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Variability in HIV-1 partial genomic sequences in Costa Rican patients: analysis with different bioinformatics tools.

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Title: Variability in HIV-1 partial genomic sequences in Costa Rican patients: analysis with different bioinformatics tools.
Alternate Title: Variabilidad de secuencias genómicas parciales del VIH-1 en pacientes costarricenses: análisis con diferentes herramientas bioinformáticas.
Authors: Taylor-Castillo, Lizeth1 MAYRA.TAYLOR@ucr.co.cr., León-Bratti, María Paz, Solano-Chinchilla, Antonio, Herrera-Martínez, Gisela, Boza-Cordero, Ricardo, León, Bernal, Luftig, Ronald B., Visoná, Kirsten
Source: Pan American Journal of Public Health / Revista Panamericana de Salud Pública. Jan2010, Vol. 27 Issue 1, p23-31. 9p.
Subjects: HIV infection genetics, HIV, BIOINFORMATICS, GENOMIC information retrieval, COMPUTATIONAL biology, GENETICS
Geographic Terms: COSTA Rica
Abstract (English): Objective. To estimate subtype and genomic variability in the HIV pol gene of Costa Rican patients by using different bioinformatics tools and to use this information to establish new policies to better manage these patients. Methods. A total of 113 pol sequences available from Costa Rican patients under highly active antiretroviral therapy were analyzed by using the Genotyping, REGA, Stanford, and MEGA programs. The pol sequences came from 77 virologic failures (VF) and 36 basal samples (BS). Of the 77 VF, 22 also were sequenced in the env region. Results. No major differences were found among the variables studied. However, there was a tendency for more variability in VF patients with a high baseline viral load. In the pol gene, 75%-83% of BS and 66%-75% of VF samples were pure B subtype by Genotyping and REGA, respectively. The other samples presented variations related mainly to circulating recombinant form CRF12 by genotyping or to CRF17 or -29 by phylogenetic analysis or a new possible BD recombinant with all programs. In the Stanford program, all variable samples showed a subtype B with high polymorphism. The variability in the env sequences was lower than that in the pol region. Conclusion. The B subtype is predominant in Costa Rican HIV-positive patients. There is high variability within sequences with potential recombination between B and F or D subtypes. The BD recombinant has not been previously reported. This high variability is likely the result of possible recombinant events, nonadherence to antiretroviral therapy, sexual intercourse without protection, and many sexual partners. Similar studies should be done in other countries in the Region, in particular in those places with extensive immigration, in order to decrease the possibility of virus variability as well as the cost of antiretroviral therapy. [ABSTRACT FROM AUTHOR]
Abstract (Spanish): Objetivos. Determinar el subtipo y la variabilidad genómica del gen pol del VIH de pacientes costarricenses mediante diferentes herramientas bioinformáticas y el uso de esta información para establecer nuevas políticas para mejorar el diagnóstico y el tratamiento de estos pacientes. Métodos. Se analizaron 113 secuencias del gen pol de pacientes costarricenses bajo tratamiento antirretrovírico de gran actividad mediante cuatro programas: Genotyping, REGA, Stanford y MEGA. Las secuencias pol analizadas provenían de 77 casos considerados fracasos virológicos (FV) y 36 muestras iniciales (MI). También se secuenció la región env de 22 de los 77 FV. Resultados. No se encontraron diferencias importantes entre las variables estudiadas. No obstante, se observó una tendencia a una mayor variabilidad en los pacientes FV que tenían una elevada carga viral inicial. Con respecto al gen pol, 77-83% de las MI y 66-75% de las muestras de los FV eran del subtipo B puro según Genotyping y REGA, respectivamente. Las otras muestras presentaron variaciones relacionadas principalmente con la forma recombinante en circulación CRF-12 según Genotyping, con la CRF-17 o la CRF-29 según el análisis filogenético, o una nueva posible forma recombinante BD según todos los programas. Con el programa Stanford, todas las muestras variables reflejaron un subtipo B con elevado polimorfismo. La variabilidad de la secuencia env fue menor que la de la región pol. Conclusiones. El subtipo B fue el predominante en los pacientes positivos al VIH en Costa Rica. Existe una alta variabilidad en las secuencias con una posible recombinación entre los subtipos B, y F o D. La forma recombinante BD no se había notificado antes. Esta elevada variabilidad parece ser el resultado de posibles eventos de recombinación, la falta de adhesión al tratamiento antirretrovírico, las relaciones sexuales sin protección y numerosas parejas sexuales. Se deben emprender estudios similares en otros países de la Región, en particular en los lugares con mucha inmigración, para reducir tanto la posibilidad de que el virus varíe como el costo del tratamiento antirretrovírico. [ABSTRACT FROM AUTHOR]
Copyright of Pan American Journal of Public Health / Revista Panamericana de Salud Pública is the property of Pan American Health Organization and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Variability in HIV-1 partial genomic sequences in Costa Rican patients: analysis with different bioinformatics tools.
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  Data: Variabilidad de secuencias genómicas parciales del VIH-1 en pacientes costarricenses: análisis con diferentes herramientas bioinformáticas.
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  Data: <searchLink fieldCode="AR" term="%22Taylor-Castillo%2C+Lizeth%22">Taylor-Castillo, Lizeth</searchLink><relatesTo>1</relatesTo><i> MAYRA.TAYLOR@ucr.co.cr.</i><br /><searchLink fieldCode="AR" term="%22León-Bratti%2C+María+Paz%22">León-Bratti, María Paz</searchLink><br /><searchLink fieldCode="AR" term="%22Solano-Chinchilla%2C+Antonio%22">Solano-Chinchilla, Antonio</searchLink><br /><searchLink fieldCode="AR" term="%22Herrera-Martínez%2C+Gisela%22">Herrera-Martínez, Gisela</searchLink><br /><searchLink fieldCode="AR" term="%22Boza-Cordero%2C+Ricardo%22">Boza-Cordero, Ricardo</searchLink><br /><searchLink fieldCode="AR" term="%22León%2C+Bernal%22">León, Bernal</searchLink><br /><searchLink fieldCode="AR" term="%22Luftig%2C+Ronald+B%2E%22">Luftig, Ronald B.</searchLink><br /><searchLink fieldCode="AR" term="%22Visoná%2C+Kirsten%22">Visoná, Kirsten</searchLink>
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  Data: <searchLink fieldCode="JN" term="%22Pan+American+Journal+of+Public+Health+%2F+Revista+Panamericana+de+Salud+Pública%22">Pan American Journal of Public Health / Revista Panamericana de Salud Pública</searchLink>. Jan2010, Vol. 27 Issue 1, p23-31. 9p.
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  Data: <searchLink fieldCode="DE" term="%22HIV+infection+genetics%22">HIV infection genetics</searchLink><br /><searchLink fieldCode="DE" term="%22HIV%22">HIV</searchLink><br /><searchLink fieldCode="DE" term="%22BIOINFORMATICS%22">BIOINFORMATICS</searchLink><br /><searchLink fieldCode="DE" term="%22GENOMIC+information+retrieval%22">GENOMIC information retrieval</searchLink><br /><searchLink fieldCode="DE" term="%22COMPUTATIONAL+biology%22">COMPUTATIONAL biology</searchLink><br /><searchLink fieldCode="DE" term="%22GENETICS%22">GENETICS</searchLink>
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  Data: <searchLink fieldCode="DE" term="%22COSTA+Rica%22">COSTA Rica</searchLink>
– Name: Abstract
  Label: Abstract (English)
  Group: Ab
  Data: Objective. To estimate subtype and genomic variability in the HIV pol gene of Costa Rican patients by using different bioinformatics tools and to use this information to establish new policies to better manage these patients. Methods. A total of 113 pol sequences available from Costa Rican patients under highly active antiretroviral therapy were analyzed by using the Genotyping, REGA, Stanford, and MEGA programs. The pol sequences came from 77 virologic failures (VF) and 36 basal samples (BS). Of the 77 VF, 22 also were sequenced in the env region. Results. No major differences were found among the variables studied. However, there was a tendency for more variability in VF patients with a high baseline viral load. In the pol gene, 75%-83% of BS and 66%-75% of VF samples were pure B subtype by Genotyping and REGA, respectively. The other samples presented variations related mainly to circulating recombinant form CRF12 by genotyping or to CRF17 or -29 by phylogenetic analysis or a new possible BD recombinant with all programs. In the Stanford program, all variable samples showed a subtype B with high polymorphism. The variability in the env sequences was lower than that in the pol region. Conclusion. The B subtype is predominant in Costa Rican HIV-positive patients. There is high variability within sequences with potential recombination between B and F or D subtypes. The BD recombinant has not been previously reported. This high variability is likely the result of possible recombinant events, nonadherence to antiretroviral therapy, sexual intercourse without protection, and many sexual partners. Similar studies should be done in other countries in the Region, in particular in those places with extensive immigration, in order to decrease the possibility of virus variability as well as the cost of antiretroviral therapy. [ABSTRACT FROM AUTHOR]
– Name: Abstract
  Label: Abstract (Spanish)
  Group: Ab
  Data: Objetivos. Determinar el subtipo y la variabilidad genómica del gen pol del VIH de pacientes costarricenses mediante diferentes herramientas bioinformáticas y el uso de esta información para establecer nuevas políticas para mejorar el diagnóstico y el tratamiento de estos pacientes. Métodos. Se analizaron 113 secuencias del gen pol de pacientes costarricenses bajo tratamiento antirretrovírico de gran actividad mediante cuatro programas: Genotyping, REGA, Stanford y MEGA. Las secuencias pol analizadas provenían de 77 casos considerados fracasos virológicos (FV) y 36 muestras iniciales (MI). También se secuenció la región env de 22 de los 77 FV. Resultados. No se encontraron diferencias importantes entre las variables estudiadas. No obstante, se observó una tendencia a una mayor variabilidad en los pacientes FV que tenían una elevada carga viral inicial. Con respecto al gen pol, 77-83% de las MI y 66-75% de las muestras de los FV eran del subtipo B puro según Genotyping y REGA, respectivamente. Las otras muestras presentaron variaciones relacionadas principalmente con la forma recombinante en circulación CRF-12 según Genotyping, con la CRF-17 o la CRF-29 según el análisis filogenético, o una nueva posible forma recombinante BD según todos los programas. Con el programa Stanford, todas las muestras variables reflejaron un subtipo B con elevado polimorfismo. La variabilidad de la secuencia env fue menor que la de la región pol. Conclusiones. El subtipo B fue el predominante en los pacientes positivos al VIH en Costa Rica. Existe una alta variabilidad en las secuencias con una posible recombinación entre los subtipos B, y F o D. La forma recombinante BD no se había notificado antes. Esta elevada variabilidad parece ser el resultado de posibles eventos de recombinación, la falta de adhesión al tratamiento antirretrovírico, las relaciones sexuales sin protección y numerosas parejas sexuales. Se deben emprender estudios similares en otros países de la Región, en particular en los lugares con mucha inmigración, para reducir tanto la posibilidad de que el virus varíe como el costo del tratamiento antirretrovírico. [ABSTRACT FROM AUTHOR]
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  Data: <i>Copyright of Pan American Journal of Public Health / Revista Panamericana de Salud Pública is the property of Pan American Health Organization and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1590/S1020-49892010000100004
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