Journal Mobile Options
Table of Contents
Vol. 55, No. 2, 2012
Issue release date: January 2012
Section title: Methods for HIV Resistance Determination and Interpretation
Intervirology 2012;55:134–137
(DOI:10.1159/000332010)

Description of Two Commercially Available Assays for Genotyping of HIV-1

Stürmer M. · Reinheimer C.
Johann Wolfgang Goethe-University Hospital, Institute for Medical Virology, Frankfurt, Germany
email Corresponding Author

Abstract

HIV-1 resistance testing is one important part in the diagnostics of antiretroviral treatment and is commonly done by genotyping. Currently, two systems are commercially available and, despite being far from easy to use, these have achieved a high degree of sophistication. Modifications of standard kit protocols might be necessary based on the clinical situation. Although resistance reports based on decision rules are a part of both systems, considerable knowledge and skills are nevertheless required by the user to establish useful clinical data out of detected resistance patterns. Both systems described here have their advantages and disadvantages; a decision for one or the other system needs to be based on individual requirements. The future might lie in so-called ‘next-generation sequencing’ systems based on pyrosequencing, which enable a high throughput and the detection of minor variants of less than 1%.

© 2012 S. Karger AG, Basel


  

Key Words

  • HIV-1
  • Genotyping
  • Drug resistance
  • Mutations
  • Assays

 Introduction

A major reason for keeping HIV replication as low as possible is to avoid the selection and emergence of resistant viral quasispecies carrying drug resistance-associated mutations (DRAMs). According to current treatment guidelines, first-line highly active antiretroviral combination therapy consists of at least 2 nucleoside reverse transcriptase inhibitors in combination with 1 protease (PR) inhibitor, normally boosted with ritonavir, or 1 nonnucleoside reverse transcriptase inhibitor:

Germany/DAIG:

www.daignet.de/site-content/hivtherapie/leitlinien-1/Leitlinien_28-05-2010_V_late.pdf

Europe/EACS:

www.europeanaidsclinicalsociety.org/images/stories/EACS-Pdf/1_treatment_of_hiv_infected_adults.pdf

USA/DHHS:

http://aidsinfo.nih.gov/contentfiles/

AdultandAdolescentGL.pdf.

However, some patients do not respond at all or only insufficiently to highly active antiretroviral combination therapy [1,2,3]. Poor adherence, maladsorption, other pharmacogenetic differences, or missing potency of the therapy regimen in the given patient context (high viral load, history of drug resistance) might contribute to insufficient drug levels allowing the virus to replicate in the presence of drugs and, consequently, might lead to the development of viral drug resistance [4,5]. In addition, the transmission of drug-resistant virus isolates in the context of primary HIV infection has been observed [6,7,8,9,10,11].

A crucial point in genotypic resistance testing is the accuracy of the test system used for the detection of DRAMs as well as the subsequent interpretation of the mutation pattern found. There are currently two commercial assays available for HIV-1 genotyping which can be performed in one’s own laboratory, the ViroSeq™ HIV-1 genotyping system version 2 (ViroSeq; Abbott GmbH, Wiesbaden, Germany) and the TruGene HIV-1 genotyping kit (TruGene; Siemens Healthcare Diagnostics GmbH, Eschborn, Germany) [12,13], both accompanied by interpretation programs employing rules-based algorithms. Although other assays are available, this review describes only these systems, and as they are most commonly used [14].

ViroSeq and TruGene are FDA-approved and – in the case of ViroSeq – CE-labeled systems for HIV-1 genotyping. They include modules for nucleic acid extraction (ViroSeq only), reverse transcription-polymerase chain reaction (RT-PCR), sequencing reaction and software for sequence alignment and drug resistance interpretation [12,13]. An automated sequencer for analyzing the sequencing products must be purchased separately; for ViroSeq capillary sequencers from Applied Biosystems Deutschland GmbH, Darmstadt, Germany, are suitable [15], the TruGene sequencing products were analyzed on the slab gel Opengene™ DNA sequencing system (Opengene), which is also available from Siemens [12,13].

The RNA extraction module supplied by ViroSeq is based on isopropanol precipitation, and both systems use two enzymes to reversely transcribe RNA into cDNA and to perform the subsequent PCR for target amplification. For ViroSeq, each RT-PCR reaction needs to be analyzed by agarose gel electrophoresis, a step not necessary when using TruGene. The sequencing reactions in both systems are based on the chain termination method by Sanger et al. [16], but use different chemistries. ViroSeq uses fluorescence-labeled chain terminators, each with a different dye. In conjunction with an automated sequencer capable of detecting the four different dyes, each sample can be sequenced in one tube. Seven primers (A–D forward direction; F–H reverse direction) are provided by ViroSeq to analyze the complete PR and most of the reverse transcriptase (RT) region (amino acids 1–335). The D primer is a backup primer in case of failure of the A primer, and has an overall poor performance rate [17,18,19,20]; therefore, we do not recommend using this primer in the initial testing. The TruGene system uses fluorescence-labeled primers; the complete PR and part of the RT (amino acids 38–247) are covered by 4 primer pairs, with differently labeled forward and reverse primers. The PR is covered by 2 primer pairs, but due to the pure performance of the PR primers, we recommend using only the P2 primer set [21]. Forward and reverse sequencing can be carried out in one tube, but each nucleotide must be analyzed in a separate reaction which means four reactions for each primer pair. The PCR product can be sequenced directly using the respective sequencing mix containing the sequencing primer, the CLIP™ reaction buffer, and the sequencing enzyme AmpliTaq FS. In contrast to ViroSeq, which needs a purification step to remove the not-incorporated chain terminators, no further purification steps are needed for TruGene, and the gel-loading buffer can be applied directly after the sequencing reaction is finished. Both systems are provided with sequence analysis software, which assembles all partial sequences for 1 patient into 1 project. They facilitate comparison with a drug-sensitive wild-type virus, editing of the consensus sequence and finally generate a drug resistance report with regard to the efficacy of the anti-HIV drugs.

To rule out a system-dependent bias in the detection of DRAMs, both systems have been compared extensively regarding general concordance, performance of the drug resistance reports and the detection of unusual insertions [22,23]. Both systems are comparable and no major discordances regarding the general performance have been described [14,24,25]. However, interpretation of DRAMs is a crucial point in the clinical application of genotypic resistance tests. It has been shown that using different interpretation systems on the same sequence results in varying resistance scores [26]. However, neither the ViroSeq nor the TruGene report was associated with serious errors in interpretation [27,28,29].

Additionally, ViroSeq and TruGene have been tested for performance in analyzing all group M subtypes [14,17,18,19,20,30,31]. Both assays are approved for the use in HIV subtype B only, and although subtype B is highly prevalent in Europe and North America, it represents only 11% of HIV-1 infections worldwide [32]. The performance in analyzing non-B subtypes is comparable for both systems, but a higher failure rate compared to subtype B has been reported. Adaptation to non-B subtypes might be a challenge for future updates.

Some modifications were necessary to take current clinical needs into account. Both systems are labeled for a viral load >1,000 copies/ml. Nowadays, clinical routine is quite different, and hence the commercial systems needed adaptations. Therefore, both assays have been tested intensely in terms of performance characteristics on different blood collection systems [33], including dried blood spot specimens [34,35,36], different extraction procedures [33,37,38,39,40] and modified PCR reactions [41]. Using dried blot samples as a source for genotyping is of major interest in the resource-limited setting. Both systems are able to reproducibly analyze samples with a viral load >10,000 copies/ml, which might be acceptable for resistance testing in this context. Modifications of the extraction procedure for ViroSeq and TruGene by either applying an ultracentrifugation step or by using sample preparation systems before the start of the procedure allow drug resistance testing in samples with viral loads down to 100 copies/ml.

As mentioned above, both the original ViroSeq and TruGene modules only cover the PR and RT regions. However, new antiretroviral drugs targeting different viral enzymes have been recently approved. Therefore, additional modules for analyzing the integrase region are available for TruGene and ViroSeq [42,43]; these modules are, however, for research only.

Taken together, we do not favor 1 system over the other. Among other things the individual choice for using ViroSeq or TruGene should depend on sample throughput and equipment which may already be available in the laboratory. Regardless of the system used, it has to be kept in mind that regular updates of the drug resistance reports are mandatory to include new drugs and/or newly described mutational pathways. Finally, all genotypic data should be accompanied by expert advice and need to be used only in the context of individual patient-related parameters including treatment history.


References

  1. d’Arminio Monforte A, Testa L, Adorni F, Chiesa E, Bini T, Moscatelli GC, Abeli C, Rusconi S, Sollima S, Balotta C, Musicco M, Galli M, Moroni M: Clinical outcome and predictive factors of failure of highly active antiretroviral therapy in antiretroviral-experienced patients in advanced stages of HIV-1 infection. AIDS 1998;12:1631–1637.
  2. van Roon EN, Verzijl JM, Juttmann JR, Lenderink AW, Blans MJ, Egberts AC: Incidence of discontinuation of highly active antiretroviral combination therapy (HAART) and its determinants. J Acquir Immune Defic Syndr Hum Retrovirol 1999;20:290–294.
  3. Wit FW, van Leeuwen R, Weverling GJ, Jurriaans S, Nauta K, Steingrover R, Schuijtemaker J, Eyssen X, Fortuin D, Weeda M, de Wolf F, Reiss P, Danner SA, Lange JM: Outcome and predictors of failure of highly active antiretroviral therapy: one-year follow-up of a cohort of human immunodeficiency virus type 1-infected persons. J Infect Dis 1999;179:790–798.
  4. Perrin L, Telenti A.: HIV treatment failure: testing for HIV resistance in clinical practice. Science 1998;280:1871–1873.
  5. Gallego O, Ruiz L, Vallejo A, Clotet B, Leal M, Soriano V: Rate of virological treatment failure and frequencies of drug resistance genotypes among human immunodeficiency virus-positive subjects on antiretroviral therapy in Spain. J Clin Microbiol 2002;40:3865–3866.
  6. Alexander CS, Dong W, Schechter MT, O’Shaughnessy MV, Strathdee SA, Mo T, Montaner JS, Harrigan PR: Prevalence of primary HIV drug resistance among seroconverters during an explosive outbreak of HIV infection among injecting drug users. AIDS 1999;13:981–985.
  7. Boden D, Hurley A, Zhang L, Cao Y, Guo Y, Jones E, Tsay J, Ip J, Farthing C, Limoli K, Parkin N, Markowitz M: HIV-1 drug resistance in newly infected individuals. JAMA 1999;282:1135–1141.
  8. Yerly S, Kaiser L, Race E, Bru JP, Clavel F, Perrin L: Transmission of antiretroviral-drug-resistant HIV-1 variants. Lancet 1999;354:729–733.
  9. Bartmeyer B, Kuecherer C, Houareau C, Werning J, Keeren K, Somogyi S, Kollan C, Jessen H, Dupke S, Hamouda O, German HIV-1 Seroconverter Study Group: Prevalence of transmitted drug resistance and impact of transmitted resistance on treatment success in the German HIV-1 Seroconverter Cohort. PLoS One 2010;5:e12718.
  10. Little SJ, Holte S, Routy JP, Daar ES, Markowitz M, Collier AC, Koup RA, Mellors JW, Connick E, Conway B, Kilby M, Wang L, Whitcomb JM, Hellmann NS, Richman DD: Antiretroviral-drug resistance among patients recently infected with HIV. N Engl J Med 2002;347:385–394.
  11. Wensing AM, Boucher CA: Worldwide transmission of drug-resistant HIV. AIDS Rev 2003;5:140–155.

    External Resources

  12. Wittek M, Stürmer M, Doerr HW, Berger A: Molecular assays for monitoring HIV infection and antiretroviral therapy (review). Expert Rev Mol Diagn 2007;7:237–246.
  13. Stürmer M, Berger A, Preiser W: HIV-1 genotyping: comparison of two commercially available assays. Expert Rev Mol Diagn 2004;4:281–291.
  14. Pandit A, Mackay WG, Steel C, van Loon AM, Schuurman R: HIV-1 drug resistance genotyping quality assessment: results of the ENVA7 Genotyping Proficiency Programme (review). J Clin Virol 2008;43:401–406.
  15. Eshleman SH, Crutcher G, Petrauskene O, Kunstman K, Cunningham SP, Trevino C, Davis C, Kennedy J, Fairman J, Foley B, Kop J: Sensitivity and specificity of the ViroSeq human immunodeficiency virus type 1 (HIV-1) genotyping system for detection of HIV-1 drug resistance mutations by use of an ABI PRISM 3100 genetic analyzer. J Clin Microbiol 2005;43:813–817.
  16. Sanger F, Nicklen S, Coulson AR: DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977;74:5463–5467.
  17. Fontaine E, Riva C, Peeters M, Schmit JC, Delaporte E, Van Laethem K, Van Vaerenbergh K, Snoeck J, Van Wijngaerden E, De Clercq E, Van Ranst M, Vandamme AM: Evaluation of two commercial kits for the detection of genotypic drug resistance on a panel of HIV type 1 subtypes A through J. J Acquir Immune Defic Syndr 2001;28:254–258.
  18. Mracna M, Becker-Pergola G, Dileanis J, Guay LA, Cunningham S, Jackson JB, Eshleman SH: Performance of Applied Biosystems ViroSeq HIV-1 Genotyping System for sequence-based analysis of non-subtype B human immunodeficiency virus type 1 from Uganda. J Clin Microbiol 2001;39:4323–4327.
  19. Jagodzinski LL, Cooley JD, Weber M, Michael NL: Performance characteristics of human immunodeficiency virus type 1 (HIV-1) genotyping systems in sequence-based analysis of subtypes other than HIV-1 subtype B. J Clin Microbiol 2003;41:998–1003.
  20. Aghokeng AF, Mpoudi-Ngole E, Chia JE, Edoul EM, Delaporte E, Peeters M: High failure rate of the ViroSeq HIV-1 genotyping system for drug resistance testing in Cameroon, a country with broad HIV-1 genetic diversity. J Clin Microbiol 2011;49:1635–1641.
  21. Ribas SG, Heyndrickx L, Ondoa P, Fransen K: Performance evaluation of the two protease sequencing primers of the TruGene HIV-1 genotyping kit. J Virol Methods 2006;135:137–142.
  22. Koch N, Tamalet C, Tivoli N, Fantini J, Yahi N: Comparison of two commercial assays for the detection of insertion mutations of HIV-1 reverse transcriptase. J Clin Virol 2001;21:153–162.
  23. Stürmer M, Staszewski S, Doerr HW, Hertogs K: A 6-base-pair insertion in the protease gene of HIV type 1 detected in a protease inhibitor-naive patient is not associated with indinavir treatment failure. AIDS Res Hum Retroviruses 2003;19:967–968.
  24. Erali M, Page S, Reimer LG, Hillyard DR: Human immunodeficiency virus type 1 drug resistance testing: a comparison of three sequence-based methods. J Clin Microbiol 2001;39:2157–2165.
  25. Grant RM, Kuritzkes DR, Johnson VA, Mellors JW, Sullivan JL, Swanstrom R, D’Aquila RT, Van Gorder M, Holodniy M, Lloyd RM Jr, Reid C, Morgan GF, Winslow DL: Accuracy of the TruGene HIV-1 genotyping kit. J Clin Microbiol 2003;41:1586–1593.
  26. Stürmer M, Doerr HW, Preiser W: Variety of interpretation systems for human immunodeficiency virus type 1 genotyping: confirmatory information or additional confusion? Curr Drug Targets Infect Disord 2003;3:373–382.
  27. Stürmer M, Doerr HW, Staszewski S, Preiser W: Comparison of nine resistance interpretation systems for HIV-1 genotyping. Antivir Ther 2003;8:239–244.
  28. Kijak GH, Rubio AE, Pampuro SE, Zala C, Cahn P, Galli R, Montaner JS, Salomón H: Discrepant results in the interpretation of HIV-1 drug-resistance genotypic data among widely used algorithms. HIV Med 2003;4:72–78.
  29. Torti C, Quiros-Roldan E, Keulen W, Scudeller L, Lo Caputo S, Boucher C, Castelli F, Mazzotta F, Pierotti P, Been-Tiktak AM, Buccoliero G, De Gennaro M, Carosi G, Tinelli C, GenPherex Study Group of the MaSTeR Cohort: Comparison between rules-based human immunodeficiency virus type 1 genotype interpretations and real or virtual phenotype: concordance analysis and correlation with clinical outcome in heavily treated patients. J Infect Dis 2003;188:194–201.
  30. Beddows S, Galpin S, Kazmi SH, Ashraf A, Johargy A, Frater AJ, White N, Braganza R, Clarke J, McClure M, Weber JN: Performance of two commercially available sequence-based HIV-1 genotyping systems for the detection of drug resistance against HIV type 1 group M subtypes. J Med Virol 2003;70:337–342.
  31. Eshleman SH, Hackett J Jr, Swanson P, Cunningham SP, Drews B, Brennan C, Devare SG, Zekeng L, Kaptué L, Marlowe N: Performance of the Celera Diagnostics ViroSeq HIV-1 genotyping system for sequence-based analysis of diverse human immunodeficiency virus type 1 strains. J Clin Microbiol 2004;42:2711–2717.
  32. Hemelaar J, Gouws E, Ghys PD, Osmanov S: Global trends in molecular epidemiology of HIV-1 during 2000–2007. WHO-UNAIDS Network for HIV Isolation and Characterisation. AIDS 2011;25:679–689.
  33. Kuritzkes DR, Grant RM, Feorino P, Griswold M, Hoover M, Young R, Day S, Lloyd RM Jr, Reid C, Morgan GF, Winslow DL: Performance characteristics of the TruGene HIV-1 genotyping kit and the Opengene DNA sequencing system. J Clin. Microbiol 2003;41:1594–1599.
  34. Hallack R, Doherty LE, Wethers JA, Parker MM: Evaluation of dried blood spot specimens for HIV-1 drug-resistance testing using the TruGene HIV-1 genotyping assay. J Clin Virol 2008;41:283–287.
  35. Johannessen A, Garrido C, Zahonero N, Naman E, de Mendoza C: HIV-1 drug resistance testing from dried blood spots collected in rural Tanzania using the ViroSeq HIV-1 genotyping system. J Antimicrob Chemother 2011;66:260–264.
  36. Lira R, Valdez-Salazar H, Vazquez-Rosales G, Rojas-Montes O, Ruiz-Tachiquin M, Torres-Ibarra R, Cano-Dominguez C, Maldonado-Rodríguez A, Gomez A, Muñoz O, Alvarez-Muñoz MT: Genotypic testing for HIV-1 drug resistance using dried blood samples. Arch Virol 2010;155:1117–1125.
  37. Stürmer M, Berger A, Doerr HW: Modifications and substitutions of the RNA extraction module in the ViroSeq HIV-1 genotyping system version 2: effects on sensitivity and complexity of the assay. J Med Virol 2003;71:475–479.
  38. Gale HB, Kan VL, Shinol RC: Performance of the TruGene human immunodeficiency virus type 1 genotyping kit and OpenGene DNA sequencing system on clinical samples diluted to approximately 100 copies per milliliter. Clin Vaccine Immunol 2006;13:235–238.
  39. Milia MG, Allice T, Gregori G, Mussino S, Orofino G, Bonora S, Ghisetti V: Magnetic silica-based nucleic acid extraction for human immunodeficiency virus type-1 drug-resistance testing in low viremic patients. J Clin Virol 2010;47:8–12.
  40. Stelzl E, Troppan KT, Winkler M, Korn K, Kessler HH: Optimized protocol for detection of HIV-1 drug mutations in patients with low viral load. J Virol Methods 2010;168:152–154.
  41. Elbeik T, Hoo BS, Campodonico ME, Dileanis J, Fay FF, Bortolozzi RL, Benetti MS, Fay OH, Marlowe N, Petrauskene O, Chernoff D, Smith L, Ng VL: In vivo emergence of drug-resistant mutations at less than 50 HIV-1 RNA copies/ml that are maintained at viral rebound in longitudinal plasma samples from human immunodeficiency virus type-1-infected patients on highly active antiretroviral therapy. J Hum Virol 2001;4:317–328.
  42. Paar C, Palmetshofer C, Flieger K, Geit M, Kaiser R, Stekel H, Berg J: Genotypic antiretroviral resistance testing for human immunodeficiency virus type 1 integrase inhibitors by use of the TruGene sequencing system. J Clin Microbiol 2008;46:4087–4090.
  43. Marlowe N, Smith P, Swanson P, Behlendorf D, Hackett J Jr, Young T: Feasibility of the ViroSeq HIV-1 integrase genotyping assay (RUO) on the 3500xL Genetic Analyser (abstract P_51). 9th European Workshop on HIV and Hepatitis Treatment Strategies and Antiviral Drug Resistance, Paphos, 2011.

  

Author Contacts

Martin Stürmer
Johann Wolfgang Goethe-University Hospital, Institute for Medical Virology
Paul-Ehrlich-Strasse 40
DE–60596 Frankfurt (Germany)
Tel. +49 69 6301 6454, E-Mail M.Stuermer@em.uni-frankfurt.de

  

Article Information

Published online: January 24, 2012
Number of Print Pages : 4
Number of Figures : 0, Number of Tables : 0, Number of References : 43

  

Publication Details

Intervirology (International Journal of Basic and Medical Virology)

Vol. 55, No. 2, Year 2012 (Cover Date: January 2012)

Journal Editor: Liebert U.G. (Leipzig)
ISSN: 0300-5526 (Print), eISSN: 1423-0100 (Online)

For additional information: http://www.karger.com/INT


Copyright / Drug Dosage / Disclaimer

Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher or, in the case of photocopying, direct payment of a specified fee to the Copyright Clearance Center.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in goverment regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.

Abstract

HIV-1 resistance testing is one important part in the diagnostics of antiretroviral treatment and is commonly done by genotyping. Currently, two systems are commercially available and, despite being far from easy to use, these have achieved a high degree of sophistication. Modifications of standard kit protocols might be necessary based on the clinical situation. Although resistance reports based on decision rules are a part of both systems, considerable knowledge and skills are nevertheless required by the user to establish useful clinical data out of detected resistance patterns. Both systems described here have their advantages and disadvantages; a decision for one or the other system needs to be based on individual requirements. The future might lie in so-called ‘next-generation sequencing’ systems based on pyrosequencing, which enable a high throughput and the detection of minor variants of less than 1%.

© 2012 S. Karger AG, Basel


  

Author Contacts

Martin Stürmer
Johann Wolfgang Goethe-University Hospital, Institute for Medical Virology
Paul-Ehrlich-Strasse 40
DE–60596 Frankfurt (Germany)
Tel. +49 69 6301 6454, E-Mail M.Stuermer@em.uni-frankfurt.de

  

Article Information

Published online: January 24, 2012
Number of Print Pages : 4
Number of Figures : 0, Number of Tables : 0, Number of References : 43

  

Publication Details

Intervirology (International Journal of Basic and Medical Virology)

Vol. 55, No. 2, Year 2012 (Cover Date: January 2012)

Journal Editor: Liebert U.G. (Leipzig)
ISSN: 0300-5526 (Print), eISSN: 1423-0100 (Online)

For additional information: http://www.karger.com/INT


Article / Publication Details

First-Page Preview
Abstract of Methods for HIV Resistance Determination and Interpretation

Published online: 1/24/2012
Issue release date: January 2012

Number of Print Pages: 4
Number of Figures: 0
Number of Tables: 0

ISSN: 0300-5526 (Print)
eISSN: 1423-0100 (Online)

For additional information: http://www.karger.com/INT


Copyright / Drug Dosage

Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher or, in the case of photocopying, direct payment of a specified fee to the Copyright Clearance Center.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in goverment regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.

References

  1. d’Arminio Monforte A, Testa L, Adorni F, Chiesa E, Bini T, Moscatelli GC, Abeli C, Rusconi S, Sollima S, Balotta C, Musicco M, Galli M, Moroni M: Clinical outcome and predictive factors of failure of highly active antiretroviral therapy in antiretroviral-experienced patients in advanced stages of HIV-1 infection. AIDS 1998;12:1631–1637.
  2. van Roon EN, Verzijl JM, Juttmann JR, Lenderink AW, Blans MJ, Egberts AC: Incidence of discontinuation of highly active antiretroviral combination therapy (HAART) and its determinants. J Acquir Immune Defic Syndr Hum Retrovirol 1999;20:290–294.
  3. Wit FW, van Leeuwen R, Weverling GJ, Jurriaans S, Nauta K, Steingrover R, Schuijtemaker J, Eyssen X, Fortuin D, Weeda M, de Wolf F, Reiss P, Danner SA, Lange JM: Outcome and predictors of failure of highly active antiretroviral therapy: one-year follow-up of a cohort of human immunodeficiency virus type 1-infected persons. J Infect Dis 1999;179:790–798.
  4. Perrin L, Telenti A.: HIV treatment failure: testing for HIV resistance in clinical practice. Science 1998;280:1871–1873.
  5. Gallego O, Ruiz L, Vallejo A, Clotet B, Leal M, Soriano V: Rate of virological treatment failure and frequencies of drug resistance genotypes among human immunodeficiency virus-positive subjects on antiretroviral therapy in Spain. J Clin Microbiol 2002;40:3865–3866.
  6. Alexander CS, Dong W, Schechter MT, O’Shaughnessy MV, Strathdee SA, Mo T, Montaner JS, Harrigan PR: Prevalence of primary HIV drug resistance among seroconverters during an explosive outbreak of HIV infection among injecting drug users. AIDS 1999;13:981–985.
  7. Boden D, Hurley A, Zhang L, Cao Y, Guo Y, Jones E, Tsay J, Ip J, Farthing C, Limoli K, Parkin N, Markowitz M: HIV-1 drug resistance in newly infected individuals. JAMA 1999;282:1135–1141.
  8. Yerly S, Kaiser L, Race E, Bru JP, Clavel F, Perrin L: Transmission of antiretroviral-drug-resistant HIV-1 variants. Lancet 1999;354:729–733.
  9. Bartmeyer B, Kuecherer C, Houareau C, Werning J, Keeren K, Somogyi S, Kollan C, Jessen H, Dupke S, Hamouda O, German HIV-1 Seroconverter Study Group: Prevalence of transmitted drug resistance and impact of transmitted resistance on treatment success in the German HIV-1 Seroconverter Cohort. PLoS One 2010;5:e12718.
  10. Little SJ, Holte S, Routy JP, Daar ES, Markowitz M, Collier AC, Koup RA, Mellors JW, Connick E, Conway B, Kilby M, Wang L, Whitcomb JM, Hellmann NS, Richman DD: Antiretroviral-drug resistance among patients recently infected with HIV. N Engl J Med 2002;347:385–394.
  11. Wensing AM, Boucher CA: Worldwide transmission of drug-resistant HIV. AIDS Rev 2003;5:140–155.

    External Resources

  12. Wittek M, Stürmer M, Doerr HW, Berger A: Molecular assays for monitoring HIV infection and antiretroviral therapy (review). Expert Rev Mol Diagn 2007;7:237–246.
  13. Stürmer M, Berger A, Preiser W: HIV-1 genotyping: comparison of two commercially available assays. Expert Rev Mol Diagn 2004;4:281–291.
  14. Pandit A, Mackay WG, Steel C, van Loon AM, Schuurman R: HIV-1 drug resistance genotyping quality assessment: results of the ENVA7 Genotyping Proficiency Programme (review). J Clin Virol 2008;43:401–406.
  15. Eshleman SH, Crutcher G, Petrauskene O, Kunstman K, Cunningham SP, Trevino C, Davis C, Kennedy J, Fairman J, Foley B, Kop J: Sensitivity and specificity of the ViroSeq human immunodeficiency virus type 1 (HIV-1) genotyping system for detection of HIV-1 drug resistance mutations by use of an ABI PRISM 3100 genetic analyzer. J Clin Microbiol 2005;43:813–817.
  16. Sanger F, Nicklen S, Coulson AR: DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977;74:5463–5467.
  17. Fontaine E, Riva C, Peeters M, Schmit JC, Delaporte E, Van Laethem K, Van Vaerenbergh K, Snoeck J, Van Wijngaerden E, De Clercq E, Van Ranst M, Vandamme AM: Evaluation of two commercial kits for the detection of genotypic drug resistance on a panel of HIV type 1 subtypes A through J. J Acquir Immune Defic Syndr 2001;28:254–258.
  18. Mracna M, Becker-Pergola G, Dileanis J, Guay LA, Cunningham S, Jackson JB, Eshleman SH: Performance of Applied Biosystems ViroSeq HIV-1 Genotyping System for sequence-based analysis of non-subtype B human immunodeficiency virus type 1 from Uganda. J Clin Microbiol 2001;39:4323–4327.
  19. Jagodzinski LL, Cooley JD, Weber M, Michael NL: Performance characteristics of human immunodeficiency virus type 1 (HIV-1) genotyping systems in sequence-based analysis of subtypes other than HIV-1 subtype B. J Clin Microbiol 2003;41:998–1003.
  20. Aghokeng AF, Mpoudi-Ngole E, Chia JE, Edoul EM, Delaporte E, Peeters M: High failure rate of the ViroSeq HIV-1 genotyping system for drug resistance testing in Cameroon, a country with broad HIV-1 genetic diversity. J Clin Microbiol 2011;49:1635–1641.
  21. Ribas SG, Heyndrickx L, Ondoa P, Fransen K: Performance evaluation of the two protease sequencing primers of the TruGene HIV-1 genotyping kit. J Virol Methods 2006;135:137–142.
  22. Koch N, Tamalet C, Tivoli N, Fantini J, Yahi N: Comparison of two commercial assays for the detection of insertion mutations of HIV-1 reverse transcriptase. J Clin Virol 2001;21:153–162.
  23. Stürmer M, Staszewski S, Doerr HW, Hertogs K: A 6-base-pair insertion in the protease gene of HIV type 1 detected in a protease inhibitor-naive patient is not associated with indinavir treatment failure. AIDS Res Hum Retroviruses 2003;19:967–968.
  24. Erali M, Page S, Reimer LG, Hillyard DR: Human immunodeficiency virus type 1 drug resistance testing: a comparison of three sequence-based methods. J Clin Microbiol 2001;39:2157–2165.
  25. Grant RM, Kuritzkes DR, Johnson VA, Mellors JW, Sullivan JL, Swanstrom R, D’Aquila RT, Van Gorder M, Holodniy M, Lloyd RM Jr, Reid C, Morgan GF, Winslow DL: Accuracy of the TruGene HIV-1 genotyping kit. J Clin Microbiol 2003;41:1586–1593.
  26. Stürmer M, Doerr HW, Preiser W: Variety of interpretation systems for human immunodeficiency virus type 1 genotyping: confirmatory information or additional confusion? Curr Drug Targets Infect Disord 2003;3:373–382.
  27. Stürmer M, Doerr HW, Staszewski S, Preiser W: Comparison of nine resistance interpretation systems for HIV-1 genotyping. Antivir Ther 2003;8:239–244.
  28. Kijak GH, Rubio AE, Pampuro SE, Zala C, Cahn P, Galli R, Montaner JS, Salomón H: Discrepant results in the interpretation of HIV-1 drug-resistance genotypic data among widely used algorithms. HIV Med 2003;4:72–78.
  29. Torti C, Quiros-Roldan E, Keulen W, Scudeller L, Lo Caputo S, Boucher C, Castelli F, Mazzotta F, Pierotti P, Been-Tiktak AM, Buccoliero G, De Gennaro M, Carosi G, Tinelli C, GenPherex Study Group of the MaSTeR Cohort: Comparison between rules-based human immunodeficiency virus type 1 genotype interpretations and real or virtual phenotype: concordance analysis and correlation with clinical outcome in heavily treated patients. J Infect Dis 2003;188:194–201.
  30. Beddows S, Galpin S, Kazmi SH, Ashraf A, Johargy A, Frater AJ, White N, Braganza R, Clarke J, McClure M, Weber JN: Performance of two commercially available sequence-based HIV-1 genotyping systems for the detection of drug resistance against HIV type 1 group M subtypes. J Med Virol 2003;70:337–342.
  31. Eshleman SH, Hackett J Jr, Swanson P, Cunningham SP, Drews B, Brennan C, Devare SG, Zekeng L, Kaptué L, Marlowe N: Performance of the Celera Diagnostics ViroSeq HIV-1 genotyping system for sequence-based analysis of diverse human immunodeficiency virus type 1 strains. J Clin Microbiol 2004;42:2711–2717.
  32. Hemelaar J, Gouws E, Ghys PD, Osmanov S: Global trends in molecular epidemiology of HIV-1 during 2000–2007. WHO-UNAIDS Network for HIV Isolation and Characterisation. AIDS 2011;25:679–689.
  33. Kuritzkes DR, Grant RM, Feorino P, Griswold M, Hoover M, Young R, Day S, Lloyd RM Jr, Reid C, Morgan GF, Winslow DL: Performance characteristics of the TruGene HIV-1 genotyping kit and the Opengene DNA sequencing system. J Clin. Microbiol 2003;41:1594–1599.
  34. Hallack R, Doherty LE, Wethers JA, Parker MM: Evaluation of dried blood spot specimens for HIV-1 drug-resistance testing using the TruGene HIV-1 genotyping assay. J Clin Virol 2008;41:283–287.
  35. Johannessen A, Garrido C, Zahonero N, Naman E, de Mendoza C: HIV-1 drug resistance testing from dried blood spots collected in rural Tanzania using the ViroSeq HIV-1 genotyping system. J Antimicrob Chemother 2011;66:260–264.
  36. Lira R, Valdez-Salazar H, Vazquez-Rosales G, Rojas-Montes O, Ruiz-Tachiquin M, Torres-Ibarra R, Cano-Dominguez C, Maldonado-Rodríguez A, Gomez A, Muñoz O, Alvarez-Muñoz MT: Genotypic testing for HIV-1 drug resistance using dried blood samples. Arch Virol 2010;155:1117–1125.
  37. Stürmer M, Berger A, Doerr HW: Modifications and substitutions of the RNA extraction module in the ViroSeq HIV-1 genotyping system version 2: effects on sensitivity and complexity of the assay. J Med Virol 2003;71:475–479.
  38. Gale HB, Kan VL, Shinol RC: Performance of the TruGene human immunodeficiency virus type 1 genotyping kit and OpenGene DNA sequencing system on clinical samples diluted to approximately 100 copies per milliliter. Clin Vaccine Immunol 2006;13:235–238.
  39. Milia MG, Allice T, Gregori G, Mussino S, Orofino G, Bonora S, Ghisetti V: Magnetic silica-based nucleic acid extraction for human immunodeficiency virus type-1 drug-resistance testing in low viremic patients. J Clin Virol 2010;47:8–12.
  40. Stelzl E, Troppan KT, Winkler M, Korn K, Kessler HH: Optimized protocol for detection of HIV-1 drug mutations in patients with low viral load. J Virol Methods 2010;168:152–154.
  41. Elbeik T, Hoo BS, Campodonico ME, Dileanis J, Fay FF, Bortolozzi RL, Benetti MS, Fay OH, Marlowe N, Petrauskene O, Chernoff D, Smith L, Ng VL: In vivo emergence of drug-resistant mutations at less than 50 HIV-1 RNA copies/ml that are maintained at viral rebound in longitudinal plasma samples from human immunodeficiency virus type-1-infected patients on highly active antiretroviral therapy. J Hum Virol 2001;4:317–328.
  42. Paar C, Palmetshofer C, Flieger K, Geit M, Kaiser R, Stekel H, Berg J: Genotypic antiretroviral resistance testing for human immunodeficiency virus type 1 integrase inhibitors by use of the TruGene sequencing system. J Clin Microbiol 2008;46:4087–4090.
  43. Marlowe N, Smith P, Swanson P, Behlendorf D, Hackett J Jr, Young T: Feasibility of the ViroSeq HIV-1 integrase genotyping assay (RUO) on the 3500xL Genetic Analyser (abstract P_51). 9th European Workshop on HIV and Hepatitis Treatment Strategies and Antiviral Drug Resistance, Paphos, 2011.