Phylogenetic Analysis of Ethiopian HIV-1 Subtype C Near Full-Length Genomes Reveals High Intrasubtype Diversity and a Strong Geographical Cluster

AIDS Research and Human Retroviruses
Wondwossen AmogneUjjwal Neogi

Abstract

In this study, we characterize HIV-1 subtype C (HIV-1C) strains at the near full-length genome (NFLG) level and perform genotypic drug resistance testing (GRT) and genotypic tropism testing (GTT) from Ethiopia (HIV-1CET). Plasma samples (n = 150) were obtained from therapy-naive individuals residing in Addis Ababa, Ethiopia in 2008. HIV-NFLG was performed in a subset of patients (n = 30). GRT (pol) and GTT (V3 env) were performed using in-house methods. GTT was analyzed by PhenoSeq-C. The phylogenetic analysis of the NLFG identified two separate clusters of HIV-1CET, although all strains formed one large overarching cluster together. At NFLG, greater diversity was found among HIV-1CET strains compared to HIV-1C strains from other geographical locations. The geographic clustering was weak in the small subgenomic (pol and env) regions. The primary drug-resistant mutations were identified at a low level (<5%). GTT identified that 12% (12/102) of the patients were predicted to be harboring X4-tropic or both R5/X4-tropic viruses.

References

Oct 13, 1990·Lancet·S AyehunieO Strannegård
Sep 12, 2008·AIDS·Rachel FontellaCarlos G Schrago
Mar 13, 2010·PloS One·Morgan N PriceAdam P Arkin
Feb 8, 2011·AIDS·Joris HemelaarUNKNOWN WHO-UNAIDS Network for HIV Isolation and Characterisation
May 31, 2011·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Irene BontellAnders Sönnerborg
Nov 24, 2011·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Ujjwal NeogiAnita Shet
Feb 26, 2015·Scientific Reports·Kieran CashinPaul R Gorry

❮ Previous
Next ❯

Citations

Dec 23, 2016·Scientific Reports·Gonzalo YebraUNKNOWN ICONIC Project
Jul 27, 2017·Scientific Reports·Ujjwal NeogiAnders Sönnerborg
May 7, 2021·Frontiers in Immunology·Elisa SacconRobert van Domselaar

❮ Previous
Next ❯

Software Mentioned

FastTree
PhenoSeq

Related Concepts

Related Feeds

Antifungals (ASM)

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

Antimicrobial Resistance (ASM)

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.

Antimicrobial Resistance

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.

Antifungals

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.