Browsing by Author "Ribeiro, Carlos"
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- Actividade gripal em Portugal no Inverno de 2000/2001 - Análise antigénica e genética das estirpes de vírus influenzaPublication . Pechirra, Pedro; Rebelo-de-Andrade, Helena; Guiomar, Raquel; Ribeiro, Carlos; Coelho, Anabela; Pedro, Sónia; George, FranciscoAs infecções por vírus influenza são uma importante causa de morbilidade em todos os grupos etários e estão associados a uma elevada mortalidade nos idosos e nos indivíduos pertencentes a grupos de risco. No presente estudo analisaram-se os dados da vigilância epidemiológica da gripe durante o Inverno de 2000/2001. Os dados clínicos, epidemiológicos e virológicos referentes aos casos de síndroma gripal foram recolhidos através do Programa Nacional de Vigilância da Gripe que se desenvolve em colaboração com a Direcção Geral da Saúde e integra a informação obtida a partir das redes Médicos-Sentinela e Serviços de Urgência. A análise dos dados recolhidos mostram que, durante a época de Inverno de 2000/2001, a actividade gripal foi baixa, sendo o período epidémico curto e de pequena intensidade e duração. As taxas de incidência do síndrome gripal subiram acima da linha de base durante três semanas e não ultrapassaram os 74 casos por 100 000 habitantes. Os vírus influenza do tipo B foram predominantes, verificando-se a presença simultânea de vírus influenza tipo AH1 e AH3. A caracterização antigénica e genética das estirpes isoladas permitiu confirmar a semelhança entre estas estirpes virais e as estirpes vacinais e detectar a extensão dos drifts antigénicos. Saliente-se que apesar da maioria das estirpes de vírus influenza B serem idênticas antigenicamente à estirpe vacinal, a caracterização genética mostrou uma evolução dirigida para a estirpe B/ Sichuan/379/99 que viria a integrar a vacina antigripal em 2001/2002. Consequentemente, observou-se a co-circulação de duas linhagens diferentes evidenciada pela análise filogenética das estirpes B isoladas no nosso país.
- An Overview of Monkeypox Virus Detection in Different Clinical Samples and Analysis of Temporal Viral Load DynamicsPublication . Cordeiro, Rita; Pelerito, Ana; de Carvalho, Isabel Lopes; Lopo, Sílvia; Neves, Raquel; Rocha, Raquel; Palminha, Paula; Verdasca, Nuno; Palhinhas, Cláudia; Borrego, Maria José; Manita, Carla; Ferreira, Idalina; Bettencourt, Célia; Vieira, Patrícia; Silva, Sónia; Água-Doce, Ivone; Roque, Carla; Cordeiro, Dora; Brondani, Greice; Santos, João Almeida; Martins, Susana; Rodrigues, Irene; Ribeiro, Carlos; Núncio, Maria Sofia; Gomes, João Paulo; Batista, Fernando da ConceiçãoMpox is a zoonotic disease caused by the Monkeypox virus (MPXV), and since May 2022, tens of thousands of cases have been reported in non-endemic countries. We aimed to evaluate the suitability of different sample types for mpox diagnostic and assess the temporal dynamics of viral load. We evaluated 1914 samples from 953 laboratory-confirmed cases. The positivity rate was higher for lesion (91.3%) and rectal swabs (86.1%) when compared with oropharyngeal swabs (69.5%) and urines (41.2%), indicating higher viral loads for the former. Supporting this, lesion and rectal swabs showed lower median PCR C values (C = 23 and C = 24), compared to oropharyngeal swabs and urines (C = 31). Stable MPXV loads were observed in swabs from lesions up to 30 days after symptoms onset, contrasting with a considerable decrease in viral load in rectal and oropharyngeal swabs. Overall, these results point to lesion swabs as the most suitable samples for detecting MPXV in the 2022-2023 multicountry outbreak and show comparable accuracy to rectal swabs up to 8 days after symptoms onset. These findings, together with the observation that about 5% of patients were diagnosed through oropharyngeal swabs while having negative lesions, suggest that multisite testing should be performed to increase diagnostic sensitivity.
- Characterisation of influenza B viruses circulating in Portugal during the 2010/2011 influenza seasonPublication . Pechirra, Pedro; Conde, Patrícia; Romero, Carla; Ribeiro, Carlos; Gonçalves, Paulo; Guiomar, Raquel
- Diagnóstico laboratorial do sarampo em Portugal, 2011-2013Publication . Palminha, Paula; Vinagre, Elsa; Cordeiro, Rita; Ribeiro, Carlos; Roque, CarlaObjetivo: Este estudo tem como objetivo descrever os casos prováveis de sarampo enviados ao INSA para confirmação laboratorial entre 2011 e 2013 em Portugal.
- Enterovirus D68 diagnosed in severe respiratory and neurological illness in children during 2015-2016 season in PortugalPublication . Guiomar, Raquel; Costa, Inês; Pechirra, Pedro; Palminha, Paula; Ribeiro, Carlos; Roque, Carla; Peres, Maria João; Viseu, Regina; Balseiro, Maria Jesus; Brito, Maria João; Neves, João; Branquinho, Paula; Côrte-Real, RitaBackground: Enterovirus D68 (EV-D68) was first isolated in 1962, and since then associated with respiratory illness. The report of severe respiratory and neurological disease including deaths associated to EV-D68 in United States and Canada during August 2014 highlighted the need of epidemiological information regarding EV-D68 circulation. In Europe information was scarce, available only for few countries. In Portugal there was no data available and was critical to know the epidemiology of EV-D68, especially in children hospitalized with severe respiratory or neurological disease. This study aims to identify EV-D68 in Enterovirus positive respiratory samples in children under 18 with clinical diagnosis of severe respiratory infection or neurological illness. Methods: During 2015/16 winter season, between November/2015 and March/2016, 29 EV positive cases were reported to the National Influenza and Other Respiratory Virus Reference Laboratory (NIC) by two hospitals located in Lisbon and Setubal districts. EV diagnosis was performed in hospitals by biomolecular methods using commercial kits (real time multiplex-PCR, FTD Respiratory pathogens 21 and CLART Pneumovir, Genomica, respectively). EV-D68 was diagnosed by an in house real-time PCR [1]. Virus isolation in RD cell line and phylogenentic analysis of the VP1/VP3 genomic regions will enable the identification of genetic groups in circulation. All samples were irreversibly anonymized. Demographic and clinical data were collected. Results: EV-D68 was confirmed in 20 respiratory samples previously positive for EV (69%; 20/29). Samples were collected from children with age ranging from 2 months to 6 years old, both genders (9 female; 11 male) with diagnosis of severe respiratory or neurological illness. Eighteen cases were hospitalized (90%; 18/20). Bronchiolitis and pneumonia were the most frequently reported diagnosis, corresponding to 70% (14/20). Two cases have neurologic diagnosis. EV-D68 was identified throughout all study period with the higher number of positive cases detected during January 2016, in week 3. Virus isolation and genetic characterization are under way with expected results in virus phylogeny and evaluation on similarity with recent circulating strains in United States, Canada and European countries. Conclusions: EV-D68 was detected in a high positive rate (69%) among EV positive cases. This positive rate of EV-D68 was higher compared to the positivity rate of 10,2 %, calculated in a European study during 2014 [2]. This finding could be linked to the selection of severe and hospitalized patients in present study, highlighting the involvement of EV-D68 with severe respiratory disease in children. The identification of EV-D68 is also crucial in respiratory samples in children with clinical diagnosis of neurological illness. This study is the first attempt to describe the prevalence of EV-D68 in severe paediatric cases, in Portugal. The strength of EV-D68 surveillance in paediatric and adult population at the national level will be important to understand the epidemiology of EV-D68, age-related susceptibility and association with disease severity.
- Enterovírus não-polio e infeções do sistema nervoso central em crianças: avaliação laboratorial, 2023-2024Publication . Palminha, Paula; Neves, Raquel; Ribeiro, Carlos; Garcia, Ana Margarida; Fontes, Inês Sousa; Gouveia, Catarina; Corte-Real, RitaOs enterovírus não-polio permanecem como os principais agentes patogénicos do sistema nervoso central (SNC) em todo o mundo, especialmente em crianças com idade inferior a 5 anos, causando desde doença ligeira a quadros graves que podem evoluir para desfechos fatais. Entre 2023 e 2024 foram analisadas no INSA fezes de 327 crianças com suspeita de infeção por enterovírus. O diagnóstico laboratorial incluiu a deteção do RNA viral por RT-PCR em tempo real e o isolamento viral. A identificação viral foi realizada por sequenciação genómica. Neste período foram identificados 109 (33,3%) casos de infeção a enterovírus, dos quais 26 casos (23,9%) corresponderam a infeções do SNC, maioritariamente em crianças com menos de 5 anos (88,5%), sem uma evidente distribuição temporal. Os enterovírus mais frequentes foram os echovírus (tipos 5, 6,7, 9, 18, 21, 25, 30, 31 e 32), detetados em 13 casos (52,0%), seguidos pelos Coxsackievírus A (tipos 4, 6, 9, 10 e 16), em 7 casos (28,0%), ambos associados a meningite e meningoencefalite. O Enterovírus 71 (EV71) foi detetado em dois casos, um de romboencefalite e um de paralisia flácida aguda (PFA), e um caso de meningite esteve associado ao EV-C99. Não se observou nenhum padrão de surto nestes dois anos. Estes resultados reforçam a relevância da identificação rápida e dirigida para enterovírus como agentes etiológicos de infeções do SNC, fundamental para uma intervenção clínica direcionada, evitando o uso desnecessário de antibióticos e de múltiplos exames complementares de diagnóstico
- Falência vacinal secundária contra o sarampo: casos identificados em 2024Publication . Neves, Raquel; Ribeiro, Carlos; Palminha, PaulaPortugal alcançou o estatuto de eliminação do sarampo em 2015, no entanto, continuam a ocorrer surtos esporádicos, incluindo casos em indivíduos previamente vacinados. O teste de avidez das IgG avalia a força de ligação das imunoglobulinas ao seu antigénio específico, a qual aumenta ao longo da resposta imunitária, permitindo assim distinguir infeções primárias de respostas imunes pré-existentes. Este estudo teve como objetivo identificar casos de falência vacinal secundária contra o sarampo que ocorreram em 2024 utilizando o teste de avidez das IgG. Em 2024 foram confirmados 35 casos de sarampo em pacientes com idades entre 1 e 61 anos. A avidez de IgG foi avaliada em 17 casos (48,6%): 14 vacinados com duas doses de VASPR e 3 com estado vacinal desconhecido. Todos os soros, exceto um, foram colhidos durante a primeira semana após o início do exantema e utilizados reagentes comerciais com ureia como agente desnaturante. O RNA do vírus do sarampo foi detetado em todos os 16 casos. A IgM foi positiva em 6 pacientes: 5 vacinados e 1 com vacinação desconhecida. IgG de baixa avidez (IA < 40%) ocorreu apenas no paciente com vacinação desconhecida e IgM positiva, indicando infeção primária. Os outros 2 pacientes com vacinação não documentada apresentaram IgG de alta avidez e IgM negativa sugerindo falência vacinal secundária ou reinfeção. Todos os 14 casos vacinados apresentaram IgG de alta avidez (IA > 60%), sendo 5 também positivos para a IgM. O estudo identificou uma infeção primária e dois casos de falência vacinal secundária ou reinfeção em indivíduos com status desconhecido. Todos os casos em vacinados ocorreram em adultos, mais de 10 anos após a segunda dose da VASPR, sendo compatíveis com uma falência vacinal secundária e representando 40% dos casos de 2024. Isso reflete o contexto pós-eliminação em Portugal, onde a baixa exposição ao vírus selvagem reduz o reforço natural da imunidade, permitindo sintomas moderados e replicação viral apesar da vacinação prévia.
- Heterogeneous Selective Pressure Acting on Influenza B Victoria- and Yamagata-Like HemagglutininsPublication . Nunes, Baltazar; Pechirra, Pedro; Coelho, Anabela; Ribeiro, Carlos; Arraiolos, Ana; Rebelo-de-Andrade, HelenaAs a consequence of immune pressure, influenza virus hemagglutinin presents some of its amino acids under positive selection. Several authors have reported the existence of influenza A hemagglutinin codons under positive selective pressure (PSP). In this framework, the present work objectives were to demonstrate the presence of PSP and evaluate its effects on Victoria- and Yamagata-like influenza B viruses. Methodology adopted consisted in estimating the acceptance rate of nonsynonymous substitutions (ω = dN/dS) that describe the strength of selective pressure and identifying codons that may be positively selected, applying a set of continuous-time Markov chain codon-substitution models. Two groups of HA1 sequences (140 from Yamagata and 60 from Victoria lineage) were used. All the model maximum-likelihood estimates were obtained using codeml software application (PAML 3.15). The hypothesis of no existence of sites under PSP was rejected for both lineages (p<0.001), using likelihood ratio tests. These results demonstrate the presence of positive selection acting on hemagglutinin of both Yamagata- and Victoria-like influenza B viruses. Several different sites were identified to be under PSP on Yamagata and Victoria hemagglutinins. Sites found with a posterior probability >0.95 were codons 197 and 199 in both lineages, codon 75 in the Yamagata lineage, and codon 129 in the Victoria lineage. The detected amino acids are located at or near antigenic sites in influenza A virus H3 hemagglutinin.
- Influenza severe cases in hospitals, between 2014 and 2016 in PortugalPublication . Guiomar, Raquel; Pechirra, Pedro; Cristóvão, Paula; Costa, Inês; Conde, Patrícia; Corte-Real, Rita; Branquinho, Paula; Silvestre, Maria José; Almeida Santos, Madalena; Fernandes, Isabel; Dias, Isabel; Rodrigues, Sónia; Sena, Nadir; Lazzara, Daniela; Sobrinho Simões, Joana; Costa, Maria do Rosário; Guimarães, João Tiago; Rodrigues, Fernando; Pereira-Vaz, João; Correia, Lurdes; Andrade, Graça; Freitas, Ludivina; Figueira, Neuza; Sanches, Raquel; Marques, Mónica; Barros, Margarida; Mota Vieira, Luísa; Cabral Veloso, Rita; Castelo Branco, Cláudia; Pimentel, Sílvia; Duarte, Joana; Pereirinha, Tânia; Bulhões, Sara; Moniz, Raquel; Brilhante, Maria José; Bruges Armas, Jácome; Pimentel Couto, Ana Rita; Santos, Margarida; Soares, Marta; Melo Cristino, José; Ribeiro, Carlos; Carvalho, Dinah; Barreto, Rosário; Ramos, Maria Helena; Castro, Ana Paula; Matos Santos, Ana Cláudia; Cunha, Mário; Martins, Luís; Almeida, Sofia; Peres, Maria João; Viseu, Regina; Inácio, Filipe; Mota, PaulaBackground: Since 2009, the Portuguese Laboratory Network (PLNID) for Influenza Diagnosis has integrated 15 Laboratories in mainland and Atlantic Islands of Azores and Madeira. This PLNID added an important contribute to the National Influenza Surveillance Program regarding severe and hospitalized influenza cases. The present study aims to describe influenza viruses detected in influenza like illness (ILI) cases: outpatients (Outp), hospitalized (Hosp), and intensive care units (ICU), between 2014 and 2016. Methods: The PLNID performs influenza virus diagnosis by biomolecular methodologies. Weekly reports to the National Influenza Reference Laboratory ILI cases tested for influenza. Reports include data on detecting viruses, hospital assistance, antiviral therapeutics, and information on death outcome. Were reported during two winter seasons 8059 ILI cases,being 3560 cases in 2014/15 (1024 in Outp, 1750 Hosp, and 606 in ICU) and 4499 cases in 2015/2016 (1933 in Outp, 1826 Hosp, and 740 in ICU). Results: The higher percentage of influenza positive cases were detected in Outp in both seasons, 18% during 2014/15 and 20% in 2015/16. In 2014/15,influenza cases were more frequent in individuals older than 65 years old and these required more hospitalizations,even in ICU. In 2015/16,the influenza cases were mainly detected in individuals between 15-64 years old. A higher proportion of influenza positive cases with hospitalization in ICU were observed in adults between 45-64 years old.During the study period,the predominant circulating influenza viruses were different in the two seasons: influenza B and A(H3) co-circulated in 2014/15,and influenza A(H1)pdm09 was predominant during 2015/16. Even when influenza A is notthe dominant virus, A(H3) and A(H1)pdm09 subtypes correlate with higher detection rate in hospitalized cases (Hosp and UCI), with higher frequencies in adults older than 45. Influenza B,detected in higher proportion in outpatients, was frequently relatedwith influenza cases in younger age groups: 0-4 and 5-14 years old. Conclusions: This study highlights the correlation of theinfluenza virus type/subtype that circulates in each season with the possible need for hospitalization and intensive care in special groups of the population. Circulation of influenza A subtypes can cause more frequentdisease in individuals older than 45, with need of hospitalization including intensive care. On the other hand, influenza B is more frequently associated with less severe cases and with infection in children and younger adults. Influenza B circulation might predict lower number of hospitalizations.The identification of influenza type in circulation,byPLNID ineach season, could guide action planning measures in population health care.
- Influenza virus type/subtype and different infection profiles by age group during 2017/2018 seasonPublication . Guiomar, Raquel; Pechirra, Pedro; Cristóvão, Paula; Costa, Inês; Conde, Patrícia; Côrte-Real, Rita; Branquinho, Paula; Garcia, David; Conde, Sílvia; Rodrigues, Fernando; Pereira-Vaz, João; Alves, José; Freitas, Ludivina; Mota Vieira, Luísa; Cabral Veloso, Rita; Bruges Armas, Jácome; Couto, Ana Rita; Ribeiro, Carlos; Barreto, Rosário; Cunha, Mário; Martins, Luís; Almeida, Sofia; Peres, Maria João; Viseu, Regina; Mota, Paula; Lopes, Paulo; Soares, Vânia; Vale, Fátima; Fonseca, Patrícia; Toscano, Cristina; Dias, AnaBackground: Influenza has a major impact in hospitalization during each influenza season. We analysed the influenza type/subtype distribution by age group and medical care wards (ambulatory, hospital, intensive care unit). Material and Methods: During 2017/2018 season, 14 hospitals from Portugal mainland and Atlantic Island (Azores and Madeira) reported to the National Influenza Centre 13747 cases of respiratory infection, all tested for influenza type and/or subtype. Epidemiological data: age, sample collection, hospital dwelling service and patient outcome were reported. Results: From the 13747 reported cases, 3717(27%) were influenza positive of which 2033 (55%) were influenza B, 722 (19%) A unsubtyped, 505 (14%) AH3, 442 (12%) AH1pdm09 and 15(0,1%) mixed infections. Influenza A was detected in 71% (204/208) of toddlers(<5 years) although in the remaining age groups influenza B was detected in more than 50% of the confirmed flu cases. Influenza B was the predominant virus in hospitalized and ICU influenza cases between 5-14 years (69% and 75%, respectively) and played a major role in elderly (65+ years) hospitalized and ICU cases(57% and 67%, respectively). AH1pdm09 virus was detected in 30% of the influenza confirmed ICU patients, 2.1 times more than in hospitalized cases in other wards and 3.3 times more than influenza AH1pdm09 cases in ambulatory care. Influenza mixed infection were detected sporadically,mainly in hospitalized and ICU patients. From 2080 known outcomes, 40(1.9%) patients deceased, influenza was confirmed in 11(28%) of these cases. Conclusions: Cocirculation of different influenza virus type/subtype may indicate different infection profiles by age groups and should guide influenza preventive/treatment measures.