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

The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability

Chromobacterium violaceum is one of millions of species of free-living microorganisms that populate the soil and water in the extant areas of tropical biodiversity around the world. Its complete genome sequence reveals (i) extensive alternative pathways for energy generation, (ii) ≈500 ORFs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) wide-spread utilization of quorum sensing for control of inducible systems, all of which underpin the versatility and adaptability of the organism. The genome also contains extensive but incomplete arrays of ORFs coding for proteins associated with mammalian pathogenicity, possibly involved in the occasional but often fatal cases of human C. violaceum infection. There is, in addition, a series of previously unknown but important enzymes and secondary metabolites including paraquat-inducible proteins, drug and heavy-metal-resistance proteins, multiple chitinases, and proteins for the detoxification of xenobiotics that may have biotechnological applications

Relationship between nutritional status and the Glasgow Prognostic Score in patients with colorectal cancer

AbstractObjectiveThe association between nutritional status and inflammation was assessed in patients with colorectal cancer and to verify their association with complications during anticancer treatment. The agreement between the Subjective Global Assessment (SGA) and different nutritional assessment methods was also evaluated.MethodsA cross-sectional, prospective, and descriptive study was performed. The nutritional status was defined by the SGA and the severity of inflammation was defined by the Glasgow Prognostic Score (GPS). The complications were classified using the Common Toxicity Criteria, version 3. Anthropometric measurements such as body mass index, triceps skinfold, midarm circumference, midarm muscle area, and adductor pollicis muscle thickness were also performed, as were handgrip strength and phase angle. The chi-square test, Fisher exact test, Spearman correlation coefficient, independent t test, analysis of variance, Gabriel test, and κ index were used for the statistical analysis. P < 0.05 was considered statistically significant.ResultsSeventy patients with colorectal cancer (60.4 ± 14.3 y old) were included. The nutritional status according to the SGA was associated with the GPS (P < 0.05), but the SGA and GPS were not related to the presence of complications. When comparing the different nutritional assessment methods with the SGA, there were statistically significant differences.ConclusionMalnutrition is highly prevalent in patients with colorectal cancer. The nutritional status was associated with the GPS

Agricultura familiar e suas potencialidades na conservação de recursos genéticos

O objectivo deste estudo era conhecer a dispersão de animais das diversas espécies, nomeadamente, animais de companhia, assim como o seu número, localização e características da exploração, dados que são relevantes na prevenção da dispersão de doenças animais. Para isso foram visitadas as explorações pecuárias do Distrito de Bragança, em Portugal, composto por 12 concelhos. A recolha de informação decorreu sob a forma de entrevista pessoal. Foram, também, recolhidos dados para georeferenciação utilizando para o efeito dois equipamentos da marca Trimble®, modelos GeoXM e GeoXT, ambos de precisão sub-métrica após correcção diferencial. O frameware e software foram desenvolvidos pela Trimble®: Terrasync, GPS PathFinder Office v.4.20. Recolheu-se a informação seguinte: nome e número de identificação fiscal do agricultor, idade, número de animais de cada espécie e localização geográfica desses animais (coordenadas GPS - Global Positioning System). Os dados correspondem aos anos de 2010 e 2011. Essa informação foi, posteriormente, transferida para computador, através do GPS PathFinder Office v.4.20 e de hardware específico Trimble. A informação foi tratada de forma a apurar o número de animais de cada espécie, nomeadamente aquelas espécies de que, normalmente, não há arrolamento, como coelhos e aves de capoeira, cães e outros animais de companhia. O erro de amostragem não ultrapassou os 10%. A generalidade das produções aqui analisadas são de muito pequena dimensão e a média de idade dos agricultores ronda os 61 anos, pelo que se considera serem explorações familiares e em boa parte dedicadas a uma economia de complementaridade com reformas e/ou a exploração agropecuária. Os resultados mais interessantes dizem respeito a aves e coelhos, quase todos criados em alojamentos tradicionais. O número de coelhos ultrapassou os 21000; de galinhas, as 114000; de patos, os 5800; e, de perus, os 500 animais. Os suínos ultrapassaram os 10000 sendo, a grande maioria, animais da raça bisara ou cruzados de bísaro. O número de animais por criador não está disponível mas sabe-se ser muito baixo. O número de burros e cavalos rondou os 6000. Em relação a outros animais de exploração não foram aqui considerados (ruminantes) por as raças em causa não estarem em perigo de extinção ou por terem programas próprios de protecção. Pode-se concluir que há uma grande abundância de pequenas explorações que criam espécies e raças diversas mas, normalmente, não são raças autóctones excepto no caso dos mamíferos. Esta discussão conduz à conclusão de que é viável a utilização deste tecido pulverizado para a produção de diversas espécies de animais e, em particular, para a produção de raças autóctones, contribuindo para o seu relançamento e, dessa forma, para a biodiversidade

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