PMID: 11337039May 5, 2001Paper

HIV-1 subtyping using phylogenetic analysis of pol gene sequences

Journal of Virological Methods
Christophe PasquierJacques Izopet

Abstract

HIV-1 pol gene sequencing is now used routinely in France to identify mutations associated with resistance to reverse transcriptase (RT) or protease (PR) inhibitors. These sequences may also provide other information, such as the HIV-1 subtype. HIV-1 subtyping was compared using the RT and PR gene sequences to heteroduplex mobility assay (HMA) of the envelope gene. The RT and PR genes of 51 samples that had been subtyped earlier by HMA were sequenced. Sequences were aligned and subtypes were determined by phylogenetic analysis with reference HIV sequences. HMA gave the following subtypes: A (20), B (19), C (1), D (3), F (1), G (3) and CRF01-AE (4). Phylogenetic analysis of the RT gene gave: A (5), B (19), C (2), D (3), F (1), G (6), J (2), CRF01_AE (4), CFR02_AG (7) and undetermined (2). PR gene analysis did not infer subtypes with sufficient confidence. HMA and RT subtyping was not in agreement in nine cases. RT subtyping can identify CFR02_AG and CRF01_AE variants from A subtype RT. It was shown that phylogenetic analysis of the RT gene could provide a useful method for HIV-1 subtyping. The length of the amplicon and the relative performance of each primer pair used in this study favoured RT sequences as a subtyping tool. One...Continue Reading

References

May 18, 1989·Nature·S Kwok, R Higuchi
Apr 1, 1995·PCR Methods and Applications·E L DelwartJ I Mullins
Jan 1, 1996·Trends in Microbiology·B D Preston, J P Dougherty
Dec 22, 1998·Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology : Official Publication of the International Retrovirology Association·J IzopetJ Puel
Apr 15, 2000·Science·D L RobertsonB Korber
Nov 16, 2002·Proceedings of the National Academy of Sciences of the United States of America·Ruy M RibeiroAlan S Perelson

❮ Previous
Next ❯

Citations

May 22, 2003·Journal of Virological Methods·Richard NjouomJacques Izopet
Jan 17, 2008·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Patrick A CoffieFrançois Dabis
Nov 7, 2003·AIDS Research and Human Retroviruses·H E VaughanR S Tedder
Apr 5, 2013·AIDS Research and Human Retroviruses·Florian LiégeoisFrançois Rouet
Dec 12, 2012·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Marie-Laure ChaixUNKNOWN ANRS PRIMO Cohort Study Group
Sep 17, 2010·The Journal of Antimicrobial Chemotherapy·Jean-Luc MeynardUNKNOWN KALESOLO Study Group
May 29, 2004·AIDS·Olivier LambotteJean-François Delfraissy
Mar 8, 2005·AIDS·Jean-Christophe PlantierFrançois Simon
Feb 16, 2007·AIDS·Bruno MarchouUNKNOWN ANRS 106 Study team
Aug 17, 2002·Antimicrobial Agents and Chemotherapy·Bernard MasquelierUNKNOWN Groupe d' Epidémiologie Clinique du SIDA en Aquitaine
Jan 4, 2007·BMC Bioinformatics·Gilles DidierIvan Laprevotte
Jun 16, 2011·Bulletin of the World Health Organization·Boubacar NacroPhilippe Msellati
Jan 14, 2005·Journal of Medical Virology·Africa HolguínVincent Soriano
Dec 24, 2005·Journal of Medical Virology·Diane DescampsDominique Costagliola
Oct 16, 2013·Journal of Medical Virology·Augustin Mouinga-OndéméFrançois Rouet
May 25, 2005·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Diane DescampsFrançoise Brun-Vézinet
Oct 7, 2004·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Africa HolguínVincent Soriano
Jun 13, 2006·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Africa HolguínThomas Klimkait

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.