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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

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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]

PMID: 30660178

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Project description:Background:South Africa has the largest population of human immunodeficiency virus (HIV) infected patients on antiretroviral therapy (ART) realising the benefits of increased life expectancy. However, this population may be susceptible to cardiovascular disease (CVD) development, due to the chronic consequences of a lifestyle-related combination of risk factors, HIV infection and ART. We predicted a 10-year cardiovascular mortality risk in an HIV-infected population on long-term ART, based on their observed metabolic risk factor profile. Methods:We extracted data from hospital medical charts for 384 randomly selected HIV-infected patients aged ??30 years. We defined metabolic syndrome (MetS) subcomponents using the International Diabetes Federation definition. A validated non-laboratory-based model for predicting a 10-year CVD mortality risk was applied and categorised into five levels, with the thresholds ranging from very low-risk (<?5%) to very high-risk scores (>?30%). Results:Among the 384 patients, with a mean (± standard deviation) age of 42.90?±?8.20 years, the proportion of patients that were overweight/obese was 53.3%, where 50.9% had low high-density lipoprotein (HDL) cholesterol and 21 (17.5%) had metabolic syndrome. A total of 144 patients with complete data allowed a definitive prediction of a 10-year CVD mortality risk. 52% (95% CI 44-60) of the patients were stratified to very low risk (<?5%) compared to 8% (95% CI 4-13) that were at a very high risk (>?30%) of 10-year CVD mortality. The CVD risk grows with increasing age (years), 57.82?±?6.27 among very high risk and 37.52?±?4.50; p?<?0.001 in very low risk patients. Adjusting for age and analysing CVD risk mortality as a continuous risk score, increasing duration of HIV infection (p?=?0.002) and ART (p?=?0.007) were significantly associated with increased predicted 10 year CVD mortality risk. However, there was no association between these factors and categorised CVD mortality risk as per recommended scoring thresholds. Conclusions:Approximately 1 in 10 HIV-infected patients is at very high risk of predicted 10-year CVD mortality in our study population. Like uninfected individuals, our study found increased age as a major predictor of 10-year mortality risk and high prevalence of metabolic syndrome. Additional CVD mortality risk due to the duration of HIV infection and ART was seen in our population, further studies in larger and more representative study samples are encouraged. It recommends an urgent need for early planning, prevention and management of metabolic risk factors in HIV populations, at the point of ART initiation.

Dataset Information

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

Publications

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

Similar Datasets

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