title: Testing a subtype-specific gp41 amplification method for genotyping individuals infected by human immunodeficiency virus type-1 in the Brazilian population of Itajaí, South Brazil.
abstract: The method used by YAGYU et al. for the subtype-specific polymerase chain reaction (PCR) amplification of the gp41 transmembrane region of the human immunodeficiency virus type-1 (HIV-1) env gene, was tested. HIV-1 proviral DNA from 100 infected individuals in Itajaí, South Brazil was used to analyze this method. Seventy individuals were determined according to this method as having PCR products at the expected size for subtypes B, C, D and F. Of these individuals, 26 (37.1%) were observed as having the expected amplification for subtype C, and 42 (60%) were observed as having the expected products for subtypes B and D. Of the subtype B and D amplicons, 16 (22.9%) were classified as subtype D, and 26 (37.1%) were classified as subtype B. Two individuals (2.9%) had amplicons that were observed after subtype F-specific amplification was performed. Sequencing and comparing the patient sequences to reference sequences confirmed the classification of sequences of subtypes C and B. However, sequences that were falsely determined as being D and F in the PCR assay were determined as being subtypes C and B, respectively, by sequence analysis. For those individuals from whom no amplified products were obtained, a low viral load that was indicated in their patient history may explain the difficulty in subtyping by PCR methods. This issue was demonstrated by the results of ANOVA when testing the effect of viral load on the success of PCR amplification. The alignment of the obtained sequences with HIV-1 reference sequences demonstrated that there is high intra-subtype diversity. This indicates that the subtype-specific primer binding sites were not conserved or representative of the subtypes that are observed in the Brazilian populations, and that they did not allow the correct classification of HIV-1 subtypes. Therefore, the proposed method by YAGYU et al. is not applicable for the classification of Brazilian HIV-1 subtypes.
authors.affiliation: Laboratório de Genética Molecular, CTTMar, Universidade do Vale do Itajaí-UNIVALI, Santa Catarina, Brazil. libarbara@usp.br
authors.forename: Liã Bárbara
authors.initials: LB
authors.lastname: Arruda
authors.forename: Laura I
authors.initials: LI
authors.lastname: Weber
authors.forename: Marisa dos
authors.initials: Md
authors.lastname: Santos
authors.forename: Edson M
authors.initials: EM
authors.lastname: Kawakubo
authors.forename: Ana Maria B
authors.initials: AM
authors.lastname: Martínez
mesh_terms: D000328:Adult; D001938:Brazil; D004279:DNA, Viral / Q000235:genetics*; D005260:Female; D005838:Genotype; D015700:HIV Envelope Protein gp41 / Q000235:genetics*; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D019562:Viral Load; D055815:Young Adult
chemical_list: D004279:DNA, Viral; D015700:HIV Envelope Protein gp41; C514787:gp41 protein, Human immunodeficiency virus 1