Copy number and mitochondria haplogroups in two HIV pediatric HIV phenotypes- rapid progressors and long term non progressors

Abstract

Whole Exome Sequencing (WES) was used to evaluate mitochondrial genetic factors associated with pediatric HIV disease progression. The Collaborative African Genomics Network (CAfGEN) is currently studying the two different phenotypes in children, Rapid Progressors (RPs) and Long Term Non Progressors (LTNPs), and trying to understand how these host genetic factors might influence HIV and disease progression. East Africa and Southern Africa are the most burdened continents in the world by HIV, causing the most deaths, hence the need for such studies in Africa, which are very minimal, whereas evidence has suggested that Africa bears the most genetic variation. Variant Calling was used to identify variants and quantify the copy number. The Mitomap database was then used to assign haplogroups. The Pearson’s Chi-Square test was used to look into the association between mtDNA and haplogroups and HIV progression, then Students T-test to assess the association between mtDNA copy number and HIV Progression. The study sought to make a contribution to the health sector and also give insights into how Copy Number and mtDNA haplogroups can be used as indicators of AIDS progression in children, which might aid in the management of potential side effects during HIV therapy. This study was able to determine copy number and mtDNA haplogroups in order to identify the host genetic factors underlying LTNPs and RPs, with the use of WES data from CAfGEN. The study was also able to determine an association between mitochondria copy number and HIV progression (p=0.01945) and the mitochondria haplogroup and HIV progression (p=5.705e-42). The paper concluded that off-target WES reads may be utilized to correctly identify the mtDNA sequence.