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Performance of the ViroSeq HIV-1 genotyping system v2.0 on HIV-1 strains circulating in Senegal.
- Source :
-
Journal of virological methods [J Virol Methods] 2013 Mar; Vol. 188 (1-2), pp. 97-103. Date of Electronic Publication: 2012 Dec 21. - Publication Year :
- 2013
-
Abstract
- The objective of this study was to investigate the performance of the ViroSeq HIV-1 Genotyping System v2.0 on HIV-1 non-B strains identified in Senegalese patients. The study involved 150 patients, and genotyping was performed using the ViroSeq HIV-1 Genotyping System v2.0 or an in-house method developed by the French National Agency on AIDS Research AC11 when the ViroSeq HIV-1 Genotyping System v2.0 failed. The sequences were edited to assess the performance of sequencing primers at their presumed binding regions. The Polymorphism was studied in the regions between the sequences of Senegalese patients and the subtype B strains used as references. The phylogenetic analysis showed a predominance of CRF02&#95;AG (88/150; 58.7%) and the circulation of 11 subtypes/CRFs, 16 unique recombinant forms (URFs) and one unclassified sample. The amplification and sequencing rates were 98% (147/150) and 96.6% (142/147), respectively. This study showed that only primer B exhibited 100% success, while the failure rate ranged from 1.4% to 71.4% for the other primers (D: 71.4%, A and H: 12.2%, F: 7.5%, G: 5.5% and C: 1.4%). These findings suggest the need for an alternative method or alternative primers for non-B strains that were not sequenced successfully using the ViroSeq HIV-1 Genotyping System v2.0.<br /> (Copyright © 2012 Elsevier B.V. All rights reserved.)
Details
- Language :
- English
- ISSN :
- 1879-0984
- Volume :
- 188
- Issue :
- 1-2
- Database :
- MEDLINE
- Journal :
- Journal of virological methods
- Publication Type :
- Academic Journal
- Accession number :
- 23266258
- Full Text :
- https://doi.org/10.1016/j.jviromet.2012.11.044