Publications des scientifiques de l'IRD

Thiam M., Diop-Ndiaye H., Kebe K., Vidal Nicole, Diakhate-Lo R., Diouara A. M., Leye N., Ndiaye O., Sow A., Ngom-Gueye N. F., Mboup S., Toure-Kane C. (2013). Performance of the ViroSeq HIV-1 genotyping system v2.0 on HIV-1 strains circulating in Senegal. Journal of Virological Methods, 188 (1-2), p. 97-103. ISSN 0166-0934.

Titre du document
Performance of the ViroSeq HIV-1 genotyping system v2.0 on HIV-1 strains circulating in Senegal
Année de publication
2013
Type de document
Article référencé dans le Web of Science WOS:000316836000018
Auteurs
Thiam M., Diop-Ndiaye H., Kebe K., Vidal Nicole, Diakhate-Lo R., Diouara A. M., Leye N., Ndiaye O., Sow A., Ngom-Gueye N. F., Mboup S., Toure-Kane C.
Source
Journal of Virological Methods, 2013, 188 (1-2), p. 97-103 ISSN 0166-0934
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 CRFO2_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.
Plan de classement
Sciences fondamentales / Techniques d'analyse et de recherche [020] ; Entomologie médicale / Parasitologie / Virologie [052] ; Biotechnologies [084]
Description Géographique
SENEGAL
Localisation
Fonds IRD [F B010060786]
Identifiant IRD
fdi:010060786
Contact