Figure S1. INSaFLU graphical output plotting the number of iSNVs at frequencies 1–50% (minor iSNV... more Figure S1. INSaFLU graphical output plotting the number of iSNVs at frequencies 1–50% (minor iSNVs) and 50–90% obtained for dataset 1. Figure S2. INSaFLU testing with artificial mixtures of A(H3N2) viruses. A. INSaFLU graphical output plotting the number of iSNVs at frequencies 1–50% (minor iSNVs) and 50–90%. B. Phylogenetic tree based on "whole-genome" consensus sequences obtained for dataset 3. (PDF 977 kb)
Table S1. A. INSaFLU genetic markers for type and subtype/lineage identification ("influenza... more Table S1. A. INSaFLU genetic markers for type and subtype/lineage identification ("influenza_typing" database). B. INSaFLU genetic markers for the assignment of segments (and references) to draft contigs ("influenza_assign_segments2contigs" database). GISAID acknowledgement tables are included in these tables. (XLSX 45 kb)
Table S2. A. Matrix of pairwise nucleotide differences between whole-genome consensus sequences o... more Table S2. A. Matrix of pairwise nucleotide differences between whole-genome consensus sequences obtained using INSaFLU versus IRMA for 137 A(H3N2) viruses from dataset 1. B. Matrix of pairwise nucleotide differences between whole-genome consensus sequences obtained using INSaFLU versus IRMA for 39 A(H1N1pdm09) viruses from dataset 2. (XLSX 100 kb)
Population immune profile for influenza is highly affected by circulating influenza viruses, thus... more Population immune profile for influenza is highly affected by circulating influenza viruses, thus changing the risk of infection for influenza. This study aim was to assess influenza immunity in the Portuguese population by age groups, during 2014 and 2015 and establish a relationship between seroprotection and circulating influenza viruses in 2014/15 and 2015/16 seasons. Conclusions: There was a correlation between virus circulation, incidence rates for each age group and the previous seroprotection for seasonal influenza viruses. Our study highlights the value of measuring the serological profile for influenza to establish risk groups for infection for which an increase preventive measures, including vaccination, should be fostered.
Background Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National... more Background Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARS-CoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementatio...
INTRODUCTION Epidemiological surveillance of influenza, a disease associated with high mortality ... more INTRODUCTION Epidemiological surveillance of influenza, a disease associated with high mortality in the elderly and individuals' belonging to risk groups, is essential for the characterization of influenza epidemics as well as for the monitoring of outbreaks and the emergence of viral strains resistant to antivirals. MATERIAL AND METHODS In the present study was analyzed the influenza surveillance data from 2010/2011 winter. The clinical, epidemiological and virological data related to cases of flu-like syndrome have been collected through the National Influenza Surveillance Programme, coordinated by the National Influenza Reference Laboratory (LNRVG) in collaboration with the Department of Epidemiology(DEP) of the National Institute of Health Doutor Ricardo Jorge (INSA) and the Directorate-General for Health (DGS). RESULTS From the analysis of the data collected during the 2010/2011 winter season, influenza activity was moderate / high with an epidemic period of 8 weeks between...
Este trabalho foi realizado no âmbito I-MOVE/I-MOVE+ financiado pelo programa Horizonte 2020 e pe... more Este trabalho foi realizado no âmbito I-MOVE/I-MOVE+ financiado pelo programa Horizonte 2020 e pelo European Centre for Disease Prevention and Control.
This report was prepared as part of the Project “Monitoring Influenza vaccine effectiveness durin... more This report was prepared as part of the Project “Monitoring Influenza vaccine effectiveness during influenza seasons and pandemics in the European Union”, financed by the European Centre for Disease Prevention and Control, and describes the results obtained in Portugal under the Protocol Agreement celebrated between EpiConcept SARL, Paris and National Health Institute Doutor Ricardo Jorge, Lisbon, signed on December 2014.
Influenza viral infections are an important cause of morbidity in all age groups and are associat... more Influenza viral infections are an important cause of morbidity in all age groups and are associated with a high mortality rate amongst the elderly and in risk groups. The current study analyses data from the epidemiological surveillance of influenza during the 2000/2001-winter season. Clinical, epidemiological and virological data relative to cases of influenza syndrome were collected via the National Influenza Surveillance Scheme, in collaboration with the General Directory of Health and integrates the information obtained by the Network of Sentinel Medical Practitioners and Emergency Units. The data analysis hereby obtained shows a low influenza activity during the 2000/2001-winter season, with an epidemiological period characterized by small duration and intensity. The incidence rate of influenza-like illnesses increased above the base line during three weeks and didn't surpass 74 cases per 1,000,000 inhabitants. Influenza B viruses were predominant with the simultaneous pres...
Background Well-established influenza surveillance systems (ISS) can be used for respiratory sync... more Background Well-established influenza surveillance systems (ISS) can be used for respiratory syncytial virus (RSV) surveillance. In Portugal, RSV cases are detected through the ISS using the European Union (EU) influenza-like illness (ILI) case definition. Aim To investigate clinical predictors for RSV infection and how three case definitions (EU ILI, a modified EU acute respiratory infection, and one respiratory symptom) performed in detecting RSV infections in Portugal. Methods This observational retrospective study used epidemiological and laboratory surveillance data (October 2010–May 2018). Associations between clinical characteristics and RSV detection were analysed using logistic regression. Accuracy of case definitions was assessed through sensitivity, specificity, and area under the receiver operating characteristic curve (AUC). A 0.05 significance level was accepted. Results The study involved 6,523 persons, including 190 (2.9%) RSV cases. Among 183 cases with age informat...
Figure S1. INSaFLU graphical output plotting the number of iSNVs at frequencies 1–50% (minor iSNV... more Figure S1. INSaFLU graphical output plotting the number of iSNVs at frequencies 1–50% (minor iSNVs) and 50–90% obtained for dataset 1. Figure S2. INSaFLU testing with artificial mixtures of A(H3N2) viruses. A. INSaFLU graphical output plotting the number of iSNVs at frequencies 1–50% (minor iSNVs) and 50–90%. B. Phylogenetic tree based on "whole-genome" consensus sequences obtained for dataset 3. (PDF 977 kb)
Table S1. A. INSaFLU genetic markers for type and subtype/lineage identification ("influenza... more Table S1. A. INSaFLU genetic markers for type and subtype/lineage identification ("influenza_typing" database). B. INSaFLU genetic markers for the assignment of segments (and references) to draft contigs ("influenza_assign_segments2contigs" database). GISAID acknowledgement tables are included in these tables. (XLSX 45 kb)
Table S2. A. Matrix of pairwise nucleotide differences between whole-genome consensus sequences o... more Table S2. A. Matrix of pairwise nucleotide differences between whole-genome consensus sequences obtained using INSaFLU versus IRMA for 137 A(H3N2) viruses from dataset 1. B. Matrix of pairwise nucleotide differences between whole-genome consensus sequences obtained using INSaFLU versus IRMA for 39 A(H1N1pdm09) viruses from dataset 2. (XLSX 100 kb)
Population immune profile for influenza is highly affected by circulating influenza viruses, thus... more Population immune profile for influenza is highly affected by circulating influenza viruses, thus changing the risk of infection for influenza. This study aim was to assess influenza immunity in the Portuguese population by age groups, during 2014 and 2015 and establish a relationship between seroprotection and circulating influenza viruses in 2014/15 and 2015/16 seasons. Conclusions: There was a correlation between virus circulation, incidence rates for each age group and the previous seroprotection for seasonal influenza viruses. Our study highlights the value of measuring the serological profile for influenza to establish risk groups for infection for which an increase preventive measures, including vaccination, should be fostered.
Background Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National... more Background Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARS-CoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementatio...
INTRODUCTION Epidemiological surveillance of influenza, a disease associated with high mortality ... more INTRODUCTION Epidemiological surveillance of influenza, a disease associated with high mortality in the elderly and individuals' belonging to risk groups, is essential for the characterization of influenza epidemics as well as for the monitoring of outbreaks and the emergence of viral strains resistant to antivirals. MATERIAL AND METHODS In the present study was analyzed the influenza surveillance data from 2010/2011 winter. The clinical, epidemiological and virological data related to cases of flu-like syndrome have been collected through the National Influenza Surveillance Programme, coordinated by the National Influenza Reference Laboratory (LNRVG) in collaboration with the Department of Epidemiology(DEP) of the National Institute of Health Doutor Ricardo Jorge (INSA) and the Directorate-General for Health (DGS). RESULTS From the analysis of the data collected during the 2010/2011 winter season, influenza activity was moderate / high with an epidemic period of 8 weeks between...
Este trabalho foi realizado no âmbito I-MOVE/I-MOVE+ financiado pelo programa Horizonte 2020 e pe... more Este trabalho foi realizado no âmbito I-MOVE/I-MOVE+ financiado pelo programa Horizonte 2020 e pelo European Centre for Disease Prevention and Control.
This report was prepared as part of the Project “Monitoring Influenza vaccine effectiveness durin... more This report was prepared as part of the Project “Monitoring Influenza vaccine effectiveness during influenza seasons and pandemics in the European Union”, financed by the European Centre for Disease Prevention and Control, and describes the results obtained in Portugal under the Protocol Agreement celebrated between EpiConcept SARL, Paris and National Health Institute Doutor Ricardo Jorge, Lisbon, signed on December 2014.
Influenza viral infections are an important cause of morbidity in all age groups and are associat... more Influenza viral infections are an important cause of morbidity in all age groups and are associated with a high mortality rate amongst the elderly and in risk groups. The current study analyses data from the epidemiological surveillance of influenza during the 2000/2001-winter season. Clinical, epidemiological and virological data relative to cases of influenza syndrome were collected via the National Influenza Surveillance Scheme, in collaboration with the General Directory of Health and integrates the information obtained by the Network of Sentinel Medical Practitioners and Emergency Units. The data analysis hereby obtained shows a low influenza activity during the 2000/2001-winter season, with an epidemiological period characterized by small duration and intensity. The incidence rate of influenza-like illnesses increased above the base line during three weeks and didn't surpass 74 cases per 1,000,000 inhabitants. Influenza B viruses were predominant with the simultaneous pres...
Background Well-established influenza surveillance systems (ISS) can be used for respiratory sync... more Background Well-established influenza surveillance systems (ISS) can be used for respiratory syncytial virus (RSV) surveillance. In Portugal, RSV cases are detected through the ISS using the European Union (EU) influenza-like illness (ILI) case definition. Aim To investigate clinical predictors for RSV infection and how three case definitions (EU ILI, a modified EU acute respiratory infection, and one respiratory symptom) performed in detecting RSV infections in Portugal. Methods This observational retrospective study used epidemiological and laboratory surveillance data (October 2010–May 2018). Associations between clinical characteristics and RSV detection were analysed using logistic regression. Accuracy of case definitions was assessed through sensitivity, specificity, and area under the receiver operating characteristic curve (AUC). A 0.05 significance level was accepted. Results The study involved 6,523 persons, including 190 (2.9%) RSV cases. Among 183 cases with age informat...
Uploads
Papers by Pedro Pechirra