**19. Correlation between phenotypic and bioinformatics tools in determining HIV coreceptor use**

Evaluation of the performances of genotypic tools to predict HIV-1 tropism has been investigated. Paired genotypic and phenotypic determination of HIV-1 coreceptor usage has been performed to assess several genotypic approaches for detecting CXCR4-using and CCR5-using viruses in a clinical setting. Excellent correlations between HIV-1 V3 genotype and phenotype have been observed. Overall, the accuracy of the bioinformatics tools to detect CXCR4-using virus was similar for ES Trofile and Trofile. However, the negative predictive values for genotypic tools with ES Trofile were slightly higher than they were with Trofile. The accuracy of genotypic algorithms for detecting CXCR4-using viruses is high when using Trofile as the reference. The concordance with ES Trofile is better with higher CD4 cell counts and non-exposure to antiretroviral therapy. The global concordance between genotypic and phenotypic data is 91% with the rule combining the amino-acid residues at positions 11/25 and V3 net charge. Gaining a better understanding of the output of these assays and correlating them with clinical progression and therapy response will provide some indication on how both genotype-based and phenotypic assays for determining HIV coreceptor usage can be improved. Deep V3 sequencing is a promising tool for identifying treatment-experienced individuals who could benefit from CCR5 antagonist-containing regimens.

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charge, which is consistent with the NSI phenotypes compared to other subtypes. Moreover, this atypical property of the subtype C envelope glycoproteins might be the reason behind the rapid expansion of the virus being currently observed. In view of this, there is need for intervention strategies that are subtype specific to curb this pandemic tailor designed for use in areas where subtype C viruses predominate. R5-using viruses have also been found to be more common in subtype A than subtype D HIV-1 infections. The emergence of X4 viruses occurs very early among subtype D-infected individuals. More so, a high proportion of subtype D infections have been shown to display D/M tropism throughout the course of disease. An inverse skewing in coreceptor usage, with an increased presence of CXCR4-using strains, has instead been reported for subtype-D HIV-1. This observation is consistent with the faster pace of disease progression reported for subtype-D infection both in Africa and abroad. An increased rate of CXCR4 usage has also been reported for CRF AE isolates common in South East Asia. There are proposals to the effect that the increase in prevalence of CXCR4-using HIV-1 variants increases with the age of the subtype epidemic. Indeed recent phylogenetic studies suggest that the proportion of patients with detectable CXCR4 using HIV-1 variants varies with subtype D having the highest CXCR4 switch rate being the oldest whilst subtype C with the lowest CXCR4 switch rate being the youngest. Subtype B predominant in North America and Europe has demonstrated that CXCR4 coreceptor usage increases with time following infection with or without concurrent use of R5 in 50% of HIV-1 infected individuals. The HIV-1 subtype-B epidemic has an intermediate pattern, both in terms of age and prevalence of CXCR4-using HIV-1 variants. This assumption is highly speculative and not supported by all the data available at present. However, if confirmed it would imply that all the subtype epidemics are evolving towards a higher prevalence of CXCR4-using HIV-1 variants although it is plausible that each epidemic would reach a point of equilibrium beyond which such

prevalence will not further increase.

compartment.

**22. HIV coreceptor usage and compartmentalization** 

Compartmentalization is the occurrence of distinct yet phylogenetically related HIV-1 phenotypes or genotypes within different anatomic sites, an observation common amongst both treated and untreated individuals. Differences in selective pressures may shape the distinct viral populations in different compartments. Anatomic compartmentalization of HIV coreceptor usage variants has been described in diverse tissues including in blood, lungs, brain, central nervous system, breast milk and genital tract. Studies have shown that the distribution of R5 and CXCR4-using variants differ in different blood compartments. Higher prevalence of predicted CXCR4-using variants in PBMC than in plasma has been reported. The limited compartmentalization and the clonal amplification of evolving functional viruses in milk indicate continual seeding of the mammary gland by blood virus variants, followed by transient local replication of these variants in the breast
