Monitoramento da qualidade da amostra para análise de RT-PCR da Covid-19 no LACEN-BA / Sample quality monitoring for Covid-19 RT-PCR analysis at LACEN-BA / Monitoreo de la calidad de la muestra para el análisis Covid-19 RT-PCR en LACEN-BA

A pandemia da Covid-19 tem se apresentado como um dos maiores desafios sanitários desse século. Em dezembro de 2019, na China, o agente etiológico foi identificado como um novo coronavírus, nomeado SARS-CoV-2. No Brasil, o primeiro caso confirmado da Covid-19 ocorreu em fevereiro de 2020 e, no mês seguinte, a Secretaria da Saúde do Estado da Bahia (Sesab) confirmou o primeiro caso na Bahia.O Laboratório Central de Saúde Pública Prof. Gonçalo Moniz (Lacen-BA) centralizou o diagnóstico laboratorial para confirmação dos casos suspeitos de Covid-19 dos 417 municípios baianos, utilizando a técnica de RT-PCR. Este estudo tem como objetivo identificar e analisar as não conformidades das amostras suspeitas de Covid-19 encaminhadas ao Lacen-BA. Trata-se de um estudo descritivo, cujos dados foram obtidos por meio de consulta aos relatórios de amostras e exames em desacordo, disponíveis no sistema Gerenciador de Ambiente Laboratorial (GAL), gerados mensalmente, no período de abril a outubro de 2020. Para garantir a qualidade das amostras recebidas, foram definidos critérios de aceitação/rejeição de amostras e criado o formulário de notificação de não conformidades, assegurando a rastreabilidade das amostras de Covid-19. Através de relatórios diários do sistema GAL, selecionou-se os nove principais motivos de não conformidades, sendo o mais frequente "requisição cancelada pela gerência do GAL devido à expiração do prazo de triagem", com 72,8% dos registros. A inserção da padronização de processos na etapa pré-analítica permite trabalhar com segurança, garantindo a qualidade da amostra a ser processada e, consequentemente, um resultado fidedigno, dentro do prazo acordado.

The Covid-19 pandemic is one of the greatest health challenges of this century. In December 2019, in China, the etiologic agent was identified as a new coronavirus, named SARS-CoV-2. In Brazil, the first case of Covid-19 was confirmed in February 2020 and, in the following month, the Department of Health of the State of Bahia (Sesab) confirms the first case in the state. The Central Public Health Laboratory Prof. Gonçalo Moniz (Lacen/BA) centralized the laboratory diagnosis to confirm the suspected cases of Covid-19 of the 417 municipalities of the state, using the RT-PCR technique. This study aims at identifying and analyzing the non-conformities of the suspected samples of Covid-19 sent to Lacen-BA. This is a descriptive study whose data were obtained by consulting there reports of samples and exams in disagreement, available in the Laboratory Environment Manager (GAL) system, generated monthly, from April to October,2020. To guarantee the quality of the samples received, acceptance / rejection criteria for the samples were defined and a form for the notification of non-conformities was created, ensuring the traceability of the Covid-19 samples. Daily reports from the Laboratory Environment Manager system based the selection of nine main reasons for non-conformities, among which "requisition canceled by the management of the GAL due to the expiration of the screening period" was present in 72.8% of the records. Process standardization, in the pre-analytical stage, allows working with security, guaranteeing the quality of the sample to be processed and a reliable result within the established period.

La pandemia del Covid-19 se ha presentado como uno de los desafíos de salud más grandes de este siglo. En diciembre de 2019, China identificó el agente etiológico del nuevo coronavirus llamado SARS-CoV-2. En Brasil, se notificó el primer caso del Covid-19 en febrero de 2020 y, al mes siguiente, la Secretaría de Salud del Estado de Bahía (Sesab) confirmaba el primer caso en Bahía. El Laboratorio Central de Salud Pública Prof. Gonçalo Moniz (Lacen/BA) centralizó el diagnóstico de laboratorio para confirmar los casos sospechosos del coronavirus de los 417 municipios de Bahía, mediante la técnica de RT-PCR. Este estudio tiene como objetivo identificar y analizar las no conformidades de las muestras sospechosas del Covid-19 enviadas al Lacen/BA. Este es un estudio descriptivo cuyos datos se obtuvieron consultando los informes de muestras y pruebas en desacuerdo disponibles en el sistema Laboratory Environment Manager (GAL), generados mensualmente, de abril a octubre/2020. Con el fin de garantizar la calidad de las muestras recibidas, se definieron criterios de aceptación/rechazo de las muestras y se elaboró un formulario para la notificación de no conformidades, asegurando la trazabilidad de las muestras. Por medio de informes diarios del sistema Laboratory Environment Manager, se seleccionaron nueve principales causas de no conformidades, de las cuales la más frecuente fue "requisición cancelada por la gerencia del GAL por vencimiento del período de cribado" con el 72,8% de los registros. La inserción de la estandarización de procesos en la etapa preanalítica permite trabajar con seguridad, garantizando la calidad de la muestra que procesar y, en consecuencia, un resultado confiable dentro del plazo acordado.

Disseminated sporotrichosis with immune reconstitution inflammatory syndrome in an HIV patient: Case report and review of the literature.

BACKGROUND: Sporotrichosis has been occurring as outbreaks in Brazil, reaching epidemic levels in some regions. Zoonotic transmission is the main route to acquire Sporothrix. CASE REPORT: We describe a case of disseminated sporotrichosis caused by Sporothrix brasiliensis in an HIV/AIDS patient, with the presentation of immune reconstitution inflammatory syndrome (IRIS). CONCLUSIONS: This case reinforces that sporotrichosis should always be suspected in patients with IRIS from endemic regions, even in patients without the typical cutaneous lesions of this mycosis.

Disseminated sporotrichosis with immune reconstitution inflammatory syndrome in an HIV patient: case report and review of the literature / Esporotricosis diseminada y síndrome inflamatorio de reconstitución inmune en un paciente con VIH: reporte de un caso y revisión de la literatura

BACKGROUND: Sporotrichosis has been occurring as outbreaks in Brazil, reaching epidemic levels in some regions. Zoonotic transmission is the main route to acquire Sporothrix. CASE REPORT: We describe a case of disseminated sporotrichosis caused by Sporothrix brasiliensis in an HIV/AIDS patient, with the presentation of immune reconstitution inflammatory syndrome (IRIS). CONCLUSIONS: This case reinforces that sporotrichosis should always be suspected in patients with IRIS from endemic regions, even in patients without the typical cutaneous lesions of this mycosis

ANTECEDENTES: La esporotricosis suele aparecer en Brasil en forma de brotes y alcanza tasas epidémicas en algunas regiones. La ruta principal de transmisión es la zoonótica. CASO CLÍNICO: Describimos un caso de esporotricosis diseminada causado por Sporothrix brasiliensis en una paciente con VIH/sida que presentó un síndrome inflamatorio de reconstitución inmune (SIRI). CONCLUSIONES: Este caso demuestra que en regiones endémicas de esporotricosis esta micosis siempre debe ser sospechada en casos de SIRI, incluso en pacientes sin las lesiones cutáneas típicas de esta enfermedad

Nontuberculous mycobacteria in patients with suspected tuberculosis and the genetic diversity of Mycobacterium avium in the extreme south of Brazil.

OBJECTIVE: Nontuberculous mycobacteria (NTM) are a heterogeneous group of bacteria that are widely distributed in nature and associated with opportunistic infections in humans. The aims of this study were to identify NTM in patients with suspected tuberculosis who presented positive cultures and to evaluate the genetic diversity of strains identified as Mycobacterium avium. METHODS: We studied pulmonary and extrapulmonary samples obtained from 1,248 patients. The samples that tested positive on culture and negative for the M. tuberculosis complex by molecular identification techniques were evaluated by detection of the hsp65 and rpoB genes and sequencing of conserved fragments of these genes. All strains identified as M. avium were genotyped using the eight-locus mycobacterial interspersed repetitive unit-variable-number tandem-repeat method. RESULTS: We found that NTM accounted for 25 (7.5%) of the 332 mycobacteria isolated. Of those 25, 18 (72%) were M. avium, 5 (20%) were M. abscessus, 1 (4%) was M. gastri, and 1 (4%) was M. kansasii. The 18 M. avium strains showed high diversity, only two strains being genetically related. CONCLUSIONS: These results highlight the need to consider the investigation of NTM in patients with suspected active tuberculosis who present with positive cultures, as well as to evaluate the genetic diversity of M. avium strains.

Histoplasma capsulatum and Mycobacterium avium co-infection in an immunocompromised patient: Case report and literature review.

We report a case of fungal and mycobacterial co-infection in an immunosuppressed patient from Southern Brazil. Histoplasmosis was diagnosed in an AIDS patient admitted to the hospital with nonspecific respiratory signs. However, 4 months post hospital discharge, the patient worsened and a co-infection with Mycobacterium avium was detected. Physicians must consider and investigate a broad spectrum of diseases which can occur as co-infections and which share the same clinical symptoms and signs in immunosuppressed patients.

Nontuberculous mycobacteria in patients with suspected tuberculosis and the genetic diversity of Mycobacterium avium in the extreme south of Brazil / Micobactérias não tuberculosas em pacientes com suspeita de tuberculose e a diversidade genética de Mycobacterium avium no extremo sul do Brasil

ABSTRACT Objective: Nontuberculous mycobacteria (NTM) are a heterogeneous group of bacteria that are widely distributed in nature and associated with opportunistic infections in humans. The aims of this study were to identify NTM in patients with suspected tuberculosis who presented positive cultures and to evaluate the genetic diversity of strains identified as Mycobacterium avium. Methods: We studied pulmonary and extrapulmonary samples obtained from 1,248 patients. The samples that tested positive on culture and negative for the M. tuberculosis complex by molecular identification techniques were evaluated by detection of the hsp65 and rpoB genes and sequencing of conserved fragments of these genes. All strains identified as M. avium were genotyped using the eight-locus mycobacterial interspersed repetitive unit-variable-number tandem-repeat method. Results: We found that NTM accounted for 25 (7.5%) of the 332 mycobacteria isolated. Of those 25, 18 (72%) were M. avium, 5 (20%) were M. abscessus, 1 (4%) was M. gastri, and 1 (4%) was M. kansasii. The 18 M. avium strains showed high diversity, only two strains being genetically related. Conclusions: These results highlight the need to consider the investigation of NTM in patients with suspected active tuberculosis who present with positive cultures, as well as to evaluate the genetic diversity of M. avium strains.

RESUMO Objetivo: As micobactérias não tuberculosas (MNT) são um grupo heterogêneo de bactérias amplamente distribuídas na natureza e relacionadas com infecções oportunistas em seres humanos. Os objetivos deste estudo foram identificar MNT em pacientes com suspeita de tuberculose e culturas positivas e avaliar a diversidade genética de cepas identificadas como Mycobacterium avium. Métodos: Foram estudadas amostras pulmonares e extrapulmonares provenientes de 1.248 pacientes. As amostras que apresentaram resultado positivo em cultura e negativo para o complexo M. tuberculosis na identificação molecular foram avaliadas por meio da detecção dos genes hsp65 e rpoB e de sequenciamento de fragmentos conservados desses genes. Todas as cepas identificadas como M. avium foram genotipadas pelo método mycobacterial interspersed repetitive unit-variable-number tandem-repeat com oito loci. Resultados: Das 332 micobactérias isoladas, 25 (7,5%) eram MNT. Dessas 25, 18 (72%) eram M. avium, 5 (20%) eram M. abscessus, 1 (4%) era M. gastri e 1 (4%) era M. kansasii. As 18 cepas de M. avium apresentaram alta diversidade, e apenas duas eram geneticamente relacionadas. Conclusões: Esses resultados mostram a necessidade de considerar a investigação de MNT em pacientes com suspeita de tuberculose ativa e culturas positivas e de avaliar a diversidade genética de cepas de M. avium.

Laboratory tools for tuberculosis control in a setting with a high burden of HIV/AIDS.

Introduction. Nosocomial transmission of Mycobacterium tuberculosis is an important health issue and the detection of tuberculosis (TB) cases is the main tool for controlling this disease.Aim. We aimed to assess the possible occurrence of nosocomial transmission of M. tuberculosis in a reference hospital for HIV/AIDS patients and evaluate both the performance of the Xpert MTB/RIF (Xpert) platform and drug resistance profiles.Methodology. We evaluated the performance of the Xpert platform. Samples that tested positive on the BACTEC MGIT 320 (MGIT320) platform were submitted for genotyping and drug susceptibility testing.Results. In this study, pulmonary and extrapulmonary samples from 407 patients were evaluated, and among these, 15.5 % were diagnosed with TB by the MGIT320 platform, with a TB/HIV coinfection rate of 52.4 %. The Xpert platform gave positive results for TB for 11 samples with negative results on the MGIT320 platform. In the genotyping results, 53.3 % of the strains clustered; of these strains, half were in two of the four clusters formed, and the patients had visited the hospital on the same day. Drug resistance was observed in 11.7 % of the strains.Conclusion. Putative nosocomial transmission of M. tuberculosis was detected, showing that genotyping is a powerful approach for understanding the dynamics of M. tuberculosis transmission, especially in a high-burden TB and HIV landscape.

Molecular and Clinical Profiles of Human Pegivirus Type 1 Infection in Individuals Living with HIV-1 in the Extreme South of Brazil.

Human pegivirus type 1 (HPgV-1) infection has been associated with a beneficial effect on the prognosis of human immunodeficiency virus type 1 (HIV-1)-coinfected individuals. However, the mechanisms involved in this protection are not yet fully elucidated. To date, circulating HPgV-1 genotypes in HIV-1-infected individuals have not yet been identified in the extreme south of Brazil. The present study aimed to determine the genotypic circulation of HPgV-1 and the influence of HPgV-1 status and persistence time on the evolution of HIV-1 infection. A retrospective cohort of 110 coinfected individuals was analyzed. Samples were subjected to viral RNA extraction, cDNA synthesis, nested PCR, and genotyping. Genotypes 1 (2.8%), 2 (47.9% of subtype 2a and 42.3% of subtype 2b), and 3 (7%) were identified. In antiretroviral treatment-naïve subjects HPgV-1 subtype 2b was associated with lower HIV-1 viral load (VL) rates (p = 0.04) and higher CD4+ T-cell counts (p = 0.03) than was subtype 2a, and the positivity for HPgV-1 was associated with higher CD4+ T-cell counts (p = 0.02). However, there was no significant difference in HIV-1 VL between HPgV-1-positive and HPgV-1-negative subjects (p = 0.08). There was no significant association between the different groups in HPgV-1 persistence and median HIV-1 VL (p = 0.66) or CD4+ T-cell counts (p = 0.15). HPgV-1 subtype 2b is associated with better prognosis of HIV-1 infection. Although HPgV-1 infection is persistent, our data suggest that the time of infection does not influence HIV-1 VL or CD4+ T-cell counts in coinfected subjects.

High prevalence and autochtonous transmission of human pegivirus (HPgV-1) in blood donors in the extreme southern of Brazil.

Recent studies have suggested that human pegivirus 1 (HPgV-1) may have some pathogenic potential. In the southernmost region of Brazil, studies on HPgV-1 are scarce, and circulating genotypes have not yet been identified. The current study aimed to evaluate the prevalence of HPgV-1 among blood donors from the southernmost region of Brazil and identify the genotypes involved with associated factors. A cross-sectional study was conducted with 281 blood donors, who had their plasma subjected to RNA extraction, complementary DNA synthesis, HPgV-1 detection by nested polymerase chain reaction, and subsequent genotyping. The observed prevalence of HPgV-1-RNA was 21.7%. The only variable that was significantly associated with virus infection was the relationship status of the donor. Single or no fixed partner blood donors were twice as likely to have HPgV-1 (95% CI, 1.12 to 4.56; P = 0.02). Genotype 2-subtypes 2b (69%) and 2a (29%)-was the most prevalent. In the absence of risk factors for parenteral transmission, it is likely that sexual transmission was the route of infection in the individuals studied. Further work will be needed to determine whether this virus is inert in the population, or if there are potential deleterious effects in infected individuals.

Prevalence of human pegivirus (HPgV) infection in patients carrying HIV-1C or non-C in southern Brazil.

Previous studies have demonstrated that coinfection with HPgV is a protective factor for human immunodeficiency virus (HIV)-infected patients, leading to slower disease progression, and longer survival after established disease. The present study sought to estimate the prevalence of HPgV infection and associated risk factors in patients harboring C or non-C HIV-1 subtypes followed-up at HU-FURG, southern Brazil. Samples from 347 HIV-1-infected subjects were subjected to plasma RNA extraction, cDNA synthesis, HPgV RNA detection, and HIV-1 genotyping. The overall prevalence of HPgV RNA was 34%. Individuals aged 18-30 years had higher chances of infection compared with those 50 years or older (95%CI 1.18-52.36, P = 0.03). The number of sexual partner between one and three was a risk factor for HPgV infection (95%CI 1.54-10.23; P < 0.01), as well as the time since diagnosis of HIV-1 ≥ 11 years (95%CI 1.01-2.89; P = 0.04). Patients infected with HIV non-C subtypes had six times more chance of being HPgV-infected when compared to subtype C-infected subjects (95%CI 2.28-14.78; P < 0.01). This was the first study conducted in southern Brazil to find the circulation of HPgV. HIV/HPgV coinfection was associated with a longer survival among HIV+ patients. Of novelty, individuals infected by HIV non-C subtypes were more susceptible to HPgV infection. However, additional studies are needed to correlate the HIV-1 subtypes with HPgV infection and to clarify cellular and molecular pathways through which such associations are ruled. J. Med. Virol 88:2106-2114, 2016. © 2016 Wiley Periodicals, Inc.

The ACTN3 R577X polymorphism affects the lipid profile and the prognosis of nutritional intervention in HIV-positive patients.

The hypothesis of the present study is that the polymorphisms in the APOC3, CEPT, ACE, and ACTN3 genes can affect the outcome of nutritional intervention and the plasma lipid profile of HIV+ patients. To test the hypothesis, genetic material was collected from buccal cells, and serum was collected for biochemical analysis. Sixty-five patients were analyzed. The incorporation of protease inhibitor (PI) was more frequent in women (77% vs 33% in men). Nutritional intervention improved anthropometric parameters independent of the genotype. Patients with the RR genotype for the ACTN3 R577X polymorphism had lower glycemia (RR = 95.4 ± 6.5 mg/dL, RX = 102.6 ± 10.6 mg/dL, XX = 110.1 ± 16.3 mg/dL; P = .03) and a greater reduction in low-density lipoproteins (LDL) after intervention (LDL: RR = -23.7 ± 15.8 mg/dL, RX = 1.32 ± 5.13 mg/dL, XX = 30.21 ± 24.4 mg/dL; P = .01). Patients using PI had a negative response to dietary intervention regarding the levels of high-density lipoprotein (-2.4 ± 1.70 with PI, 2.56 ± 1.60 mg/dL without PI; P = .02), very low density lipoprotein (0.84 ± 2.73 with IP, -5.46 ± 3.37 mg/dL without PI; P = .03), and triglycerides (1.79 ± 13.22 with PI, -34.00 ± 17.67 mg/dL without PI; P = .052). This response was also independent of the genotype (P > 0.05) and suggested the need for oral lipid-lowering drugs in all HIV+ patients using PI. Our results indicate that the ACTN3 R577X polymorphism is a good predictor of both the lipid profile and the prognosis of nutritional intervention in reducing LDL in HIV+ patients.

Virologic and immunologic effectiveness at 48 weeks of darunavir-ritonavir-based regimens in treatment-experienced persons living with HIV-1 infection in clinical practice: a multicenter Brazilian cohort.

INTRODUCTION: Published data addressing the effectiveness of darunavir-ritonavir (DRV/r)-based therapy for multiexperienced patients in developing countries are scarce. This study evaluated the 48-week virologic and immunologic effectiveness of salvage therapy based on DRV/r for the treatment of multidrug-experienced HIV-1-infected adults in Brazil. MATERIALS AND METHODS: A multicenter retrospective cohort study was carried out with multidrug-experienced adults who were on a failing antiretroviral therapy and started a DRV/r-based salvage therapy between 2008 and 2010. The primary effectiveness end point was the proportion of patients with virologic success (plasma HIV-1 RNA <50 copies/mL at week 48). RESULTS: At 48 weeks, 73% of the patients had HIV-RNA <50 copies/mL and a mean increase of 108 CD4 cells/mm(3). Higher baseline viral load, lower baseline CD4 count, younger age, and 3 or more DRV/r-associated resistance mutations were significantly predictive of virologic failure. Concomitant use of raltegravir was strongly associated with virologic success. CONCLUSION: The use of DRV/r-based regimens for salvage therapy is an effective strategy in the clinical care setting of a developing country.

Genetic markers associated to dyslipidemia in HIV-infected individuals on HAART.

This study evaluated the impact of 9 single nucleotide polymorphisms (SNPs) in 6 candidate genes (APOB, APOA5, APOE, APOC3, SCAP, and LDLR) over dyslipidemia in HIV-infected patients on stable antiretroviral therapy (ART) with undetectable viral loads. Blood samples were collected from 614 patients at reference services in the cities of Porto Alegre, Pelotas, and Rio Grande in Brazil. The SNPs were genotyped by conventional polymerase chain reaction (PCR) and real-time PCR. The prevalence of dyslipidemia was particularly high among the protease inhibitors-treated patients (79%). APOE (rs429358 and rs7412) genotypes and APOA5 -1131T>C (rs662799) were associated with plasma triglycerides (TG) and low-density-lipoprotein cholesterol levels (LDL-C). The APOA5 -1131T>C (rs662799) and SCAP 2386A>G (rs12487736) polymorphisms were significantly associated with high-density-lipoprotein cholesterol levels. The mean values of the total cholesterol and LDL-C levels were associated with both the APOB SP Ins/Del (rs17240441) and APOB XbaI (rs693) polymorphisms. In conclusion, our data support the importance of genetic factors in the determination of lipid levels in HIV-infected individuals. Due to the relatively high number of carriers of these risk variants, studies to verify treatment implications of genotyping before HAART initiation may be advisable to guide the selection of an appropriate antiretroviral therapy regimen.

Expression levels of the innate response gene RIG-I and its regulators RNF125 and TRIM25 in HIV-1-infected adult and pediatric individuals.

OBJECTIVE: TLRs (Toll-like receptors) and RLRs (RIG-I-like receptors) mediate innate immune responses by detecting microorganism invasion. RIG-I activation results in the production of interferon (IFN) type 1 and IFN responsive genes (ISGs). As the ubiquitin ligases RNF125 and TRIM25 are involved in regulating RIG-I function, our aim was to assess whether the levels of these three genes vary between healthy and HIV-infected individuals and whether these levels are related to disease progression. DESIGN: Gene expression analyses for RIG-I, RNF125, and TRIM25 were performed for HIV-infected adults and the children's peripheral blood mononuclear cells (PBMCs). METHODS: Reverse transcription-quantitative PCRs (RT-qPCRs) were performed in order to quantify the expression levels of RIG-I, RNF125 and TRIM25 from PBMCs purified from control or HIV-infected individuals. RESULTS: Controls express higher levels of the three genes when compared to HIV-infected patients. These expressions are clearly distinct between healthy and progressors, and are reproduced in adults and children. In controls, RNF125 is the highest expressed gene, whereas in progressors, RIG-I is either the highest expressed gene or is expressed similarly to RNF125 and TRIM25. CONCLUSION: A pattern of expression of RIG-I, RNF125, and TRIM25 genes in HIV patients is evident. The high expression of RNF125 in healthy individuals reflects the importance of keeping RIG-I function off, inhibiting unnecessary IFN production. Consistent with this assumption, RNF125 levels are lower in HIV patients and importantly, the RNF125/RIG-I ratio is lower in patients who progress to AIDS. Our results might help to predict disease progression and unveil the role of poorly characterized host genes during HIV infection.

Phenotypic susceptibility to antiretrovirals among clades C, F, and B/F recombinant antiretroviral-naive HIV type 1 strains.

To evaluate antiretroviral phenotypic susceptibility of wild-type HIV-1 strains circulating in Brazil, samples from antiretroviral-naive individuals infected with subtypes C (n=16), F (n=9), or B/F (n=7), where reverse transcriptase is B and protease is F, were phenotyped using the Antivirogram Assay (Virco, Mechelen, Belgium). Reduced susceptibility to protease inhibitors (PIs) was observed in one C and three F isolates. None of these samples had any known PI resistance mutations. The phenotypic fold change to one PI was above the biological cut-off in three of 96 (3.1%) clade F phenotypic determinations and in one of 96 (1.0%) clade C. Phenotypic resistance to at least one nucleoside reverse transcriptase inhibitor (NRTI) was found for two B/F, four C, and three F isolates. The phenotypic fold change in susceptibility to NRTIs was above the cut-off value in nine of 111 (8.1%) clade C determinations, as compared to three of 63 (4.8%) for clade F and two of 49 (4.1%) for clade B. The phenotypic fold change to non-NRTI (NNRTI) was above the cut-off in seven of 32 (21.9%) of C isolates determinations, whereas none of the F isolates had a decrease of susceptibility. Only two of the 16 C samples had a known NNRTI resistance mutation. The NNRTI fold change was above the cut-off value in three of 14 (21.4%) phenotypic determinations of Brazilian B/F recombinants, representing clade B reverse transcriptase. NNRTI susceptibility should be better investigated in clade C and B/F recombinants.

Connection subdomain mutations in HIV-1 subtype-C treatment-experienced patients enhance NRTI and NNRTI drug resistance.

Mutations in the connection subdomain (CN) and RNase H domain (RH) of HIV-1 reverse transcriptase (RT) from subtype B-infected patients enhance nucleoside and nonnucleoside RT inhibitor (NRTI and NNRTI) resistance by affecting the balance between polymerization and RNase H activity. To determine whether CN mutations in subtype C influence drug sensitivity, single genome sequencing was performed on Brazilian subtype C-infected patients failing RTI therapy. CN mutations identified were similar to subtype B, including A376S, A400T, Q334D, G335D, N348I, and A371V, and increased AZT resistance in the presence of thymidine analog mutations. CN mutations also enhanced NNRTI resistance in the presence of classical NNRTI mutations: etravirine resistance was enhanced 6- to 11-fold in the presence of L100I/K103N/Y181C. These results indicate that selection of CN mutations in treatment-experienced patients also occurs in subtype-C-infected patients and are likely to provide valuable information in predicting clinical RTI resistance.

Heterosexual transmission of human immunodeficiency virus type 1 subtype C in southern Brazil.

BACKGROUND: Human immunodeficiency virus type 1 (HIV-1) subtype B predominates in Brazil, but in the southern region subtype C is the most frequent, followed by subtypes B, F1 and recombinant forms. In southern Brazil, these subtypes co-circulate in subjects with homogeneous demographic and clinical features, enabling a better understanding of the role of HIV-1 subtypes on the characteristics of infection. OBJECTIVES: To evaluate the prevalence of different HIV-1 subtypes in subjects with recent diagnosis for HIV infection in the extreme south of Brazil, and to study their association with demographic, behavioral, clinical and laboratorial characteristics. STUDY DESIGN: We have determined the genetic sequence of viral protease and reverse transcriptase (polymerase, connection and RNase H domains) isolated from studied subjects. Viral subtype was inferred by comparison with reference HIV sequences, and recombination was determined with Simplot analysis. The association of HIV-1 subtypes with studied characteristics was evaluated by chi-square, Fisher's exact, Student's t and Kruskal-Wallis tests. RESULTS: Two hundred and forty-five HIV isolates were molecularly characterized, and the association with variables was studied for 233 (95.1%) patients. Of those, 46.8% followed AIDS defining criteria. HIV-1C was responsible for 56.3% of infections, and was associated with heterosexual transmission (p=0.001) and with higher CD4(+) T-cell counts (p=0.02). CONCLUSIONS: The molecular epidemiology of HIV-1 in the southernmost Brazil is currently steady with predominance of HIV-1C. This is the first study showing a robust association of the infection by this subtype and heterosexual transmission in the state of Rio Grande do Sul, Brazil.

Genetic polymorphisms in estrogen receptors and sexual dimorphism in fat redistribution in HIV-infected patients on HAART.

OBJECTIVE: To investigate genetic single nucleotide polymorphisms (SNPs) in estrogen receptor-α (ERα) (ESR1, rs2234693, rs1801132, rs7757956 and rs2813544) and ERß (ESR2, rs3020450, rs7154455 and rs4986938) genes and relate them to the adverse effects lipodystrophy, dyslipidemia and metabolic syndrome as well as to differences in their prevalence between sexes in HIV-infected individuals on HAART. DESIGN: Cross-sectional study. METHODS: Blood samples and anthropometric measurements were collected from 614 patients at reference services in the cities of Porto Alegre, Pelotas and Rio Grande in Brazil. The SNPs were genotyped by real-time PCR. RESULTS: The lipodystrophy subtype frequencies in patients of different sexes showed statistically significant differences; the atrophic pattern was more prevalent in men, and the hypertrophic pattern was more prevalent in women. Furthermore, metabolic syndrome prevalence was higher in women than in men. The ESR1 rs2813544 G-allele was associated with higher measurements of several anthropometric variables in women: BMI, total subcutaneous fat and subcutaneous fat of limbs. Additionally, patients who were AA homozygous for ESR2 rs3020450 presented an increased risk for developing lipoatrophy (prevalence ratio 1.37, 95% confidence interval 1.09-1.73, P = 0.007). CONCLUSION: Significant differences in lipodystrophy and metabolic syndrome prevalence were detected between sexes. Moreover, the ESR1 gene (rs2813544) presented significant sex-specific associations with anthropometric variables, and the ESR2 gene (rs3020450) was associated with an increased risk of developing lipoatrophy. Our results suggest that these genes are in part responsible for the sexual dimorphism in fat tissue redistribution and patterns of lipodystrophy.

Short communication: UGT1A1*28 variant allele is a predictor of severe hyperbilirubinemia in HIV-infected patients on HAART in southern Brazil.

Highly active antiretroviral therapy (HAART) has increased the survival of HIV-infected patients. However, adverse effects play a major role in adherence to HAART. Some protease inhibitors (mainly atazanavir and indinavir) act as inhibitors of uridine diphosphate-glucuronosyltransferase (UGT1A1), the enzyme responsible for hepatic conjugation of bilirubin. Variations in the promoter region of the UGT1A1 gene (UGT1A1*28, rs8175347) can influence bilirubin plasma levels, modulating the susceptibility to hyperbilirubinemia. Aiming to analyze the association between UGT1A1*28 allele and hyperbilirubinemia in individuals exposed to HAART, we evaluated 375 HIV-positive individuals on antiretroviral therapy. Individuals carrying the UGT1A1*28 allele had a higher risk of developing severe hyperbilirubinemia [prevalence ratio (PR)=2.43, 95% confidence interval (CI) 1.08-5.45, p=0.032] as well as atazanavir users (PR=7.72, 95% CI=3.14-18.98, p<0.001). This is the first description of such an association in Brazilian HIV patients, which shows that in African-American and Euroamerican HAART users, the UGT1A1*28 allele also predisposes to severe hyperbilirubinemia, especially in those exposed to atazanavir.

Primary HIV-1 drug resistance in the C-terminal domains of viral reverse transcriptase among drug-naïve patients from Southern Brazil.

BACKGROUND: Major and accessory drug resistance mutations have been recently characterized in the C-terminal RT subdomains of HIV-1, connection and RNase H. However, their presence in treatment-naïve patients infected with HIV-1 non-B subtypes remains largely unknown. OBJECTIVES: To characterize the patterns of primary resistance at the C-terminal RT subdomains of HIV-1 infecting subjects in the southern region of Brazil, where HIV-1 subtypes B and C co-circulate. STUDY DESIGN: Plasma viral RNA was extracted from patients recently diagnosed for HIV infection (2005-2008). The protease and reverse transcriptase regions were PCR-amplified and sequenced. Infecting HIV subtypes were assigned by phylogenetic inference and drug resistance mutations were determined following the IAS consensus and recent reports on C-terminal RT mutations. RESULTS: The major mutation to NNRTI T369I/V was found in 1.8% of patients, while A376S was present in another 8.3%. In the RNase H domain, the compensatory mutation D488E was more frequently observed in subtype C than in subtype B (p=0.038), while the inverse was observed for mutation Q547K (p<0.001). The calculated codon genetic barrier showed that 22% of subtype B isolates, but no subtype C, carried T360, requiring two transitions to change into the resistance mutation 360V. CONCLUSIONS: Major resistance-conferring mutations to NNRTI were detected in 10% of RT connection domain viral sequences from treatment-naïve subjects. We showed for the first time that the presence of specific polymorphisms can constrain the acquisition of definite resistance mutations in the connection and RNase H subdomains of HIV-1 RT.