Hybrid approach for predicting coreceptor used by HIV-1 from its V3 loop amino acid sequence.

<h4>Background</h4>HIV-1 infects the host cell by interacting with the primary receptor CD4 and a coreceptor CCR5 or CXCR4. Maraviroc, a CCR5 antagonist binds to CCR5 receptor. Thus, it is important to identify the coreceptor used by the HIV strains dominating in the patient. In past, a...

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Autores principales:	Ravi Kumar, Gajendra P S Raghava
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e02801e0573948c0947001f0178e783c
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spelling	oai:doaj.org-article:e02801e0573948c0947001f0178e783c2021-11-18T07:49:30ZHybrid approach for predicting coreceptor used by HIV-1 from its V3 loop amino acid sequence.1932-620310.1371/journal.pone.0061437https://doaj.org/article/e02801e0573948c0947001f0178e783c2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23596523/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>HIV-1 infects the host cell by interacting with the primary receptor CD4 and a coreceptor CCR5 or CXCR4. Maraviroc, a CCR5 antagonist binds to CCR5 receptor. Thus, it is important to identify the coreceptor used by the HIV strains dominating in the patient. In past, a number of experimental assays and in-silico techniques have been developed for predicting the coreceptor tropism. The prediction accuracy of these methods is excellent when predicting CCR5(R5) tropic sequences but is relatively poor for CXCR4(X4) tropic sequences. Therefore, any new method for accurate determination of coreceptor usage would be of paramount importance to the successful management of HIV-infected individuals.<h4>Results</h4>The dataset used in this study comprised 1799 R5-tropic and 598 X4-tropic third variable (V3) sequences of HIV-1. We compared the amino acid composition of both types of V3 sequences and observed that certain types of residues, e.g., Asparagine and Isoleucine, were preferred in R5-tropic sequences whereas residues like Lysine, Arginine, and Tryptophan were preferred in X4-tropic sequences. Initially, Support Vector Machine-based models were developed using amino acid composition, dipeptide composition, and split amino acid composition, which achieved accuracy up to 90%. We used BLAST to discriminate R5- and X4-tropic sequences and correctly predicted 93.16% of R5- and 75.75% of X4-tropic sequences. In order to improve the prediction accuracy, a Hybrid model was developed that achieved 91.66% sensitivity, 81.77% specificity, 89.19% accuracy and 0.72 Matthews Correlation Coefficient. The performance of our models was also evaluated on an independent dataset (256 R5- and 81 X4-tropic sequences) and achieved maximum accuracy of 84.87% with Matthews Correlation Coefficient 0.63.<h4>Conclusion</h4>This study describes a highly efficient method for predicting HIV-1 coreceptor usage from V3 sequences. In order to provide a service to the scientific community, a webserver HIVcoPred was developed (http://www.imtech.res.in/raghava/hivcopred/) for predicting the coreceptor usage.Ravi KumarGajendra P S RaghavaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 4, p e61437 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ravi Kumar Gajendra P S Raghava Hybrid approach for predicting coreceptor used by HIV-1 from its V3 loop amino acid sequence.
description	<h4>Background</h4>HIV-1 infects the host cell by interacting with the primary receptor CD4 and a coreceptor CCR5 or CXCR4. Maraviroc, a CCR5 antagonist binds to CCR5 receptor. Thus, it is important to identify the coreceptor used by the HIV strains dominating in the patient. In past, a number of experimental assays and in-silico techniques have been developed for predicting the coreceptor tropism. The prediction accuracy of these methods is excellent when predicting CCR5(R5) tropic sequences but is relatively poor for CXCR4(X4) tropic sequences. Therefore, any new method for accurate determination of coreceptor usage would be of paramount importance to the successful management of HIV-infected individuals.<h4>Results</h4>The dataset used in this study comprised 1799 R5-tropic and 598 X4-tropic third variable (V3) sequences of HIV-1. We compared the amino acid composition of both types of V3 sequences and observed that certain types of residues, e.g., Asparagine and Isoleucine, were preferred in R5-tropic sequences whereas residues like Lysine, Arginine, and Tryptophan were preferred in X4-tropic sequences. Initially, Support Vector Machine-based models were developed using amino acid composition, dipeptide composition, and split amino acid composition, which achieved accuracy up to 90%. We used BLAST to discriminate R5- and X4-tropic sequences and correctly predicted 93.16% of R5- and 75.75% of X4-tropic sequences. In order to improve the prediction accuracy, a Hybrid model was developed that achieved 91.66% sensitivity, 81.77% specificity, 89.19% accuracy and 0.72 Matthews Correlation Coefficient. The performance of our models was also evaluated on an independent dataset (256 R5- and 81 X4-tropic sequences) and achieved maximum accuracy of 84.87% with Matthews Correlation Coefficient 0.63.<h4>Conclusion</h4>This study describes a highly efficient method for predicting HIV-1 coreceptor usage from V3 sequences. In order to provide a service to the scientific community, a webserver HIVcoPred was developed (http://www.imtech.res.in/raghava/hivcopred/) for predicting the coreceptor usage.
format	article
author	Ravi Kumar Gajendra P S Raghava
author_facet	Ravi Kumar Gajendra P S Raghava
author_sort	Ravi Kumar
title	Hybrid approach for predicting coreceptor used by HIV-1 from its V3 loop amino acid sequence.
title_short	Hybrid approach for predicting coreceptor used by HIV-1 from its V3 loop amino acid sequence.
title_full	Hybrid approach for predicting coreceptor used by HIV-1 from its V3 loop amino acid sequence.
title_fullStr	Hybrid approach for predicting coreceptor used by HIV-1 from its V3 loop amino acid sequence.
title_full_unstemmed	Hybrid approach for predicting coreceptor used by HIV-1 from its V3 loop amino acid sequence.
title_sort	hybrid approach for predicting coreceptor used by hiv-1 from its v3 loop amino acid sequence.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/e02801e0573948c0947001f0178e783c
work_keys_str_mv	AT ravikumar hybridapproachforpredictingcoreceptorusedbyhiv1fromitsv3loopaminoacidsequence AT gajendrapsraghava hybridapproachforpredictingcoreceptorusedbyhiv1fromitsv3loopaminoacidsequence
_version_	1718422942323310592

Hybrid approach for predicting coreceptor used by HIV-1 from its V3 loop amino acid sequence.

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