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Machine learning in predicting severe acute respiratory infection outbreaks
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Silva, Amauri Duarte da

; Gomes, Marcelo Ferreira da Costa

; Gregianini, Tatiana Schäffer

; Martins, Leticia Garay

; Veiga, Ana Beatriz Gorini da

Cadernos de Saúde Pública

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2024, Volume 40 Nº 1 elocation e00122823

Resumo: En Es Pt | Texto: En Es Pt | PDF: En | PDF: Es | PDF: Pt

Abstract: Severe acute respiratory infection (SARI) outbreaks occur annually, with seasonal peaks varying among geographic regions. Case notification is important to prepare healthcare networks for patient attendance and hospitalization. Thus, health managers need adequate resource planning tools for SARI seasons. This study aims to predict SARI outbreaks based on models generated with machine learning using SARI hospitalization notification data. In this study, data from the reporting of SARI hospitalization cases in Brazil from 2013 to 2020 were used, excluding SARI cases caused by COVID-19. These data were prepared to feed a neural network configured to generate predictive models for time series. The neural network was implemented with a pipeline tool. Models were generated for the five Brazilian regions and validated for different years of SARI outbreaks. By using neural networks, it was possible to generate predictive models for SARI peaks, volume of cases per season, and for the beginning of the pre-epidemic period, with good weekly incidence correlation (R2 = 0.97; 95%CI: 0.95-0.98, for the 2019 season in the Southeastern Brazil). The predictive models achieved a good prediction of the volume of reported cases of SARI; accordingly, 9,936 cases were observed in 2019 in Southern Brazil, and the prediction made by the models showed a median of 9,405 (95%CI: 9,105-9,738). The identification of the period of occurrence of a SARI outbreak is possible using predictive models generated with neural networks and algorithms that employ time series.

Resumen: Brotes de síndrome respiratorio agudo grave (SRAG) ocurren todos los años, con picos estacionales que varían entre regiones geográficas. La notificación de los casos es importante para preparar las redes de atención a la salud para el cuidado y hospitalización de los pacientes. Por lo tanto, los gestores de salud deben tener herramientas adecuadas de planificación de recursos para las temporadas de SRAG. Este estudio tiene el objetivo de predecir brotes de SRAG con base en modelos generados con aprendizaje automático utilizando datos de hospitalización por SRAG. Se incluyeron datos sobre casos de hospitalización por SRAG en Brasil desde 2013 hasta 2020, salvo los casos causados por la COVID-19. Se prepararon estos datos para alimentar una red neural configurada para generar modelos predictivos para series temporales. Se implementó la red neural con una herramienta de canalización. Se generaron los modelos para las cinco regiones brasileñas y se validaron para diferentes años de brotes de SRAG. Con el uso de redes neurales, se pudo generar modelos predictivos para los picos de SRAG, el volumen de casos por temporada y para el inicio del periodo pre-epidémico, con una buena correlación de incidencia semanal (R2 = 0,97; IC95%: 0,95-0,98, para la temporada de 2019 en la Región Sudeste). Los modelos predictivos tuvieron una buena predicción del volumen de casos notificados de SRAG; así, se observaron 9.936 casos en 2019 en la Región Sur, y la predicción de los modelos mostró una mediana de 9.405 (IC95%: 9.105-9.738). La identificación del periodo de ocurrencia de un brote de SRAG es posible a través de modelos predictivos generados con el uso de redes neurales y algoritmos que aplican series temporales.

Resumo: Surtos de síndrome respiratória aguda grave (SRAG) ocorrem anualmente, com picos sazonais variando entre regiões geográficas. A notificação dos casos é importante para preparar as redes de atenção à saúde para o atendimento e internação dos pacientes. Portanto, os gestores de saúde precisam ter ferramentas adequadas de planejamento de recursos para as temporadas de SRAG. Este estudo tem como objetivo prever surtos de SRAG com base em modelos gerados com aprendizado de máquina usando dados de internação por SRAG. Foram incluídos dados sobre casos de hospitalização por SRAG no Brasil de 2013 a 2020, excluindo os casos causados pela COVID-19. Estes dados foram preparados para alimentar uma rede neural configurada para gerar modelos preditivos para séries temporais. A rede neural foi implementada com uma ferramenta de pipeline. Os modelos foram gerados para as cinco regiões brasileiras e validados para diferentes anos de surtos de SRAG. Com o uso de redes neurais, foi possível gerar modelos preditivos para picos de SRAG, volume de casos por temporada e para o início do período pré-epidêmico, com boa correlação de incidência semanal (R2 = 0,97; IC95%: 0,95-0,98, para a temporada de 2019 na Região Sudeste). Os modelos preditivos obtiveram uma boa previsão do volume de casos notificados de SRAG; dessa forma, foram observados 9.936 casos em 2019 na Região Sul, e a previsão feita pelos modelos mostrou uma mediana de 9.405 (IC95%: 9.105-9.738). A identificação do período de ocorrência de um surto de SRAG é possível por meio de modelos preditivos gerados com o uso de redes neurais e algoritmos que aplicam séries temporais.

https://doi.org/10.1590/0102-311xen122823

Machine learning in predicting severe acute respiratory infection outbreaks
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Silva, Amauri Duarte da

; Gomes, Marcelo Ferreira da Costa

; Gregianini, Tatiana Schäffer

; Martins, Leticia Garay

; Veiga, Ana Beatriz Gorini da

Cadernos de Saúde Pública

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2024, Volume 40 Nº 1 elocation e00122823

Resumo: En Es Pt | Texto: En Es Pt | PDF: En | PDF: Es | PDF: Pt

https://doi.org/10.1590/0102-311xen122823

Influenza A(H3N2) infection followed by separate COVID-19 infection
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Gregianini, Tatiana Schäffer

; Salvato, Richard Steiner

; Baethgen, Ludmila Fiorenzano

; Piazza, Cláudia Fasolo

; Barcellos, Regina Bones

; Godinho, Fernanda Marques

; Veiga, Ana Beatriz Gorini da

Revista Panamericana de Salud Pública

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2023, Volume 47 elocation e61

Resumo: Es Pt En | Texto: Es Pt En | PDF: Es | PDF: Pt | PDF: En

RESUMEN Este estudio describe el caso de un profesional de la salud que contrajo la infección primero por el virus de la gripe A (H3N2) y a continuación por el coronavirus 2 del síndrome respiratorio agudo grave (SARS-CoV-2) 11 días después. Se recogieron muestras respiratorias y datos clínicos del paciente y sus contactos cercanos. Se extrajo ARN de muestras y se utilizó la reacción en cadena de la polimerasa cuantitativa con transcripción inversa (RT-qPCR, por su sigla en inglés) para investigar los virus. El paciente presentó dos procesos infecciosos distintos: el primero se caracterizó por fiebre, dolor corporal y torácico, postración y cansancio, que cesó en el noveno día. La prueba mediante RT-qPCR solo fue positiva en el virus de la gripe A (H3N2). Once días después del inicio de los primeros síntomas, el paciente manifestó dolor de garganta, congestión nasal, catarro, picazón nasal, estornudos y tos. Una segunda prueba mediante RT-qPCR solo fue positiva para el SARS-CoV-2 y durante este segundo proceso los síntomas duraron 11 días. La secuenciación del SARS-CoV-2 identificó el linaje ómicron BA.1. De los contactos del paciente, uno presentaba una coinfección por el virus de la gripe A (H3N2) y el linaje BA.1.15 del SARS-COV-2, y los otros dos presentaban infecciones únicamente por SARS-CoV-2, uno también del linaje ómicron BA.1.15 y el otro de BA.1.1. Estos hallazgos refuerzan la importancia de realizar pruebas para detectar diferentes virus en casos de sospecha de infección viral respiratoria durante la vigilancia epidemiológica de rutina porque las manifestaciones clínicas comunes de COVID-19 son similares a las de otros virus, como en el caso de la gripe.

RESUMO Este estudo descreve o caso de uma profissional de saúde infectada primeiro pelo vírus influenza A (H3N2) e, 11 dias depois, pelo coronavírus da síndrome respiratória aguda grave 2 (SARS-CoV-2). Amostras respiratórias e dados clínicos foram coletados da paciente e de contatos próximos. RNA foi extraído das amostras, e o método de reação em cadeia da polimerase via transcriptase reversa quantitativa (RT-qPCR) foi utilizado para investigar os vírus. A paciente apresentou dois quadros clínicos distintos. O primeiro foi caracterizado por febre, dor no peito e no corpo, prostração e fadiga, que cessou no nono dia. A RT-qPCR foi positiva apenas para o vírus da influenza A (H3N2). Onze dias após o início dos primeiros sintomas, a paciente apresentou dor de garganta, congestão nasal, coriza, prurido nasal, espirros e tosse. Um segundo teste de RT-qPCR foi positivo apenas para SARS-CoV-2. No segundo evento, os sintomas duraram 11 dias. O sequenciamento do SARS-CoV-2 identificou a cepa Ômicron BA.1. Dentre os contatos da paciente, um teve coinfeção por influenza A (H3N2) e SARS-COV-2 (cepa BA.1.15), e os outros dois foram infectados apenas por SARS-CoV-2 (um também pela cepa Ômicron BA.1.15 e o outro pela BA.1.1). Nossos achados reforçam a importância de testes para a detecção de diferentes vírus em casos de suspeita de infecção viral respiratória durante a vigilância epidemiológica de rotina, visto que as manifestações clínicas comuns da COVID-19 imitam as de outros vírus, como o vírus influenza.

ABSTRACT This study describes the case of a health professional infected first by influenza virus A(H3N2) and then by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 11 days later. Respiratory samples and clinical data were collected from the patient and from close contacts. RNA was extracted from samples and reverse transcription–quantitative polymerase chain reaction (RT-qPCR) was used to investigate the viruses. The patient presented with two different illness events: the first was characterized by fever, chest and body pain, prostration and tiredness, which ceased on the ninth day; RT-qPCR was positive only for influenza virus A(H3N2). Eleven days after onset of the first symptoms, the patient presented with sore throat, nasal congestion, coryza, nasal itching, sneezing and coughing, and a second RT-qPCR test was positive only for SARS-CoV-2; in the second event, symptoms lasted for 11 days. SARS-CoV-2 sequencing identified the Omicron BA.1 lineage. Of the patient’s contacts, one was coinfected with influenza A(H3N2) and SARS-CoV-2 lineage BA.1.15 and the other two were infected only with SARS-CoV-2, one also with Omicron BA.1.15 and the other with BA.1.1. Our findings reinforce the importance of testing for different viruses in cases of suspected respiratory viral infection during routine epidemiological surveillance because common clinical manifestations of COVID-19 mimic those of other viruses, such as influenza.

https://doi.org/10.26633/rpsp.2023.61

SARS-CoV-2 laboratory surveillance during the first year of the COVID-19 pandemic in southern Brazil
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Baethgen, Ludmila Fiorenzano

; Veiga, Ana Beatriz Gorini da

; Salvato, Richard Steiner

; Carvalho, Talita Giacomet de

; Rispoli, Thaiane

; Schiefelbein, Sun Hee

; Martins, Letícia Garay

; Nunes, Zenaida Marion Alves

; Schaurich, Anelise Praetzel

; Timm, Loeci Natalina

; Ramos, Rosane Campanher

; Bastos, Cynthia Goulart Molina

; Gregianini, Tatiana Schäffer

Revista da Sociedade Brasileira de Medicina Tropical

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2023, Volume 56 elocation e0146-2022

Resumo: En | Texto: En | PDF: En

ABSTRACT Background: Brazil has one of the highest numbers of COVID-19 cases and deaths. Rio Grande do Sul (RS) in southern Brazil is one of the leading states in terms of case numbers. As part of the national public health network, the State Central Laboratory (LACEN-RS) changed its routine in 2020 to focus on the diagnosis of COVID-19. This study evaluated the laboratory surveillance of COVID-19 suspected cases analyzed at the LACEN-RS in 2020. Methods: Viral detection was performed using RT-qPCR in samples from patients with respiratory infection who met the study criteria. Viral RNA was isolated using commercial manual kits or automated extractors, and SARS-CoV-2 RT-qPCR was performed using the Bio-Manguinhos/Rio de Janeiro, IBMP/Paraná, or Allplex 2019-nCoV assay. In total, 360 representative SARS-CoV-2 samples were sequenced using the Illumina platform. Results: In total, 31,197 of 107,578 (positivity rate = 29%) tested positive for SARS-CoV-2. The number of RT-qPCR tests performed per month followed the COVID-19 epidemic curve observed for the state, with peaks in July-August and December. Females accounted for 63% of the samples, whereas the positivity rate was higher among males (33.1% males vs. 26.5% females). The positivity rate was higher in adults aged 50-79 years compared to the overall positivity rate. The majority of cases were observed in the capital, Porto Alegre, and the metropolitan region. Ten distinct lineages were identified, with B.1.1.28, B.1.1.33, and P.2 being the most frequent. Conclusions: Here, we describe laboratory surveillance of COVID-19 to identify priorities for epidemiological surveillance actions in RS.

https://doi.org/10.1590/0037-8682-0146-2022

Chikungunya virus infection in the southernmost state of Brazil was characterised by self-limited transmission (2017-2019) and a larger 2021 outbreak
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Gregianini, Tatiana Schäffer

; Salvato, Richard Steiner

; Barcellos, Regina Bones

; Godinho, Fernanda Marques

; Ruivo, Amanda Pellenz

; de Melo, Viviane Horn

; Schroder, Júlio Augusto

; Martiny, Fernanda Letícia

; Möllmann, Erica Bortoli

; Favreto, Cátia

; Baethgen, Ludmila Fiorenzano

; Ferreira, Vithoria Pompermaier

; de Lima, Lívia Eidt

; Piazza, Cláudia Fasolo

; Machado, Taís Raquel Marcon

; Becker, Irina Marieta

; Ramos, Raquel Rocha

; Frölich, Guilherme Carey

; Rossetti, Alana Fraga

; Almeida, Lucas da Cunha

; Rodrigues, Tahiana Machado Antunes

; Bragança, Isabella Tabelli

; Campos, Aline Alves Scarpellini

; Manzoni, Verônica Baú

; Machado, Lais Ceschini

; da Silva, Luisa Maria Inácio

; de Oliveira, André Luiz Sá

; Paiva, Marcelo Henrique Santos

; Nunes, Zenaida Marion Alves

; de Almeida, Paula Rodrigues

; Demoliner, Meriane

; Gularte, Juliana Schons

; da Silva, Mariana Soares

; Filippi, Micheli

; Pereira, Vyctoria Malayhka de Abreu Góes

; Spilki, Fernando Rosado

; da Veiga, Ana Beatriz Gorini

; Wallau, Gabriel Luz

Memórias do Instituto Oswaldo Cruz

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2023, Volume 118 elocation e220259

Resumo: En | Texto: En | PDF: En

BACKGROUND Chikungunya is a mosquito-borne virus that has been causing large outbreaks in the Americas since 2014. In Brazil, Asian-Caribbean (AC) and East-Central-South-African (ECSA) genotypes have been detected and lead to large outbreaks in several Brazilian states. In Rio Grande do Sul (RS), the southernmost state of Brazil, the first cases were reported in 2016. OBJECTIVES AND METHODS We employed genome sequencing and epidemiological investigation to characterise the Chikungunya fever (CHIKF) burden in RS between 2017-2021. FINDINGS We detected an increasing CHIKF burden linked to travel associated introductions and communitary transmission of distinct lineages of the ECSA genotype during this period. MAIN CONCLUSIONS Until 2020, CHIKV introductions were most travel associated and transmission was limited. Then, in 2021, the largest outbreak occurred in the state associated with the introduction of a new ECSA lineage. CHIKV outbreaks are likely to occur in the near future due to abundant competent vectors and a susceptible population, exposing more than 11 million inhabitants to an increasing infection risk.

https://doi.org/10.1590/0074-02760220259

Storage protein variability in natural populations of maté (Ilex paraguariensis) in Brazil
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Gregianini, Tatiana Schäffer

; Winge, Helga

Ciência Rural

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2019, Volume 49 Nº 2 elocation e20180451

Resumo: Pt En | Texto: Pt En | PDF: Pt | PDF: En

RESUMO: A variabilidade de proteínas de reserva das sementes foi analisada em 168 árvores de quatro populações naturais de erva-mate (Ilex paraguariensis) dos estados brasileiros Rio Grande do Sul, Santa Catarina, Paraná e Mato Grosso do Sul. Estes marcadores foram utilizados para estimar o grau de diferenciação entre e dentro da espécie porque são relativamente estáveis ao longo da evolução. Dados sobre presença e ausência de bandas de 80 diferentes polipeptídios foram utilizados para calcular o coeficiente de similaridade de Jaccard. Encontramos alto grau de variabilidade genética dentro de cada uma das quatro populações de árvores (SJ intra=0.374). Menores níveis de diversidade foram observados entre as populações (SJ inter=0.308). A diversidade total da espécie Ilex foi Hsp=0,264, estimada pela medida de Shannon. A partição deste valor revelou que 95% da diversidade total é intrapopulacional, enquanto somente 5% é entre populações. O fenograma, baseado nas distâncias de King, indica certo grau de diferenciação geográfica. Este trabalho representa o primeiro estudo de variabilidade em proteínas de reserva de I. paraguariensis e pode ser utilizado para orientar a escolha de espécimes para compor bancos de germoplasma e programas de melhoramento genético da espécie.

ABSTRACT: Samples of 168 maté trees (Ilex paraguariensis) from four natural populations of different states of Brazil (Rio Grande do Sul, Santa Catarina, Paraná and Mato Grosso do Sul) were analyzed for their variability in storage proteins seed, which were used to estimate the degree of differentiation among and within species, because are relatively stable during evolution. Data on band presence/absence from 80 different polypeptides were used to perform similarity coefficient of Jaccard. A high level of genetic variability was reported within sampled populations (SJ intra=0.374). Lower levels of diversity were observed between populations (SJ inter=0.308). Total genetic diversity of maté was Hsp=0.264 estimated by Shannon measure. Partition of that value disclosed that 95 % of the total diversity is within-population, and only 5% to between-populations. The phenogram based on King’s distances indicates a certain degree of geographic differentiation. This represents the first study on storage protein variability in I. paraguariensis and guides the choice of the specimens to increment germoplasm banks and genetic improvement programs.

https://doi.org/10.1590/0103-8478cr20180451 705 downloads

Drug susceptibility in emerging fungal infections: tests with fluconazole, itraconazole, and amphotericin B
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Fay, Vanessa da Silva

; Rodrigues, Diana Mara Garcia

; Gonçalves, Stela Maris Bottin

; Gregianini, Tatiana Schaffer

; Bonamigo, Renan Rangel

Anais Brasileiros de Dermatologia

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Jun 2018, Volume 93 Nº 3 Páginas 462 - 464

Resumo: En | Texto: En | PDF: En

Abstract: The number of new cases of emerging fungal infections has increased considerably in recent years, mainly due to the large number of immunocompromised individuals. The objective of this study was to evaluate the susceptibility of emerging fungi to fluconazole, itraconazole and amphotericin B by disk diffusion method. In 2015, 82 emerging fungi were evaluated in IPB-LACEN/RS and 13 (15.8%) were resistant: 10/52 were from superficial mycoses and 3/30 from systemic mycoses. The data from the study point to the need for permanent vigilance regarding the careful evaluation in the prescription and clinical and laboratory follow-up of patients affected by fungal infections.

https://doi.org/10.1590/abd1806-4841.20187364 832 downloads

Human metapneumovirus in Southern Brazil
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Gregianini, Tatiana Schäffer

; Seadi, Claudete Farina

; Menegolla, Ivone

; Martins, Letícia Garay

; Ikuta, Nilo

; Wolf, Jonas Michel

; Lunge, Vagner Ricardo

Revista da Sociedade Brasileira de Medicina Tropical

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Fev 2018, Volume 51 Nº 1 Páginas 30 - 38

Resumo: En | Texto: En | PDF: En

Abstract INTRODUCTION Infections caused by respiratory viruses are important problems worldwide, especially in children. Human metapneumovirus (hMPV) is a respiratory pathogen and causes severe infections with nonspecific symptoms. This study reports the hMPV occurrence and dissemination in southern Brazil and compares the frequency of occurrence of this virus and the human respiratory syncytial virus (hRSV) in the epidemiological weeks in a three-year period (2009-2011). METHODS: In total, 545 nasopharyngeal (NP) specimens from individuals with Severe Acute Respiratory Syndrome (SARS) who were negative for other seven respiratory viruses were analyzed for the presence of hMPV. Human metapneumovirus was detected by direct immunofluorescence and real-time reverse transcription polymerase chain reaction. RESULTS: hMPV was detected in 109 patients from the main geographic regions of the southernmost state of Brazil, presenting similar overall prevalence in males (46.8%) and females (53.2%). Among children who were less than six years old, hMPV was detected in 99 samples of all age groups, with a higher frequency in infants who were less than one year old (45.7%) compared to all other age groups until six years. hMPV and hRSV infection occurred in almost the same epidemiological weeks (EWs) of each year, with peaks of incidence between EW 31/37 and EW 26/38 for the years 2009 and 2011, respectively. hMPV was further detected in several cases of SARS and it was the only virus detected in three deaths. CONCLUSIONS These findings indicate that hMPV is in circulation in southern Brazil and highlight the importance of diagnosing hMPV for influenza-like illness in the population.

https://doi.org/10.1590/0037-8682-0435-2017 1641 downloads

Prevalence of hepatitis C virus and human immunodeficiency virus in a group of patients newly diagnosed with active tuberculosis in Porto Alegre, Southern Brazil
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Costi, Cintia

; Grandi, Tarciana

; Halon, Maria Laura

; Silva, Márcia Susana Nunes

; Silva, Cláudia Maria Dornelles da

; Gregianini, Tatiana Schäffer

; Possuelo, Lia Gonçalves

; Jarczewski, Carla Adriane

; Niel, Christian

; Rossetti, Maria Lucia Rosa

Memórias do Instituto Oswaldo Cruz

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Abr 2017, Volume 112 Nº 4 Páginas 255 - 259

Resumo: En | Texto: En | PDF: En

BACKGROUND Porto Alegre is the Brazilian state capital with second highest incidence of tuberculosis (TB) and the highest proportion of people infected with human immunodeficiency virus (HIV) among patients with TB. Hepatitis C virus (HCV) infection increases the risk of anti-TB drug-induced hepatotoxicity, which may result in discontinuation of the therapy. OBJECTIVES The aim of this study was (i) to estimate prevalence of HCV and HIV in a group of patients newly diagnosed with active TB in a public reference hospital in Porto Alegre and (ii) to compare demographic, behavioural, and clinical characteristics of patients in relation to their HCV infection status. METHODS One hundred and thirty-eight patients with TB were tested for anti-HCV antibody, HCV RNA, and anti-HIV1/2 antibody markers. HCV RNA from real-time polymerase chain reaction (PCR)-positive samples was submitted to reverse transcription and PCR amplification. The 5′ non-coding region of the HCV genome was sequenced, and genotypes of HCV isolates were determined. FINDINGS Anti-HCV antibody, HCV RNA, and anti-HIV antibodies were detected in 27 [20%; 95% confidence interval (CI), 13-26%], 17 (12%; 95% CI, 7-18%), and 34 (25%; 95% CI, 17-32%) patients, respectively. HCV isolates belonged to genotypes 1 (n = 12) and 3 (n = 4). Some characteristics were significantly more frequent in patients infected with HCV. Among them, non-white individuals, alcoholics, users of illicit drugs, imprisoned individuals, and those with history of previous TB episode were more commonly infected with HCV (p < 0.05). MAIN CONCLUSIONS HCV screening, including detection of anti-HCV antibody and HCV RNA, will be important to improving the management of co-infected patients, given their increased risk of developing TB treatment-related hepatotoxicity.

https://doi.org/10.1590/0074-02760160352 1401 downloads

10.

Performance of direct immunofluorescence assay for the detection of human metapneumovirus under clinical laboratory settings
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Wolf, Jonas Michel

; Gregianini, Tatiana Schäffer

; Seadi, Claudete Maria Farina

; Tumioto, Gabriela Luchiari

; Dambrós, Bibiana Paula

; Lehmann, Fernanda Kieling Moreira

; Carli, Silvia De

; Ikuta, Nilo

; Lunge, Vagner Ricardo

Revista da Sociedade Brasileira de Medicina Tropical

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Dez 2015, Volume 48 Nº 6 Páginas 762 - 764

Resumo: En | Texto: En | PDF: En

ABSTRACT INTRODUCTION: Human metapneumovirus (hMPV) is an emergent human respiratory pathogen. This study aimed to evaluate the performance of direct immunofluorescence (DIF) to detect hMPV in a clinical laboratory setting. METHODS: Nasopharyngeal aspirate samples (448) of children and adults with respiratory illness were used to detect hMPV by using DIF and real time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assays. RESULTS: In all, 36 (8%) samples were positive by DIF and 94 (21%) were positive by qRT-PCR. Direct immunofluorescence specificity was 99% and sensitivity was 38%. CONCLUSIONS: DIF is not very sensitive under clinical laboratory settings.

https://doi.org/10.1590/0037-8682-0107-2015 1884 downloads

11.

Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance
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Souza, Thiago Moreno Lopes e

; Fintelman-Rodrigues, Natalia

; Resende, Paola Cristina

; Mesquita, Milene

; Gregianini, Tatiana Schaffer

; Bozza, Fernando A

; Pecego, Ana Carla

; Fernandes, Sandra Bianchini

; Cury, Ana Luisa Furtado

; Riediger, Irina Nastassja

; Siqueira, Marilda M

Memórias do Instituto Oswaldo Cruz

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Fev 2015, Volume 110 Nº 1 Páginas 101 - 105

Resumo: En | Texto: En | PDF: En

The 2009 pandemic influenza A virus outbreak led to the systematic use of the neuraminidase (NA) inhibitor oseltamivir (OST). Consequently, OST-resistant strains, carrying the mutation H275Y, emerged in the years after the pandemics, with a prevalence of 1-2%. Currently, OST-resistant strains have been found in community settings, in untreated individuals. To spread in community settings, H275Y mutants must contain additional mutations, collectively called permissive mutations. We display the permissive mutations in NA of OST-resistant A(H1N1)pdm09 virus found in Brazilian community settings. The NAs from 2013 are phylogenetically distinct from those of 2012, indicating a tendency of positive selection of NAs with better fitness. Some previously predicted permissive mutations, such as V241I and N369K, found in different countries, were also detected in Brazil. Importantly, the change D344N, also predicted to compensate loss of fitness imposed by H275Y mutation, was found in Brazil, but not in other countries in 2013. Our results reinforce the notion that OST-resistant A(H1N1)pdm09 strains with compensatory mutations may arise in an independent fashion, with samples being identified in different states of Brazil and in different countries. Systematic circulation of these viral strains may jeopardise the use of the first line of anti-influenza drugs in the future.

https://doi.org/10.1590/0074-02760140330 1914 downloads

12.

Tumour necrosis factor -308 and -238 promoter polymorphisms are predictors of a null virological response in the treatment of Brazilian hepatitis C patients
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Grandi, Tarciana

; Silva, Cláudia Maria Dornelles da

; Amaral, Karine Medeiros

; Picon, Paulo Dornelles

; Costi, Cintia

; Fré, Nicole Nascimento da

; Fiegenbaum, Marilu

; Gregianini, Tatiana Schäffer

; Niel, Christian

; Rossetti, Maria Lucia Rosa

Memórias do Instituto Oswaldo Cruz

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Jun 2014, Volume 109 Nº 3 Páginas 345 - 351

Resumo: En | Texto: En | PDF: En

Certain host single nucleotide polymorphisms (SNPs) affect the likelihood of a sustained virological response (SVR) to treatment in subjects infected with hepatitis C virus (HCV). SNPs in the promoters of interleukin (IL)-10 (-1082 A/G, rs1800896), myxovirus resistance protein 1 (-123 C/A, rs17000900 and -88 G/T, rs2071430) and tumour necrosis factor (TNF) (-308 G/A, rs1800629 and -238 G/A, rs361525) genes and the outcome of PEGylated α-interferon plus ribavirin therapy were investigated. This analysis was performed in 114 Brazilian, HCV genotype 1-infected patients who had a SVR and in 85 non-responders and 64 relapsers. A significantly increased risk of having a null virological response was observed in patients carrying at least one A allele at positions -308 [odds ratios (OR) = 2.58, 95% confidence intervals (CI) = 1.44-4.63, p = 0.001] or -238 (OR = 7.33, 95% CI = 3.59-14.93, p < 0.001) in the TNF promoter. The risk of relapsing was also elevated (-308: OR = 2.87, 95% CI = 1.51-5.44, p = 0.001; -238: OR = 4.20, 95% CI = 1.93-9.10, p < 0.001). Multiple logistic regression of TNF diplotypes showed that patients with at least two copies of the A allele had an even higher risk of having a null virological response (OR = 16.43, 95% CI = 5.70-47.34, p < 0.001) or relapsing (OR = 6.71, 95% CI = 2.18-20.66, p = 0.001). No statistically significant association was found between the other SNPs under study and anti-HCV therapy response.

https://doi.org/10.1590/0074-0276130372 1541 downloads

13.

Oseltamivir-resistant influenza A(H1N1)pdm09 virus in southern Brazil
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Marx, Camila

; Gregianini, Tatiana Schaffer

; Lehmann, Fernanda Kieling Moreira

; Lunge, Vagner Ricardo

; Carli, Silvia de

; Dambros, Bibiana Paula

; Tumioto, Gabriela Luchiari

; Seadi, Claudete

; Fonseca, Andre Salvador Kazantzi

; Ikuta, Nilo

Memórias do Instituto Oswaldo Cruz

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Mai 2013, Volume 108 Nº 3 Páginas 392 - 394

Resumo: En | Texto: En | PDF: En

The neuraminidase (NA) genes of A(H1N1)pdm09 influenza virus isolates from 306 infected patients were analysed. The circulation of oseltamivir-resistant viruses in Brazil has not been reported previously. Clinical samples were collected in the state of Rio Grande do Sul (RS) from 2009-2011 and two NA inhibitor-resistant mutants were identified, one in 2009 (H275Y) and the other in 2011 (S247N). This study revealed a low prevalence of resistant viruses (0.8%) with no spread of the resistant mutants throughout RS.

https://doi.org/10.1590/S0074-02762013000300021 2362 downloads Citado 1 vez em SciELO

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