Reliable Genotypic Tropism Tests for the Major HIV-1 Subtypes

Cashin, Kieran; Gray, Lachlan Robert; Harvey, Katherine; Perez-Bercoff, Danielle; Lee, Guinevere Q.; Sterjovski, Jasminka; Roche, Michael; Demarest, James F.; Drummond, Fraser; Harrigan, P. Richard; Churchill, Melissa; Gorry, Paul R

doi:10.1038/srep08543

Cited by 36 publications

(44 citation statements)

References 74 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…More sophisticated models have been developed that outperform the 11/25 rule, e.g. position specific scoring matrix (PSSM) [34] and PhenoSeq [35]. The most widely used geno2pheno and PSSM tools are highly concordant (>85%) [36].…”

Section: Discussionmentioning

confidence: 99%

Monophylogenetic HIV-1C epidemic in Ethiopia is dominated by CCR5-tropic viruses–an analysis of a prospective country-wide cohort

et al. 2017

View full text Add to dashboard Cite

BackgroundCCR5 coreceptor using HIV-1 subtype C (HIV-1C) has been reported to dominate the Ethiopian epidemic. However, almost all data have been obtained from two large cities in the central and north-west regions and recent data is lacking.MethodsPlasma were obtained from 420 treatment-naïve patients recruited 2009–2011 to a large country-wide Ethiopian cohort. The V3 region was sequenced and the co-receptor tropism was predicted by the clinical and clonal models of the geno2pheno tool at different false positive rates (fpr) and for subtype. In an intention to treat analysis the impact of baseline tropism on outcome of antiretroviral therapy was evaluated.ResultsV3 loop sequencing was successful in 352 (84%) patients. HIV-1C was found in 350 (99.4%) and HIV-1A in two (0.6%) patients. When comparing the geno2pheno fpr10% clonal and clinical models, 24.4% predictions were discordant. X4-virus was predicted in 17.0 and 19.0%, respectively, but the predictions were concordant in only 6%. At fpr5%, concordant X4-virus predictions were obtained in 3.1%. The proportion of X4-tropic virus (clonal fpr10%) increased from 5.6 to 17.3% (p < 0.001) when 387 Ethiopian V3 loop sequences dated from 1984 to 2003 were compared with ours. In an intention to treat analysis, 67.9% reached treatment success at month 6 and only 50% at month 12. Only age and not tropism predicted therapy outcome and no difference was found in CD4+ cell gain between R5-tropic and X4-tropic infected patients. At viral failure, R5 to X4 switch was rare while X4 to R5 switch occurred more frequently (month 6: p = 0.006; month 12: p = 0.078).ConclusionThe HIV-1C epidemic is monophylogenetic in all regions of Ethiopia and R5-tropic virus dominates, even in patients with advanced immunodeficiency, although the proportion of X4-tropic virus seems to have increased over the last two decades. Geno2pheno clinical and clonal prediction models show a large discrepancy at fpr10%, but not at fpr5%. Hence further studies are needed to assess the utility of genotypic tropism testing in HIV-1C. In ITT analysis only age and not tropism influenced the outcome.

show abstract

Section: Discussionmentioning

confidence: 99%

Monophylogenetic HIV-1C epidemic in Ethiopia is dominated by CCR5-tropic viruses–an analysis of a prospective country-wide cohort

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Only a small minority of sequences were predicted to be as CXCR4-using by PhenoSeq-B (28). These results were highly concordant with those predicted by G2P using an FPR cut-off of 10% (Table S3 in Supplementary Material).…”

Section: Resultsmentioning

confidence: 99%

HIV-1 and SIV Predominantly Use CCR5 Expressed on a Precursor Population to Establish Infection in T Follicular Helper Cells

Phetsouphanh

Suzuki

et al. 2017

Front. Immunol.

Self Cite

View full text Add to dashboard Cite

BackgroundT follicular helper (Tfh) cells are increasingly recognized as a major reservoir of HIV infection that will likely need to be addressed in approaches to curing HIV. However, Tfh express minimal CCR5, the major coreceptor for HIV-1, and the mechanism by which they are infected is unclear. We have previously shown that macaque Tfh lack CCR5, but are infected in vivo with CCR5-using SIV at levels comparable to other memory CD4+ T cells. Similarly, human splenic Tfh cells are highly infected with HIV-1 DNA. Therefore, we set out to examine the mechanism of infection of Tfh cells.MethodologyTfh and other CD4+ T cell subsets from macaque lymph nodes and spleens, splenic Tfh from HIV+ subjects, and tonsillar Tfh from HIV-uninfected subjects were isolated by cell sorting prior to cell surface and molecular characterization. HIV proviral gp120 sequences were submitted to genotypic and phenotypic tropism assays. Entry of CCR5- and CXCR4-using viruses into Tfh from uninfected tonsillar tissue was measured using a fusion assay.ResultsPhylogenetic analysis, genotypic, and phenotypic analysis showed that splenic Tfh cells from chronic HIV+ subjects were predominantly infected with CCR5-using viruses. In macaques, purified CCR5+PD-1intermediate(int)+ memory CD4+ T cells were shown to include pre-Tfh cells capable of differentiating in vitro to Tfh by upregulation of PD-1 and Bcl6, confirmed by qRT-PCR and single-cell multiplex PCR. Infected PD-1int cells survive, carry SIV provirus, and differentiate into PD-1hi Tfh after T cell receptor stimulation, suggesting a pathway for SIV infection of Tfh. In addition, a small subset of macaque and human PD-1hi Tfh can express low levels of CCR5, which makes them susceptible to infection. Fusion assays demonstrated CCR5-using HIV-1 entry into CCR5+ Tfh and pre-Tfh cells from human tonsils.ConclusionThe major route of infection of Tfh in macaques and humans appears to be via a CCR5-expressing pre-Tfh population. As the generation of Tfh are important for establishing effective immune responses during primary infections, Tfh are likely to be an early target of HIV-1 following transmission, creating an important component of the reservoir that has the potential to expand over time.

show abstract

“…Sensitivity analyses were also performed to examine whether a different RIP window size (100), a different HIV-1 subtyping tool (REGA), a different and subtype-specific algorithm to infer viral tropism (PhenoSeq [25]), different g2p fpr % cutoffs (5%, 10%, 15%, 20%), different definitions of virologic suppression (50 and 500 copies HIV RNA/mL), or a different measure of CD4 recovery (time to first of two consecutive post-therapy CD4 above baseline) would yield different observations. In summary, all yielded trends similar to our primary analysis regardless of HIV gene used to infer subtype, g2p fpr % cutoff values, and the definition of virologic suppression or CD4 recovery (results not shown).…”

Section: Resultsmentioning

confidence: 99%

“…In the same study [24], we also showed that adjusting the algorithms’ cutoff value may further optimize sensitivity and specificity for each subtype. Hence in the current study, we performed sensitivity analyses by redefining tropism with g2p cutoffs at 5%, 10%, 15% and 20%, and with a subtype-specific tropism inference tool PhenoSeq [25]; overall, all yielded trends similar to our primary analysis with g2p cutoff at 5.75%.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Non-R5-tropic HIV-1 in subtype A1 and D infections were associated with lower pretherapy CD4+ cell count but not with PI/(N)NRTI therapy outcomes in Mbarara, Uganda

Lee

Lachowski

Cai

et al. 2016

Aids

Self Cite

View full text Add to dashboard Cite

Background Previous studies suggest that infection with non-R5-tropic subtype B HIV-1, compared to R5, is associated with a more rapid decline in CD4 count, but does not affect PI/(N)NRTI therapy outcome. Here, we explored clinical correlates associated with viral tropism in subtype A1 and D infections. Methods HIV-1 subtype A1 (n=196) and D (n=143) pre-therapy plasma samples and up to 7.5 years of post-therapy virologic and CD4 data were collected from a cross-sectional cohort in Mbarara, Uganda. Tropism and subtype were inferred using env V3 (geno2pheno) and gp41 (RIP) Sanger sequences. For each subtype, R5 infection was compared with non-R5 in terms of: Pre-therapy viral load and CD4 count (Mann-Whitney tests), and therapy outcomes including time to virologic suppression, post-suppression virologic rebound, CD4 decline and CD4 recovery (Log-rank tests). Results 94% of all patients in this study achieved virologic suppression within median 3 months post-therapy. In both subtypes, non-R5 infection was associated with lower pre-therapy CD4 count (non-R5 versus R5; A: median 57 versus 147 cells/µL p=0.005; D: 80 versus 128 cells/µL p=0.006). Multivariable linear regression confirmed that tropism, not subtype nor the interaction between subtype and tropism, was a significant predictor of pre-therapy CD4 count (p<0.0001). None of pre-therapy viral load, time to virologic suppression, virologic rebound, CD4 decline nor CD4 recovery was significantly different (all p>0.09). Conclusion Regardless of HIV-1 subtype or tropism, the majority of patients in this Ugandan cohort responded to therapy, even though non-R5 infection was associated with lower pre-therapy CD4 count.

show abstract

Reliable Genotypic Tropism Tests for the Major HIV-1 Subtypes

Cited by 36 publications

References 74 publications

Monophylogenetic HIV-1C epidemic in Ethiopia is dominated by CCR5-tropic viruses–an analysis of a prospective country-wide cohort

Monophylogenetic HIV-1C epidemic in Ethiopia is dominated by CCR5-tropic viruses–an analysis of a prospective country-wide cohort

HIV-1 and SIV Predominantly Use CCR5 Expressed on a Precursor Population to Establish Infection in T Follicular Helper Cells

Non-R5-tropic HIV-1 in subtype A1 and D infections were associated with lower pretherapy CD4+ cell count but not with PI/(N)NRTI therapy outcomes in Mbarara, Uganda

Contact Info

Product

Resources

About