Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy
Genre
Journal ArticleDate
2018-12-18Author
Tzou, PLRhee, SY
Pond, SLK
Manasa, J
Shafer, RW
Subject
Anti-HIV AgentsHIV Envelope Protein gp41
HIV Infections
HIV-1
Humans
Mutation
Sequence Analysis, Protein
Sequence Analysis, RNA
gag Gene Products, Human Immunodeficiency Virus
Permanent link to this record
http://hdl.handle.net/20.500.12613/4621
Metadata
Show full item recordDOI
10.1038/sdata.2018.147Abstract
© 2018, The Author(s). Most HIV-1-infected individuals with virological failure on a pharmacologically-boosted protease inhibitor (PI) regimen do not develop PI-resistance protease mutations. One proposed explanation is that HIV-1 gag or gp41 cytoplasmic domain mutations might also reduce PI susceptibility. In a recent study of paired gag and gp41 sequences from individuals with virological failure on a PI regimen, we did not identify PI-selected mutations and concluded that if such mutations existed, larger numbers of paired sequences from multiple studies would be needed for their identification. In this study, we generated site-specific amino acid profiles using gag and gp41 published sequences from 5,338 and 4,242 ART-naïve individuals, respectively, to assist researchers identify unusual mutations arising during therapy and to provide scripts for performing established and novel maximal likelihood estimates of dN/dS substitution rates in paired sequences. The pipelines used to generate the curated sequences, amino acid profiles, and dN/dS analyses will facilitate the application of consistent methods to paired gag and gp41 sequence datasets and expedite the identification of potential sites under PI-selection pressure.Citation to related work
Springer Science and Business Media LLCHas part
Scientific DataADA compliance
For Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.eduae974a485f413a2113503eed53cd6c53
http://dx.doi.org/10.34944/dspace/4603