Genotypic prediction of HIV-1 subtype D tropism
<p>Abstract</p> <p>Background</p> <p>HIV-1 subtype D infections have been associated with rapid disease progression and phenotypic assays have shown that CXCR4-using viruses are very prevalent. Recent studies indicate that the genotypic algorithms used routinely to asse...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-07-01
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| Series: | Retrovirology |
| Online Access: | http://www.retrovirology.com/content/8/1/56 |
| _version_ | 1818807742470553600 |
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| author | Chaix Marie-Laure Delobel Pierre Raymond Stéphanie Cazabat Michelle Encinas Stéphanie Bruel Patrick Sandres-Sauné Karine Marchou Bruno Massip Patrice Izopet Jacques |
| author_facet | Chaix Marie-Laure Delobel Pierre Raymond Stéphanie Cazabat Michelle Encinas Stéphanie Bruel Patrick Sandres-Sauné Karine Marchou Bruno Massip Patrice Izopet Jacques |
| author_sort | Chaix Marie-Laure |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>HIV-1 subtype D infections have been associated with rapid disease progression and phenotypic assays have shown that CXCR4-using viruses are very prevalent. Recent studies indicate that the genotypic algorithms used routinely to assess HIV-1 tropism may lack accuracy for non-B subtypes. Little is known about the genotypic determinants of HIV-1 subtype D tropism.</p> <p>Results</p> <p>We determined the HIV-1 coreceptor usage for 32 patients infected with subtype D by both a recombinant virus phenotypic entry assay and V3-loop sequencing to determine the correlation between them. The sensitivity of the Geno2pheno10 genotypic algorithm was 75% and that of the combined 11/25 and net charge rule was 100% for predicting subtype D CXCR4 usage, but their specificities were poor (54% and 68%). We have identified subtype D determinants in the V3 region associated with CXCR4 use and built a new simple genotypic rule for optimizing the genotypic prediction of HIV-1 subtype D tropism. We validated this algorithm using an independent GenBank data set of 67 subtype D V3 sequences of viruses of known phenotype. The subtype D genotypic algorithm was 68% sensitive and 95% specific for predicting X4 viruses in this data set, approaching the performance of genotypic prediction of HIV-1 subtype B tropism.</p> <p>Conclusion</p> <p>The genotypic determinants of HIV-1 subtype D coreceptor usage are slightly different from those for subtype B viruses. Genotypic predictions based on a subtype D-specific algorithm appear to be preferable for characterizing coreceptor usage in epidemiological and pathophysiological studies.</p> |
| first_indexed | 2024-12-18T19:30:30Z |
| format | Article |
| id | doaj.art-d31be9dda61e473c839a8aa318668aab |
| institution | Directory Open Access Journal |
| issn | 1742-4690 |
| language | English |
| last_indexed | 2024-12-18T19:30:30Z |
| publishDate | 2011-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Retrovirology |
| spelling | doaj.art-d31be9dda61e473c839a8aa318668aab2022-12-21T20:55:45ZengBMCRetrovirology1742-46902011-07-01815610.1186/1742-4690-8-56Genotypic prediction of HIV-1 subtype D tropismChaix Marie-LaureDelobel PierreRaymond StéphanieCazabat MichelleEncinas StéphanieBruel PatrickSandres-Sauné KarineMarchou BrunoMassip PatriceIzopet Jacques<p>Abstract</p> <p>Background</p> <p>HIV-1 subtype D infections have been associated with rapid disease progression and phenotypic assays have shown that CXCR4-using viruses are very prevalent. Recent studies indicate that the genotypic algorithms used routinely to assess HIV-1 tropism may lack accuracy for non-B subtypes. Little is known about the genotypic determinants of HIV-1 subtype D tropism.</p> <p>Results</p> <p>We determined the HIV-1 coreceptor usage for 32 patients infected with subtype D by both a recombinant virus phenotypic entry assay and V3-loop sequencing to determine the correlation between them. The sensitivity of the Geno2pheno10 genotypic algorithm was 75% and that of the combined 11/25 and net charge rule was 100% for predicting subtype D CXCR4 usage, but their specificities were poor (54% and 68%). We have identified subtype D determinants in the V3 region associated with CXCR4 use and built a new simple genotypic rule for optimizing the genotypic prediction of HIV-1 subtype D tropism. We validated this algorithm using an independent GenBank data set of 67 subtype D V3 sequences of viruses of known phenotype. The subtype D genotypic algorithm was 68% sensitive and 95% specific for predicting X4 viruses in this data set, approaching the performance of genotypic prediction of HIV-1 subtype B tropism.</p> <p>Conclusion</p> <p>The genotypic determinants of HIV-1 subtype D coreceptor usage are slightly different from those for subtype B viruses. Genotypic predictions based on a subtype D-specific algorithm appear to be preferable for characterizing coreceptor usage in epidemiological and pathophysiological studies.</p>http://www.retrovirology.com/content/8/1/56 |
| spellingShingle | Chaix Marie-Laure Delobel Pierre Raymond Stéphanie Cazabat Michelle Encinas Stéphanie Bruel Patrick Sandres-Sauné Karine Marchou Bruno Massip Patrice Izopet Jacques Genotypic prediction of HIV-1 subtype D tropism Retrovirology |
| title | Genotypic prediction of HIV-1 subtype D tropism |
| title_full | Genotypic prediction of HIV-1 subtype D tropism |
| title_fullStr | Genotypic prediction of HIV-1 subtype D tropism |
| title_full_unstemmed | Genotypic prediction of HIV-1 subtype D tropism |
| title_short | Genotypic prediction of HIV-1 subtype D tropism |
| title_sort | genotypic prediction of hiv 1 subtype d tropism |
| url | http://www.retrovirology.com/content/8/1/56 |
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