title: Genotyping of B and non-B subtypes of human immunodeficiency virus type 1.
abstract: Current HIV-1 genotyping assays were developed using subtype B viruses prevalent in Western countries. It is not clear whether these assays are appropriate for use among African patients, who are likely to be infected with non-B subtypes. We evaluated the Bayer TRUGENE HIV-1 genotyping (TG) assay using prospectively collected samples from HIV-1-infected individuals who acquired infection in either sub-Saharan Africa or the West (Europe, North America, and Australia). Plasma samples from 208 individuals with an HIV-1 viral load of >1,000 copies/ml were tested using version 1 primers supplied with the TG assay. If these failed, an alternative primer set version 1.5 was used. Of the 208 individuals, the likely origin of infection was Africa (n = 104), Western (n = 87) and "Others" (i.e., all other geographic locations or origin not certain; n = 17). Among the three groups, the version 1 primers were successful in 85 (82%), 77 (89%), and 13 (76%) individuals, respectively (P = 0.1). Of the remaining 32 samples, 30 were successfully amplified by using the version 1.5 primers. HIV-1 subtypes deduced from the reverse transcriptase sequences correlated with the likely origin of infection: Africa (28A, 3B, 33C, 13D, 6G, 4J, 2K, 5CRF01_AE, and 10CRF02_AG), Western (86B and 1K), and Others (1A and 16B). The success of the version 1 primers correlated with viral load (P < 0.014) and not with HIV-1 subtypes. A protocol based on version 1 primers, followed by 1.5 primers, was successful in sequencing 99% of the samples in this cohort.
authors.affiliation: Department of Infection, St. Thomas' Hospital, London, UK.
authors.forename: C Y W
authors.initials: CY
authors.lastname: Tong
authors.forename: J
authors.initials: J
authors.lastname: Mullen
authors.forename: R
authors.initials: R
authors.lastname: Kulasegaram
authors.forename: A
authors.initials: A
authors.lastname: De Ruiter
authors.forename: S
authors.initials: S
authors.lastname: O'Shea
authors.forename: I L
authors.initials: IL
authors.lastname: Chrystie
mesh_terms: D000293:Adolescent; D000328:Adult; D001315:Australia; D002648:Child; D017931:DNA Primers; D024882:Drug Resistance, Viral / Q000235:genetics*; D005060:Europe; D005260:Female; D005838:Genotype; D015658:HIV Infections / Q000821:virology*; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000145:classification* / Q000187:drug effects / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D009656:North America; D012367:RNA, Viral / Q000097:blood; D011933:Reagent Kits, Diagnostic; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D012367:RNA, Viral; D011933:Reagent Kits, Diagnostic; D054303:HIV Reverse Transcriptase