title: Performance of the ViroSeq HIV-1 genotyping system v2.0 on HIV-1 strains circulating in Senegal.
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_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.
authors.affiliation: Laboratory of Bacteriology and Virology, Le Dantec Hospital, Dakar, Senegal.
authors.forename: Moussa
authors.initials: M
authors.lastname: Thiam
authors.forename: Halimatou
authors.initials: H
authors.lastname: Diop-Ndiaye
authors.forename: Khady
authors.initials: K
authors.lastname: Kebe
authors.forename: Nicole
authors.initials: N
authors.lastname: Vidal
authors.forename: Rokhaya
authors.initials: R
authors.lastname: Diakhate-Lô
authors.forename: Abou Abdallah Malick
authors.initials: AA
authors.lastname: Diouara
authors.forename: Nafissatou
authors.initials: N
authors.lastname: Leye
authors.forename: Ousseynou
authors.initials: O
authors.lastname: Ndiaye
authors.forename: Amina
authors.initials: A
authors.lastname: Sow
authors.forename: Ndeye Fatou
authors.initials: NF
authors.lastname: Ngom-Gueye
authors.forename: Souleymane
authors.initials: S
authors.lastname: Mboup
authors.forename: Coumba
authors.initials: C
authors.lastname: Toure-Kane
mesh_terms: D000328:Adult; D000368:Aged; D017931:DNA Primers / Q000235:genetics; D014644:Genetic Variation; D005838:Genotype; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D058889:Molecular Typing / Q000379:methods*; D012675:Senegal; D017422:Sequence Analysis, DNA; D055815:Young Adult
chemical_list: D017931:DNA Primers