title: An improved algorithm for determining HIV type 1 subtypes in a primary laboratory in Uganda.
abstract: A pilot study was undertaken with the objective of developing a simple, economical, and efficient algorithm through which to subtype HIV-1 in a large epidemiological cohort study in Uganda. A peptide enzyme immunoassay (PEIA) employing both V3 and gp41 regions and a heteroduplex mobility assay (HMA) were evaluated in comparison with DNA sequencing. Of 146 samples selected, 115 (79%) were successfully sequenced. Taking sequence data as the "gold standard," other assays were compared with these data. The HMA correctly identified 95 (83%) of the samples, and only 1 sample was wrongly identified. The V3 PEIA alone and in combination with gp41 peptides correctly identified 76 and 78% of the samples, respectively; however, the number of wrongly identified samples was four times less with the combination compared with V3 peptides alone (4 versus 16%). The sensitivity, specificity, and positive and negative predictive values for serotype A and D samples were greater for the combination than V3 peptides alone. We have described a new algorithm to segregate subtypes A and D. This algorithm uses the two peptide assays followed by HMA and then DNA sequencing for untypable samples, giving an accuracy of 95% at a cost of 37 and 21% for consumables compared with subtyping all the samples by HMA or DNA sequencing, respectively. This proposed approach is suitable for epidemiological studies in Uganda and other regions with a predominance of A and D subtypes.
authors.affiliation: Medical Research Council Programme on AIDS in Uganda, Uganda Virus Research Institute, Entebbe. mrc@starcom.co.ug
authors.forename: P
authors.initials: P
authors.lastname: Kaleebu
authors.forename: D
authors.initials: D
authors.lastname: Yirrell
authors.forename: N
authors.initials: N
authors.lastname: French
authors.forename: F
authors.initials: F
authors.lastname: Lyagoba
authors.forename: A
authors.initials: A
authors.lastname: Rutebemberwa
authors.forename: R
authors.initials: R
authors.lastname: Cheingsong-Popov
authors.forename: C
authors.initials: C
authors.lastname: Gilks
authors.forename: B
authors.initials: B
authors.lastname: Biryahwaho
authors.forename: J
authors.initials: J
authors.lastname: Weber
authors.forename: J
authors.initials: J
authors.lastname: Whitworth
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D015699:HIV Envelope Protein gp120 / Q000737:chemistry / Q000235:genetics / Q000276:immunology; D015700:HIV Envelope Protein gp41 / Q000737:chemistry / Q000235:genetics / Q000276:immunology; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000276:immunology; D020180:Heteroduplex Analysis; D006801:Humans; D007124:Immunoenzyme Techniques; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry / Q000235:genetics / Q000276:immunology; D010455:Peptides / Q000276:immunology; D010865:Pilot Projects; D011237:Predictive Value of Tests; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D012703:Serotyping; D014454:Uganda / Q000453:epidemiology
chemical_list: D015699:HIV Envelope Protein gp120; D015700:HIV Envelope Protein gp41; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments; D010455:Peptides