Machine learning in predicting severe acute respiratory infection outbreaks / Aprendizado de máquina na previsão de surtos de síndrome respiratória aguda grave / Aprendizaje automático en la predicción de brotes de síndrome respiratorio agudo grave

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.

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.

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.

Tracking the emergence of antigenic variants in influenza A virus epidemics in Brazil.

Influenza A virus (IAV) circulation patterns differ in North America and South America, with influenza seasons often characterized by different subtypes and strains. However, South America is relatively undersampled considering the size of its population. To address this gap, we sequenced the complete genomes of 220 IAVs collected between 2009 and 2016 from hospitalized patients in southern Brazil. New genetic drift variants were introduced into southern Brazil each season from a global gene pool, including four H3N2 clades (3c, 3c2, 3c3, and 3c2a) and five H1N1pdm clades (clades 6, 7, 6b, 6c, and 6b1). In 2016, H1N1pdm viruses belonging to a new 6b1 clade caused a severe influenza epidemic in southern Brazil that arrived early and spread rapidly, peaking mid-autumn. Inhibition assays showed that the A/California/07/2009(H1N1) vaccine strain did not protect well against 6b1 viruses. Phylogenetically, most 6b1 sequences that circulated in southern Brazil belong to a single transmission cluster that rapidly diffused across susceptible populations, leading to the highest levels of influenza hospitalization and mortality seen since the 2009 pandemic. Continuous genomic surveillance is needed to monitor rapidly evolving IAVs for vaccine strain selection and understand their epidemiological impact in understudied regions.

Epidemiologic Profile of Severe Acute Respiratory Infection in Brazil During the COVID-19 Pandemic: An Epidemiological Study.

Background: The COVID-19 is a significant public health issue, and monitoring confirmed cases and deaths is an essential epidemiologic tool. We evaluated the features in Brazilian hospitalized patients due to severe acute respiratory infection (SARI) during the COVID-19 pandemic in Brazil. We grouped the patients into the following categories: Influenza virus infection (G1), other respiratory viruses' infection (G2), other known etiologic agents (G3), SARS-CoV-2 infection (patients with COVID-19, G4), and undefined etiological agent (G5). Methods: We performed an epidemiological study using data from DataSUS (https://opendatasus.saude.gov.br/) from December 2019 to October 2021. The dataset included Brazilian hospitalized patients due to SARI. We considered the clinical evolution of the patients with SARI during the COVID-19 pandemic according to the SARI patient groups as the outcome. We performed the multivariate statistical analysis using logistic regression, and we adopted an Alpha error of 0.05. Results: A total of 2,740,272 patients were hospitalized due to SARI in Brazil, being the São Paulo state responsible for most of the cases [802,367 (29.3%)]. Most of the patients were male (1,495,416; 54.6%), aged between 25 and 60 years (1,269,398; 46.3%), and were White (1,105,123; 49.8%). A total of 1,577,279 (68.3%) patients recovered from SARI, whereas 701,607 (30.4%) died due to SARI, and 30,551 (1.3%) did not have their deaths related to SARI. A major part of the patients was grouped in G4 (1,817,098; 66.3%) and G5 (896,207; 32.7%). The other groups account for <1% of our sample [G1: 3,474 (0.1%), G2: 16,627 (0.6%), and G3: 6,866 (0.3%)]. The deaths related to SARI were more frequent in G4 (574,887; 34.7%); however, the deaths not related to SARI were more frequent among the patients categorized into the G3 (1,339; 21.3%) and G5 (25,829; 4.1%). In the multivariate analysis, the main predictors to classify the patients in the G5 when compared with G4 or G1-G4 were female sex, younger age, Black race, low educational level, rural place of residence, and the use of antiviral to treat the clinical signs. Furthermore, several features predict the risk of death by SARI, such as older age, race (Black, Indigenous, and multiracial background), low educational level, residence in a flu outbreak region, need for intensive care unit, and need for mechanical ventilatory support. Conclusions: The possible COVID-19 underreporting (G5) might be associated with an enhanced mortality rate, more evident in distinct social groups. In addition, the patients' features are unequal between the patients' groups and can be used to determine the risk of possible COVID-19 underreporting in our population. Patients with a higher risk of death had a different epidemiological profile when compared with patients who recovered from SARI, like older age, Black, Indigenous, and multiracial background races, low educational level, residence in a flu outbreak region, need for intensive care unit and need for mechanical ventilatory support.

Perinatal Outcomes of Asynchronous Influenza Vaccination, Ceará, Brazil, 2013-2018.

In Ceará, Brazil, seasonal influenza transmission begins before national annual vaccination campaigns commence. To assess the perinatal consequences of this misalignment, we tracked severe acute respiratory infection (SARI), influenza, and influenza immunizations during 2013-2018. Among 3,297 SARI cases, 145 (4.4%) occurred in pregnant women. Statewide vaccination coverage was >80%; however, national vaccination campaigns began during or after peak influenza season. Thirty to forty weeks after peak influenza season, birthweights decreased by 40 g, and rates of prematurity increased from 10.7% to 15.5%. We identified 61 children born to mothers with SARI during pregnancy; they weighed 10% less at birth and were more likely to be premature than 122 newborn controls. Mistiming of influenza vaccination campaigns adversely effects perinatal outcomes in Ceará. Because Ceará is the presumptive starting point for north-to-south seasonal influenza transmission in Brazil, earlier national immunization campaigns would provide greater protection for pregnant women and their fetuses in Ceará and beyond.

Epidemiology of influenza B infection in the state of Rio Grande do Sul, Brazil, from 2003 to 2019.

Influenza B virus (IBV) causes respiratory tract infections with mild, moderate, or life-threatening symptoms. This study describes the epidemiology of IBV infection in Rio Grande do Sul (RS), Brazil, over 17 years. Nasopharyngeal samples were collected from outpatients presenting acute respiratory illness (ARI) between 2003 and 2019, and from inpatients with severe acute respiratory infection (SARI) from 2009 to 2019. IBV was detected by immunofluorescence assay or quantitative real-time polymerase chain reaction; demographic and clinical data were analyzed. In total, 48,656 cases of respiratory infection were analyzed, of which 20.45% were ARI, and 79.46% were SARI. Respiratory viruses accounted for 22.59% and 37.47% of the cases of ARI and SARI, respectively. Considering respiratory viral infections, 17.10% of ARI and 3.06% of SARI were associated with IBV. IBV circulated year-round in RS, with an increase in autumn and winter, peaking in July (p = .005). IBV infection showed an association with age, and most outpatients positive for IBV were between 10 and 49 years old, whereas IBV infection in SARI affected mainly individuals ≤ 1 year or ≥ 60 years old. No significant association was found between sex and IBV infection. Coryza, sore throat, and myalgia were associated with ARI (p < .001). Moreover, 3.18% of the deaths associated with respiratory virus infection were positive for IBV; notably, cardiopathy (p < .001), metabolic disease (p < .001), and smoking (p = .003) were associated to fatality in IBV infection. IBV is an important cause of severe respiratory infections, and the fatality risk is high in individuals with cardiopathy and metabolic diseases.

Epidemiology of respiratory viruses in patients with severe acute respiratory infections and influenza-like illness in Suriname.

BACKGROUND: Influenza has been well studied in developed countries with temperate climates, in contrast to low- and middle-income (LMIC) countries, thus hampering the effort to attain representative global data. Furthermore, data on non-influenza respiratory infections are also limited. Insight in viral respiratory infections in Suriname, a tropical LMIC in South America, would contribute to improved local preventive measures and a better global understanding of respiratory viruses. METHODS: From May 2016 through April 2018, all patients (n = 1096) enrolled in the national severe acute respiratory infection and influenza-like illness surveillance were screened for the presence of 10 respiratory viruses with singleplex RT-PCR. RESULTS: The overall viral-positive detection rate was 45.3%, specified as RSV (19.4%), influenza (15.5%), hMPV (4.9%), AdV (4.6%), and parainfluenza (3.8%). Co-infections were detected in 6.2% of the positive cases. Lower overall positivity was observed in the SARI vs ILI surveillance and influenza prevalence was higher in outpatients (45.0% vs 6.7%), while RSV exhibited the reverse (4.8% vs 23.8%). Respiratory infections in general were more common in children than in adults (54.4% vs 29.5%), although children were significantly less affected by influenza (11.5% vs 22.7%). None of the respiratory viruses displayed a clear seasonal pattern, and viral interference was observed between RSV and influenza. CONCLUSIONS: The comprehensive information presented for Suriname, including first data on non-influenza respiratory viruses, displayed distinct differences between the viruses, in seasonality, within age groups and between SARI/ILI, accentuating the need, especially for tropical LMIC countries to continue ongoing surveillance and accumulate local data.

Fatores associados à Síndrome Respiratória Aguda Grave em uma Região Central do Brasil / Factors associated with Severe Acute Respiratory Syndrome in a Brazilian central region

Resumo A Síndrome Respiratória Aguda Grave (SRAG) deve ser notificada e investigada. O objetivo do estudo foi analisar o perfil epidemiológico e fatores associados à internação e óbitos por SRAG notificados em Goiás. Estudo de coorte retrospectiva, com dados das fichas de investigação do Sistema de Informação de Agravos de Notificação Influenza Web. Métodos de análise multivariada foram realizados para verificar a associação entre variáveis de exposição com os desfechos internação em UTI e óbito. Entre 2013 e 2018 foram notificados 4.832 casos de SRAG em Goiás. O principal diagnóstico etiológico foi influenza A (22,3%) com o subtipo A (H1N1pdm09) predominante, seguido pelo Vírus Sincicial Respiratório. 34,6% dos pacientes necessitaram de internação em UTI e 19% evoluíram para o óbito. Maior tempo de início do tratamento com antiviral foi associado à maior chance de internação em UTI, enquanto a não vacinação prévia contra a influenza, maior tempo para início do antiviral e idade mais avançada foram associados à maior chance de óbito. O estudo mostrou uma elevada frequência de doenças respiratórias provocadas pelo vírus Influenza no estado de Goiás e que a gravidade da síndrome, caracterizada pela internação em UTI e óbitos, está associada com o tempo de início do tratamento com o antiviral, o status vacinal e a idade do paciente.

Abstract Severe Acute Respiratory Infection (SARI) is a notifiable syndrome that must be investigated. This study aimed to analyze the epidemiological profile and factors associated with SARI-related hospitalization and deaths reported in Goiás. Retrospective cohort study, with data from the investigation files of the Notifiable Diseases Information System's Influenza Web. Multivariate analysis methods were employed to verify the association between exposure variables with the outcomes of ICU admission and death. A total of 4,832 SARI cases were reported in Goiás from 2013 to 2018. The primary etiological diagnosis was Influenza A (22.3%) with the predominant subtype A (H1N1pdm09), followed by the Respiratory Syncytial Virus. A total of 34.6% of the patients required ICU admission, and 19% died. A longer time to start treatment with antivirals was associated with a higher likelihood to have an ICU admission, while a previous non-vaccination against Influenza, longer time to start treatment, and older age were associated with a higher likelihood to suffer death. The study showed a high frequency of respiratory diseases caused by the Influenza virus in Goiás and that the severity of the syndrome, characterized by ICU admission and deaths, is associated with the start of antiviral treatment vaccine status, and patient's age.

A 28-year study of human parainfluenza in Rio Grande do Sul, Southern Brazil.

PROBLEM: Human parainfluenza virus (hPIV) is an important pathogen in respiratory infections, however the health burden of hPIV is underestimated. This study describes the infections by hPIV1-3 in Rio Grande do Sul, Brazil, from 1990 to 2017, providing data of the frequency and seasonality of cases and associated clinical symptoms. METHOD OF STUDY: Nasopharyngeal samples of patients with respiratory infection were collected, clinical data were analyzed, and immunofluorescence was used to detect hPIV. RESULTS: Respiratory viruses were detected in 33.63% of respiratory infections. In a total of 11 606 cases of viral respiratory infection, 781 were positive for hPIV; hPIV prevalence ranged from 2.14% to 27% of viral respiratory infections. hPIV1 circulates mainly during fall; hPIV3 circulation, in turn, starts in fall and peaks during spring; and cases of hPIV2 are reported along the year, with peaks in fall and early spring. The most affected age group was children, with hPIV prevalence of 74.23% in patients for less than 1 year. A higher proportion of girls were infected than boys, however, no difference by sex was observed considering all age groups. The most frequent type was hPIV3, especially in hospitalized patients. Both hPIV1 and 3 were associated with dyspnea, while hPIV2 caused mild symptoms mainly in nonhospitalized patients. Nineteen fatalities occurred, 89.5% of them associated with risk factors (prematurity; chronic diseases; age, <1 or >60 years). CONCLUSION: hPIV causes a high number of respiratory infections, leading to hospitalization especially in children; epidemiological and surveillance studies are important for the control and management of respiratory infections.

The occurrence of polyomaviruses WUPyV and KIPyV among patients with severe respiratory infections.

In 2007, the new polyomaviruses WUPyV and KIPyV were identified in patients with acute respiratory infections. The aim of this study was to investigate these viruses in hospitalized patients with severe acute respiratory infection (SARI). A retrospective study was conducted with 251 patients, from April 2009 to November 2010, using nasopharyngeal aspirates, naso- and oropharyngeal swab samples from hospitalized patients (children < 12 years and adults) who had SARI within 7 days of the onset of symptoms, including fever (> 38.8 °C), dyspnea, and cough. Clinical and epidemiological information was obtained through standardized questionnaire. Enrolled patients were initially suspected to have influenza A(H1N1)pdm09 infections. WUPyV and KIPyV were detected by real-time PCR. Samples were also tested for influenza A and B viruses, human respiratory syncytial virus, rhinovirus, metapneumovirus, coronavirus, adenovirus, and parainfluenza viruses. WUPyV and KIPyV were detected in 6.77% (4.78% and 1.99%, respectively) of hospitalized patients with SARI. All samples from children showed coinfections (rhinovirus was the most commonly detected). Six adults had polyomavirus infection and four (1.6%) had monoinfection. Of them, 3 reported comorbidities including immunosuppression and 1 patient had worse outcome, requiring ICU admission. These preliminary data may suggest a possible role of polyomaviruses in SARI among immunocompromised adult patients.

Viral detection profile in children with severe acute respiratory infection.

OBJECTIVES: The role of viral co-detection in children with severe acute respiratory infection is not clear. We described the viral detection profile and its association with clinical characteristics in children admitted to the Pediatric Intensive Care Unit (PICU) during the 2009 influenza A(H1N1) pandemic. METHOD: Longitudinal observational retrospective study, with patients aged 0-18 years, admitted to 11 PICUs in Rio de Janeiro, with suspected H1N1 infection, from June to November, 2009. The results of respiratory samples which were sent to the Laboratory of Fiocruz/RJ and clinical data extracted from specific forms were analyzed. RESULTS: Of 71 samples, 38% tested positive for H1N1 virus. Of the 63 samples tested for other viruses, 58 were positive: influenza H1N1 (43.1% of positive samples), rhinovirus/enterovirus (41.4%), respiratory syncytial vírus (12.1%), human metapneumovirus (12.1%), adenovirus (6.9%), and bocavirus (3.5%). Viral codetection occured in 22.4% of the cases. H1N1-positive patients were of a higher median age, had higher frequency of fever, cough and tachypnea, and decreased leukometry when compared to H1N1-negative patients. There was no difference in relation to severity outcomes (number of organic dysfunctions, use of mechanical ventilation or amines, hospital/PICU length of stay or death). Comparing the groups with mono-detection and co-dection of any virus, no difference was found regarding the association with any clinical variable. CONCLUSIONS: Other viruses can be implicated in SARI in children. The role of viral codetection has not yet been completely elucidated.

Viral detection profile in children with severe acute respiratory infection

ABSTRACT Objectives: The role of viral co-detection in children with severe acute respiratory infection is not clear. We described the viral detection profile and its association with clinical characteristics in children admitted to the Pediatric Intensive Care Unit (PICU) during the 2009 influenza A(H1N1) pandemic. Method: Longitudinal observational retrospective study, with patients aged 0-18 years, admitted to 11 PICUs in Rio de Janeiro, with suspected H1N1 infection, from June to November, 2009. The results of respiratory samples which were sent to the Laboratory of Fiocruz/RJ and clinical data extracted from specific forms were analyzed. Results: Of 71 samples, 38% tested positive for H1N1 virus. Of the 63 samples tested for other viruses, 58 were positive: influenza H1N1 (43.1% of positive samples), rhinovirus/enterovirus (41.4%), respiratory syncytial vírus (12.1%), human metapneumovirus (12.1%), adenovirus (6.9%), and bocavirus (3.5%). Viral codetection occured in 22.4% of the cases. H1N1-positive patients were of a higher median age, had higher frequency of fever, cough and tachypnea, and decreased leukometry when compared to H1N1-negative patients. There was no difference in relation to severity outcomes (number of organic dysfunctions, use of mechanical ventilation or amines, hospital/PICU length of stay or death). Comparing the groups with mono-detection and co-dection of any virus, no difference was found regarding the association with any clinical variable. Conclusions: Other viruses can be implicated in SARI in children. The role of viral codetection has not yet been completely elucidated.

Hospitalization costs due to severe acute respiratory infection (SARI) in three Central American countries / Costos de hospitalización de infección respiratoria aguda grave (IRAG) en tres países de América Central

Objective: To estimate the direct medical costs of severe acute respiratory infection (SARI) in children and adults from three Central American countries with a bottom-up costing approach. Methods: The costs of inpatients treatment were estimated through the retrospective bottom-up costing in a randomized sample of clinical records from SARI patients treated in teaching tertiary hospitals during 2009 - 2011 period. Activities incurred per patient were registered and a setting-specific cost per activity was acquired. Average cost per patient in the group of children and elderly adults was estimated for each country. In Nicaragua, only the pediatric population was included. Costs were expressed in local currency (2011), American dollars, and international dollars (2005) for country comparison. Results: The care cost per case in children in Guatemala was the cheaper (I$971.95) compared to Nicaragua (I$1,431.96) and Honduras (I$1,761.29). In adults, the treatment cost for Guatemala was the more expensive: I$4,065.00 vs. I$2,707.91 in Honduras. Conclusion: Bottom-up costing of SARI cases allowed the mean estimates per treated case that could have external validity for the target population diagnosed in hospitals with similar epidemiological profiles and level of complexity for the study countries. This information is very relevant for the decision-making.

Objetivo: Estimar los costos directos de la atención de infección respiratoria aguda (IRAG) en niños y adultos en tres países de América Central. Métodos: Los costos de pacientes hospitalizados fueron estimados a través de análisis retrospectivo en una muestra aleatoria de registros de historias clínicas de casos de IRAG tratado en hospitales universitarios durante el periodo 2009-2011. Las actividades incurridas por paciente fueron registradas y un costo especifico para cada sitio fue estimado. El costo por cada niño y adulto mayor fue estimado para cada país. En Nicaragua sólo se incluyó población pediátrica. Los costos fueron expresados en moneda local (2011), dolar americano y dolar internacional (2005). Resultados: El costo por caso en niños en Guatemala fue el más barato (I$971.95) comparado al de Nicaragua (I$1,431.96) y Honduras (I$1,761.29). En adultos, el costo de tratamiento para Guatemala fue el más costoso: I$4,065.00 vs. I$2,707.91 en Honduras. Conclusión: Los costos de tratar casos IRAG estimados a partir de costos promedios pro caso pueden tener validez externa para hospitales con perfiles epidemiologicos similares y nivel de complejidad de atención para los países del estudio. Esta información es muy relevante para la toma de decisiones.

Comparison of the nasopharynx microbiome between influenza and non­influenza cases of severe acute respiratory infections: a pilot study

Aims: Influenza A virus (IAV) can cause severe acute respiratory infection (SARI), and disease outcome may be associated with changes in the microbiome of the nasopharynx. This is a pilot study to characterize the microbiome of the nasopharynx in patients hospitalized with SARI, infected and not infected by IAV. Methods and Results: Using target sequencing of the 16S rRNA gene, we assessed the bacterial community of nasopharyngeal aspirate samples and compared the microbiome of patients infected with IAV with the microbiome of patients who were negative for IAV. We observed differences in the relative abundance of Proteobacteria and Firmicutes between SARI patients, with Streptococcus being enriched and Pseudomonas underrepresented in IAV patients compared with patients who were not infected with IAV. Conclusion: Pseudomonas taxon seems to be in high frequency on the nasopharynx of SARI patients with non­IAV infection and might present a negative association with Streptococcus taxon. Microbial profile appears to be different between SARI patients infected or not infected with IAV.

Global Influenza Hospital-based Surveillance Network (GIHSN): results of surveillance of influenza and other respiratory viruses in hospitalised patients in Brazil, 2015.

BACKGROUND: Influenza-like illness occurs annually worldwide, with peak timing and severity varying seasonally, resulting in significant annual mortality. OBJECTIVES: There were three objectives: (1) to describe the epidemiological and clinical features of hospitalised patients with severe acute respiratory infection caused by influenza and other respiratory viruses (ORVs); (2) to report the influenza seasonality in the region and (3) to correlate findings of influenza circulation and immunisation time in Brazil. PATIENTS/METHODS: This study took place in three Brazilian hospitals located in cities with different climatic conditions (Curitiba (south), Rio de Janeiro (south-east) and Fortaleza (north-east)). Patients presenting with an acute process with indication for admission consisting of a predefined set of conditions potentially associated with recent influenza infection were enrolled. RESULTS: We screened 1666 patients, with 595 meeting the inclusion criteria. Influenza viruses and ORVs were detected in 6.5% and 59% of patients, respectively. Influenza-positive cases fell into the severe spectrum as compared with those with ORVs (30% vs 11%), but without any difference in mortality rates. Epidemiological results revealed variations in the peak time of influenza infections between north-east (Fortaleza) and south (Curitiba) Brazil, basically following the rain period of each region. In north-east Brazil, viral circulation was prevalent in the first 4 months of the year, indicating that the vaccination campaign occurred in a postseasonal period, possibly explaining the low effectiveness. CONCLUSIONS: The active-surveillance model is a valuable tool for investigating respiratory virus impact on hospitalised patients, with influenza-infection monitoring enabling implementation of adequate preventive measures.

Human coronavirus and severe acute respiratory infection in Southern Brazil.

Human coronaviruses (HCoVs) are an important cause of respiratory tract infection and are responsible for causing the common cold in the general population. Thus, adequate surveillance of HCoV is essential. This study aimed to analyze the impact of HCoV infections and their relation to severe acute respiratory infection (SARI) in a hospitalized population in Southern Brazil. A cross-sectional study was conducted at a tertiary care hospital, and assessed inpatients under investigation for SARI by the hospital epidemiology department, and all patients who had nasopharyngeal aspirates collected from January 2012 to December 2013 to detect respiratory viruses (RVs). Viral infection was detected by multiplex reverse transcriptase polymerase chain reaction (RT-PCR), with primers specific to the subtypes HCoV-229E/NL63 and OC43/HKU1. The overall positivity rate was 58.8% (444/755), and HCoVs were detected in 7.6% (n = 34) of positive samples. Children below two years of age were most frequently affected (62%). Comorbidities were more likely to be associated with HCoVs than with other RVs. Immunosuppression was an independent risk factor for HCoV infection (OR = 3.5, 95% CI 1.6-7.6). Dyspnea was less frequently associated with HCoV infection (p < 0.001), and HCoV accounted for 6% of the SARI cases. Three patients infected with HCoV (9%) died from respiratory infection. HCoVs are important respiratory pathogens, especially in hospitalized children under 2 years of age and in immunosuppressed patients. They may account for a small proportion of SARI diagnoses, increased need for mechanical ventilation, intensive care unit admission, and death.

Costos de tratamiento hospitalario de la infección respiratoria aguda grave en niños de Nicaragua / Cost of treatment for severe acute respiratory infection in Nicaraguan children

Objetivo: Estimar los costos de tratamiento hospitalario de la infección respiratoria aguda grave (IRAG) en niños en Nicaragua. Métodos: Se estimaron costos de tratamiento de pacientes hospitalizados a partir del microcosteo retrospectivo de una muestra aleatoria de casos ocurridos durante el periodo 2009-2011 en Nicaragua y atendidos en un hospital pediátrico universitario de alta complejidad. Se calculó una muestra aleatoria de pacientes con diagnósticos de IRAG (CIE-10), según parámetros extraídos de la literatura. En esta, se estimó el costo promedio por paciente. Los costos fueron expresados en moneda local de 2011 y dólares americanos. Resultados: El costo promedio total de atención de caso en niños fue de 314,9 US$ (intervalo de confianza [IC] 95%: 280,1-349,7 US$) y de 971,6 (655,5-1.287,8 US$) para los que requirieron UCI. El 41% de los costos en los que solo requieren hospitalización general se explican por gastos de hotelería, mientras que en los que requieren UCI el 52% es por medicamentos. Conclusión: El microcosteo de los casos incluidos de IRAG permitió estimar un valor medio por caso tratado, con sus respectivos IC y estos podrían tener validez para el total de la población atendida por estos diagnósticos en hospitales con similar perfil epidemiológico y similar nivel de complejidad en Nicaragua.

Objective: To estimate the costs of treatment for severe acute respiratory infection (SARI) in children in Nicaragua. Methods: A cost assessment was carried out on a random sample of inpatients during 2009-2011 who were treated in one pediatric universitary hospital in Nicaragua. A random sample of patients diagnosed with SARI (ICD-10) was calculated based on parameters from the literature. The average cost per patient was estimated. Costs were expressed in local currency and US dollar values in 2011. Results: The total average cost of healthcare per case was US$314.9 (confidence interval [CI]95%: 280.10-US$349.70) and US$971.60 (655.50-US$1287.80) for those requiring intensive care unit (ICU). Around 41% of the general hospitalization costs are due to the cost of the hospitalization while for those costs involving ICU care, 52% are due to drugs costs. Conclusion: We estimated an average cost per case expressed with their respective CI by microcosts analysis for SARI health care in Nicaraguan children. These costs may be representative of the population with this diagnosis in Nicaraguan hospitals with similar epidemiological profile.

Mortalidad por Influenza pA(H1N1) 2009 en el noreste de México / Mortality from pandemic influenza A (H1N1) in northeast of Mexico

Objetivo. Determinar los factores asociados a la mortalidad por influenzapA(H1N1) en los pacientes hospitalizados por infección respiratoria agudagrave (IRAG) confirmada por reacción en cadena de la polimerasa (PCR)en el Instituto Mexicano del Seguro Social (IMSS).Material y métodos. En el IMSS en la delegación de Nuevo León entre el1 de junio de 2009 y 9 de marzo de 2010 se realizó un estudio observacionalretrospectivo de casos y controles, utilizando la base de datos del Sistemade Información en Línea para la Vigilancia Epidemiológica de Influenza(SINOLAVE). Se incluyeron 278 pacientes hospitalizados con IRAG (controles)y 50 pacientes con IRAG que fallecieron (casos) debido a la infecciónpor virus influenza pA(H1N1).Resultados. Los factores asociados a la mortalidad en los pacientes hospitalizadospor IRAG debida a influenza pA(H1N1) fueron la edad (OR: 1,03IC95% 1,01-1,05) y la obesidad (OR: 4,44 IC95% 1,85-1,6), utilizando unmodelo de regresión logística.Conclusión. Podemos concluir que en la delegación de Nuevo León delIMSS, la influenza pA(H1N1) afectó principalmente a adultos jóvenes, sinembargo las muertes se presentaron en mayor número en los pacientes alincrementar la edad y en pacientes con alguna comorbilidad.Palabras clave: Influenza pandémica A(H1N1), mortalidad, infección respiratoriaaguda grave, factores de riesgo, razón de probabilidad.

Objective. To determine factors associated with mortality from pAinfluenzA(H1N1) – confirmed by polymerase chain reaction (PCR) – Inhospitalized patients with severe acute respiratory infection (SARI) in theMexican Social Security Institute (IMSS). Methods. In the IMSS in the Delegation of Nuevo Leon between June 1, 2009 and March9, 2010 a retrospective observational case-control study was conducted using the database ofOnline Information System for Epidemiological Surveillance of Influenza (SINOLAVE). 278inpatients with SARI (controls) and 50 SARI patients who died (cases) due to infection withinfluenza virus pA(H1N1) were included.Results. In the logistic regression model factors associated with mortality in patientshospitalized due to SARI pA influenzA(H1N1) were age (OR: 1.03 95% CI 1.01-1.05) andobesity (OR: 4.44 95 1.85 to 1%, 0.6).Conclusion. We can conclude that the delegation of Nuevo León of the IMSS, pAinfluenzA(H1N1) affects mainly young adults, though the deaths occurred in greater numbersin patients with increasing age and in patients with comorbidities.

Infección respiratoria aguda grave en pacientes cubanos durante la ola de influenza pandémica A (H1N1) en Cuba, 2009 / Severe acute respiratory infection in Cuban patients during the influenza A (H1N1) pandemic in Cuba, 2009

INTRODUCCIÓN: en abril de 2009 las autoridades de salud de México reportan a la Organización Panamericana de la Salud un incremento de las hospitalizaciones por neumonía con tasas elevadas de mortalidad. El Sistema Nacional de Vigilancia Epidemiológica, notó que este incremento se presentaba fundamentalmente en las edades de 20 a 40 años. Se identificó un nuevo virus influenza A de origen porcino subtipo (H1N1) como agente causal de la primera pandemia del siglo XXI. El 26 de abril de 2009 el plan nacional de enfrentamiento a la pandemia por influenza (H1N1) es activado por las autoridades nacionales de salud de la República de Cuba y el 7 de mayo se diagnosticó el caso índice de influenza pandémica (H1N1) en Cuba. Se estableció un sistema de vigilancia integrada con confirmación de laboratorio. OBJETIVOS: detectar e identificar el virus de la influenza pandémica durante la ola pandémica. MÉTODOS: durante las semanas epidemiológicas de la 37 a la 41 se observó un alza en el número de atenciones médicas. En este período se seleccionaron para este análisis solo las muestras colectadas de pacientes con diagnóstico clínico de infección respiratoria aguda grave divididas en tres grupos fundamentales, 370 niños y adultos graves, 55 gestantes graves y 30 fallecidos. El diagnóstico fue realizado por reacción en cadena de la polimerasa en tiempo real para los virus de influenza pandémica y reacción en cadena de la polimerasa convencional para otros virus respiratorios. RESULTADOS: el virus de la influenza pandémica se detectó en 65, 20 y 9 casos, respectivamente. El virus de la influenza estacional A (H3N2) en 81 casos de infección respiratoria aguda grave, donde se incluyeron pacientes de todas las edades; 10 gestantes graves y en 5 fallecidos, los cuales fueron detectados por reacción en cadena de la polimerasa en tiempo real. Otros virus respiratorios también fueron monitoreados por reacción en cadena de la polimerasa a punto final. CONCLUSIONES: el análisis integral de estos resultados constituye un aporte a la vigilancia nacional y regional de los virus respiratorios para el perfeccionamiento de los programas de prevención y control de las infecciones respiratorias agudas.

INTRODUCTION: on April 2009, the Mexican health authorities reported increased hospitalization indexes caused by pneumonia with high mortality rates to the Pan-American Health Organization (PAHO). The National Epidemiological Surveillance System of Mexico noticed that this increase mainly occurred in the 20-40 year old population. A new type of swine influenza A (H1N1) virus was identified by laboratory studies as the etiological agent of the first pandemic of the 21st century. On April 26 2009, the National Anti-pandemic Plan was activated by the Cuban Ministry of Public Health, and on May 7th, the lab-confirmed index case appeared. An integrated surveillance system with laboratory confirmation was set up. OBJECTIVES: to detect pandemic influenza virus during the pandemic wave. METHODS: the epidemiological weeks 37 to 41 witnessed a rise of the number of sick people seen by the medical services. In this period, the samples taken from patients clinically diagnosed with severe acute respiratory infection were selected for this analysis; they were divided into three groups, that is, 370 children and adults in critical condition, 55 pregnant women in severe condition and 30 fatal cases. The diagnosis of the pandemic virus was performed by Real Time Polymerase Chain Reaction Test (PCR). Other respiratory viruses were tested by conventional PCR. RESULTS: the pandemic influenza virus was detected in 65 children and adults, 20 pregnant women and 9 fatal cases. The seasonal influenza A (H3N2) virus was identified in 81 cases of severe acute respiratory infection covering all age groups, 10 pregnant women and 5 deceased on the basis of real time polymerase chain reaction test. Other respiratory viruses were also monitored by the end-point polymerase chain reaction. CONCLUSIONS: the comprehensive analysis of these results contributes to the national and regional surveillance of respiratory viruses for the improvement of the prevention and control programs of the acute respiratory infections.