title: Molecular genotyping of HIV-1 in 61 patients with AIDS from Lomé, Togo.
abstract: To study the distribution of HIV types and genotypes, in Lomé, Togo, a random population of patients who met the clinical criteria of the Bangui definition of AIDS and were positive with two independent screening assays for antibodies to HIV-1 group M, HIV-2, and HIV-1 group O was selected. HIV RNA from serum samples was reverse-transcribed and amplified with degenerate primers annealing to conserved regions of the HIV-1, HIV-2, and HIV-O gag gene. Amplicons were directly sequenced using an automated sequencer. A 262-271-bp (strain-dependent) fragment of the gag gene from each patient was phylogenetically analyzed and compared to the corresponding gag sequences of published HIV-1 sequences of known African genotypes. Genotype A was found in 48 of 60 patient amplicons (80%), subdivided into two clusters. Ten patients (16.7%) were HIV-1 genotype G; one was genotype D and one genotype H. HIV-1 genotype B was not found. Amplicons from two patients contained sequence ambiguities, requiring cloning and sequencing of the gag insert. One patient (T52) was apparently infected with HIV-1 genotypes A and G; whereas HIV-1 from patient T139 was of genotype A, with 2/10 clones having a three-codon insertion at nucleotide position 1142 of the gag gene. HIV-1 genotype A is dominant in Togo; genotype G is frequent and genotype B has not been found.
authors.affiliation: Department of Haematology, University of Cambridge, England.
authors.forename: F J
authors.initials: FJ
authors.lastname: Davies
authors.forename: O
authors.initials: O
authors.lastname: d'Almeida
authors.forename: E
authors.initials: E
authors.lastname: Timmers
authors.forename: J
authors.initials: J
authors.lastname: d'Ameida
authors.forename: M
authors.initials: M
authors.lastname: Fasken
authors.forename: K
authors.initials: K
authors.lastname: Bassabi
authors.forename: H
authors.initials: H
authors.lastname: Lee
authors.forename: J P
authors.initials: JP
authors.lastname: Allain
mesh_terms: D000163:Acquired Immunodeficiency Syndrome / Q000453:epidemiology / Q000821:virology*; D000328:Adult; D000914:Antibodies, Viral / Q000097:blood; D000918:Antibody Specificity; D005260:Female; D015750:Genes, gag / Q000235:genetics; D005838:Genotype; D015497:HIV-1 / Q000235:genetics* / Q000276:immunology; D015498:HIV-2 / Q000276:immunology; D006801:Humans; D008297:Male; D017720:Molecular Epidemiology; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000097:blood / Q000235:genetics; D014037:Togo / Q000453:epidemiology
chemical_list: D000914:Antibodies, Viral; D012367:RNA, Viral