title: Development, evaluation, and validation of an oligonucleotide probe hybridization assay to subtype human immunodeficiency virus type 1 circulating recombinant form CRF02_AG.
abstract: We have developed and validated an oligonucleotide probe hybridization assay for human immunodeficiency virus type 1 (HIV-1) circulating recombinant form (CRF) CRF02_AG. In the p17 coding region of the gag gene, a CRF02_AG-specific signature pattern was observed. Five working probes were designed to discriminate CRF02_AG infections from infections by all other documented subtypes and CRFs in an enzyme-linked immunosorbent assay-based oligonucleotide probe hybridization assay. Nucleic acids were extracted from a panel of HIV-1-positive plasma samples from Cameroon, Bénin, Côte d'Ivoire, Kenya, Zambia, and Belgium and from blood spots from The Gambia. CRF02_AG (n = 147) and non-CRF02 (n = 100) samples were analyzed to evaluate and validate the oligonucleotide probe hybridization assay. The CRF02_AG-specific oligonucleotide probe hybridization assay has a high sensitivity and specificity, with good positive and negative predictive values in regions of high and low prevalence. A validation of the assay with West and West Central African samples indicated a sensitivity of 98.4% and a specificity of 96.7%. The oligonucleotide probe hybridization assay as a diagnostic tool will allow for rapid screening for CRF02_AG. This could be used to track the HIV epidemic in terms of documenting the real prevalence of CRF02_AG strains and will complement efforts in vaccine development. Moreover, this technology can easily be applied in laboratories in developing countries.
authors.affiliation: Department of Microbiology, Institute of Tropical Medicine, Antwerp.
authors.forename: Harr F
authors.initials: HF
authors.lastname: Njai
authors.forename: Gert
authors.initials: G
authors.lastname: Van der Auwera
authors.forename: Chiambah A
authors.initials: CA
authors.lastname: Ngong
authors.forename: Leo
authors.initials: L
authors.lastname: Heyndrickx
authors.forename: Souleymane
authors.initials: S
authors.lastname: Sawadago
authors.forename: Hilton
authors.initials: H
authors.lastname: Whittle
authors.forename: Phillipe
authors.initials: P
authors.lastname: Nyambi
authors.forename: Robert
authors.initials: R
authors.lastname: Colebunders
authors.forename: Guido
authors.initials: G
authors.lastname: van der Groen
authors.forename: Wouter
authors.initials: W
authors.lastname: Janssens
mesh_terms: D001483:Base Sequence; D015683:Gene Products, gag / Q000235:genetics; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization / Q000379:methods*; D015345:Oligonucleotide Probes / Q000235:genetics*; D011995:Recombination, Genetic; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
chemical_list: D015683:Gene Products, gag; D015345:Oligonucleotide Probes