Work

1 Analysis of intra-patient, full length HIV gagsequences identifies regions of variability

Year: 2016

Type: article

Abstract: Background: HIV Gag polyprotein is central to assembly, budding, and maturation of HIV virions, and there is substantial interest in Gag as a therapeutic target.Previously, maturation inhibitors have been limited by natural polymorphisms in gag.A more comprehensive analysis of intra-patient gag genetic variation, including linkage analysis is essential to inform novel approaches to therapeutics.As a first step, we developed a new single genome sequencing (SGS) assay to analyze full length HIV gag to investigate intra-patient genetic variation, localize regions of variability, and determine linkage patterns.Methods: Antiretroviral naïve individuals with detectable HIV RNA were recruited at NIH and Walter Reed National Military Medical Center and underwent phlebotomy.Plasma derived HIV RNA was subjected to cDNA synthesis and PCR primers were designed to amplify the entire 1.5kb fragment from upstream p17 through p6.SGS (9-21 sequences per patient) were aligned (CLUSTAL W), and subjected to phylogenetic (MEGA) and population genetics (DNASP) analyses.Results: Patients (N=22, median age 30 years, 37% non-white, median baseline CD4=568 cells/μl, median HIV RNA=3.9 log10 copies/ml) were enrolled, and 181 sequences from 13 patients have been analyzed thus far (average: 14 sequences/patient).Full length gag sequences were genetically diverse (average pairwise difference range 0.4% to 1.59%, one acute patient excluded).Although diversity was present throughout gag, most of the variation was attributed to p6.On the protein level, translated p6 sequences had significantly higher average pairwise difference (APD) compared to translated full length gag (1.7-fold p=0.041,Students t-test).Indels were common in p6, including PTAP duplications and contribute additional variability.Polymorphisms were common, (mean 45 segregating sites/patient dataset) but no significant linkage between gag polymorphisms was detected (Fisher's exact=NS, Bonferroni corrected).Conclusions: Intra-patient gag genetic diversity is substantial but overall variability is largely limited to p6.No significant linkage between polymorphic positions was detected, indicating that populations were in linkage equilibrium.Next generation sequencing approaches focusing on specific regions in gag will be useful in characterizing intra-patient diversity.

Source: Journal of Virus Eradication

DOI: 10.1016/s2055-6640(20)30946-8

Authors: E. Anderson, M. Gouzoulis, A. Ganesan, C. Rehm, S. Jones, F. Maldarelli

Institutions: National Cancer Institute, Walter Reed National Military Medical Center, National Institute of Allergy and Infectious Diseases, Leidos Biomedical Research Inc. (United States)

Language: English

Topic: HIV Research and Treatment

Subfield: Virology

Field: Immunology and Microbiology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $2,950