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 analyz...
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ftdoajarticles:oai:doaj.org/article:d732468d279047beb8714d9869bd1219 2023-05-15T15:18:31+02:00 Liã Bárbara Arruda Laura I. Weber Marisa dos Santos Edson M. Kawakubo Ana Maria B. Martínez 2013-04-01T00:00:00Z https://doaj.org/article/d732468d279047beb8714d9869bd1219 EN PT eng por Universidade de São Paulo http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0036-46652013000200091 https://doaj.org/toc/0036-4665 https://doaj.org/toc/1678-9946 0036-4665 1678-9946 https://doaj.org/article/d732468d279047beb8714d9869bd1219 Revista do Instituto de Medicina Tropical de São Paulo, Vol 55, Iss 2, Pp 91-99 (2013) HIV-1 gp41 Viral load Subtypes PCR South Brazil Arctic medicine. Tropical medicine RC955-962 article 2013 ftdoajarticles 2023-01-08T01:30:26Z 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. A metodologia para amplificação subtipo-específica por PCR da região transmembrana do gene env ... Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English Portuguese |
topic |
HIV-1 gp41 Viral load Subtypes PCR South Brazil Arctic medicine. Tropical medicine RC955-962 |
spellingShingle |
HIV-1 gp41 Viral load Subtypes PCR South Brazil Arctic medicine. Tropical medicine RC955-962 Liã Bárbara Arruda Laura I. Weber Marisa dos Santos Edson M. Kawakubo Ana Maria B. Martínez |
topic_facet |
HIV-1 gp41 Viral load Subtypes PCR South Brazil Arctic medicine. Tropical medicine RC955-962 |
description |
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. A metodologia para amplificação subtipo-específica por PCR da região transmembrana do gene env ... |
format |
Article in Journal/Newspaper |
author |
Liã Bárbara Arruda Laura I. Weber Marisa dos Santos Edson M. Kawakubo Ana Maria B. Martínez |
author_facet |
Liã Bárbara Arruda Laura I. Weber Marisa dos Santos Edson M. Kawakubo Ana Maria B. Martínez |
author_sort |
Liã Bárbara Arruda |
publisher |
Universidade de São Paulo |
publishDate |
2013 |
url |
https://doaj.org/article/d732468d279047beb8714d9869bd1219 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Revista do Instituto de Medicina Tropical de São Paulo, Vol 55, Iss 2, Pp 91-99 (2013) |
op_relation |
http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0036-46652013000200091 https://doaj.org/toc/0036-4665 https://doaj.org/toc/1678-9946 0036-4665 1678-9946 https://doaj.org/article/d732468d279047beb8714d9869bd1219 |
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1766348719550103552 |