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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

Journal Metrics
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2024, Volume 40 N. 1 elocation e00122823

Abstract: Es En Pt | Text: Es En Pt | PDF: Es | PDF: En | PDF: Pt

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. Resumen (SRAG geográficas pacientes tanto 201 2020 COVID19. COVID19 COVID 19. 19 COVID-19 temporales canalización preepidémico, preepidémico pre epidémico, epidémico pre-epidémico R2 R (R 0,97 097 0 97 IC95% IC95 IC 0,950,98, 095098 0,95 0,98, 95 98 0,95-0,98 Sudeste. Sudeste . Sudeste) así 9936 9 936 9.93 Sur 9405 405 9.40 (IC95% 9.1059.738. 91059738 9.105 9.738 105 738 9.105-9.738) 20 202 COVID1 1 COVID-1 0,9 09 IC9 950 0,950,98 09509 095 098 0,98 0,95-0,9 993 93 9.9 940 40 9.4 (IC95 1059 9.1059.738 9105973 9105 9.10 9738 9.73 10 73 9.105-9.738 2 COVID- 0, 0,950,9 0950 0,95-0, 99 9. 94 4 (IC9 9.1059.73 910597 910 9.1 973 9.7 7 9.105-9.73 0,950, 0,95-0 (IC 9.1059.7 91059 91 9.105-9.7 0,950 0,95- 9.1059. 9.105-9. 9.1059 9.105-9 9.105-

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. Abstract (SARI annually Thus seasons 201 202 used COVID19. COVID19 COVID 19. 19 COVID-19 series tool preepidemic pre epidemic R2 R (R 0.97 097 0 97 95%CI 95CI CI 95 0.950.98, 095098 0.95 0.98, 98 0.95-0.98 Brazil. . Brazil) accordingly 9936 9 936 9,93 9405 405 9,40 (95%CI 9,1059,738. 91059738 9,105 9,738 105 738 9,105-9,738) 20 COVID1 1 COVID-1 0.9 09 950 0.950.98 09509 095 098 0.98 0.95-0.9 993 93 9,9 940 40 9,4 1059 9,1059,738 9105973 9105 9,10 9738 9,73 10 73 9,105-9,738 2 COVID- 0. 0.950.9 0950 0.95-0. 99 9, 94 4 9,1059,73 910597 910 9,1 973 9,7 7 9,105-9,73 0.950. 0.95-0 9,1059,7 91059 91 9,105-9,7 0.950 0.95- 9,1059, 9,105-9, 9,1059 9,105-9 9,105-

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. Resumo (SRAG anualmente geográficas pacientes Portanto 201 2020 COVID19. COVID19 COVID 19. 19 COVID-19 temporais pipeline préepidêmico, préepidêmico pré epidêmico, epidêmico pré-epidêmico R2 R (R 0,97 097 0 97 IC95% IC95 IC 0,950,98, 095098 0,95 0,98, 95 98 0,95-0,98 Sudeste. Sudeste . Sudeste) forma 9936 9 936 9.93 Sul 9405 405 9.40 (IC95% 9.1059.738. 91059738 9.105 9.738 105 738 9.105-9.738) 20 202 COVID1 1 COVID-1 0,9 09 IC9 950 0,950,98 09509 095 098 0,98 0,95-0,9 993 93 9.9 940 40 9.4 (IC95 1059 9.1059.738 9105973 9105 9.10 9738 9.73 10 73 9.105-9.738 2 COVID- 0, 0,950,9 0950 0,95-0, 99 9. 94 4 (IC9 9.1059.73 910597 910 9.1 973 9.7 7 9.105-9.73 0,950, 0,95-0 (IC 9.1059.7 91059 91 9.105-9.7 0,950 0,95- 9.1059. 9.105-9. 9.1059 9.105-9 9.105-

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 N. 1 elocation e00122823

Abstract: En Es Pt | Text: En Es Pt | PDF: En | PDF: Es | PDF: Pt

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

The health burden of natural and technological disasters in Brazil from 2013 to 2021 201 202 20 2
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Freitas, Abner Willian Quintino de

; Witt, Regina Rigatto

; Veiga, Ana Beatriz Gorini da

Cadernos de Saúde Pública

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2023, Volume 39 N. 4 elocation e00154922

Abstract: Es En Pt | Text: Es En Pt | PDF: Es | PDF: En | PDF: Pt

Los desastres afectan profundamente la salud de la población y la economía de un país. La carga sanitaria de los desastres en Brasil está subestimada, y se necesitan más estudios para elaborar políticas y acciones para reducir el riesgo de desastres. Este estudio analiza y describe los desastres ocurridos en Brasil entre 2013 y 2021. Del Sistema Integrado de Información de Desastres (S2iD) se recogió datos demográficos, datos de desastres, según la Clasificación y Codificación Brasileña de Desastres (COBRADE), y datos de resultados de salud (muertos, heridos, enfermos, personas sin hogar, desplazados, desaparecidos y otros afectados). La preparación y análisis de los datos se realizó en Tableau. El estudio muestra que ocurrieron el 98,62% (50.481) de los desastres registrados en Brasil entre 2013 y 2021 fueron naturales, con un aumento significativo en 2020 y 2021 a causa de la pandemia del COVID-19, considerada un desastre biológico. Este grupo de desastre también causó el mayor número de muertos (321.111), así como el mayor número de heridos (208.720) y enfermos (7.041.099). Al analizar los datos de cada región del país, se constataron diferencias en cuanto a la frecuencia y los resultados en salud de los desastres. Mientras los desastres climatológicos son los más frecuentes en el país (23.452 eventos) y ocurren principalmente en la región Nordeste, los desastres geológicos frecuentes en el Sudeste son los más letales. En el Sur y Sudeste del país, los desastres más comunes son los meteorológicos e hidrológicos. Este estudio muestra que los mayores resultados en salud se asocian con los desastres previstos en tiempo y espacio, y que los impactos pueden reducirse con las políticas públicas de prevención y gestión de desastres. subestimada 201 S2iD SiD S iD (S2iD demográficos COBRADE, COBRADE , (COBRADE) muertos, (muertos hogar desplazados afectados. afectados . afectados) Tableau 9862 98 62 98,62 50.481 50481 50 481 (50.481 202 naturales COVID19, COVID19 COVID 19, 19 COVID-19 biológico 321.111, 321111 321.111 321 111 (321.111) 208.720 208720 208 720 (208.720 7.041.099. 7041099 7.041.099 7 041 099 (7.041.099) 23.452 23452 23 452 (23.45 eventos Nordeste letales hidrológicos espacio 20 (COBRADE 986 9 6 98,6 50.48 5048 5 48 (50.48 COVID1 1 COVID-1 32111 321.11 32 11 (321.111 208.72 20872 72 (208.72 704109 7.041.09 04 09 (7.041.099 23.45 2345 2 45 (23.4 98, 50.4 504 4 (50.4 COVID- 3211 321.1 3 (321.11 208.7 2087 (208.7 70410 7.041.0 0 (7.041.09 23.4 234 (23. 50. (50. 321. (321.1 208. (208. 7041 7.041. (7.041.0 23. (23 (50 (321. (208 704 7.041 (7.041. (2 (5 (321 (20 70 7.04 (7.041 ( (32 7.0 (7.04 (3 7. (7.0 (7. (7

Disasters deeply impact the health of the affected population and the economy of a country. The health burden of disasters in Brazil is underestimated and more studies are needed to underpin policies and actions for disaster risk reduction. This study analyzes and describes disasters that occurred in Brazil from 2013 to 2021. The Integrated Disaster Information System (S2iD) was accessed to obtain demographic data, disaster data according to Brazilian Classification and Codification of Disasters (COBRADE), and health outcome data (number of dead, injured, sick, unsheltered, displaced, and missing individuals and other outcomes). Database preparation and analysis were performed in Tableau. In total, 98.62% (50,481) of the disasters registered in Brazil from 2013 to 2021 are natural, with a significant increase in 2020 and 2021 due to the COVID-19 pandemic, a biological disaster. This disaster group also caused the highest number of deaths (321,111), as well as injured (208,720) and sick (7,041,099) people. By analyzing data for each geographic region, we observed differences regarding disasters frequency and their health outcomes. In Brazil, climatological disasters are the most frequent (23,452 events) and occur mainly in the Northeast region. Geological disasters have the highest lethality, which are more common in the Southeast; however, the most common disasters in the South and Southeast are those of the meteorological and hydrological groups. Therefore, since the greatest health outcomes are associated with disasters predicted in time and space, public policies for the prevention and management of disasters can reduce the impacts of these events. country reduction 201 S2iD SiD S iD (S2iD COBRADE, COBRADE , (COBRADE) dead unsheltered displaced . outcomes) Tableau total 9862 98 62 98.62 50,481 50481 50 481 (50,481 202 natural COVID19 COVID 19 COVID-1 pandemic 321,111, 321111 321,111 321 111 (321,111) 208,720 208720 208 720 (208,720 7,041,099 7041099 7 041 099 (7,041,099 people region 23,452 23452 23 452 (23,45 events lethality however groups Therefore space 20 (COBRADE 986 9 6 98.6 50,48 5048 5 48 (50,48 COVID1 1 COVID- 32111 321,11 32 11 (321,111 208,72 20872 72 (208,72 7,041,09 704109 04 09 (7,041,09 23,45 2345 2 45 (23,4 98. 50,4 504 4 (50,4 3211 321,1 3 (321,11 208,7 2087 (208,7 7,041,0 70410 0 (7,041,0 23,4 234 (23, 50, (50, 321, (321,1 208, (208, 7,041, 7041 (7,041, 23, (23 (50 (321, (208 7,041 704 (7,041 (2 (5 (321 (20 7,04 70 (7,04 ( (32 7,0 (7,0 (3 7, (7, (7

Desastres afetam profundamente a saúde da população afetada e a economia de um país. A carga de saúde dos desastres no Brasil é subestimada e mais estudos são necessários para fundamentar políticas e ações para a redução do risco de desastres. Este estudo analisa e descreve desastres ocorridos no Brasil entre 2013 e 2021. O Sistema Integrado de Informações sobre Desastres (S2iD) foi acessado para obtenção de dados demográficos, dados de desastres, de acordo com a Classificação e Codificação Brasileira de Desastres (COBRADE), e dados de resultados de saúde (mortos, feridos, doentes, desabrigados, deslocados, desaparecidos e outros afetados). A preparação e a análise do banco de dados foram realizadas no Tableau. O estudo mostra que 98,62% (50.481) dos desastres registrados no Brasil entre 2013 e 2021 foram naturais, com um aumento significativo em 2020 e 2021 por causa da pandemia de COVID-19, que é um desastre biológico. Este grupo de desastres também causou o maior número de mortes (321.111), bem como de feridos (208.720) e doentes (7.041.099). Ao analisar os dados para cada região geográfica, observaram-se diferenças em relação à frequência e aos resultados de saúde dos desastres. Por exemplo, enquanto os desastres climatológicos são os mais frequentes no país (23.452 eventos) e ocorrem principalmente na Região Nordeste, a maior letalidade é observada para desastres geológicos, que são mais comuns no Sudeste. No Sul e Sudeste, os desastres mais comuns são meteorológicos e hidrológicos. Este estudo mostra que os maiores resultados de saúde estão associados a desastres previstos no tempo e no espaço e, portanto, os impactos podem ser reduzidos com políticas públicas de prevenção e gestão de desastres. 201 S2iD SiD S iD (S2iD demográficos COBRADE, COBRADE , (COBRADE) mortos, mortos (mortos desabrigados deslocados afetados. afetados . afetados) Tableau 9862 98 62 98,62 50.481 50481 50 481 (50.481 202 naturais COVID19, COVID19 COVID 19, 19 COVID-19 biológico 321.111, 321111 321.111 321 111 (321.111) 208.720 208720 208 720 (208.720 7.041.099. 7041099 7.041.099 7 041 099 (7.041.099) geográfica observaramse observaram se exemplo 23.452 23452 23 452 (23.45 eventos Nordeste geológicos Sudeste hidrológicos portanto 20 (COBRADE 986 9 6 98,6 50.48 5048 5 48 (50.48 COVID1 1 COVID-1 32111 321.11 32 11 (321.111 208.72 20872 72 (208.72 704109 7.041.09 04 09 (7.041.099 23.45 2345 2 45 (23.4 98, 50.4 504 4 (50.4 COVID- 3211 321.1 3 (321.11 208.7 2087 (208.7 70410 7.041.0 0 (7.041.09 23.4 234 (23. 50. (50. 321. (321.1 208. (208. 7041 7.041. (7.041.0 23. (23 (50 (321. (208 704 7.041 (7.041. (2 (5 (321 (20 70 7.04 (7.041 ( (32 7.0 (7.04 (3 7. (7.0 (7. (7

https://doi.org/10.1590/0102-311xen154922

Chikungunya virus infection in the southernmost state of Brazil was characterised by self-limited transmission (2017-2019) and a larger 2021 outbreak selflimited self limited 20172019 2017 2019 (2017-2019 202 2017201 201 (2017-201 20 201720 (2017-20 2 20172 (2017-2 (2017- (2017 (201 (20 (2 (
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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

Abstract: En | Text: 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. mosquitoborne mosquito borne 2014 Brazil AsianCaribbean Asian Caribbean AC (AC EastCentralSouthAfrican East Central South African (ECSA states RS, , (RS) 2016 (CHIKF 20172021. 20172021 2017 2021. 2021 2017-2021 period 2020 limited Then lineage population 1 risk 201 (RS 2017202 202 2017-202 20 201720 2017-20 2 20172 2017-2 2017-

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

SARS-CoV-2 laboratory surveillance during the first year of the COVID-19 pandemic in southern Brazil SARSCoV2 SARSCoV SARS CoV 2 SARS-CoV- COVID19 COVID 19 COVID-1 SARS-CoV COVID1 1 COVID-
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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

Abstract: En | Text: 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. Background COVID19 COVID 19 COVID-1 deaths RS (RS network LACENRS LACEN (LACEN-RS 202 COVID19. 19. Methods RTqPCR RT qPCR criteria extractors SARSCoV2 SARSCoV SARS CoV 2 SARS-CoV- BioManguinhos/Rio BioManguinhosRio Bio Manguinhos/Rio Manguinhos Janeiro IBMPParaná IBMP Paraná IBMP/Paraná 2019nCoV nCoV 2019 assay total 36 platform Results 31197 31 197 31,19 107578 107 578 107,57 29% 29 SARSCoV2. 2. state JulyAugust July August December 63 33.1% 331 33 1 (33.1 vs 265 26 5 26.5 females. females . females) 5079 50 79 50-7 capital Alegre region identified B1128 B 28 B.1.1.28 B1133 B.1.1.33 P2 P P. frequent Conclusions Here COVID1 COVID- 20 SARS-CoV BioManguinhos ManguinhosRio 201 3 3119 31,1 10757 10 57 107,5 6 33.1 (33. 26. 507 7 50- B112 B.1.1.2 B113 B.1.1.3 311 31, 1075 107, 33. (33 B11 B.1.1. (3 B1 B.1.1 ( B.1. B.1 B.

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

The health burden of natural and technological disasters in Brazil from 2013 to 2021
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Freitas, Abner Willian Quintino de

; Witt, Regina Rigatto

; Veiga, Ana Beatriz Gorini da

Cadernos de Saúde Pública

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2023, Volume 39 N. 4 elocation e00154922

Abstract: Pt Es En | Text: Pt Es En | PDF: Pt | PDF: Es | PDF: En

https://doi.org/10.1590/0102-311xen154922

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

Abstract: Es Pt En | Text: 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

Gene expression evaluation of antioxidant enzymes in patients with hepatocellular carcinoma: RT-qPCR and bioinformatic analyses
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Alves, Andressa de Freitas

; Moura, Ana Carolina de

; Andreolla, Huander Felipe

; Veiga, Ana Beatriz Gorini da

; Fiegenbaum, Marilu

; Giovenardi, Márcia

; Almeida, Silvana

Genetics and Molecular Biology

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2021, Volume 44 N. 2 elocation e20190373

Abstract: En | Text: En | PDF: En

Abstract Any condition leading to chronic liver disease is a potential oncogenic agent for hepatocellular carcinoma (HCC). Alterations in the expression of antioxidant enzymes could alter the redox balance. Our aim was to evaluate the expression of the genes GPX1, GPX4, SEP15, SELENOP, SOD1, SOD2, GSR, CAT, and NFE2L2 in patients with HCC. Differential gene expression analysis was performed using RNA-Seq data from the TCGA and GTEx databases, and RT-qPCR data from HCC patient samples. Bioinformatic analysis revealed significant differential expression in most genes. GPX4 expression was significantly increased (p=0.02), while SOD2 expression was significantly decreased (p=0.04) in experimental data. In TCGA samples, alpha-fetoprotein levels (mg/dL) were negatively correlated with the expression of SEP15 (p<0.001), SELENOP (p<0.001), SOD1 (p<0.001), SOD2 (p<0.001), CAT (p<0.001), and NFE2L2 (p=0.004). Alpha-fetoprotein levels were positively correlated with the expression of GPX4 (p=0.02) and SELENOP (p=0.01) in the experimental data. Low expression of GPX1 (p=0.006), GPX4 (p=0.01), SELENOP (p=0.006), SOD1 (p=0.007), CAT (p<0.001), and NFE2L2 (p<0.001), and higher levels of GSR, were associated with low overall survival at 12 months. These results suggest a significant role for these antioxidant enzymes in HCC pathogenesis and severity.

https://doi.org/10.1590/1678-4685-gmb-2019-0373 412 downloads

Control and prevention of infectious diseases from a One Health perspective
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Ellwanger, Joel Henrique

; Veiga, Ana Beatriz Gorini da

; Kaminski, Valéria de Lima

; Valverde-Villegas, Jacqueline María

; Freitas, Abner Willian Quintino de

; Chies, José Artur Bogo

Genetics and Molecular Biology

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2021, Volume 44 N. 1 elocation e20200256

Abstract: En | Text: En | PDF: En

Abstract The ongoing COVID-19 pandemic has caught the attention of the global community and rekindled the debate about our ability to prevent and manage outbreaks, epidemics, and pandemics. Many alternatives are suggested to address these urgent issues. Some of them are quite interesting, but with little practical application in the short or medium term. To realistically control infectious diseases, human, animal, and environmental factors need to be considered together, based on the One Health perspective. In this article, we highlight the most effective initiatives for the control and prevention of infectious diseases: vaccination; environmental sanitation; vector control; social programs that encourage a reduction in the population growth; control of urbanization; safe sex stimulation; testing; treatment of sexually and vertically transmitted infections; promotion of personal hygiene practices; food safety and proper nutrition; reduction of the human contact with wildlife and livestock; reduction of social inequalities; infectious disease surveillance; and biodiversity preservation. Subsequently, this article highlights the impacts of human genetics on susceptibility to infections and disease progression, using the SARS-CoV-2 infection as a study model. Finally, actions focused on mitigation of outbreaks and epidemics and the importance of conservation of ecosystems and translational ecology as public health strategies are also discussed.

https://doi.org/10.1590/1678-4685-gmb-2020-0256 2561 downloads

10.

Identification of hepatitis B virus A1762T/G1764A double mutant strain in patients in Southern Brazil
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Silva Souza, Adaliany Cecília da

; Souza Marasca, Giórgia de

; Kretzmann-Filho, Nélson Alexandre

; Dall-Bello, Aline

; Kliemann, Dimas Alexandre

; Tovo, Cristiane Valle

; Veiga, Ana Beatriz Gorini da

Brazilian Journal of Infectious Diseases

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oct 2017, Volume 21 N. 5 Pages 525 - 529

Abstract: En | Text: En | PDF: En

Abstract Infection by hepatitis B virus (HBV) is a worldwide public health problem. Chronic HBV infection with high viral replication may lead to cirrhosis and/or hepatocellular carcinoma. Mutant HBV strains, such as the HBV A1762T/G1764A double mutant, have been associated with poor prognosis and higher risk of the patient for developing cirrhosis and/or hepatocellular carcinoma. This study analyzed the presence of the HBV A1762T/G1764A double mutant in patients with chronic HBV and its association with clinical parameters such as viral load, aminotransferases, and HBV antigens. A total of 49 patients with chronic hepatitis B were included in the study, and the HBV A1762T/G1764A double mutant strain was detected in four samples (8.16%) by polymerase chain reaction followed by restriction fragment length analysis (PCR-RFLP). The viral load was not significantly different between patients with or without the double mutant strain (p = 0.43). On the other hand, carriers of the HBV A1762T/G1764A double mutant had higher levels of ALT (p = 0.0028), while AST levels did not differ between groups (p = 0.051). In this study, 75% of the samples with the HBV A1762T/G1764A double mutation were HBeAg negative and anti-HBe positive, reflecting seroconversion even though they still displayed high viral loads. Our study has shown that the HBV A1762T/G1764A double mutant strain circulates in Brazilian patients, and is associated with elevated levels of ALT and HBeAg seroconversion.

https://doi.org/10.1016/j.bjid.2017.05.002 521 downloads

11.

FREQUENCY OF THE MDR1 GENE POLYMORPHISM RS1045642 (C3435T) IN HCV-HIV CO-INFECTED PATIENTS
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MARASCA, Giórgia de Souza

; MACHADO, André Luiz

; KRETZMANN FILHO, Nélson Alexandre

; SOUZA, Adaliany Cecília da Silva

; MATTOS, Angelo Alves de

; KLIEMANN, Dimas

; TOVO, Cristiane Valle

; VEIGA, Ana Beatriz Gorini da

Arquivos de Gastroenterologia

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dec 2016, Volume 53 N. 4 Pages 246 - 249

Abstract: Pt En | Text: Pt En | PDF: Pt | PDF: En

RESUMO Contexto Em virtude da elevada prevalência da coinfecção pelos vírus da hepatite C (HCV) e da imunodeficiência humana (HIV) e às inúmeras complicações que esses vírus acarretam, é fundamental o maior entendimento do comportamento biológico dos mesmos. O polimorfismo de nucleotídeo único rs1045642 C3435T do gene de resistência a múltiplas drogas MDR1, no qual ocorre modificação do códon ATC para ATT, parece estar relacionado à resposta virológica sustentada ao tratamento do HCV em coinfectados HCV-HIV. Objetivo Mapear o polimorfismo C3435T do gene MDR1 em pacientes coinfectados HCV-HIV e correlacionar com dados clínicos e laboratoriais. Métodos Foram analisados 99 pacientes coinfectados HCV-HIV. A identificação molecular do polimorfismo de nucleotídeo único rs1045642 do gene MDR1 foi realizada pela técnica de PCR em tempo real (qPCR) alelo-específico com primers e sondas específicos para a identificação desse polimorfismo. Fatores de risco para a aquisição do HCV e a resposta virológica sustentada ao tratamento do HCV com interferon-alfa peguilado e ribavirina foram analisados. Resultados Dentre os pacientes avaliados, 54 (54,5%) eram do gênero masculino e 45 (45,5%) do gênero feminino. A média de idade foi de 46,1 anos (±9,8). As frequências dos genótipos CC, CT e TT foram 28,3%, 47,5% e 24,2% respectivamente, e as frequências alélicas foram 52% para alelo C e 48% para alelo T. Não houve associação entre o gene MDR1 e a resposta virológica sustentada (P=0,308). Conclusão Neste estudo, o polimorfismo C3435T no gene MDR1 não apresentou associação com a resposta virológica sustentada ao tratamento em indivíduos coinfectados HCV-HIV.

ABSTRACT Background Due to the high prevalence of co-infection by hepatitis C virus (HCV) and human immunodeficiency virus (HIV) and the severity of these infections, the understanding of the biological mechanisms involved in these processes, including viral behavior and host genetic profile, is of great importance for patient treatment and for public health policies.Some single nucleotide polymorphisms (SNPs) in the human genome, such as the SNP rs1045642 (C3435T) in the MDR1 gene, have been reported to be associated to the sustained virological response (SVR) to HCV treatment in HCV-HIV co-infected patients. Objective The present study analyzes the MDR1 gene C3435T polymorphism in HCV-HIV co-infected patients. Methods A total of 99 HCV-HIV patients were included in the study. The DNA was extracted from blood samples, and the SNP rs1045642 was assessed by Real Time PCR (qPCR). Risk factors for acquiring the virus and the SVR after HCV treatment with pegylated interferon-alpha and ribavirin were also analyzed. Results Among the patients, 54 (54.5%) were male and 45 (45.5%) were female. The average age was 46.1±9.8 years. The SVR after HCV treatment was 40%. The frequencies of MDR1 genotypes CC, CT and TT were 28.3%, 47.5% and 24.2%, respectively. Allele frequencies were 52% for the C allele and 48% for the T allele. No association was found for SNP rs1045642 (C3435T) regarding response to treatment (P=0.308). Conclusion - In this study, the C3435T polymorphism in the MDR1 gene appears not to be associated with SVR in HCV-HIV co-infected individuals.

https://doi.org/10.1590/S0004-28032016000400007 3882 downloads

12.

Transcriptional expression study in the central nervous system of rats: what gene should be used as internal control?
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Moura, Ana Carolina de

; Lazzari, Virgínia Meneghini

; Agnes, Grasiela

; Almeida, Silvana

; Giovenardi, Márcia

; Veiga, Ana Beatriz Gorini da

einstein (São Paulo)

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sep 2014, Volume 12 N. 3 Pages 336 - 341

Abstract: Pt En | Text: Pt En | PDF: Pt | PDF: En

Objetivo Um número crescente de artigos publicados relaciona a expressão de genes específicos com diferentes padrões de comportamento em ratos. Os níveis de transcritos de ácido ribonucleico mensageiro são geralmente analisados por transcrição reversa, seguida de reação em cadeia da polimerase, e quantificados após a normalização com um controle interno ou gene de referência (gene housekeeping). No entanto, os genes housekeeping exibem expressão diferencial no sistema nervoso central, dependendo das condições fisiológicas e da área do cérebro a ser estudada. A escolha de um bom gene de controle interno é essencial para a obtenção de resultados confiáveis. Este estudo avaliou a expressão de três genes housekeeping (beta-actina, ciclofilina A e ubiquitina C) em diferentes áreas do sistema nervoso central de ratos (bulbo olfatório, hipocampo, estriado e córtex pré-frontal). Métodos Foram usadas ratas Wistar (fêmeas virgens, n=6) durante o período de diestro. O ácido ribonucleico total foi extraído a partir de cada região do cérebro; o ácido desoxirribonucleico complementar foi sintetizado por transcrição reversa e amplificado por reação em cadeia da polimerase quantitativo em tempo real utilizando SYBR® Green e primers específicos para cada um dos genes de referência. A estabilidade de expressão foi determinada utilizando NormFinder. Resultados A beta-actina foi o gene mais estável no hipocampo e estriado, enquanto a ciclofilina A e a ubiquitina C apresentaram maior estabilidade no córtex pré-frontal e no bulbo olfatório, respectivamente. Conclusão Com base em nosso trabalho, estudos posteriores de expressão gênica utilizando ratos como modelos animais devem levar estes resultados em conta na escolha de um gene de controle interno confiável.

Objective A growing number of published articles report the expression of specific genes with different behavior patterns in rats. The levels of messenger ribonucleic acid transcripts are usually analyzed by reverse transcription followed by polymerase chain reaction and quantified after normalization with an internal control or reference gene (housekeeping gene). Nevertheless, housekeeping genes exhibit different expression in the central nervous system, depending on the physiological conditions and the area of the brain to be studied. The choice of a good internal control gene is essential for obtaining reliable results. This study evaluated the expression of three housekeeping genes (beta-actin, cyclophilin A, and ubiquitin C) in different areas of the central nervous system in rats (olfactory bulb, hippocampus, striatum, and prefrontal cortex). Methods Wistar rats (virgin females, n=6) during the diestrum period were used. Total ribonucleic acid was extracted from each region of the brain; the complementary deoxyribonucleic acid was synthesized by reverse transcription and amplified by real-time quantitative polymerase chain reaction using SYBR™ Green and primers specific for each one of the reference genes. The stability of the expression was determined using NormFinder. Results Beta-actin was the most stable gene in the hippocampus and striatum, while cyclophilin A and ubiquitin C showed greater stability in the prefrontal cortex and the olfactory bulb, respectively. Conclusion Based on our study, further studies of gene expression using rats as animal models should take into consideration these results when choosing a reliable internal control gene.

https://doi.org/10.1590/s1679-45082014ao3042 5947 downloads

13.

MELTING CURVE ANALYSIS FOR THE SCREENING OF HEPATITIS B VIRUS GENOTYPES A, D AND F IN PATIENTS FROM A GENERAL HOSPITAL IN SOUTHERN BRAZIL
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BECKER, Carlos Eduardo

; KRETZMANN, Nelson Alexandre

; MATTOS, Angelo Alves de

; VEIGA, Ana Beatriz Gorini da

Arquivos de Gastroenterologia

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sep 2013, Volume 50 N. 3 Pages 219 - 225

Abstract: Pt En | Text: Pt En | PDF: Pt | PDF: En

Contexto O vírus da hepatite B pode causar hepatite fulminante, cirrose e carcinoma hepatocelular, sendo uma das causas mais frequentes de doença aguda e crônica do fígado. As variantes genéticas do VHB podem ser determinantes para a evolução da doenças assim como para a eleição da terapêutica. Objetivos O objetivo deste estudo foi padronizar e avaliar uma metodologia “in house”, através da utilização da curva de melting de reação em cadeia da polimerase (PCR) em tempo real (qPCR), como rastreamento para análise dos genótipos A, D e F do vírus da hepatite B em pacientes do Rio Grande do Sul. Métodos Foram avaliados 104 pacientes supostamente com infecção crônica pelo VHB. O DNA foi extraído com kit comercial, os genótipos e as mutações foram determinados utilizando diferentes protolocos baseados em PCR. Resultados Foi padronizada uma metodologia baseada em PCR para a análise dos genótipos A, D e F do VHB. A técnica consistiu de uma PCR Nested incluindo uma etapa final de PCR em tempo real Multiplex, utilizando a curva de melting como ferramenta para a definição dos fragmentos. Foi observada uma maior frequência do genótipo D (44,4%), seguido do genótipo A (22,2%) e do genótipo F (3,7%) na amostra analisada. Conclusão O ensaio padronizado fornece um método rápido e preciso para diferenciar genótipos do VHB mais frequentes no sul do Brasil – A, D e F – usando um PCR Nested Multiplex com primers específicos, o qual apresenta potencial aplicação na prática clínica.

Context Hepatitis B virus (HBV) can cause fulminant hepatitis, cirrhosis and hepatocellular carcinoma, and is one of the most common causes of acute and chronic liver failure. The genetic variants of HBV can be decisive for the evolution of these diseases as well as for the election of therapy. Objectives The aim of this study was to evaluate and standardize an in house methodology based on the analysis of the melting curve polymerase chain reaction (PCR) of real-time (qPCR) to screen for genotypes A, D and F of HBV in patients from a hospital in Rio Grande do Sul, Brazil. Methods We evaluated 104 patients presumably with HBV chronic infection. Viral DNA was extracted from plasma and viral genotypes and different mutations were determined using PCR-based protocols. Results A PCR-based methodology was standardized for the analysis of genotypes A, D and F of HBV. The technique was based in a nested PCR with the final step consisting of a multiplex real-time PCR, using the melting curve as a tool for the differentiation of fragments. A higher frequency of genotype D (44.4%), followed by genotype A (22.2%) and genotype F (3.7%) was observed. Conclusion The standardized assay, a nested PCR-multiplex qPCR using specific primers, provides a rapid and accurate method for the differentiation of HBV genotypes that are more frequent in Southern Brazil – A, D and F. This method can be applied in the clinical practice.

https://doi.org/10.1590/S0004-28032013000200039 5849 downloads Cited 1 time in SciELO

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