fabbiani M et al. Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping. Retrovirology 2010; 7: 56.
6. Verhofstede C, Brudney D, Reynaerts J et al. Concordance between HIV-1 genotypic coreceptor tropism predictions based on plasma RNA and proviral DNA. HIV Med 2011; 12: 544-52.
7. Parisi SG, Andreoni C, Sarmati L et al. HIV coreceptor tropism in paired plasma, peripheral blood mononuclear cell, and cerebrospinal fluid isolates from antiretroviral-naive subjects. J ClinMicrobiol 2011; 49: 1441-5.
8. Raymond S, Delobel P, Mavigner M et al. Prediction of HIV type 1 subtype C tropism by genotypic algorithms built from subtype B viruses. J Acquir Immune Defic Syndr 2010; 53: 167-75.
9. Neogi U, Bontell I, Shet A et al. Molecular epidemiology of HIV-1 subtypes in India: origin and evolutionary history of the predominant subtype C. PLoS One 2012; 7: e39819.
10. Neogi U, Sahoo PN, Arumugam K et al. Higher prevalence of predicted X4-tropic strains in perinatally infected older children with HIV-1 subtype C in India. J Acquir Immune Defic Syndr 2012; 59: 347-53.
11. Svicher V, Alteri C, Montano M et al. Performance of genotypic tropism testing on proviral DNA in clinical practice: results from the DIVA study group. New Microbiol 2012; 35: 17-25.
12. Baroncelli S, Galluzzo CM, Weimer LE et al. Evolution of proviral DNA HIV-1 tropism under selective pressure of maraviroc-based therapy. J Antimicrob Chemother 2012; 67: 1479-85.
13. Seclen E, Del Mar Gonzalez M, De Mendoza C et al. Dynamics of HIV tropism under suppressive antiretroviral therapy: implications for tropism testing in subjects with undetectable viraemia. J Antimicrob Chemother 2010; 65: 1493-6.
14. Soulie C, Fourati S, Lambert-Niclot S et al. Factors associated with proviral DNA HIV-1 tropism in antiretroviral therapy-treated patients with fully suppressed plasma HIV viral load: implications for the clinical use of CCR5 antagonists. J Antimicrob Chemother 2010; 65: 749-51.
15. Swenson LC, Dong WW, Mo T et al. Use of cellular HIV DNA to predict virologic response to maraviroc: performance of population-based and deep sequencing. Clin Infect Dis 2013; doi:10.1093/cid/cit105.
16. Paar C, Geit M, Stekel H et al. Genotypic prediction of human immunodeficiency virus type 1 tropism by use of plasma and peripheral blood mononuclear cells in the routine clinical laboratory. J Clin Microbiol 2011; 49: 2697-9.
17. Saracino A, Monno L, Punzi G et al. HIV-1 biological phenotype and predicted coreceptor usage based on V3 loop sequence in paired PBMC and plasma samples. Virus Res 2007; 130: 34-42.
18. Verhofstede C, Vandekerckhove L, Eygen VV et al. CXCR4-using HIV type 1 variants are more commonly found in peripheral blood mononuclear cell DNA than in plasma RNA. J Acquir Immune Defic Syndr 2009; 50: 126-36.
19. Sanchez V, Masia M, Robledano C et al. Performance of genotypic algorithms for predicting HIV-1 tropism measured against the enhanced-sensitivity Trofile coreceptor tropism assay. J Clin Microbiol 2010; 48: 4135-9.
20. 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.