Application of PolyPRep tools on HIV protease polyproteins using molecular docking / Aplicação da ferramenta PolyPRep em poliproteínas de protease de HIV usando docking molecular

Abstract In recent years, the development of high-throughput technologies for obtaining sequence data leveraged the possibility of analysis of protein data in silico. However, when it comes to viral polyprotein interaction studies, there is a gap in the representation of those proteins, given their size and length. The prepare for studies using state-of-the-art techniques such as Machine Learning, a good representation of such proteins is a must. We present an alternative to this problem, implementing a fragmentation and modeling protocol to prepare those polyproteins in the form of peptide fragments. Such procedure is made by several scripts, implemented together on the workflow we call PolyPRep, a tool written in Python script and available in GitHub. This software is freely available only for noncommercial users.

Resumo Nos últimos anos, o desenvolvimento de tecnologias de alto rendimento para obtenção de dados sequenciais potencializou a possibilidade de análise de dados proteicos in silico. No entanto, quando se trata de estudos de interação de poliproteínas virais, existe uma lacuna na representação dessas proteínas, devido ao seu tamanho e comprimento. Para estudos utilizando técnicas de ponta como o Aprendizado de Máquina, uma boa representação dessas proteínas é imprescindível. Apresentamos uma alternativa para este problema, implementando um protocolo de fragmentação e modelagem para preparar essas poliproteínas na forma de fragmentos de peptídeos. Tal procedimento é feito por diversos scripts, implementados em conjunto no workflow que chamamos de PolyPRep, uma ferramenta escrita em script Python e disponível no GitHub. Este software está disponível gratuitamente apenas para usuários não comerciais.

Genetic diversity and primary resistance among HIV-1-positive patients from Maringá, Paraná, Brazil / Diversidade genética e resistência primária entre pacientes HIV-1-positivos de Maringá, Paraná, Brasil

The objective of this study is to identify subtypes of Human Immunodeficiency Virus type 1 (HIV-1) and to analyze the presence of mutations associated to antiretroviral resistance in the protease (PR) and reverse transcriptase (RT) regions from 48 HIV-1 positive treatment naïve patients from an outpatient clinic in Maringá, Paraná, Brazil. Sequencing was conducted using PR, partial RT and group-specific antigen gene (gag) nested PCR products from retrotranscribed RNA. Transmitted resistance was determined according to the Surveillance Drug Resistance Mutation List (SDRM) algorithm. Phylogenetic and SimPlot analysis of concatenated genetic segments classified sequences as subtype B 19/48 (39.6%), subtype C 12/48 (25%), subtype F 4/48 (8.3%), with 13/48 (27.1%) recombinant forms. Most recombinant forms were B mosaics (B/F 12.5%, B/C 10.4%), with one C/F (2.1%) and one complex B/C/F mosaic (2.1%). Low levels of transmitted resistance were found in this study, 2/48 (2.1% to NRTIs and 2.1% for PI). This preliminary data may subsidize the monitoring of the HIV evolution in the region.

O objetivo foi identificar subtipos do Vírus da Imunodeficiência Humana tipo-1 (HIV-1) e analisar a presença de mutações/polimorfismos nas regiões da protease (PR) e transcriptase reversa (TR) de 48 pacientes virgens de tratamento atendidos no município de Maringá, Paraná, Brasil. O sequenciamento foi conduzido usando produtos de nested PCR dos genes da PR, TR parcial e group-specific antigen gene (gag) de RNA retrotranscrito. A interpretação da resistência transmitida foi realizada segundo o algoritmo Surveillance Drug Resistance Mutation List (SDRM). As análises filogenética e SimPlot dos segmentos concatenados classificaram as sequências como subtipo B 19/48 (39,6%), subtipo C 12/48 (25%), subtipo F 4/48 (8,3%), com 13/48 (27,1%) formas recombinantes. A maioria das formas recombinantes era mosaicos B (B/F 12,5%, B/C 10,4%), com um C/F (2,1%) e um mosaico complexo B/C/F (2,1%). A prevalência de resistência transmitida foi de 4,2% (2,1% para ITRN e 2,1% para IP). Baixos níveis de resistência transmitida foram encontrados nesse estudo, 2/48 (2,1% para INTR e 2,1% para IP). Esses achados, embora preliminares, podem contribuir no monitoramento da epidemia de HIV na região.

Primary resistance of HIV to antiretrovirals among individuals recently diagnosed at voluntary counselling and testing centres in the metropolitan region of Recife, Pernambuco

Determining the prevalence and type of antiretroviral (ARV) resistance among ARV-naïve individuals is important to assess the potential responses of these individuals to first-line regimens. The prevalence of primary resistance and the occurrence of recent infections among individuals with human immunodeficiency virus (HIV)/acquired immune deficiency syndrome (AIDS) were identified among recently diagnosed patients at five sexually transmitted disease/AIDS testing and counselling centres in the metropolitan region of Recife (RMR), Pernambuco, Brazil, between 2007-2009. One-hundred and eight samples were analysed using the Calypte® BED assay. Males predominated (56%), as did patients aged 31-50 years. Twenty-three percent presented evidence of a recent HIV infection. The median CD4+ T lymphocyte count was 408 cells/mm³ and the median viral load was 3.683 copies/mL. The prevalence of primary resistance was 4.6% (confidence interval 95% = 1-8.2%) based on criteria that excluded common polymorphisms in accordance with the surveillance drug resistance mutation criteria. The prevalence of resistance to non-nucleoside reverse transcriptase, nucleoside/nucleotide reverse transcriptase and protease inhibitors were 3.8%, 1.5% and 0.8%, respectively. Fifty-seven percent of strains were from clade B, 37.7% were clade F and 3.1% were clade C; there were no statistically significant differences with respect to resistance between clades. Recent infection tended to be more common in men (p = 0.06) and in municipalities in the south of the RMR (Jaboatão dos Guararapes and Cabo de Santo Agostinho) (p = 0.046). The high prevalence of recent infection and the high prevalence of non-B strains in this poor Brazilian region merit further attention.

HIV transmitted drug resistance in adult and pediatric populations in Panama / Farmacorresistencia transmitida del VIH en poblaciones adultas y pediátricas en Panamá

Objetivo. Investigar la prevalencia de farmacorresistencia transmitida del VIH en adultos en Panamá mediante un estudio del umbral modificado de la Organización Mundial de la Salud (OMS) e investigar las tasas de resistencia inicial en lactantesseropositivos para el VIH en Panamá.Métodos. En el Instituto Conmemorativo Gorgas, en 47 adultos seropositivos al VIH se efectuó la genotipificación de las mutaciones asociadas con la farmacorresistencia transmitida en los genes de la transcriptasa inversa y la proteasa del VIH-1, según las directrices del estudio umbral de la OMS, modificadas para incluir a las personas ≤ 26 años de edad. Las tasas de prevalencia de las mutaciones farmacorresistentes contra tres clases de fármacos antirretroviral —inhibidores de la transcriptasa inversaanálogos de nucleósidos, inhibidores de la transcriptasa inversa no análogos de nucleósidos e inhibidores de la proteasa— se clasificaron en bajas (< 5,0%), moderadas (5,0%–15,0%) o altas (> 15,0%). También se llevó a cabo genotipificación y se calcularonlas tasas de prevalencia de las mutaciones causantes de farmacorresistencia en 25 lactantes.Resultados. En los adultos de Panamá la farmacorresistencia transmitida fue moderada: 6 de 47 adultos seropositivos para el VIH presentaron una o más mutacionesasociadas con farmacorresistencia transmitida. Las mutaciones farmacorresitentes de transmisión horizontal fueron moderadas para los inhibidores de la transcriptasainversa análogos de nucleósidos y los inhibidores de la transcriptasa inversa no análogos de nucleósidos, y bajas para los inhibidores de la proteasa. En Panamá la transmisiónvertical del VIH ha disminuido en el período 2002–2007, pero la prevalenciade la farmacorresistencia del VIH transmitida por vía vertical es moderada (12,0%) y está surgiendo como un problema debido a la cobertura antirretroviral incompletadurante el embarazo...

Objective. To investigate the prevalence of transmitted drug-resistant HIV among adults in Panama by using a modified World Health Organization Threshold Survey (WHO-TS) and to investigate rates of initial resistance among HIV-positive infants in Panama.Methods. At the Gorgas Memorial Institute, 47 HIV-positive adults were genotyped for mutations associated with transmitted drug resistance (TDR) in the reverse transcriptase andprotease genes of HIV-1, according to WHO-TS guidelines, modified to include patients ≤ 26 years old. Prevalence rates for drug-resistance mutations against three classes of antiretroviraldrugs—nucleoside analog reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), and protease inhibitors—were calculated as low (< 5.0%), moderate (5.0%–15.0%), and high (> 15.0%). Twenty-five infant patients were also genotyped and prevalence rates for drug-resistance mutations were calculated. Results. TDR among Panamanian adults was moderate: 6 of 47 HIV-positive adultsshowed one or more mutations associated with TDR. Horizontal TDR mutations were moderate for NRTIs and NNRTIs and low for protease inhibitors. Vertical transmission of HIV inPanama has decreased for 2002–2007, but vertical HIV TDR prevalence is moderate (12.0%) and is emerging as a problem due to incomplete antiretroviral coverage in pregnancy. Conclusions. The prevalence of HIV TDR indicated by this study, combined with knownrates of HIV infection in Panama, suggests more extensive surveys are needed to identify risk factors associated with transmission of HIV drug resistance. Specific WHO-TS guidelines for monitoring vertical transmission of drug-resistant HIV should be established.

A first case of protease codon 35 amino acid insertion in a HIV-1 subtype B sequence detected in the Bauru region, state of São Paulo, Brazil: case report / Primeiro caso de inserção de aminoácidos no codon 35 da protease em uma sequência de HIV-1 do subtipo B detectada na região de Bauru, estado de São Paulo, Brasil: relato de caso

Amino acid insertions in the protease have rarely been described in HIVinfected patients. One of these insertions has recently been described in codon 35, although its impact on resistance remains unknown. This study presents a case of an HIV variant with an insertion in codon 35 of the protease, described for the first time in Bauru, State of Sao Paulo, Brazil, circulating in a 38-year-old caucasian male with asymptomatic HIV infection since 1997. The variant isolated showed a codon 35 insertion of two amino acids in the protease: a threonine and an aspartic acid, resulting in the amino acid sequence E35E_TD.

Inserções de aminoácidos na protease têm sido raramente descritas em pacientes infectados pelo HIV. Uma destas inserções foi, recentemente, descrita no codon 35, embora seu impacto na resistência mantém-se pouco conhecido. Este trabalho apresenta um caso de uma variante viral com inserção no codon 35 da protease, descrita pela primeira vez em Bauru, São Paulo, Brasil, circulante em um homem, caucasiano, com 38 anos, o qual apresenta infecção assintomática pelo HIV desde 1997. A variante isolada mostrou uma inserção no codon 35 da protease de dois aminoácidos: uma treonina e um ácido aspártico, resultando na sequência de aminoácidos E35E_TD.

Resistencia a los inhibidores de la integración del Virus de la Inmunodeficiencia Humana Tipo I: [revisión] / Resistance to inhibitors of the Human Immunodeficiency Virus Type I integration: [review]

En esta revisión, se resume el rol de la integrasa en la infección por VIH-1, el mecanismo de los inhibidores de la integrasa y la resistencia, con énfasis en el Raltegravir (RAL), el primer inhibidor de la integrasa autorizado para tratar la infección por VIH-1.

This review will summarize the role of integrase in HIV-1 infection, the mechanism of integrase inhibitors and resistance with an emphasis on Raltegravir (RAL), the first integrase inhibitor licensed to treat HIV-1 infection.

HIV-1 genotypic resistance profile of patients failing antiretroviral therapy in Paraná, Brazil

Antiretroviral therapy (ART) has reduced morbidity and mortality related to human immunodeficiency virus (HIV) infection, but in spite of this advance, HIV mutations decrease antiretroviral susceptibility, thus contributing to treatment failure in patients. Genotyping HIV-1 allows the selection of new drugs after initial drug failure. This study evaluated the genotypic profile of HIV-1 isolates from treated (drug-experienced) patients in Paraná, Brazil. The prevalence of mutations in reverse transcriptase (RT) and protease (PR) genes were assessed. We analyzed 467 genotypes of patients with HIV-1 viral loads above 1,000 copies/mL. Mutations at HIV-1 RT and PR genes and previously used ART regimens were recorded. The most prevalent RT mutations were: 184V (68.31 percent), 215YF (51.6 percent), 103NS (46 percent), 41L (39.4 percent), 67N (38.54 percent), 210W (23.5 percent), 190ASE (23.2 percent), and 181C (17.4 percent). PR mutations were 90M (33.33 percent), 82ATFS (29 percent), 46I (26.8 percent) and 54V (22.2 percent). The prevalence of mutations was in line with previous national and international reports, except to nonnucleoside analogue reverse transcriptase inhibitors related mutations, which were more prevalent in this study. Previous exposure to antiretroviral drugs was associated with genotypic resistance to specific drugs, leading to treatment failure in HIV patients.

Genetic diversity of human immunodeficiency virus-1 isolates in Paraná, Brazil

OBJECTIVE: Because epidemiological data on circulating HIV subtypes among HIV-positive patients in the state of Paraná were not known until now, the aims of this study were to describe the genetic diversity profile of HIV-1 in treated patients in Paraná, Brazil, and report the differences in protease (PR) and reverse transcriptase (RT) mutations in HIV-1 subtypes. PATIENTS AND METHODS: A cross-sectional study was conducted from 2003 to 2006. Plasma viral RNA of 389 patients was extracted and PR and RT genes were polymerase chain reaction-amplified and sequenced. Sequences were subtyped and examined for antiretroviral resistance mutations. Data on gender of patient harboring the viruses and past history of antiretroviral treatment were also collected. RESULTS: Most viruses were either subtype B (61.44 percent) or subtype C (20.57 percent). Subtype C and F were more frequent in women (p < 0.00). The prevalence of subtypes was similar over the years studied. The most frequent RT mutations in all subtypes were M184V and mutations at codons 215, 41, 103, 67, 219, and 190. Mutations 41L, 210W, 215YF, and 74V were significantly more prevalent on subtype B, and the mutation 106M was significantly more prevalent on subtype C. The most frequent major PI mutations in all subtypes occurred at codons 46, 82, and 90. PR mutations 32I, 46I, and 84V were significantly more prevalent on subtype B. The minor PI mutations on codons 36, 93, and 63 were more prevalent on subtypes F, C, and B, respectively. CONCLUSION: We concluded that the predominant strain of HIV-1 in Paraná is subtype B, followed by subtype C. Some mutations at PR and TR had subtype predominance in accordance with other authors' report.

Prevalence of resistance-associated mutations in Human Immunodeficiency Virus type 1-positive individuals failing HAART in Rio de Janeiro, Brazil

We investigated the occurrence of HIV-1 antiretroviral resistance in individuals failing to respond to highly active antiretroviral therapy (HAART) attended by RENAGENO from 2001-2004. One hundred and seventeen patients were selected for this study; their plasma viral RNA was extracted and the PR and RT genes sequenced to examine subtype, genetic polymorphisms and mutations associated with resistance to antiretroviral drugs. HIV-1 sequence analysis showed that 86/100 (86 percent) were infected with subtype B, 7/100 (7 percent) with subtype F and 7/100 (7 percent) with RT/PR hybrid forms (2 D/B, 2 F/B, 2 B/F and 1 D/F). In 14 (12 percent) of the samples, the subtype was not determined. The prevalence of resistance mutations was high (93.1 percent), mainly in the RT gene. The most prevalent resistance mutations were: M184V (60.7 percent), T215Y (49.6 percent) and M41L (46.7 percent) in the RT gene and L90M (19.6 percent), M46I (16.2 percent) and D30N (12.8 percent) in the PR gene. The frequency of resistance mutations tended to increase from the first to the second therapeutic scheme failure (p=0.079); but it stabilized after subsequent failures (p=0.875). Our finding of a high frequency of drug resistant HIV-1 samples supports the need for continuous genotypic monitoring of patients failing HAART.

Antiretroviral resistance in individuals presenting therapeutic failure and subtypes of the human immunodeficiency virus type 1 in the Northeast Region of Brazil

This study aimed to analyze human immunodeficiency virus (HIV) mutation profiles related to antiretroviral resistance following therapeutic failure, and the distribution of hiv subtypes in the Northeast Region of Brazil. A total of 576 blood samples from AIDS patients presenting therapeutic failure between 2002 and 2004 were analyzed. The genotyping kit viroSeq® was used to perform viral amplification in order to identify mutations related to hiv pol gene resistance. An index of 91.1 percent of the patients presented mutations for nucleoside reverse transcriptase inhibitors (nrti), 58.7 percent for non-nucleoside reverse transcriptase inhibitors (nnrti), and 94.8 percent for protease inhibitors (pi). The most prevalent mutations were 184V and 215E for nrti, 103N and 190A for nnrti. Most mutations associated with PIs were secondary, but significant frequencies were observed in codons 90 (25.2 percent), 82 (21.1 percent), and 30 (16.2 percent). The resistance index to one class of antiretrovirals was 14 percent, to two classes of antiretrovirals 61 percent, and to three classes 18.9 percent. Subtype B was the most prevalent (82.4 percent) followed by subtype F (11.8 percent). The prevalence of mutations related to nrti and nnrti was the same in the two subtypes, but codon analysis related to PI showed a higher frequency of mutations in codon 63 in subtype B and in codon 36 in subtype F. The present study showed that there was a high frequency of primary mutations, which offered resistance to nrti and nnrti. Monitoring patients with treatment failure is an important tool for aiding physicians in rescue therapy.

Detección de resistencia primaria en pacientes chilenos infectados por VIH / Detection of primary antiretroviral resistance in Chilean patients recently infected with human immunodeficiency virus (HIV)

Background: In countries with universal access to antiretroviral therapy a progressive increase in the number of patients that are infected with resistant virus, is observed. Aim To detect the presence of primary resistance to antiretroviral drugs among patients with a recent diagnosis of HIV infection. Material and methods: Twenty five male patients aged 25 to 45 years, with a diagnosis of a recent HIV infection, done between 2004 and 2005, were studied. Genotypic resistance to antiretroviral drugs was studied using the Genetic Resistance Test TRUGENE® from Bayer. Results: Resistance mutations were detected in 10 patients. All had an university title or had university studies. All lived in northeastern Santiago and had risky sexual behaviors while traveling abroad. Seven mutations were detected in reverse transcriptase. Of these, three were associated to a high resistance level and four, to an intermediate or low resistance, were also detected. Conclusions: A high frequency of genotypic resistance was detected in this group of Chilean patients recently infected with HIV. A higher socioeconomic status and lifestyle could have influenced these results.

Comparison of the epidemiology, profile of mutations, and clinical response to antiretrovirals among subtypes B and F of the human immunodeficiency virus type 1

The authors compared demographic aspects and profile of mutations in 80 patients with subtypes B and F of human immunodeficiency type 1 (HIV-1). Genotyping of the pol region of the reverse transcriptase was performed using the ViroSeqTM Genotyping System. A total of 61 (76.2 percent) patients had subtype B and 19 (23.8 percent) subtype F of the HIV-1. Subtype F tended to be more frequent in heterosexuals and women with a low educational level, but without statistical significance. The frequency of mutations related to nucleoside reverse transcriptase inhibitors and protease inhibitors (PI) was the same in the two subtypes, but mutations related to PI at the codons 63, 77, and 71 were more frequent in subtype B, while mutations at the codons 36 and 20 predominated in subtype F. Sixty-two of the 80 patients infected with subtypes B and F were submitted to antiretroviral therapy for an average of 18-22 months. Undetectable viral loads at the end of follow-up were similar in the two groups, representing 63.8 percent of subtype B and 73.3 percent of subtype F (p = 0.715). CD4 lymphocyte counts before and after treatment were similar in the two groups. This study, despite pointing to possible epidemiological and genetic differences among subtypes B and F of HIV-1, suggests that the use of highly active antiretroviral therapy is equally effective against these subtypes.

Genotype testing and antiretroviral resistance profiles from HIV-1 patients experiencing therapeutic failure in northeast Brazil

Genotype testing for HIV-1 drug resistance is useful for selecting antiretroviral drug regimens for patients experiencing therapeutic failure, but the optimal means for interpreting the test results is unknown because many HIV-1 protease and reverse transcriptase (RT) mutations contribute to drug resistance. This study identified common combinations of resistance mutations related to antiretroviral resistance profiles. From April 2002 to March 2004, 101 protease and RT sequences were determined for HIV-1 isolates from patients who were failing antiretroviral therapy. The resistance profile was evaluated using the Stanford Database program. Male patients predominated (76.2 percent), the median age was 38 years, the average CD4 count was 279.21 cells/mm³ and the average viral load was 4.49 log. In relation to protease inhibitors (IP) 31 mutation patterns were detected, 49 mutation patterns were detected in Nucleoside RT Inhibitors (NRTI), and 17 patterns were found in the Non Nucleoside RT Inhibitors (NNRTI). K65R was detected in 5.9 percent of the isolates. The most frequent mutations were: L90M, M184V and K103N related to PI's, NRTI's and NNRTI's, respectively. The best antiretroviral susceptibility was found to be Lopinavir in the PI class and Tenofovir in the NRTI class. The top six mutation patterns accounted for 49 percent of the resistance to PI's, for 38.5 percent of NRTI resistance, and the top two mutation patterns accounted for 40.9 percent of resistance to NNRTI's.

Primary resistance of human immunodeficiency virus type 1 in a reference center in Recife, Pernambuco, Brazil

To assess the prevalence of primary resistance of human immunodeficiency virus type 1 (HIV-1) to antiretrovirals, 84 patients chronically infected with HIV without prior antiretroviral treatment from Northeast Brazil were studied. Genotyping was performed using the ViroSeqTM Genotyping System. Thimidine analog mutations occurred in 3 (3.6 percent) patients. Accessory mutations related to NRTI occurred in 6 (7.1 percent) and related to PI in 67 (79.8 percent). Subtypes B (72.6 percent), F (22.6 percent), B/F 3 (3.6 percent), and C (1.2 percent) were detected. A low prevalence of major mutations related to NRTI in patients chronically infected by HIV was observed.

Caracterização de leveduras de cavidade oral de crianças infectadas pelo HIV-1, antes e durante o uso de inibidor de protease / Characterization of candida oral flora in HIV-1 infected children in the HAART era

O presente estudo caracterizou a flora oral de Candida em 52 crianças infectadas pelo HIV-1 em dois períodos, definidos como período I antes da introdução de inibidores de protease no esquema de terapia antiretroviral para HIV-1 e período II após a introdução de inibidores de protease. Comparou-se as espécies de Candida identificadas nos períodos I e II. Isolados do períodos I foram identificados e as crianças em sua maioria (80 por cento) estavam colonizadas por C. albicans. Redução no percentual de colonização por C. albicans de 80 por cento para 52 por cento, nos períodos I e II respectivamente, sugere mudança na colonização oral por Candida após a introdução da terapêutica com inibidores de protease HIV (IP). Destaca-se particularmente o aumento da incidência de isolados Não?albicans (p=0.005) no período II. No período I haviam 8 crianças que estavam colonizadas por espécies Não-albicans e no período II haviam 20 crianças colonizadas com isolados Não-albicans. Investigou-se a prevalência de C. dubliniensis na família de uma das crianças que estava colonizada por esta levedura. Do total de 52 crianças 38.4 por cento mostraram manifestação oral associada a colonização por Candida. Observou-se alta sensibilidade dos isolados aos agentes antifúngicos testados, mas 4 por cento dos isolados exibiram resistência ao fluconazol. Documentou...

This study characterized the Candida oral flora from 52 Brazilian HIV 1-infected children, comparing the Candida species identified in two periods before (PI) and under (PII) the introduction of the HIV Protease Inhibitor therapy. The majority (80 percent) of the children from the PI group were colonized by C. albicans. Children in the PII (52 percent) were colonized by C. albicans and 28 percent of them carried on mixed colonization (C. albicans and Non?albicans isolates). Therefore when we compared the periods I and II, after the inhibitor protease usage there was an important decrease in the percentile of colonization for C. albicans of 80 porcent to 52 percent, suggesting an important change of the Candida oral colonization after the HIV protease inhibitors introduction. Particularly with increase of the Non-albicans isolates incidence (p=0.005) in the period II. In PI there were 8 children that were colonized by Non-albicans species and in the PII there were 20 children colonized with Non?albicans isolates. Rare Candida species were identified, particularly we investigated the C. dubliniensis prevalence in a HIV-infected child?s family. Of 52 children in this study 20 (38.4 percent) of them showed oral lesions associated to the Candida colonization. In spite of the high susceptibility of the isolates to the antifungal agents tested in this study, 4.4 percent (n=2) exhibited resistance...

A genotyping study of human immunodeficiency virus type-1 drug resistance in a small Brazilian municipality

In Brazil, surveillance studies on antiretroviral drug resistance among drug-naïve and treatment-experienced patients have focused primarily on patients living in large urban centers. As the epidemic spreads towards small municipalities and the innermost parts of the country, it will be essential to monitor the prevalence of antiretroviral drug resistance in these areas. We report the first survey on the prevalence of antiretroviral drug resistance in a small Brazilian municipality. Between July 1999 and March 2005, 72 adult human immunodeficiency virus type-1(HIV-1)-infected patients received care at the Municipal HIV/AIDS Program of the small, southeastern municipality of Miracema, state of Rio de Janeiro. A genotyping study of antiretroviral drug resistance was performed in 54 patients. Among 27 samples from treatment-experienced patients, 9 (33.3 percent) harbored strains with reduced drug susceptibility. Among these, 6 had reduced susceptibility to reverse transcriptase (RT) inhibitors and 3 to both RT and protease inhibitors. No primary antiretroviral drug resistance was recorded among 27 drug-naïve subjects. The relatively low prevalence of resistance mutations in the Miracema cohort argues against the concern that resource-poor settings should not implement widespread accessibility to standard of care antiretroviral combinations due to the possibility of sub-optimal adherence leading to the emergence and spread of drug-resistant strains.

Study of antiretroviral mutants in HIV patients with treatment failures and the effect of risk factors in the virological failures

En Costa Rica no se tiene información a cerca de genotipos de resistencia para los tratamientos anti-retrovirales disponibles y la influencia de diferentes factores de riego en la falla virológica (FV) de pacientes VIH positivos previo o durante su tratamiento.Ochenta y nueve muestras, 72 FV y 17 basales, fueron analizadas con Trugene o LIPA para la detección de mutantes de resistencia en la transcriptasa reversa (TR) y en la proteasa (PT) del VIH.Se seleccionaron sesenta y ocho controles y se recolectó información relevante en un cuestionario. La mala adherencia, la presencia de mutaciones y el número de cambios de tratamiento fueron los únicos factores con significancia encontrados. (p = 0.03, 0.04 and 0.04 respectively). De 66 muestras secuenciadas, 78%, 50% y 50% mostraron resistencia a los inhibidores análogos y no análogos de nucleótidos para la TR y la PT respectivamente. La mutaciones más frecuentes fueron M41L, M184V, y T215FY en la TR y L62PI, L10FIRV y M36I en la PT. La adherencia fue el factor más importante relacionado con la respuesta al tratamiento. Las mutaciones encontradas en la TR estaban relacionadas al tratamiento mientras que las de la PT fueron mutaciones secundarias que propician la aparición de las mutaciones asociadas a resistencia en esa región. Este estudio revela la necesidad de detectar mutantes de resistencia en pacientes con FV y de estudiar las muestras basales. Además la importancia de reforzar la adherencia en los pacientes para una mejor respuesta al tratamiento.

Antiretroviral resistance mutations in human immunodeficiency virus type 1 infected patients enrolled in genotype testing at the Central Public Health Laboratory, São Paulo, Brazil: preliminary results

Antiretroviral resistance mutations (ARM) are one of the major obstacles for pharmacological human immunodeficiency virus (HIV) suppression. Plasma HIV-1 RNA from 306 patients on antiretroviral therapy with virological failure was analyzed, most of them (60 percent) exposed to three or more regimens, and 28 percent of them have started therapy before 1997. The most common regimens in use at the time of genotype testing were AZT/3TC/nelfinavir, 3TC/D4T/nelfinavir and AZT/3TC/efavirenz. The majority of ARM occurred at protease (PR) gene at residue L90 (41 percent) and V82 (25 percent); at reverse transcriptase (RT) gene, mutations at residue M184 (V/I) were observed in 64 percent. One or more thymidine analogue mutations were detected in 73 percent. The number of ARM at PR gene increased from a mean of four mutations per patient who showed virological failure at the first ARV regimens to six mutations per patient exposed to six or more regimens; similar trend in RT was also observed. No differences in ARM at principal codon to the three drug classes for HIV-1 clades B or F were observed, but some polymorphisms in secondary codons showed significant differences. Strategies to improve the cost effectiveness of drug therapy and to optimize the sequencing and the rescue therapy are the major health priorities.

Analysis of HIV- type 1 protease and reverse transcriptase in Brazilian children failing highly active antiretroviral therapy (HAART)

O objetivo deste estudo foi avaliar o perfil de resistência genotípica do HIV-1 em crianças com falha terapêutica ao tratamento anti-retroviral (HAART). Quarenta e uma crianças (idade mediana = 67 meses) em uso de HAART foram submetidas ao teste de genotipagem no momento da detecção de falha ao tratamento. Foi realizada extração de cDNA de células periféricas mononucleares e amplificação do mesmo (regiões da transcriptase reversa e protease do gene pol) através de PCR-nested. O perfil genotípico foi determinado através do seqüenciamnto de nucleotídeos. De acordo com a análise genotípica, 12/36 (33,3%) e 6/36 (16,6%) crianças apresentaram, respectivamente, resistência e possível resistência ao AZT; 5/36 (14%) e 4/36 (11,1%), respectivamente, eram resistentes e possivelmente resistentes ao ddI; 4/36 %11,1%) apresentaram resistência ao 3TC e D4T, e 3/36 (8,3%) eram resistentes ao ABC. Uma alta porcentagem de crianças (54%) apresentou mutações relacionadas à resistência aos inibidores da trancriptase reversa não-análogos de nucleosídeos. As taxas de resistência e possível resistência aos inibidores da protease foram, respectivamente: RTV (12,2%; 7,3%); APV (2,4%; 12,1%); SQV (0%; 12,1%); IDV (14,6%; 4,9%); NFV (22%; 4,9%); LPV/RTV (2,4%; 12,1%). No total, 37/41 (90%) crianças apresentaram vírus com mutações relacionadas à resistência a alguma droga, sendo que 9% delas tinham vírus resistentes às três classes de drogas anti-retrovirais disponíveis.

Human immunodeficiency virus type 1 (HIV-1) genotyping in Rio de Janeiro, Brazil: assessing subtype and drug-resistance associated mutations in HIV-1 infected individuals failing highly active antiretroviral therapy

In order to assess the human immunodeficiency virus type 1 (HIV-1) drug resistance mutation profiles and evaluate the distribution of the genetic subtypes in the state of Rio de Janeiro, Brazil, blood samples from 547 HIV-1 infected patients failing antiretroviral (ARV) therapy, were collected during the years 2002 and 2003 to perform the viral resistance genotyping at the Renageno Laboratory from Rio de Janeiro (Oswaldo Cruz Foundation). Viral resistance genotyping was performed using ViroSeqTM Genotyping System (Celera Diagnostic-Abbott, US). The HIV-1 subtyping based on polymerase (pol) gene sequences (protease and reverse transcriptase-RT regions) was as follows: subtype B (91.2 percent), subtype F (4.9 percent), and B/F viral recombinant forms (3.3 percent). The subtype C was identified in two patients (0.4 percent) and the recombinant CRF_02/AG virus was found infecting one patient (0.2 percent). The HIV-1 genotyping profile associated to the reverse transcriptase inhibitors has shown a high frequency of the M184V mutation followed by the timidine-associated mutations. The K103N mutation was the most prevalent to the non-nucleoside RT inhibitor and the resistance associated to protease inhibitor showed the minor mutations L63P, L10F/R, and A71V as the more prevalent. A large proportion of subtype B was observed in HIV-1 treated patients from Rio de Janeiro. In addition, we have identified the circulation of drug-resistant HIV-1 subtype C and are presenting the first report of the occurrence of an African recombinant CRF_02/AG virus in Rio de Janeiro, Brazil. A clear association between HIV-1 subtypes and protease resistance mutations was observed in this study. The maintenance of resistance genotyping programs for HIV-1 failing patients is important to the management of ARV therapies and to attempt and monitor the HIV-1 subtype prevalence in Brazil.