This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Holguín, A.
Right arrow Articles by Soriano, V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Holguín, A.
Right arrow Articles by Soriano, V.

 Previous Article  |  Next Article 

Journal of Clinical Microbiology, December 2008, p. 3896-3899, Vol. 46, No. 12
0095-1137/08/$08.00+0     doi:10.1128/JCM.00515-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Reliability of Rapid Subtyping Tools Compared to That of Phylogenetic Analysis for Characterization of Human Immunodeficiency Virus Type 1 Non-B Subtypes and Recombinant Forms{triangledown}

África Holguín,1,2* Marisa López,1 and Vincent Soriano1

Department of Infectious Diseases. Hospital Carlos III,1 HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Hospital Universitario Ramón y Cajal and CIBER-ESP, Madrid, Spain2

Received 17 March 2008/ Returned for modification 17 May 2008/ Accepted 30 September 2008

Human immunodeficiency virus type 1 (HIV-1) subtyping is often estimated on the basis of pol sequences by using online websites instead of phylogenetic analysis (phy). We evaluated the reliability of distinct rapid subtyping tools versus phy with a large panel of HIV-1 non-B subtypes and circulating recombinant forms (CRF). pol sequences (277 protease [PR] and 171 reverse transcriptase [RT] sequences) previously assigned by phy to eight distinct HIV-1 non-B subtypes were obtained from 277 HIV-infected patients. Phy was run again to identify CRF. Subtyping was then performed using three rapid tools (the Stanford, NCBI, and REGA online tools). Thirty-three additional clade B sequences were tested as controls. New phylogenetic analyses reclassified two-thirds of pol sequences previously assigned to HIV-1 non-B clades as CRF. CRF02_AG variants were correctly assigned by the Stanford and NCBI tools for 92 to 97% and 96 to 99% of PR-RT sequences, respectively, while they were correctly assigned by the REGA tool for only 18 to 32% of PR-RT sequences. The Stanford, NCBI, and REGA tools failed to assign pure non-B clades correctly for 24 to 33%, 35%, and 57 to 64% of PR-RT sequences, respectively. For PR-RT sequences from CRF other than CRF02_AG, discrepancies occurred in 98 to 100%, 18 to 43%, and 80 to 87% of sequences, respectively. The concordance between those tools and phy was almost complete for subtype B assignment. Rapid subtyping tools show relatively low agreement with phy in identifying HIV-1 non-B clades and CRF other than CRF02_AG. The Stanford tool shows the best concordance with phy for the assignment of pure non-B clades, while the NCBI tool performs better at identifying CRF. Before entering routine clinical use, rapid subtyping tools should be optimized and updated periodically. Larger numbers of different non-B subtypes and CRF sequences should be included.

* Corresponding author. Mailing address: HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Hospital Ramón y Cajal, Crta. Colmenar Viejo Km. 9.100, 28034, Madrid, Spain. Phone: 34-91-3368832. Fax: 34-91-3368809. E-mail: aholguin.hciii{at}salud.madrid.org

{triangledown} Published ahead of print on 8 October 2008.

Journal of Clinical Microbiology, December 2008, p. 3896-3899, Vol. 46, No. 12
0095-1137/08/$08.00+0     doi:10.1128/JCM.00515-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.





Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»