Unknown

Dataset Information

0

Characterization of APOBEC3 variation in a population of HIV-1 infected individuals in northern South Africa.


ABSTRACT: BACKGROUND:The apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3 (APOBEC3) genes A3D, A3F, A3G and A3H have all been implicated in the restriction of human immunodeficiency virus type 1 (HIV-1) replication. Polymorphisms in these genes are likely to impact viral replication and fitness, contributing to viral diversity. Currently, only a few studies indicate that polymorphisms in the A3 genes may be correlated with infection risk and disease progression. METHODS:To characterize polymorphisms in the coding regions of these APOBEC3 genes in an HIV-1 infected population from the Limpopo Province of South Africa, APOBEC3 gene fragments were amplified from genomic DNA of 192 HIV-1 infected subjects and sequenced on an Illumina MiSeq platform. SNPs were confirmed and compared to SNPs in other populations reported in the 1000 Genome Phase III and HapMap databases, as well as in the ExAC exome database. Hardy-Weinberg Equilibrium was calculated and haplotypes were inferred using the LDlink 3.0 web tool. Linkage Disequilibrium (LD) for these SNPS were calculated in the total 1000 genome and AFR populations using the same tool. RESULTS:Known variants compared to the GRCh37 consensus genome sequence were detected at relatively high frequencies (>?5%) in all of the APOBEC3 genes. A3H showed the most variation, with several of the variants present in both alleles in almost all of the patients. Several minor allele variants (

SUBMITTER: Matume ND 

PROVIDER: S-EPMC6339282 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

altmetric image

Publications

Characterization of APOBEC3 variation in a population of HIV-1 infected individuals in northern South Africa.

Matume Nontokozo D ND   Tebit Denis M DM   Gray Laurie R LR   Turner Stephen D SD   Rekosh David D   Bessong Pascal O PO   Hammarskjöld Marie-Louise ML  

BMC medical genetics 20190119 1


<h4>Background</h4>The apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3 (APOBEC3) genes A3D, A3F, A3G and A3H have all been implicated in the restriction of human immunodeficiency virus type 1 (HIV-1) replication. Polymorphisms in these genes are likely to impact viral replication and fitness, contributing to viral diversity. Currently, only a few studies indicate that polymorphisms in the A3 genes may be correlated with infection risk and disease progression.<h4>Methods</h4>To  ...[more]

Similar Datasets

2020-01-28 | E-MTAB-8757 | biostudies-arrayexpress
| S-EPMC7804374 | biostudies-literature
| S-EPMC3826734 | biostudies-literature
| S-EPMC4051661 | biostudies-literature
| S-EPMC6712739 | biostudies-literature
| S-EPMC4139789 | biostudies-literature
| S-EPMC6916025 | biostudies-literature
| S-EPMC5278732 | biostudies-literature
| S-EPMC3818088 | biostudies-literature
2019-10-17 | GSE138949 | GEO