9 documents found, page 1 of 1
Dengue and Oropouche virus co-infection in a traveller from Cuba to Portugal
Zé-Zé, Líbia; Laranjinha, Joana; Borges, Vítor; Graça, Ana Luísa; Sobral, Daniel; Santos, João Dourado; Carvalho, Ana Cláudia; Faria, Nuno R.In 2024, unprecedented outbreaks of dengue and Oropouche were reported in the Americas. We describe a documented co-infection with dengue and Oropouche viruses in a 35-year-old traveller from Cuba detected in Portugal. RT-PCR and next-generation sequencing confirmed both viruses. Our findings highlight the need for multiplex arboviral diagnostics in travellers from regions with concurrent outbreaks.
Multi-country and intersectoral assessment of cluster congruence between pipeli...
Mixão, Verónica; Pinto, Miguel; Brendebach, Holger; Sobral, Daniel; Santos, João Dourado; Radomski, Nicolas; Uldall, Anne Sophie MajgaardDifferent laboratories employ different Whole-Genome Sequencing (WGS) pipelines for Food and Waterborne disease (FWD) surveillance, casting doubt on the comparability of their results and hindering optimal communication at intersectoral and international levels. Through a collaborative effort involving eleven European institutes spanning the food, animal, and human health sectors, we aimed to assess the inter-p...
Probe-based metagenomic pathogen detection: advancing laboratory capacity for c...
Ferreira, Rita; Coelho, Luís; Santos, João Dourado; Sobral, Daniel; Isidro, Joana; Mixão, Verónica; Pinto, Miguel; Nunes, Alexandra; Borrego, Maria JoséProbe-based pathogen enrichment, followed by NGS, is a promising tool for complex diagnosis, overcoming traditional challenges of shotgun metagenomics, namely small microbial/human genetic material ratio and demanding computational resources. Here, we assessed the combined detection performance of two Illumina probe-based panels, the Respiratory and the Urinary Pathogen ID panels (RPIP and UPIP), using 99 clini...
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic d...
Santos, João Dourado; Sobral, Daniel; Pinheiro, Miguel; Isidro, Joana; Bogaardt, Carlijn; Pinto, Miguel; Eusébio, Rodrigo; Santos, André; Mamede, RafaelBackground: Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and deve...
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic d...
Santos, João Dourado; Sobral, Daniel; Pinheiro, Miguel; Isidro, Joana; Bogaardt, Carlijn; Pinto, Miguel; Eusébio, Rodrigo; Santos, André; Mamede, RafaelBackground: Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and deve...
Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in...
Borges, Vítor; Duque, Mariana Perez; Martins, João Vieira; Vasconcelos, Paula; Ferreira, Rita; Sobral, Daniel; Pelerito, Ana; de Carvalho, Isabel LopesPathogen genome sequencing during epidemics enhances our ability to identify and understand suspected clusters and investigate their relationships. Here, we combine genomic and epidemiological data of the 2022 mpox outbreak to better understand early viral spread, diversification and transmission dynamics. By sequencing 52% of the confirmed cases in Portugal, we identified the mpox virus sublineages with the hi...
Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in...
Borges, Vítor; Duque, Mariana Perez; Martins, João Vieira; Vasconcelos, Paula; Ferreira, Rita; Sobral, Daniel; Pelerito, Ana; de Carvalho, Isabel LopesPathogen genome sequencing during epidemics enhances our ability to identify and understand suspected clusters and investigate their relationships. Here, we combine genomic and epidemiological data of the 2022 mpox outbreak to better understand early viral spread, diversification and transmission dynamics. By sequencing 52% of the confirmed cases in Portugal, we identified the mpox virus sublineages with the hi...
Phylogenomic characterization and signs of microevolution in the 2022 multi-cou...
Isidro, Joana; Borges, Vítor; Pinto, Miguel; Sobral, Daniel; Santos, João Dourado; Nunes, Alexandra; Mixão, Verónica; Ferreira, Rita; Santos, DanielaThe largest monkeypox virus (MPXV) outbreak described so far in non-endemic countries was identified in May 2022 (refs. 1-6). In this study, shotgun metagenomics allowed the rapid reconstruction and phylogenomic characterization of the first MPXV outbreak genome sequences, showing that this MPXV belongs to clade 3 and that the outbreak most likely has a single origin. Although 2022 MPXV (lineage B.1) clustered ...
Kin structure and roost fidelity in greater noctule bats
Santos, João Dourado; Meyer, Christoph F. J.; Ibáñez, Carlos; Popa-Lisseanu, Ana G.; Juste, JavierRoost fidelity is an important aspect of mammalian biology. Studying the mechanisms underlying philopatry can help us understand a species’ energetic requirements, ecological constraints and social organisation. Temperate bat species notably exhibit a high degree of female philopatry considering their size, resulting in maternity colonies segregated at the mitochondrial level. We focus on the greater noctule, N...