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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

Arruda, Liã Bárbara ; Weber, Laura I ; Santos, Marisa dos ; Kawakubo, Edson M ; Martínez, Ana Maria B

Revista do Instituto de Medicina Tropical de São Paulo, 2013-03, Vol.55 (2), p.91-99 [Periódico revisado por pares]

Brazil: Instituto de Medicina Tropical de Sao Paulo

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  • Título:
    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
  • Autor: Arruda, Liã Bárbara ; Weber, Laura I ; Santos, Marisa dos ; Kawakubo, Edson M ; Martínez, Ana Maria B
  • Assuntos: Adult ; Brazil ; DNA, Viral - genetics ; Female ; Genotype ; HIV Envelope Protein gp41 - genetics ; HIV Infections - virology ; HIV-1 - genetics ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; Polymerase Chain Reaction ; Reproducibility of Results ; Sequence Analysis, DNA ; TROPICAL MEDICINE ; Viral Load ; Young Adult
  • É parte de: Revista do Instituto de Medicina Tropical de São Paulo, 2013-03, Vol.55 (2), p.91-99
  • Notas: ObjectType-Article-1
    SourceType-Scholarly Journals-1
    ObjectType-Feature-2
    content type line 23
  • Descrição: 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.
  • Editor: Brazil: Instituto de Medicina Tropical de Sao Paulo
  • Idioma: Inglês;Português
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