Browsing by Issue Date, starting with "2020-11-27"
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- Portuguese National Serological Survey to Coronavirus Disease-19Publication . Rodrigues, Ana Paula; Guiomar, Raquel; INS COVID-19 groupIntroduction: Seroepidemiological studies allow estimating more precise cumulative incidence when compared with results obtained from the SARS-CoV-2 RNA detection test. In this context, the first Portuguese COVID-19 National Serological Survey (ISN-COVID-19) had as primary objectives to: characterize the extent of SARS-CoV-2 infection; determine seroprevalence in specific age groups and Health Regions; and determine the proportion of asymptomatic SARS-CoV-2 infections within Portuguese population. Methods: ISN-COVID-19 was an observational, cross-sectional study. A non-probabilistic sample of 2,301 people residing in Portugal, aged over 1 year old, was analyzed. Sociodemographic, epidemiological and clinical data were collected using a questionnaire and a blood sample was collected from each participant, at 114 collection points, between May 21-July 8, 2020. SARS-Cov-2 specific IgG and IgM were measured in serum by ELISA. Results: National seroprevalence was 2.9% (2.0-4.2%), being higher than the accumulated incidence of the infection reported by the National Surveillance System (0.44%). The estimated seroprevalence was higher in males than in females (4.1% vs 1.8%). It ranged from 2.2% (0.8-5.5) in the 10-19 age group to 3.2% (1.5-6.7) in the 40-59 age group. At the regional level, seroprevalence varied between 1.2% (0.3-4.0) in Alentejo and 3.5% (1.9-6.3) in Lisbon and Tagus Valley. Age and regional differences were not statistical significant. About 44% of individuals with SARS-CoV-2 antibodies did not report previous COVID-19 symptoms. Conclusions: The estimated value is compatible with a limited extent of infection in the Portuguese population, between March and June. Differences observed between seroprevalence and cumulative incidence of the infection are consistent with the evidence of lesser capacity to capture mild or asymptomatic cases by surveillance systems. These results advise universal maintenance of protection measures.
- Alternative Splicing: Expanding the Landscape of Cancer Biomarkers and TherapeuticsPublication . Bessa, Cláudia; Matos, Paulo; Jordan, Peter; Gonçalves, VâniaAlternative splicing (AS) is a critical post-transcriptional regulatory mechanism used by more than 95% of transcribed human genes and responsible for structural transcript variation and proteome diversity. In the past decade, genome-wide transcriptome sequencing has revealed that AS is tightly regulated in a tissue- and developmental stage-specific manner, and also frequently dysregulated in multiple human cancer types. It is currently recognized that splicing defects, including genetic alterations in the spliced gene, altered expression of both core components or regulators of the precursor messenger RNA (pre-mRNA) splicing machinery, or both, are major drivers of tumorigenesis. Hence, in this review we provide an overview of our current understanding of splicing alterations in cancer, and emphasize the need to further explore the cancer-specific splicing programs in order to obtain new insights in oncology. Furthermore, we also discuss the recent advances in the identification of dysregulated splicing signatures on a genome-wide scale and their potential use as biomarkers. Finally, we highlight the therapeutic opportunities arising from dysregulated splicing and summarize the current approaches to therapeutically target AS in cancer.
- Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistancePublication . Pinto, Miguel; Borges, Vítor; Isidro, Joana; Rodrigues, João Carlos; Vieira, Luís; Borrego, Maria José; Gomes, João PauloNeisseria gonorrhoeae, the bacterium responsible for the sexually transmitted disease gonorrhoea, has shown an extraordinary ability to develop antimicrobial resistance (AMR) to multiple classes of antimicrobials. With no available vaccine, managing N. gonorrhoeae infections demands effective preventive measures, antibiotic treatment and epidemiological surveillance. The latter two are progressively being supported by the generation of whole-genome sequencing (WGS) data on behalf of national and international surveillance programmes. In this context, this study aims to perform N. gonorrhoeae clustering into genogroups based on WGS data, for enhanced prospective laboratory surveillance. Particularly, it aims to identify the major circulating WGS-genogroups in Europe and to establish a relationship between these and AMR. Ultimately, it enriches public databases by contributing with WGS data from Portuguese isolates spanning 15 years of surveillance. A total of 3791 carefully inspected N. gonorrhoeae genomes from isolates collected across Europe were analysed using a gene-by-gene approach (i.e. using cgMLST). Analysis of cluster composition and stability allowed the classification of isolates into a two-step hierarchical genogroup level determined by two allelic distance thresholds revealing cluster stability. Genogroup clustering in general agreed with available N. gonorrhoeae typing methods [i.e. MLST (multilocus sequence typing), NG-MAST (N. gonorrhoeae multi-antigen sequence typing) and PubMLST core-genome groups], highlighting the predominant genogroups circulating in Europe, and revealed that the vast majority of the genogroups present a dominant AMR profile. Additionally, a non-static gene-by-gene approach combined with a more discriminatory threshold for potential epidemiological linkage enabled us to match data with previous reports on outbreaks or transmission chains. In conclusion, this genogroup assignment allows a comprehensive analysis of N. gonorrhoeae genetic diversity and the identification of the WGS-based genogroups circulating in Europe, while facilitating the assessment (and continuous monitoring) of their frequency, geographical dispersion and potential association with specific AMR signatures. This strategy may benefit public-health actions through the prioritization of genogroups to be controlled, the identification of emerging resistance carriage, and the potential facilitation of data sharing and communication.