A reliable phenotype predictor for human immunodeficiency virus type 1 subtype C based on envelope V3 sequences.

Journal of Virology
Mark A JensenJames I Mullins

Abstract

In human immunodeficiency virus type 1 (HIV-1) subtype B infections, the emergence of viruses able to use CXCR4 as a coreceptor is well documented and associated with accelerated CD4 decline and disease progression. However, in HIV-1 subtype C infections, responsible for more than 50% of global infections, CXCR4 usage is less common, even in individuals with advanced disease. A reliable phenotype prediction method based on genetic sequence analysis could provide a rapid and less expensive approach to identify possible CXCR4 variants and thus increase our understanding of subtype C coreceptor usage. For subtype B V3 loop sequences, genotypic predictors have been developed based on position-specific scoring matrices (PSSM). In this study, we apply this methodology to a training set of 279 subtype C sequences of known phenotypes (228 non-syncytium-inducing [NSI] CCR5(+) and 51 SI CXCR4(+) sequences) to derive a C-PSSM predictor. Specificity and sensitivity distributions were estimated by combining data set bootstrapping with leave-one-out cross-validation, with random sampling of single sequences from individuals on each bootstrap iteration. The C-PSSM had an estimated specificity of 94% (confidence interval [CI], 92% to 96%) and ...Continue Reading

References

Oct 25, 1990·Nucleic Acids Research·T D Schneider, R M Stephens
May 1, 1994·The Journal of Infectious Diseases·D D Richman, S A Bozzette
Jan 24, 1998·Nature·E A BergerR A Weiss
Mar 20, 2003·AIDS Research and Human Retroviruses·Satish PillaiJacques Corbeil

❮ Previous
Next ❯

Citations

Jun 10, 2008·Nature Biotechnology·Mark A Jensen
Feb 2, 2012·Journal of Biomolecular Structure & Dynamics·Balasubramanian ChandramouliAlessandro Desideri
Aug 11, 2012·Journal of Biomolecular Structure & Dynamics·Balasubramanian ChandramouliAlessandro Desideri
May 1, 2008·The Journal of Infectious Diseases·Jessica D ChurchSusan H Eshleman
Mar 3, 2007·AIDS Research and Human Retroviruses·Mia CoetzerLynn Morris
Feb 15, 2008·AIDS Research and Human Retroviruses·Maria LahuertaDenise Naniche
Feb 1, 2007·AIDS Research and Human Retroviruses·J A M BrandfulP L Moore
Sep 10, 2011·AIDS Research and Human Retroviruses·Somi Sankaran PrakashKalpana Luthra
Jul 3, 2013·AIDS Research and Human Retroviruses·Chris A KieslichDimitrios Morikis
Apr 27, 2013·AIDS Research and Human Retroviruses·Anthony Kebira NyamacheSamoel A Khamadi
Jun 4, 2013·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·E Liana FalconeH Clifford Lane
Mar 21, 2013·The Journal of Antimicrobial Chemotherapy·Francisco Díez-FuertesMichael M Thomson
Jan 6, 2010·Current Opinion in HIV and AIDS·Nina H Lin, Daniel R Kuritzkes
Apr 23, 2008·AIDS·Bridgette J ConnellMaria A Papathanasopoulos
Dec 22, 2010·AIDS·Rebecca R GrayMaureen M Goodenow
Oct 6, 2010·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Mia CoetzerDonald E Mosier
May 21, 2010·Journal of Clinical Microbiology·L SarmatiM Andreoni
May 15, 2009·Journal of Clinical Microbiology·Stéphanie RaymondJacques Izopet
Apr 6, 2007·Journal of Virology·E S GrayUNKNOWN CAPRISA 002 Study Team
Feb 15, 2013·Journal of Virology·Penny L MooreLynn Morris
Mar 4, 2008·BMC Infectious Diseases·Job C J CalisMarion Cornelissen
Feb 10, 2011·Journal of Translational Medicine·Hanneke SchuitemakerPaolo Lusso
Apr 3, 2007·PLoS Computational Biology·Oliver SanderFrancisco S Domingues
Jun 17, 2010·PloS One·Concepción CasadoCecilio López-Galíndez

❮ 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.