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Covariance of charged amino acids at positions 322 and 440 of HIV-1 Env contributes to coreceptor specificity of subtype B viruses, and can be used to improve the performance of V3 sequence-based coreceptor usage prediction algorithms.

Cashin K, Sterjovski J, Harvey KL, Ramsland PA, Churchill MJ, Gorry PR - PLoS ONE (2014)

Bottom Line: We demonstrate a significant covariant association between charged amino acids at position 322 in V3 and position 440 in the C4 Env region that contributes to the specificity of HIV-1 subtype B strains for CCR5 or CXCR4.We further demonstrate that inclusion of a "440 rule" can improve the sensitivity of several V3 sequence-based genotypic algorithms for predicting coreceptor usage of subtype B HIV-1 strains, without compromising specificity, and significantly improves the AUROC of the geno2pheno algorithm when set to its recommended false positive rate of 5.75%.Together, our results provide further mechanistic insights into the intra-molecular interactions within Env that contribute to coreceptor specificity of subtype B HIV-1 strains, and demonstrate that incorporation of Env determinants outside V3 can improve the reliability of coreceptor usage prediction algorithms.

View Article: PubMed Central - PubMed

Affiliation: Center for Biomedical Research, Burnet Institute, Melbourne, Australia; Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia.

ABSTRACT
The ability to determine coreceptor usage of patient-derived human immunodeficiency virus type 1 (HIV-1) strains is clinically important, particularly for the administration of the CCR5 antagonist maraviroc. The envelope glycoprotein (Env) determinants of coreceptor specificity lie primarily within the gp120 V3 loop region, although other Env determinants have been shown to influence gp120-coreceptor interactions. Here, we determined whether conserved amino acid alterations outside the V3 loop that contribute to coreceptor usage exist, and whether these alterations improve the performance of V3 sequence-based coreceptor usage prediction algorithms. We demonstrate a significant covariant association between charged amino acids at position 322 in V3 and position 440 in the C4 Env region that contributes to the specificity of HIV-1 subtype B strains for CCR5 or CXCR4. Specifically, positively charged Lys/Arg at position 322 and negatively charged Asp/Glu at position 440 occurred more frequently in CXCR4-using viruses, whereas negatively charged Asp/Glu at position 322 and positively charged Arg at position 440 occurred more frequently in R5 strains. In the context of CD4-bound gp120, structural models suggest that covariation of amino acids at Env positions 322 and 440 has the potential to alter electrostatic interactions that are formed between gp120 and charged amino acids in the CCR5 N-terminus. We further demonstrate that inclusion of a "440 rule" can improve the sensitivity of several V3 sequence-based genotypic algorithms for predicting coreceptor usage of subtype B HIV-1 strains, without compromising specificity, and significantly improves the AUROC of the geno2pheno algorithm when set to its recommended false positive rate of 5.75%. Together, our results provide further mechanistic insights into the intra-molecular interactions within Env that contribute to coreceptor specificity of subtype B HIV-1 strains, and demonstrate that incorporation of Env determinants outside V3 can improve the reliability of coreceptor usage prediction algorithms.

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Correlation between charged amino acids at Env positions 322/440 and coreceptor usage for phenotypically characterized C-HIV, D-HIV and AE-HIV strains.Values represent the percentage of R5 or CXCR4-using Envs within C-HIV (A), D-HIV (B) and AE-HIV (C) subtypes that have the indicated type of amino acid (+, positively charged; −, negatively charged; o, neutral) at position 440 out of all Envs with the indicated type of amino acid at position 322. Subscript values represent the percentage of R5 or CXCR4-using Envs within each subtype that have the indicated combination of amino acid types at positions 322/440. Amino acids are colored according to charge, as described in the legend for Figure 1.
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pone-0109771-g005: Correlation between charged amino acids at Env positions 322/440 and coreceptor usage for phenotypically characterized C-HIV, D-HIV and AE-HIV strains.Values represent the percentage of R5 or CXCR4-using Envs within C-HIV (A), D-HIV (B) and AE-HIV (C) subtypes that have the indicated type of amino acid (+, positively charged; −, negatively charged; o, neutral) at position 440 out of all Envs with the indicated type of amino acid at position 322. Subscript values represent the percentage of R5 or CXCR4-using Envs within each subtype that have the indicated combination of amino acid types at positions 322/440. Amino acids are colored according to charge, as described in the legend for Figure 1.

Mentions: We next investigated whether these potentially covariant sites influence coreceptor usage of non-B HIV-1 subtypes. Unfortunately, the paucity of phenotypically characterized sequences containing positions 322/440 in non-B HIV-1 subtypes limited our analysis to C-, D- and AE-HIV strains (Figure 5). Unlike B-HIV, we found that C-HIV R5 Envs have preference for a -322/o440 genotype (61%), yet similar to B-HIV, emergence of CXCR4-using C-HIV Envs was associated with a preference for o322/o440 (31%). Covariance at 322/440 in D-HIV was not associated with coreceptor usage, as both the majority of R5 and CXCR4-using D-HIV sequences exhibited a preference for the same +322/−440 genotype, similar to CXCR4-using B-HIV. However, considering that there was a marked difference in frequency of CXCR4-using D-HIV Envs with a −322/+440 genotype (67%) compared to R5 Envs (26%), these findings suggest that R5 D-HIV viruses may be predisposed for emergence of CXCR4-using viruses, which may explain the high incidence of CXCR4-using strains in the D-HIV epidemic. Similarly, 322/440 preferences within AE-HIV strains could not distinguish R5 from CXCR4-using strains, with both phenotypes exhibiting a relatively high frequency of -322/o440 genotype.


Covariance of charged amino acids at positions 322 and 440 of HIV-1 Env contributes to coreceptor specificity of subtype B viruses, and can be used to improve the performance of V3 sequence-based coreceptor usage prediction algorithms.

Cashin K, Sterjovski J, Harvey KL, Ramsland PA, Churchill MJ, Gorry PR - PLoS ONE (2014)

Correlation between charged amino acids at Env positions 322/440 and coreceptor usage for phenotypically characterized C-HIV, D-HIV and AE-HIV strains.Values represent the percentage of R5 or CXCR4-using Envs within C-HIV (A), D-HIV (B) and AE-HIV (C) subtypes that have the indicated type of amino acid (+, positively charged; −, negatively charged; o, neutral) at position 440 out of all Envs with the indicated type of amino acid at position 322. Subscript values represent the percentage of R5 or CXCR4-using Envs within each subtype that have the indicated combination of amino acid types at positions 322/440. Amino acids are colored according to charge, as described in the legend for Figure 1.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4196930&req=5

pone-0109771-g005: Correlation between charged amino acids at Env positions 322/440 and coreceptor usage for phenotypically characterized C-HIV, D-HIV and AE-HIV strains.Values represent the percentage of R5 or CXCR4-using Envs within C-HIV (A), D-HIV (B) and AE-HIV (C) subtypes that have the indicated type of amino acid (+, positively charged; −, negatively charged; o, neutral) at position 440 out of all Envs with the indicated type of amino acid at position 322. Subscript values represent the percentage of R5 or CXCR4-using Envs within each subtype that have the indicated combination of amino acid types at positions 322/440. Amino acids are colored according to charge, as described in the legend for Figure 1.
Mentions: We next investigated whether these potentially covariant sites influence coreceptor usage of non-B HIV-1 subtypes. Unfortunately, the paucity of phenotypically characterized sequences containing positions 322/440 in non-B HIV-1 subtypes limited our analysis to C-, D- and AE-HIV strains (Figure 5). Unlike B-HIV, we found that C-HIV R5 Envs have preference for a -322/o440 genotype (61%), yet similar to B-HIV, emergence of CXCR4-using C-HIV Envs was associated with a preference for o322/o440 (31%). Covariance at 322/440 in D-HIV was not associated with coreceptor usage, as both the majority of R5 and CXCR4-using D-HIV sequences exhibited a preference for the same +322/−440 genotype, similar to CXCR4-using B-HIV. However, considering that there was a marked difference in frequency of CXCR4-using D-HIV Envs with a −322/+440 genotype (67%) compared to R5 Envs (26%), these findings suggest that R5 D-HIV viruses may be predisposed for emergence of CXCR4-using viruses, which may explain the high incidence of CXCR4-using strains in the D-HIV epidemic. Similarly, 322/440 preferences within AE-HIV strains could not distinguish R5 from CXCR4-using strains, with both phenotypes exhibiting a relatively high frequency of -322/o440 genotype.

Bottom Line: We demonstrate a significant covariant association between charged amino acids at position 322 in V3 and position 440 in the C4 Env region that contributes to the specificity of HIV-1 subtype B strains for CCR5 or CXCR4.We further demonstrate that inclusion of a "440 rule" can improve the sensitivity of several V3 sequence-based genotypic algorithms for predicting coreceptor usage of subtype B HIV-1 strains, without compromising specificity, and significantly improves the AUROC of the geno2pheno algorithm when set to its recommended false positive rate of 5.75%.Together, our results provide further mechanistic insights into the intra-molecular interactions within Env that contribute to coreceptor specificity of subtype B HIV-1 strains, and demonstrate that incorporation of Env determinants outside V3 can improve the reliability of coreceptor usage prediction algorithms.

View Article: PubMed Central - PubMed

Affiliation: Center for Biomedical Research, Burnet Institute, Melbourne, Australia; Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia.

ABSTRACT
The ability to determine coreceptor usage of patient-derived human immunodeficiency virus type 1 (HIV-1) strains is clinically important, particularly for the administration of the CCR5 antagonist maraviroc. The envelope glycoprotein (Env) determinants of coreceptor specificity lie primarily within the gp120 V3 loop region, although other Env determinants have been shown to influence gp120-coreceptor interactions. Here, we determined whether conserved amino acid alterations outside the V3 loop that contribute to coreceptor usage exist, and whether these alterations improve the performance of V3 sequence-based coreceptor usage prediction algorithms. We demonstrate a significant covariant association between charged amino acids at position 322 in V3 and position 440 in the C4 Env region that contributes to the specificity of HIV-1 subtype B strains for CCR5 or CXCR4. Specifically, positively charged Lys/Arg at position 322 and negatively charged Asp/Glu at position 440 occurred more frequently in CXCR4-using viruses, whereas negatively charged Asp/Glu at position 322 and positively charged Arg at position 440 occurred more frequently in R5 strains. In the context of CD4-bound gp120, structural models suggest that covariation of amino acids at Env positions 322 and 440 has the potential to alter electrostatic interactions that are formed between gp120 and charged amino acids in the CCR5 N-terminus. We further demonstrate that inclusion of a "440 rule" can improve the sensitivity of several V3 sequence-based genotypic algorithms for predicting coreceptor usage of subtype B HIV-1 strains, without compromising specificity, and significantly improves the AUROC of the geno2pheno algorithm when set to its recommended false positive rate of 5.75%. Together, our results provide further mechanistic insights into the intra-molecular interactions within Env that contribute to coreceptor specificity of subtype B HIV-1 strains, and demonstrate that incorporation of Env determinants outside V3 can improve the reliability of coreceptor usage prediction algorithms.

Show MeSH
Related in: MedlinePlus