PMID: 12757914May 22, 2003Paper

Assessment of HIV-1 subtyping for Cameroon strains using phylogenetic analysis of pol gene sequences

Journal of Virological Methods
R NjouomJ Izopet

Abstract

Phylogenetic analysis of human immunodeficiency virus type 1 (HIV-1) pol gene is a useful method for subtyping European strains of HIV-1. The suitability of this method for genetically diverse African strains was evaluated by comparing HIV-1 subtyping of Cameroon strains using a long fragment of the pol gene sequence to the findings obtained using env gene sequences. When the pol gene could not be amplified, the reverse transcriptase (RT) or the protease (PR) genes were used. Phylogenetic analysis of the env C2/V3 gene sequences of 60 HIV-1 isolates showed 52 to be subtype A, 2 subtype G, plus one each of subtypes C, F2 and H, with 3 subtypes not determined. A long fragment of the pol gene was amplified successfully and sequenced in 23% of cases. The RT region was amplified for 42% of the samples that could not be typed by analysing the long fragment, and the PR gene was amplified for 40% of them. Thus, 63% of samples were typable. Env and pol gene subtypings were in agreement in 86% of cases. It is concluded that the phylogenetic analysis of pol gene sequences is not a practical method for HIV-1 subtyping in areas of high subtype diversity, despite the good agreement between the env and pol gene subtypings. However, it can be ...Continue Reading

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Citations

Aug 3, 2005·AIDS Research and Human Retroviruses·Magdi D SaadJean K Carr
Oct 9, 2007·AIDS Research and Human Retroviruses·Fabio TramutoUNKNOWN Group for HIV-1 Antiretroviral Studies in Sicily
Apr 24, 2007·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·J H K ChenW C Yam
May 11, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Andrea-Clemencia Pineda-PeñaAnne-Mieke Vandamme
Jun 9, 2006·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Hsi-Hsun LinLinqi Zhang
Jul 10, 2004·AIDS Research and Human Retroviruses·Frank A J Konings, Phillipe N Nyambi

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