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Routine HIV-1 genotyping as a tool to identify dual infections

Cornelissen, Mariona; Jurriaans, Suzannea; Kozaczynska, Karolinaa; Prins, Jan Mb; Hamidjaja, Raditijo Aa; Zorgdrager, Foklaa; Bakker, Margreeta; Back, Nicolea; van der Kuyl, Antoinette Ca

doi: 10.1097/QAD.0b013e3280f3c08a
Basic Science

Objectives: The incidence of HIV-1 dual infections is generally thought to be low, but as dual infections have been associated with accelerated disease progression, its recognition is clinically important. Methods to identify HIV-1 dual infections are time consuming and are not routinely performed.

Design: Genotyping of the HIV-1 protease and reverse transcriptase (prot/RT) genes is commonly performed in the western world to detect drug-resistance mutations in clinical isolates. In our hospital, prot/RT baseline sequencing is part of the patient care for all newly infected patients in the Amsterdam region since 2003. We reasoned that degenerate base codes in this sequence could indicate either extensive viral evolution or infection with multiple HIV-1 strains.

Methods: We amplified, cloned and sequenced multiple HIV-1 envelope (env)-V3 and gag sequences from patients with 34 or more (range 34–99) degenerate base codes in the ViroSeq genotyping RT sequence (37 out of 1661 available records) to estimate the number of HIV-1 dual infections in this group.

Results: Of the 37 patients included in this study, 16 (43.2%, equal to 1% of the 1661 total records) had an HIV-1 dual infection based on phylogenetic analysis of env-V3/gag sequences. If only sequences with 45 or more degenerate base codes were taken into account, 73.3% of patients showed evidence of a dual infection.

Conclusion: We describe an additional use of routinely performed HIV-1 genotyping. In patients with a high number of degenerate bases (≥ 34) in RT it is important to consider the possibility of a dual HIV-1 infection.

From the aLaboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam, Amsterdam, the Netherlands

bDepartment of Internal Medicine, Division of Infectious Diseases, Tropical Medicine and AIDS, Academic Medical Centre of the University of Amsterdam, Amsterdam, the Netherlands.

Received 1 June, 2006

Revised 24 August, 2006

Accepted 6 September, 2006

Correspondence to Antoinette C. van der Kuyl, Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre of the University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands. Tel: +31 20 5666778; fax: +31 20 5669064; e-mail:

© 2007 Lippincott Williams & Wilkins, Inc.