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(See the editorial commentary by Hodskog and Albert, on pages 163-5.) Background. The prevalence and correlates of CXCR4-use in recently diagnosed patients and the impact of X4/DM transmission remain largely unknown. Method. Genotypic coreceptor use determination on the baseline sample of 539 recently diagnosed individuals. Correlation of coreceptor use with clinical, viral and epidemiological data and with information on transmission events as obtained through phylogenetic analysis of protease and reverse transcriptase sequences. Results. CXCR4-use was predicted in 12 to 19% of the patients, depending on the interpretative cutoff used. CXCR4-use was correlated with lower CD4(+) T cell counts and subtype 01_AE infection. No association with viral load was observed. Seven (11%) of 63 transmission clusters and 4 (31%) of 13 donor-source pairs resulted from X4/DM transmission. Conclusion. The results confirmed the relation between CXCR4-use at diagnosis and low baseline CD4+ T cell counts. Significantly more CXCR4-use was predicted in 01_AE infections, which may impose constraints on the use of CCR5 antagonists in certain regions of the world. Observations from the transmission cluster analysis contradict the hypothesis that R5 viruses are selected at transmission, and support the idea that R5 or X4/DM infections result from a stochastic process. [ABSTRACT FROM AUTHOR]

Abstract Background The number of HIV-1 infected individuals in the Western world continues to rise. More in-depth understanding of regional HIV-1 epidemics is necessary for the optimal design and adequate use of future prevention strategies. The use of a combination of phylogenetic analysis of HIV sequences, with data on patients' demographics, infection route, clinical information and laboratory results, will allow a better characterization of individuals responsible for local transmission. Methods Baseline HIV-1 pol sequences, obtained through routine drug-resistance testing, from 506 patients, newly diagnosed between 2001 and 2009, were used to construct phylogenetic trees and identify transmission-clusters. Patients' demographics, laboratory and clinical data, were retrieved anonymously. Statistical analysis was performed to identify subtype-specific and transmission-cluster-specific characteristics. Results Multivariate analysis showed significant differences between the 59.7% of individuals with subtype B infection and the 40.3% non-B infected individuals, with regard to route of transmission, origin, infection with Chlamydia (p = 0.01) and infection with Hepatitis C virus (p = 0.017). More and larger transmission-clusters were identified among the subtype B infections (p < 0.001). Overall, in multivariate analysis, clustering was significantly associated with Caucasian origin, infection through homosexual contact and younger age (all p < 0.001). Bivariate analysis additionally showed a correlation between clustering and syphilis (p < 0.001), higher CD4 counts (p = 0.002), Chlamydia infection (p = 0.013) and primary HIV (p = 0.017). Conclusions Combination of phylogenetics with demographic information, laboratory and clinical data, revealed that HIV-1 subtype B infected Caucasian men-who-have-sex-with-men with high prevalence of sexually transmitted diseases, account for the majority of local HIV-transmissions. This finding elucidates observed epidemiological trends through molecular analysis, and justifies sustained focus in prevention on this high risk group.

Background: Determination of HIV-1 co-receptor use is a necessity before initiation of a CCR5 antagonist but the longevity of a CCR5-use prediction remains unknown., Methods: Genotypic co-receptor tropism determination was performed in 225 newly diagnosed individuals consulting an AIDS Reference Centre. Samples were collected at diagnosis and at initiation of antiretroviral therapy or just before closure of the study for patients who did not initiate therapy. For individuals with a discordant tropism prediction on the two longitudinal samples, analysis of intermediate samples and single genome sequencing of proviral DNA was performed to confirm the tropism switch. Deep sequencing was done to identify minor CXCR4 or CCR5-using populations in the initial sample., Results: Overall, tropism switches were rare (7.6%). Only a geno2pheno false positive rate of <50% at baseline was retained as predictive for a subsequent switch from CCR5-use only to predicted CXCR4-use. Minor CXCR4-using virus populations were detected in the first sample of 9 of the 14 R5-to-X4 switchers but the subsequent outgrowth of these minor populations was documented in only 3., Conclusions: With the current guidelines for treatment initiation at CD4(+) T cell counts of <500 cells/mm(3), co-receptor switch between diagnosis and starting antiretroviral therapy is rare. Patients with R5 viruses and a geno2pheno FPR of <50% are more prone to subsequent co-receptor switch than patients with an FPR of >50% and will need repeat tropism testing if initiation of maraviroc is considered and previous testing dates from more than a year before.

A cluster of four patients acutely infected with a genetically almost identical virus, allowed us to investigate genetic variability and disease progression in early HIV-1 infection with minimal interference of virus specific factors. Two of the patients were heterozygous for the 32-bp deletion in the CCR5 coreceptor gene. Both showed a slower disease progression with lower viral load levels and a reduced rate of genetic evolution compared to the patients with normal CCR5 alleles. During 3 years of treatment-free follow-up, the mean pairwise genetic distance increased with 1.45% and 1.58% in the two patients with a 32-bp deletion allele compared to 3.05% and 3.57% in the two patients with normal CCR5 alleles. The observed relation between slower disease progression and a reduced evolutionary rate illustrates the influence of the virus replicative capacity, here most possibly hampered by the CCR5 heterozygosity in two of the four individuals, on the genetic evolution of the virus in the host.