Puesta a punto PCR Multiplex para el diagnóstico de 14 virus respiratorios

L’objectiu d’aquesta tesi es descriure l’epidemiologia de les infeccions respiratòries víriques, tant de les infeccions lleus del tracte respiratori superior com de les infeccions greus del tracta respiratori inferior que requereixen hospitalització en pacients pediàtrics de Manhiça, una zona rural del sud de Moçambic. Els resultats d’aquesta tesi indiquen que la carrega de malaltia associada als virus respiratoris a l’Hospital Distrital de Manhiça és elevada: aproximadament la meitat dels pacients pediàtrics atesos a l’Hospital Distrital de Manhiça amb símptomes d’infecció respiratòria detectem al menys un virus respiratori. La incidència de les infeccions respiratòries augmenta durant l’estació de pluges, i és durant aquesta estació que es produeixen els brots anulars del virus influenza i del virus respiratori sincitial. Les co-infeccions víriques, les infeccions invasives bacterianes i la infecció per l’HIV (virus de la immunodeficiència humana) s’associen a una major severitat i pitjor prognosi de les infeccions respiratòries víriques. / The main objective of this thesis is to describe the epidemiology of viral respiratory infection, both mild upper respiratory infections and severe lower respiratory tract infections requiring hospitalization, in paediatric patients in Manhiça, a rural area of southern Mozambique. Results of this work show that the burden of disease associated with respiratory viruses in Mahiça District Hospital in high: Approximately half of paediatric patients visited at Manhiça District Hospital with respiratory symptoms had, at least, one respiratory virus detected. Incidence of respiratory infections increases during the rainy season and outbreaks of influenza and respiratory syncytial virus also occur during this season. Viral co-infections, invasive bacterial infections and HIV (human immunodeficiency virus) infection are associated with more severe viral respiratory infections and a worse prognosis of such infections.

Objective: To study the presence of 8 respiratory viruses (Influenza-A, Influenza-B, RSV-A, RSV-B, Adenovirus, Parainfluenza-1, Parainfluenza-2 and Parainfluenza-3) and atypical bacteria (Mycoplasma pneumonia and Chlamydia pneumonia) in samples from Peruvian children under 5 years-old previously analyzed for Bordetella. Pertussis. Methods: A secondary data analysis was performed from a previous cross-sectional study conducted in children with a probable diagnosis of Pertussis from January 2010 to July 2012. All samples were analyzed via Polymerase Chain Reaction (PCR) for the following etiologies: Influenza-A, Influenza-B, RSV-A, RSV-B, Adenovirus, Parainfluenza 1 virus, Parainfluenza 2 virus, Parainfluenza 3 virus, Mycoplasma pneumoniae and Chlamydia pneumoniae. Results: A total of 288 patients were included. The most common pathogen isolated was Adenovirus (49%), followed by Bordetella pertussis (41%) from our previous investigation; the most prevalent microorganisms were Mycoplasma pneumonia (26%) and Influenza-B (19.8%). Coinfections were reported in 58% of samples and the most common association was found between B. pertussis and Adenovirus (12.2%). Conclusions: There was a high prevalence of Adenovirus, Mycoplasma pneumoniae and other etiologies in patients with a probable diagnosis of pertussis. Despite the presence of persistent cough lasting at least two weeks and other clinical characteristics highly suspicious of pertussis, secondary etiologies should be considered in children under 5 years-old in order to give a proper treatment. / Objetivo: Estudiar la presencia de 8 virus respiratorios (Influenza-A, Influenza-B, RSV-A, RSV-B, Adenovirus, Parainfluenza-1, Parainfluenza-2 y Parainfluenza-3) y bacterias atípicas (Mycoplasma pneumoniae y Chlamydia pneumonia) en muestras de niños peruanos menores de 5 años analizados previamente para Bordetella pertussis Métodos: se realizó un análisis de datos secundarios de un estudio transversal previo realizado en niños con un diagnóstico probable de Pertussis desde enero del 2010 hasta julio del 2012. Todas las muestras se analizaron mediante reacción en cadena de la polimerasa (PCR) para las siguientes etiologías: Influenza-A, Influenza-B, RSV-A, RSV-B, Adenovirus, virus Parainfluenza 1, virus Parainfluenza 2, virus Parainfluenza 3, Mycoplasma pneumoniae y Chlamydia pneumoniae. Resultados: un total de 288 pacientes fueron incluidos en el estudio. El patógeno aislado más común fue el Adenovirus (49%), seguido de Bordetella pertussis (41%) de nuestra investigación previa; los microorganismos más prevelantes fueron Mycoplasma pnemoniae (26%) e Influenza-B (19.8%). Las coinfecciones fueron reportadas en el 58% de las muestras y la asociación más común se encontró entre B. pertussis y Adenovirus (12.2%). Conclusiones: hubo una alta prevalencia de Adenovirus, Mycoplasma pneumoniae y otras etiologías en pacientes con un diagnóstico probable de pertussis. A pesar de la presencia de tos persistente que dura por lo menos dos semanas y otras características clínicas altamente sospechosas de pertussis, se deben considerar las etiologías secundarias en niños menores de 5 años para poder administrar un tratamiento adecuado. / Tesis

Introducción: Las infecciones agudas del tracto respiratorio (IRA) son muy prevalentes, las IRAs bajas constituyen la cuarta causa de muerte a nivel mundial. Los agentes causales más comunes en niños son el Rinovirus (RV) y el Virus sincitial respiratorio (VSR). Existen tres especies de RV (A, B, C), estudios recientes han demostrado que la sintomatología y severidad de la enfermedad varía dependiendo de la especie de RV por la que hayan sido infectados los pacientes. Objetivo: Evaluar la prevalencia de Rinovirus en muestras de hisopado nasofaríngeo de niños con diagnóstico clínico de IRA en Lima, Perú durante el periodo 2009-2010. Materiales y métodos: Estudio retrospectivo de muestras de hisopado nasofaríngeo en niños, procesadas por la técnica RT-PCR para identificación de RV y sus especies. La población está compuesta por pacientes pediátricos en el Hospital Nacional Cayetano Heredia. Se analizó las variables por medio de la prueba de Chi cuadrado y Fischer. Resultados: RVA se detectó en 10.26%, RVB en 16.67%, RVC 73.9%. Grupo etario más prevalente fue de 0-5 meses. Signos y síntomas más comunes fueron tos, fiebre, rinorrea y dificultad respiratoria. Se encontró asociación entre sibilancias y RVA; tos, sibilancias e inyección conjuntival con RVC. Se halló pico de casos por RVC durante marzo, junio y noviembre. Conclusión: Se encontró alta prevalencia de infección por RVC en pacientes pediátricos, principalmente en pacientes de 0-5 meses. Distribución mensual muestra aumento de casos en marzo y junio. Se sugiere realizar vigilancia epidemiológica y estudios longitudinales para el estudio de este patógeno. / Introduction: Acute respiratory tract infections (ARTI) are a very prevalent group of diseases, lower ARTI represent the fourth cause of death worldwide. In children, the two most usual agents are Rhinovirus (RV) and Syncytial respiratory virus (SRV). RV is responsible for most is related with lower respiratory tract infections. Scientists have identified three RV species (A, B, C), recent studies have reported that symptomatology and severity vary within RV species. Objective: Asses the prevalence of Rhinovirus on nasopharyngeal swab samples of children with clinical diagnosis of ARTI in Lima, Peru during 2009-2010. Materials and method: Retrospective study about nasopharyngeal swab on children, which were processed through RT-PCR technique to identify RV and its species. The study population was pediatric patients, with clinical diagnosis of ARTI, at Hospital Nacional Cayetano Heredia. This investigation project will be revised by the ethics committee from Universidad Peruana de Ciencias Aplicadas. Results: RVA was detected in 10.26% of cases, RVB 16-67% and RVC in 73.9%. The most prevalent age group was the 0-5 months old. The most common signs and symptoms were cough, fever, rhinorrhea, and respiratory distress. The study found association between wheezing and RVA infection, cough, wheezing and conjunctival injection and RVC infection. There was a peak in RVC cases during the March, June, and November. Conclusion: We found a high prevalence for RVC infection, mainly in children between 0-5 months old. Monthly distribution showed an increase of RVC cases during March and June; epidemiological surveillance and longitudinal studies should be encouraged. / Tesis

Objetivo: Describir la distribución de patógenos responsables de IRA durante el período 2009-2010 en Cajamarca, Perú: en el contexto de la pandemia del virus de la Influenza AH1N1 2009. Resultados: Se encontraron 17 patógenos respiratorios (14 virus y 3 bacterias) en 124 niños, de los cuales el 50% eran hombres y el 50% mujeres, con un 55,6% (69/124) de 1 a 5 años y un 15,3% (19/124) de 6 a 11 años. Los patógenos más comunes fueron: Influenza A (20,2%, 25/124), Mycoplasma pneumoniae (14,5%, 18/124), RSV-A (12,1%, 15/124), Chlamydia pneumoniae (9,7%, 12/124). No se pudo identificar un patógeno específico en el 33,8% de los pacientes (42/124). Los signos y síntomas más comunes fueron fiebre 90,3%, tos 85,5%, rinorrea 74,2% y malestar 66,9%. El distrés respiratorio y la hospitalización fueron las complicaciones más comunes con 37,1% y 28,2% de los casos. Se informó una sola muerte de un niño diagnosticado con el virus de la influenza A. Además, se identificaron 12 casos de coinfecciones: 9 con 2 patógenos, 2 con tres patógenos y 1 con 4. Conclusión: Los patógenos respiratorios más comunes encontrados durante la pandemia de la Influenza AH1N1 2009-2010 fueron Influenza A, Mycoplasma pneumoniae, RSV-A y Chlamydia pneumoniae. La mayoría de patógenos presentan un perfil clínico similar Se detectaron varios casos de coinfecciones, con hasta 4 patógenos en un solo paciente. / Objective: To describe the distribution of pathogens responsible for ARI during the 2009-2010 period in Cajamarca, Peru: in the context of the 2009 AH1N1 influenza virus pandemic. Results: 17 respiratory pathogens (14 viruses and 3 bacteria) were found in 124 children, of which 50% were men and 50% women, with 55.6% (69/124) aged 1 to 5 years and a 15.3% (19/124) from 6 to 11 years old. The most common pathogens were Influenza A (20.2%, 25/124), Mycoplasma pneumoniae (14.5%, 18/124), RSV-A (12.1%, 15/124), Chlamydia pneumoniae (9,7%, 12/124). A specific pathogen could not be identified in 33.8% of patients (42/124). The most common signs and symptoms were fever 90.3%, cough 85.5%, rhinorrhea 74.2% and discomfort 66.9%. Respiratory distress and hospitalization were the most common complications with 37.1% and 28.2% of the cases. A single death was reported in a child diagnosed with influenza A virus. In addition, 12 cases of coinfections were identified: 9 with 2 pathogens, 2 with 3 pathogens, and 1 with 4. Conclusion: The most common respiratory pathogens encountered during the 2009-2010 AH1N1 influenza pandemic were influenza A, Mycoplasma pneumoniae, RSV-A, and Chlamydia pneumoniae. Most pathogens have a similar clinical profile. Several cases of coinfections were detected, with up to 4 pathogens in a single patient. / Tesis

This dissertation is related to mathematical modelling of the spread of respiratory syncytial virus (RSV) in Valencia and is still causing a large number of hospitalizations of children in this community. A mathematical model based on a system of nonlinear differential equations of first order has been built. This model considers the population divided into two age groups to pay particular attention to children under one year who are the most affected by this disease. This model has been fitted with hospitalizations data of Valencia and has been used to perform a cost analysis of a potential vaccination strategy. We also propose a complete network model to study the seasonal evolution of RSV epidemics in which seasonal parameters were fitted with the previous continuous model. Both developments are contrasted. On the complete network model we propose a strategy for vaccination of children based on the administration of three doses, and develop a cost-effectiveness study for different vaccination rates. Finally we have defined a SIRS model for RSV epidemics on a random social network of contacts among individuals. In this model has not forced the seasonality. The seasonality arises naturally for certain values of the duration of immunity of a patient recovered, the number of contacts and the likelihood of infection from a contact in a day. In this social network model only a narrow range of parameters can support RSV epidemic seasons. / Moraño Fernández, JA. (2010). Mathematical modelling of Respiratory Syncytial Virus spread in the Spanish region of Valencia. Preventive applications [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/8638