Coreceptor utilization and primary cell tropism by HIV-1 subtype C strains.

Abstract

Human immunodeficiency virus type 1 (HIV-1) isolates can be differentiated based

on their ability to use particular coreceptors – R5 viruses use CCR5, X4 viruses use

CXCR4 and R5X4 (dual tropic) viruses use both CCR5 and CXCR4. It is widely

reported that HIV-1 subtype C (HIV-1C) has a unique viral coreceptor evolution

pattern in that a complete switch from the predominant CCR5 (R5) to CXCR4 (X4)

phenotype is less common for this subtype compared to other subtypes. However,

dual tropic HIV-1C isolates have occasionally been described. Furthermore, it has

been reported that certain highly active antiretroviral drugs (HAART) may select for

X4 viral variants. Therefore, this thesis study was undertaken to better understand the

functional and genotypic characteristics of dual tropic HIV-1C isolates, and to

characterize drug resistance and coreceptor usage patterns in HAART-naïve versus

HAART-failing HIV-1C infected patients.

Thirty-five functional HIV-1 env clones derived from seven dual tropic HIV-1C

strains were generated and their coreceptor usage characterized in transformed cell

lines. All 35 env clones efficiently infected transformed cells expressing CXCR4.

Twenty of 35 clones (57%) also utilized the CCR5 receptor. No R5-only clones were

detected. Functional coreceptor usage data was correlated to env gene sequence data.

The ability of the HIV-1C env clones to facilitate infection of primary lymphocytes

and monocyte-derived macrophages was next investigated. The majority of clones

characterized as X4 or R5X4 on cell lines used either CXCR4 alone or CXCR4 and

CCR5, respectively, in primary cells. A few viruses displayed comparable CCR5 and

CXCR4 usage and clones from one virus preferred CCR5 usage in macrophages.

Thus in a few cases coreceptor phenotyping in transformed cell lines does not predict

usage in primary cells. Genetic determinants for coreceptor usage in primary cells

require further investigation.

Finally the patterns of drug resistance mutations were studied and coreceptor usage

among 45 HAART-naïve and 45 HAART-failing HIV-1C infected patients analyzed.

Ninety-five percent of HAART-failing patients had viruses with at least one drug

resistance mutation. Thymidine analog resistance mutations (TAMs) were present in

55% of patients. HAART-failing patients had significantly higher prevalence (59%)

of X4/R5X4-utilizing viruses compared to HAART-naïve patients (30%) (p<0.02)

using the Trofile Co-receptor Tropism Assay while 41% of HAART-failing patients

used CCR5 and 70% of HAART-naïve patients used CCR5. Functional results

correlated with predictive algorithm methods.

This study enhances our understanding of HIV-1 pathogenesis and the results have

important implications for the use of coreceptor antagonists for the clinical

management of HIV-1C infection.