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Antimicrobial Agents and Chemotherapy, February 2006, p. 694-701, Vol. 50, No. 2
0066-4804/06/$08.00+0     doi:10.1128/AAC.50.2.694-701.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Discordances between Interpretation Algorithms for Genotypic Resistance to Protease and Reverse Transcriptase Inhibitors of Human Immunodeficiency Virus Are Subtype Dependent

Joke Snoeck,¹ Rami Kantor,² Robert W. Shafer,² Kristel Van Laethem,¹ Koen Deforche,¹ Ana Patricia Carvalho,³ Brian Wynhoven,⁴ Marcelo A. Soares,⁵ Patricia Cane,⁶ John Clarke,⁷ Candice Pillay,⁸ Sunee Sirivichayakul,⁹ Koya Ariyoshi,¹⁰ Africa Holguin,¹¹ Hagit Rudich,¹² Rosangela Rodrigues,¹³ Maria Belen Bouzas,¹⁴ Françoise Brun-Vézinet,¹⁵ Caroline Reid,¹⁶ Pedro Cahn,¹⁴ Luis Fernando Brigido,¹³ Zehava Grossman,¹² Vincent Soriano,¹¹ Wataru Sugiura,¹⁰ Praphan Phanuphak,⁹ Lynn Morris,⁸ Jonathan Weber,⁷ Deenan Pillay,¹⁷ Amilcar Tanuri,⁵ Richard P. Harrigan,⁴ Ricardo Camacho,³ Jonathan M. Schapiro,¹⁸ David Katzenstein,² and Anne-Mieke Vandamme^1*

Rega Institute for Medical Research, Leuven, Belgium,¹ Stanford University, Stanford, California,² Hospital Egas Moniz, Lisbon, Portugal,³ BC Center for Excellence in HIV/AIDS, Vancouver, Canada,⁴ Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil,⁵ Health Protection Agency, Salisbury, United Kingdom,⁶ Wright Fleming Institute, London, United Kingdom,⁷ National Institute for Communicable Diseases, Johannesburg, South Africa,⁸ Chulalongkorn University, Bangkok, Thailand,⁹ National Institute of Infectious Diseases, Tokyo, Japan,¹⁰ Hospital Carlos III, Madrid, Spain,¹¹ Ministry of Health, Tel Aviv, Israel,¹² Instituto Adolfo Lutz, Sao Paulo, Brazil,¹³ Fundación Huesped, Buenos Aires, Argentina,¹⁴ Laboratory of Virology, Bichat, Claude Bernard Hospital, Paris, France,¹⁵ Bayer Health Care-Diagnostics, Toronto, Canada,¹⁶ HPA Antiviral Susceptibility Reference Unit, Birmingham, United Kingdom,¹⁷ National Hemophilia Center, Sheba Medical Center, Tel Aviv, Israel,¹⁸

Received 5 May 2005/ Returned for modification 25 August 2005/ Accepted 26 November 2005

The major limitation of drug resistance genotyping for human immunodeficiency virus remains the interpretation of the results. We evaluated the concordance in predicting therapy response between four different interpretation algorithms (Rega 6.3, HIVDB-08/04, ANRS [07/04], and VGI 8.0). Sequences were gathered through a worldwide effort to establish a database of non-B subtype sequences, and demographic and clinical information about the patients was gathered. The most concordant results were found for nonnucleoside reverse transcriptase (RT) inhibitors (93%), followed by protease inhibitors (84%) and nucleoside RT inhibitor (NRTIs) (76%). For therapy-naive patients, for nelfinavir, especially for subtypes C and G, the discordances were driven mainly by the protease (PRO) mutational pattern 82I/V + 63P + 36I/V for subtype C and 82I + 63P + 36I + 20I for subtype G. Subtype F displayed more discordances for ritonavir in untreated patients due to the combined presence of PRO 20R and 10I/V. In therapy-experienced patients, subtype G displayed a lot of discordances for saquinavir and indinavir due to mutational patterns involving PRO 90 M and 82I. Subtype F had more discordance for nelfinavir attributable to the presence of PRO 88S and 82A + 54V. For the NRTIs lamivudine and emtricitabine, CRF01_AE had more discordances than subtype B due to the presence of RT mutational patterns 65R + 115 M and 118I + 215Y, respectively. Overall, the different algorithms agreed well on the level of resistance scored, but some of the discordances could be attributed to specific (subtype-dependent) combinations of mutations. It is not yet known whether therapy response is subtype dependent, but the advice given to clinicians based on a genotypic interpretation algorithm differs according to the subtype.

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* Corresponding author. Mailing address: Rega Institute for Medical Research, Minderbroedersstraat 10, 3000 Leuven, Belgium. Phone: 32 16332160. Fax: 32 16332131. E-mail: annemie.vandamme{at}uz.kuleuven.ac.be.

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Antimicrobial Agents and Chemotherapy, February 2006, p. 694-701, Vol. 50, No. 2
0066-4804/06/$08.00+0     doi:10.1128/AAC.50.2.694-701.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

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