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Journal of Clinical Microbiology, September 2005, p. 4623-4627, Vol. 43, No. 9
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.9.4623-4627.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Genotyping of B and Non-B Subtypes of Human Immunodeficiency Virus Type 1

C. Y. W. Tong,1* J. Mullen,1 R. Kulasegaram,2 A. De Ruiter,2 S. O'Shea,1 and I. L. Chrystie1

Department of Infection,1 Department of Genitourinary Medicine, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom2

Received 13 April 2005/ Returned for modification 17 May 2005/ Accepted 1 June 2005

Current HIV-1 genotyping assays were developed using subtype B viruses prevalent in Western countries. It is not clear whether these assays are appropriate for use among African patients, who are likely to be infected with non-B subtypes. We evaluated the Bayer TRUGENE HIV-1 genotyping (TG) assay using prospectively collected samples from HIV-1-infected individuals who acquired infection in either sub-Saharan Africa or the West (Europe, North America, and Australia). Plasma samples from 208 individuals with an HIV-1 viral load of >1,000 copies/ml were tested using version 1 primers supplied with the TG assay. If these failed, an alternative primer set version 1.5 was used. Of the 208 individuals, the likely origin of infection was Africa (n = 104), Western (n = 87) and "Others" (i.e., all other geographic locations or origin not certain; n = 17). Among the three groups, the version 1 primers were successful in 85 (82%), 77 (89%), and 13 (76%) individuals, respectively (P = 0.1). Of the remaining 32 samples, 30 were successfully amplified by using the version 1.5 primers. HIV-1 subtypes deduced from the reverse transcriptase sequences correlated with the likely origin of infection: Africa (28A, 3B, 33C, 13D, 6G, 4J, 2K, 5CRF01_AE, and 10CRF02_AG), Western (86B and 1K), and Others (1A and 16B). The success of the version 1 primers correlated with viral load (P < 0.014) and not with HIV-1 subtypes. A protocol based on version 1 primers, followed by 1.5 primers, was successful in sequencing 99% of the samples in this cohort.

* Corresponding author. Mailing address: Department of Infection, 5th Floor, North Wing, St. Thomas' Hospital, London SE1 7EH, United Kingdom. Phone: 44 (20) 71883147. Fax: 44 (20) 71883146. E-mail: william.tong{at}gstt.nhs.uk.

Journal of Clinical Microbiology, September 2005, p. 4623-4627, Vol. 43, No. 9
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.9.4623-4627.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Perrin, L., Pawlotsky, J. M., Bouvier-Alias, M., Sarrazin, C., Zeuzem, S., Colucci, G. (2006). Multicenter Performance Evaluation of a New TaqMan PCR Assay for Monitoring Human Immunodeficiency Virus RNA Load. J. Clin. Microbiol. 44: 4371-4375 [Abstract] [Full Text]  


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