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Emerg Infect Dis ; 28(8): 1669-1672, 2022 08.
Article in English | MEDLINE | ID: covidwho-1963350


During July-December 2021, after COVID-19 restrictions were removed in England, invasive pneumococcal disease incidence in children <15 years of age was higher (1.96/100,000 children) than during the same period in 2020 (0.7/100,000 children) and in prepandemic years 2017-2019 (1.43/100,000 children). Childhood vaccine coverage should be maintained to protect the population.

COVID-19 , Pneumococcal Infections , COVID-19/epidemiology , Child , England/epidemiology , Humans , Incidence , Infant , Pandemics , Pneumococcal Infections/epidemiology , Pneumococcal Infections/prevention & control , Pneumococcal Vaccines
Viruses ; 14(5)2022 04 20.
Article in English | MEDLINE | ID: covidwho-1792408


Coronavirus disease 2019 (COVID-19) pandemic has caused immeasurable impacts on the health and socioeconomic system. The real-time identification and characterization of new Variants of Concern (VOCs) are critical to comprehend its emergence and spread worldwide. In this sense, we carried out a national epidemiological surveillance program in Brazil from April to October 2021. Genotyping by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and sequencing were performed to monitor the dynamics and dissemination of VOCs in samples from 15 federative units. Delta VOC was first detected on June 2021 and took sixteen weeks to replace Gamma. To assess the transmissibility potential of Gamma and Delta VOCs, we studied the dynamics of RT-qPCR cycle threshold (Ct) score in the dominance period of each variant. The data suggest that Delta VOC has a higher transmission rate than Gamma VOC. We also compared relevant symptom patterns in individuals infected with both VOCs. The Delta-infected subjects were less likely to have low oxygen saturation or fatigue, altered results on chest computed tomography, and a propensity for altered X-rays. Altogether, we described the replacement of Gamma by Delta, Delta enhanced transmissibility, and differences in symptom presentation.

COVID-19 , SARS-CoV-2 , Brazil/epidemiology , COVID-19/epidemiology , Epidemiological Monitoring , Humans , SARS-CoV-2/genetics
Public Health ; 205: 187-191, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1676893


OBJECTIVES: Case definitions are vital in a pandemic to effectively identify, isolate, and contact trace, particularly where testing is slow, scant, or not available. While case definitions have been developed in the COVID-19 pandemic, their diagnostic properties have not been adequately assessed. This study's objective is to determine the diagnostic properties of local and World Health Organization (WHO) COVID-19 case definitions in the large metropolitan area of Mexico City. METHODS: We calculated the diagnostic properties of five COVID-19 definitions (three of the Mexican government and two of the WHO) using open data of suspected COVID-19 cases in Mexico City from March 24th, 2020, until May 15th, 2021. RESULTS: All 2,564,782 people included in the analysis met the WHO suspected case definition (sensitivity: 100%, specificity: 0%). The WHO probable case definition was met by 1.2%, while the first and second Mexican suspected case had sensitivities of 61% and specificities of 61% and 67%, respectively. Confirmed case by epidemiological contact had a low sensitivity (32%) but slightly higher specificity (81%). CONCLUSIONS: Case definitions should maximize sensitivity, especially in a high-transmission area such as Mexico City. The WHO suspected case definition has the potential for detecting most symptomatic cases. We underline the need for routine evaluation of case definitions as new evidence arises to maximize their usefulness.

COVID-19 , COVID-19/diagnosis , COVID-19/epidemiology , Humans , Mexico/epidemiology , Pandemics , Sensitivity and Specificity , World Health Organization
Epidemiol. serv. saúde ; 29(3): e2020066, 2020. tab, graf
Article in English, Portuguese | WHO COVID, LILACS (Americas) | ID: covidwho-1406041


Objetivo: avaliar os atributos do sistema de vigilância da síndrome respiratória aguda grave (SRAG) no Brasil, no período 2014-2016. Métodos: estudo de avaliação segundo o guia do Centro de Controle de Doenças (Centers for Disease Control and Prevention - CDC) dos Estados Unidos; utilizaram-se dados do sistema de informação Influenza Web, notificados entre 2014 e 2016; avaliaram-se os atributos simplicidade, completude, inconsistência, oportunidade, aceitabilidade, representatividade, valor preditivo positivo (VPP) da definição de caso de SRAG e utilidade. Resultados: observou-se estrutura simples; boa completude (100% nas variáveis obrigatórias; >95% nas não obrigatórias); baixa inconsistência (3,2%); não oportunidade (68,2%); aceitabilidade baixa (média de 70,4%); representatividade do território (capaz de análises de grupos de risco); alto VPP (29,1%); e utilidade (por cumprir objetivos do sistema). Conclusão: os atributos avaliados indicam que o sistema é capaz de fornecer informações completas, representativas e úteis sobre influenza, adequadas para balizar respostas do sistema de saúde.

Objetivo: evaluar los atributos del sistema del sistema de vigilancia del Síndrome Agudo Respiratorio Severo (SARS) en Brasil, entre 2014-2016. Método: estudio de evaluación según la guía del Centro para el Control y la Prevención de Enfermedades (Centers for Disease Control and Prevention - CDC) dos Estados Unidos. Se utilizaron datos del sistema de información Influenza Web, notificados entre 2014-2016. Se evaluaron los atributos simplicidad, completitud, inconsistencia, oportunidad, aceptabilidad, representatividad, valor predictivo positivo (VPP) de definición de caso de SARS y utilidad. Resultados: se observó estructura simple; buena completitud (100% en variables obligatorias; >95% en variables no obligatorias); baja inconsistencia (3.2%); no oportunidad (68,2%); baja aceptabilidad (promedio de 70.4%); representatividad de territorio (capaz de analizar grupos de riesgo); VPP alto (29.1%); y utilidad (por cumplir los objetivos del sistema). Conclusión: los atributos evaluados indican que el sistema es capaz de suministrar informaciones completas, representativas y útiles sobre la influenza en Brasil, adecuadas para orientar respuestas del sistema de salud.

Objective: to evaluate attributes of the severe acute respiratory syndrome (SARS) surveillance system in Brazil, 2014-2016. Method: this was an evaluation study conducted according to United States Centers for Disease Control and Prevention guidelines. Data from the Influenza Web information system notified for the period 2014-2016 were used. The simplicity, completeness, inconsistency, timeliness, acceptability, representativeness, positive predictive value (PPV) of the SARS case definition attributes and usefulness were evaluated. Results: a simple structure was found with good completeness (100% for required variables; >95% for optional variables); low inconsistency (3.2%); lack of timeliness (68.2%); low acceptability (average of 70.4%); representative of the territory (capable of analyzing risk groups); high PPV (29.1%); useful (fulfils system objectives). Conclusion: the attributes evaluated indicate that the system is capable of providing complete, representative and useful information about influenza, adequate for guiding national health responses.

Humans , Severe Acute Respiratory Syndrome/epidemiology , Epidemiologic Surveillance Services , Influenza, Human/epidemiology , Brazil/epidemiology , Program Evaluation , Evaluation Study
Evol Med Public Health ; 9(1): 267-275, 2021.
Article in English | MEDLINE | ID: covidwho-1376294


INTRODUCTION: The coronavirus disease 2019 (COVID-19) pandemic is a global public health emergency causing a disparate burden of death and disability around the world. The viral genetic variants associated with outcome severity are still being discovered. METHODS: We downloaded 155 958 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from GISAID. Of these genomes, 3637 samples included useable metadata on patient outcomes. Using this subset, we evaluated whether SARS-CoV-2 viral genomic variants improved prediction of reported severity beyond age and region. First, we established whether including genomic variants as model features meaningfully increased the predictive power of our model. Next, we evaluated specific variants in order to determine the magnitude of association with severity and the frequency of these variants among SARS-CoV-2 genomes. RESULTS: Logistic regression models that included viral genomic variants outperformed other models (area under the curve = 0.91 as compared with 0.68 for age and gender alone; P < 0.001). We found 84 variants with odds ratios greater than 2 for outcome severity (17 and 67 for higher and lower severity, respectively). The median frequency of associated variants was 0.15% (interquartile range 0.09-0.45%). Altogether 85% of genomes had at least one variant associated with patient outcome. CONCLUSION: Numerous SARS-CoV-2 variants have 2-fold or greater association with odds of mild or severe outcome and collectively, these variants are common. In addition to comprehensive mitigation efforts, public health measures should be prioritized to control the more severe manifestations of COVID-19 and the transmission chains linked to these severe cases.Lay summary: This study explores which, if any, SARS-CoV-2 viral genomic variants are associated with mild or severe COVID-19 patient outcomes. Our results suggest that there are common genomic variants in SARS-CoV-2 that are more often associated with negative patient outcomes, which may impact downstream public health measures.

Sci Total Environ ; 796: 148887, 2021 Nov 20.
Article in English | MEDLINE | ID: covidwho-1301004


Wastewater-based epidemiology (WBE) is an emerging tool that gives temporal and spatial information on a population's health status. Here, we report the epidemiological dynamics of a population of ~1.2 million residents in the metropolitan region of Mendoza province, Argentina, within the period July 2020 to January 2021. We combined the use of WBE of two wastewater treatment plants with epidemiological surveillance of the corresponding populations. We applied two viral concentration methods (polyethylene glycol precipitation and aluminum-based adsorption-flocculation) and RNA isolation methods in each wastewater sample to increase the possibility of detection and quantification of nucleocapsid markers (N1 and N2) of SARS-CoV-2 by RT-qPCR. Overall, our results allowed us to trace the rise, exponential growth, plateau, and fall of SARS-CoV-2 infections for 26 weeks. Individual analysis for each wastewater treatment plant showed a positive correlation between the viral load of SARS-CoV-2 genetic markers and COVID-19 cases that were diagnosed per week. Our findings indicate that WBE is a useful epidemiological indicator to anticipate the increase in COVID-19 cases and monitor the advance of the pandemic and different waves of infections.

COVID-19 , Waste Water , Argentina/epidemiology , Humans , RNA, Viral , SARS-CoV-2
Epidemiol Health ; 43: e2021024, 2021.
Article in English | MEDLINE | ID: covidwho-1273605


OBJECTIVES: A coronavirus disease 2019 (COVID-19) outbreak triggered by religious activities occurred in Daegu, Korea in February 2020. This outbreak spread rapidly to the community through high-risk groups. This study describes the characteristics of COVID-19 cases based on S religious group membership and summarizes the Daegu municipal government's processes and responses to control the outbreak. METHODS: The epidemiological characteristics of confirmed cases were obtained through basic and in-depth epidemiological surveys. General characteristics, the proportion of asymptomatic cases, the case-fatality rate, and the time-to-event within each group were presented after stratifying confirmed cases according to S religious group membership. RESULTS: Overall, 7,008 COVID-19 cases were confirmed in Daegu from February 18, 2020 to June 30, 2020, and 61.5% (n= 4,309) were S religious group members. Compared with non-members, members had a higher proportion of female (p< 0.001) and younger age (p< 0.001), as well as lower disease prevalence. At the time of the investigation, 38.4% of cases in members were asymptomatic versus 23.7% of cases in non-members (p< 0.001). The case-fatality rate of non-members aged ≥ 60 years was significantly higher than that of members (p< 0.001). Compared with non-members, members had longer intervals from symptom onset to diagnosis (p< 0.001) and from diagnosis to admission (p< 0.001), and a shorter interval from admission to discharge (p< 0.001). CONCLUSIONS: The epidemiological features of S religious group members, including the proportion of asymptomatic cases, case-fatality rate, and time-to-event, differed from non-members. The Daegu authorities prevented further COVID-19 spread through immediate isolation and active screening tests of all S religious group members.

COVID-19/epidemiology , Disease Outbreaks , Epidemiological Monitoring , Religion , Adolescent , Adult , Aged , Aged, 80 and over , Child , Child, Preschool , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , Republic of Korea/epidemiology , Young Adult
Cad. Saúde Pública (Online) ; 37(3): e00238720, 2021. tab
Article in Spanish | WHO COVID, LILACS (Americas) | ID: covidwho-1138609


El objetivo fue describir las características de la infección por SARS-CoV-2 entre miembros de hogares, con un caso confirmado primario de COVID-19, en distritos de baja carga de casos en Lima, Perú, en comparación con un distrito de alta carga. Estudio retrospectivo de revisión de base de datos secundaria. Se recolectó información proveniente de una actividad de vigilancia epidemiológica en contactos cercanos (cohabitantes), en 52 hogares de Lima, con un solo miembro con COVID-19. En 10 hogares se realizó una reevaluación. Se evaluaron variables epidemiológicas y clínicas; y su asociación con el resultado a la prueba serológica rápida (presencia de IgG, IgM o ambas). En 40 hogares se encontraron casos secundarios, lo que representa un 49,9% de identificación en promedio por hogar. Se encontró una tasa de ataque secundaria entre cohabitantes de 53% (125 casos), siendo sintomáticos un 77,6% de casos (razón sintomáticos/asintomáticos: 3,5). La presencia de fiebre y/o escalofríos se encontró en el 40% de las personas con resultado positivo, seguido del dolor de garganta en el 39,2%. La ageusia y anosmia estuvieron presentes en el 22,4% y 20,8% de los casos, respectivamente. Al tener un caso primario de COVID-19 en el hogar, la tasa de ataque secundaria de esta infección es de 53%; sin embargo, en una proporción importante de hogares evaluados no hubo un caso positivo, más allá del caso primario. Las características epidemiológicas y clínicas encontradas en este caso estuvieron acorde a lo ya reportado en otras series internacionales.

O objetivo foi descrever as características da infecção por SARS-CoV-2 entre os membros de domicílios, com um caso primário confirmado de COVID-19, em distritos com baixa carga de casos em Lima, Peru, em comparação com um distrito com alta carga. Estudo retrospectivo de revisão de banco de dados secundário. As informações foram coletadas em uma atividade de vigilância epidemiológica em contatos próximos (coabitantes), em 52 domicílios em Lima, com um único membro com COVID-19. Foi realizada uma reavaliação em 10 domicílios. Variáveis ​​epidemiológicas e clínicas foram avaliadas; e sua associação com o resultado do teste sorológico rápido (presença de IgG, IgM ou ambos). Os casos secundários foram encontrados em 40 domicílios, representando uma taxa média de identificação de 49,9% por domicílio. Foi encontrada uma taxa de ataque secundário entre coabitantes de 53% (125 casos), com 77,6% dos casos sendo sintomáticos (relação sintomático/assintomático: 3,5). A presença de febre e/ou calafrios foi encontrada em 40% das pessoas com resultado positivo, seguida de dor de garganta em 39,2%. Ageusia e anosmia estiveram presentes em 22,4% e 20,8% dos casos, respectivamente. Quando há um caso primário de COVID-19 em casa, a taxa de ataque secundário para essa infecção é de 53%; No entanto, em uma proporção significativa dos domicílios avaliados não houve caso positivo, além do caso primário. As características epidemiológicas e clínicas encontradas neste caso foram consistentes com o que já foi relatado em outras séries internacionais.

The study aimed to describe the characteristics of SARS-CoV-2 transmission among members of households with a confirmed primary case of COVID-19 in districts with low burden of cases in Lima, Peru, compared to a district with high burden. This was a retrospective study with a secondary database review. Information was collected from an epidemiological surveillance activity in close contacts (household members) in 52 households in Lima, with a single member with COVID-19. Reevaluation was conducted in 10 households. The study evaluated epidemiological and clinical variables and their association with the result of the rapid serological test (presence of IgG, IgM, or both). Secondary cases were found in 40 households, representing mean identification of 49.9% per household. Secondary attack rate in household members was 53% (125 cases), and symptomatic individuals accounted for 77.6% of cases (symptomatic/asymptomatic ratio: 3.5). Presence of fever and/or chills was found in 40% of persons with positive test results, followed by sore throat with 39.2%. Ageusia and anosmia were present in 22.4% and 20.8% of cases, respectively. When there was a primary case of COVID-19 in the household, the secondary attack rate was 53%; however, in an important proportion of households there were no positive cases other than the primary case. The epidemiological and clinical findings were consistent with reports from other international series.

Humans , SARS-CoV-2 , COVID-19 , Peru/epidemiology , Brazil , Retrospective Studies
Cad. Saúde Pública (Online) ; 36(4): e00070120, 2020. graf
Article in Portuguese | WHO COVID, LILACS (Americas) | ID: covidwho-818358


Resumo: A vigilância de síndrome respiratória aguda grave (SRAG) no Brasil visa a caracterizar a circulação dos vírus Influenza A e B em casos hospitalizados e óbitos, tendo sido ampliada em 2012 para incluir outros vírus respiratórios. A COVID-19 foi detectada no Brasil pela primeira vez na 9ª semana epidemiológica de 2020 e o teste para o vírus SARS-CoV-2 foi incluído no protocolo de vigilância a partir da 12ª semana epidemiológica. O objetivo deste estudo foi investigar o padrão de hospitalizações por SRAG no país após a entrada do SARS-CoV-2, comparando o perfil temporal, etário e de resultados laboratoriais com os anos de 2010 a 2019. Em 2020, a hospitalização por SRAG, contabilizada desde a data do primeiro caso de COVID-19 confirmado até a 12ª semana, superou o observado, no mesmo período, em cada um dos 10 anos anteriores. A faixa etária acima de 60 anos foi a mais acometida, em nível acima do histórico. Houve um aumento considerável de testes laboratoriais negativos, sugerindo a circulação de um vírus diferente dos presentes no painel. Concluímos que o aumento das hospitalizações por SRAG, a falta de informação específica sobre o agente etiológico e a predominância de casos entre idosos, no mesmo período de tempo em que cresce o número de casos novos de COVID-19, é coerente com a hipótese de que os casos graves da doença já estejam sendo detectados pela vigilância de SRAG com sobrecarga para o sistema de saúde. A inclusão da testagem para SARS-CoV-2 no protocolo de vigilância de SRAG e sua efetiva implementação são de grande importância para acompanhar a evolução dos casos graves da doença no país.

Resumen: La vigilancia del síndrome respiratorio agudo grave (SRAG) en Brasil tiene como objetivo caracterizar la circulación de los virus de la Influenza A y B en casos y muertes hospitalizadas, y se expandió en 2012 para incluir otros virus respiratorios. La COVID-19 se detectó en Brasil por la primera vez en la 9ª semana epidemiológica de 2020, y el examen test para el virus SARS-CoV-2 se incluyó en el protocolo de vigilancia a partir de la 12ª semana epidemiológica. El objetivo de este estudio fue investigar el patrón de hospitalizaciones por SRAG en Brasil desde la entrada de SARS-CoV-2, comparando el perfil temporal y de edad y los resultados de laboratorio entre los años 2010 a 2019. En 2020, las hospitalizaciones por SRAG, compiladas a partir de la fecha del primer caso confirmado de COVID-19 hasta la 12ª semana, excedió los números observados durante el mismo período en cada uno de los 10 años anteriores. El grupo de edad mayor de 60 años fue el más afectado, a niveles superiores a los históricos. Hubo un aumento considerable en las pruebas de laboratorio negativas, lo que sugiere la circulación de un virus diferente de los que ya están presentes en el panel. Se concluye que el aumento de las hospitalizaciones por SRAG, la falta de información específica sobre el agente etiológico y el predominio de casos entre los ancianos en el mismo período en que hubo un aumento de casos nuevos de COVID-19 se entiende que con esta hipótesis de que los casos graves de COVID-19 ya estén siendo monitorados por la vigilancia de SRAG, lo que genera una sobrecarga en el sistema de salud. La inclusión de los exámenes para SARS-CoV-2 en el protocolo de vigilancia de SRAG y la eficacia de implementación son de grande importancia para monitorear la evolución de los casos graves de COVID-19 en Brasil.

Abstract: Surveillance of the severe acute respiratory illness (SARI) in Brazil aims to characterize the circulation of the Influenza A and B viruses in hospitalized cases and deaths, having been expanded in 2012 to include other respiratory viruses. COVID-19 was detected in Brazil for the time in the 9th epidemiological week of 2020, and the test for the SARS-CoV-2 virus was included in the surveillance protocol starting in the 12th epidemiological week. This study's objective was to investigate the pattern of hospitalizations for SARI in Brazil since the entry of SARS-CoV-2, comparing the temporal and age profiles and laboratory results to the years 2010 through 2019. In 2020, hospitalizations for SARI, compiled from the date of the first confirmed case of COVID-19 up to the 12th week, exceeded the numbers observed during the same period in each of the previous 10 years. The age bracket over 60 years was the most heavily affected, at higher than historical levels. There was a considerable increase in negative laboratory tests, suggesting circulation of a different virus from those already present in the panel. We concluded that the increase in hospitalizations for SARI, the lack of specific information on the etiological agent, and the predominance of cases among the elderly during the same period in which there was an increase in the number of new cases of COVID-19 are all consistent with the hypothesis that severe cases of COVID-19 are already being detected by SARI surveillance, placing an overload on the health system. The inclusion of testing for SARS-CoV-2 in the SARI surveillance protocol and the test's effective nationwide deployment are extremely important for monitoring the evolution of severe COVID-19 cases in Brazil.

Humans , Male , Female , Infant, Newborn , Infant , Child, Preschool , Child , Adolescent , Adult , Young Adult , Pneumonia, Viral/epidemiology , Coronavirus Infections/epidemiology , Severe Acute Respiratory Syndrome/epidemiology , Betacoronavirus , Hospitalization/statistics & numerical data , Time Factors , Brazil/epidemiology , Age Distribution , Influenza, Human/epidemiology , Pandemics , Epidemiological Monitoring , SARS-CoV-2 , COVID-19 , Middle Aged