SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

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 SARSCoV-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 implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).info:eu-repo/semantics/publishedVersio

Exploring a capacity to screen of the European Portuguese version of the 15-item Geriatric Depression Scale

Abstract: The aim of this study was to analyze the screening performance of the European Portuguese version of the 15-item Geriatric Depression Scale (GDS-15) against DSM-5 diagnostic criteria for major depressive episode. The study was multicentre and involved 139 older adults recruited in the context of primary healthcare. Twenty-three participants were diagnosed with clinical depression. Sensitivity and specificity for different cut-off points were determined based on ROC curve analyses. The cut-off point ≥ 4.5 provided optimal sensitivity (95.7%) and specificity (52.6%) rates. After exclusion from the analysis of illiterate participants’ data, the optimal cut-off point remained unchanged. The European Portuguese version of GDS-15 is an effective tool for depression screening in older adults. Further studies are needed to verify if there are factors, other than formal education, that may influence the scale’s performance. Resumen: Exploración de la capacidad de screening de la versión europea portuguesa de la Geriatric Depression Scale de 15 items. El objetivo del estudio fue comparar la capacidad de cribado de la versión europea portuguesa de la Geriatric Depression Scale de 15 ítems (GDS-15) respecto a los criterios del DSM-5 en relación con el trastorno depresivo mayor. El estudio fue multicéntrico e incluyó 139 ancianos (23 con diagnóstico de depresión) reclutados en un contexto de atención primaria. La sensibilidad y la especificidad para diferentes puntos de corte fueron obtenidas a través de curvas ROC. La relación de sensibilidad y especificidad reveló ser mejor en el punto de corte ≥ 4.5, resultante en sensibilidad del 95.7% y especificidad del 52.6%. Después de excluirse del análisis de los datos los participantes sin educación formal, el punto de corte óptimo permaneció sin cambios. La versión europea portuguesa de la escala GDS-15 es una herramienta efectiva para el screening de la depresión en ancianos. Se necesitan más estudios para verificar si hay otros factores que puedan influir en el rendimiento de la escala

Anti-HIV-1 Activity of pepRF1, a Proteolysis-Resistant CXCR4 Antagonist Derived from Dengue Virus Capsid Protein

There is an urgent need for the development of new anti-HIV drugs that can complement existing medicines to be used against resistant strains. Here, we report the anti-HIV-1 peptide pepRF1, a human serum-resistant peptide derived from the Dengue virus capsid protein. In vitro, pepRF1 shows a 50% inhibitory concentration of 1.5 nM with a potential therapeutic window higher than 53 000. This peptide is specific for CXCR4-tropic strains, preventing viral entry into target cells by binding to the viral coreceptor CXCR4, acting as an antagonist of this receptor. pepRF1 is more effective than T20, the only peptide-based HIV-1 entry inhibitor approved, and excels in inhibiting a HIV-1 strain resistant to T20. Potentially, pepRF1 can be used alone or in combination with other anti-HIV drugs. Furthermore, one can also envisage its use as a novel therapeutic strategy for other CXCR4-related diseases.This work was supported by Fundação para a Ciência e a Tecnologia (FCT-MCTES, Portugal) project PTDC/QEQMED/4412/2014, and by the Institut National de la Santé et de la Recherche Medicale (Inserm). I.C.C., J.M.F., T.N.F., and I.B. acknowledge fellowships SFRH/BPD/65531/2009, SFRH/BD/70423/2010, SFRH/BD/5283/2013, and SFRH/BPD/76225/2011, respectively, funded by FCT-MCTES. A.T. is the recipient of a fellowship from Agence Nationale de Recherche sur le Sida et les Hepatites Virales (ANRS). A.S.V. acknowledges funding under the Investigator Programme (IF/00803/2012) from FCT-MCTES. Work at Pompeu Fabra University was supported by grants AGL2014-52395-C2 and AGL2017-84097-C2-2-R and by the “María de Maeztu” Program for Units of Excellence in R&D from the Spanish Ministry of Innovation and Competitiveness (MINECO).info:eu-repo/semantics/publishedVersio

Anti-HIV-1 activity of pepRF1, a proteolysis-resistant CXCR4 antagonist derived from Dengue virus capsid protein

Copyright © 2020 American Chemical SocietyThere is an urgent need for the development of new anti-HIV drugs that can complement existing medicines to be used against resistant strains. Here, we report the anti-HIV-1 peptide pepRF1, a human serum-resistant peptide derived from the Dengue virus capsid protein. In vitro, pepRF1 shows a 50% inhibitory concentration of 1.5 nM with a potential therapeutic window higher than 53 000. This peptide is specific for CXCR4-tropic strains, preventing viral entry into target cells by binding to the viral coreceptor CXCR4, acting as an antagonist of this receptor. pepRF1 is more effective than T20, the only peptide-based HIV-1 entry inhibitor approved, and excels in inhibiting a HIV-1 strain resistant to T20. Potentially, pepRF1 can be used alone or in combination with other anti-HIV drugs. Furthermore, one can also envisage its use as a novel therapeutic strategy for other CXCR4-related diseases.This work was supported by Fundação para a Ciência e aTecnologia (FCT-MCTES, Portugal) project PTDC/QEQ-MED/4412/2014, and by the Institut National de la Santéetde la Recherche Médicale (Inserm). I.C.C., J.M.F., T.N.F., and I.B. acknowledge fellowships SFRH/BPD/65531/2009,SFRH/BD/70423/2010, SFRH/BD/5283/2013, and SFRH/BPD/76225/2011, respectively, funded by FCT-MCTES. A.T. is the recipient of a fellowship from Agence Nationale de Recherche sur le Sida et les Hépatites Virales (ANRS). A.S.V.acknowledges funding under the Investigator Programme (IF/00803/2012) from FCT-MCTES. Work at Pompeu Fabra University was supported by grants AGL2014-52395-C2 and AGL2017-84097-C2-2-R and by the“María de Maeztu”Program for Units of Excellence in R&D from the Spanish Ministry of Innovation and Competitiveness (MINECO).info:eu-repo/semantics/publishedVersio

Characterisation of microbial attack on archaeological bone

As part of an EU funded project to investigate the factors influencing bone preservation in the archaeological record, more than 250 bones from 41 archaeological sites in five countries spanning four climatic regions were studied for diagenetic alteration. Sites were selected to cover a range of environmental conditions and archaeological contexts. Microscopic and physical (mercury intrusion porosimetry) analyses of these bones revealed that the majority (68%) had suffered microbial attack. Furthermore, significant differences were found between animal and human bone in both the state of preservation and the type of microbial attack present. These differences in preservation might result from differences in early taphonomy of the bones. © 2003 Elsevier Science Ltd. All rights reserved