European Cohorts of patients and schools to Advance Response to Epidemics (EuCARE): a cluster randomised interventional and observational study protocol to investigate the relationship between schools and SARS-CoV-2 infection

Publisher Copyright: © 2023, The Author(s).Following publication of the original article [1], the authors identified an error in the author name of Claudia Dellavia. The incorrect author name is: Claudia Dallavia. The correct author name is: Claudia Dellavia. The author group has been updated above and the original article [1] has been corrected.publishersversionpublishe

a cluster randomised interventional and observational study protocol to investigate the relationship between schools and SARS-CoV-2 infection

Funding Information: Open Access funding enabled and organized by Projekt DEAL. This research received the contribution of the EuCARE Project funded by the European Union´s Horizon Europe Research and Innovation Programme under Grant Agreement No 101046016. The study is funded by the European Union and the study proposal has undergone a competitive peer review process. Role of the funder: the EU has launched a call for projects to which the study proposal answered. The call defined the general themes of research for the applying projects. The EU periodically carries out reviews on the advancement status of the study and quality assessment of its deliverables. The EU does not interfere with the scientific decisions and conduct of the study nor in the analysis of the results. The funding is administered to the participant centres by the study coordinator EuResist Network GEIE. This work was partially supported by the Italian Ministry of Health with Ricerca Corrente and 5X1000 funds. The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript. Funding Information: Eucare WP4: Maria Chiara Mommo, Michael Böhm, Michal Rosen-Zvi, Yishai Shimoni, Sivan Ravid, Tal Kozlovski, Sofia Seabra, Victor Pimentel, Mafalda Miranda, Dora Vaz, Giuseppina Tucci, Juan Manuel Baez, Carmen Romero, Francesco Vairo, Martina Spaziante, Valeria Gabellone, Giulia Vaglio, Fabrizio Fedele. We would like to thank school personnel, students and parents for participating in the EuCARE study. Participating schools up to now are the following: Scuola Maria Ausiliatrice (Lodi), Liceo Scientifico G. Gandini (Lodi), Scuola Infanzia Pio XII (Lodi), Fondazione Scuola materna (Rivolta D'Adda), Istituto Tecnico Industriale Statale Enrico Mattei (San Donato), Liceo Leonardo da Vinci (Casalecchio di Reno), I.C. Ammirato Falcone (Lecce), Direzione didattica statale 5° circolo “Livio Tempesta” (Lecce), I.C 1° Polo “S. Colonna”(Monteroni di Lecce), I.C. E. De Amicis (Squinzano), I.C. Magistrato Giovanni Falcone (Copertino), I.C. Castro dei Volsci, Agrupamento de Escolas Dr. Azevedo Neves (Amadora, Portugal). Funding Information: The EuCARE consortium involves 18 partners from 10 different countries and has been funded by the European Commission in the frame of the research aimed at fighting SARS-CoV2 virus and its variants, in the context of the EuCARE project, “European Cohorts of Patients and Schools to Advance Response to Epidemics”. The project’s ultimate goal is to find solutions to safely support school reopening within the COVID-19 pandemic on the basis of scientific evidence, taking in consideration the impact that a prolonged school closure can have on education, wellbeing and personal development of children. Publisher Copyright: © 2022, The Author(s).Background: Contradictory results were reported on the role of school closure/reopening on the overall SARS-CoV-2 transmission rate, as well as on which kind and level of mitigation measures implemented in schools may be effective in limiting its diffusion. Some recent studies were reassuring, showing that opening did not increase the community spread, although teachers and families are worried about the high class density. On the other hand, distance learning was associated with a negative impact on learning, sociability and psychological health, especially in vulnerable children. As it becomes clear that the SARS-CoV-2 pandemic will last for a long time, there is a high need for studies and solutions to support safe schools opening based on scientific evidence of harms and benefits. The Lolli-Methode (LM) is a strategy for epidemiological surveillance and early intervention aiming at SARS-CoV-2 outbreaks’ reduction in schools, relying on polymerase chain reaction analysis of saliva samples. Methods: In this cluster randomised trial protocol, we aim to determine whether the LM is useful to support schools opening and to reduce clusters and attack rates in schools, compared with the standard of care (SoC) surveillance by public health departments. This multicenter study will enrol 440 classes (around 8800 students, teachers and other personnel) from two countries, cluster randomised to LM or SoC. The samples from the pools will be collected and tested using PCR-based techniques. Test results will be combined with questionnaires filled in by children, parents, schoolteachers, and principals, concerning ongoing mitigation measures, their perceived psychological impact and other health and socio-economic information. An ancillary observational study will be carried out to study the prevalence of SARS-CoV-2 in schools, frequencies and size of clusters and attack rates, to compare the effectiveness of the different preventive measures adopted and to evaluate psychological issues in students and teachers in relation to the pandemic’s containment measures. Discussion: By the end of this study, we will have defined and characterised the applicability of the LM for SARS-CoV-2 surveillance, as well as the impact of pandemic preventive measures on children and teachers. Trial registration International Standard Randomised Controlled Trial Number: NCT05396040, 27.05.2022.publishersversionpublishe

Genetic lineage characterization and spatiotemporal dynamics of the recently established Brevihamaparvovirus genus

Copyright © 2022 Elsevier B.V. All rights reserved.The analysis of the viruses allocated to the recently established Brevihamaparvovirus genus (Parvoviridae family), which includes all previously known brevidensoviruses, has not yet been carried out on an extensive basis. As a result, no detailed genetic lineage characterization has ever been performed for this group of insect-specific viruses. Using a wide range of molecular tools, we have explored this taxon by calculating Shannon entropy values, intra- and inter-taxon genetic distances, analysed sequence polymorphisms, and evaluated selective pressures acting on the viral genome. While the calculated Brevihamaparvovirus mutation rates were within the range of those of other parvoviruses, their genomes look to be under strong purifying selection, and are also characterized by low diversity and entropy. Furthermore, even though recombination events are quite common among parvoviruses, no evidence of recombination (either intra or intergenic) was found in the Brevihamaparvoviruses sequences analyzed. An extended taxonomic analysis and reevaluation of existing Brevihamaparvoviruses sequences, many still unclassified, was performed using cut-off values defining NS1 identity between viral sequences from the Parvovirus family. Two existing genetic lineages, Dipteran Brevihamaparvovirus 1 and Dipteran Brevihamaparvovirus 2, were rearranged and the creation of a new one, Dipteran Brevihamaparvovirus 3, was suggested. Finally, despite the uncertainties associated with both the time estimates of the most recent common ancestors, which could span from twenty thousand years before the current era to way earlier (in the last century), and the dispersal routes proposed for Brevihamaparvoviruses sequences by phylodynamic reconstruction, the analyses here presented could help define how future studies should be conducted as more isolates continue to be identified in the future, and contribute to eliminating possible analytical biases.publishersversionpublishe

Readdressing the genetic diversity and taxonomy of the Mesoniviridae family, as well as its relationships with other nidoviruses and putative mesonivirus-like viral sequences

Copyright © 2022 Elsevier B.V. All rights reserved.Research on the recently established Mesoniviridae family (Order Nidovirales), RNA genome insect-specific viruses, has been steadily growing in the last decade. However, after the last detailed phylogenetic characterization of mesoniviruses in 2014, numerous new sequences, even in organisms other than mosquitos, have been identified and characterized. In this study, we analyzed nucleotide and protein sequences of mesoniviruses with a wide range of molecular tools including genetic distance, Shannon entropy, selective pressure analysis, polymorphism identification, principal coordinate analysis, likelihood mapping and phylodynamic reconstruction. We also sought to revaluate new mesoniviruses sequence positions within the family, proposing a taxonomic revision. The different sub-lineages of mosquito mesoniviruses sequences presented low sequence diversity and entropy, with incongruences to the existing taxonomy being found after an extensive phylogenetic characterization. High sequence discrepancy and differences in genome organization were found between mosquito mesoniviruses and other mesoniviruses, so their future classification, as other meso-like viruses that are found in other organisms, should be approached with caution. No evidence of frequent recombination was found, and mesonivirus genomes seem to evolve under strong purifying selection. Insufficient data by root-to-tip analysis did not yet allow for an adequate phylogeographic reconstruction.publishersversionpublishe

Marine Conservation in the Azores: Evaluating Marine Protected Area Development in a Remote Island Context

In the Archipelago of the Azores, over 110,000 km2 of marine areas presently benefit from some form of protection, including a suite of coastal habitats, offshore areas, seamounts, hydrothermal vents, and large parcels of mid-ocean ridge. These areas are integrated in the recently established network of marine protected areas (MPAs), which stands as the cornerstone of Azorean marine conservation policies. This article describes and analyses the process of MPA establishment in the Azores and the current network of protected areas. Three phases of MPA development are identified, progressing from individual MPA establishment with little scientific support in the 1980s, the increasing scope of scientific research during the 1990s under European Union initiatives and the gradual implementation of an MPA network in the 2000s. Expert critical evaluation of the contemporary situation demonstrates that this network must be integrated within a wider regional marine management strategy, with MPA success being contingent upon the implementation of management plans, appropriate enforcement and monitoring, and bridging gaps in scientific knowledgeThisworkispartoftheresearchproject“2020:toward ecosystem-basedmanagementoftheAzoresmarine resources,biodiversityandhabitatsM2.1.2/I/026/2011.” FCT/MCTESprovidedindividualfundingsupporttoRA (SFRH/BD/46621/2008),ACwassupportedbyProgram InvestigadorFCT(IF/00029/2014/CP1230/CT0002)from FCTandPA(Ciência2007and2008).IMAR-DOP/UAz isResearchandDevelopmentunitno.531andLARSyS- AssociatedLaboratoryno.9fundedbythePortuguese FoundationforScienceandTechnology(FCT)through FCT—Pest/OE/EEI/LA0009/2011–2014(COMPETE,QERN, andOE)andbytheAzoresFundScienceandTechnology (FRTC)Pro-ConvergenciaandRAA

Monitoring invasive macroalgae in southern Portugal: drivers and citizen science contribution

Under certain environmental and oceanographic conditions, macroalgae can overgrow and accumulate in massive quantities on beaches, causing serious ecological and economic impacts. To address this problem, a citizen science monitoring platform was created to determine the spatial and temporal distribution of macroalgae accumulations along the beaches of Algarve in southern Portugal, with the aim to assess the extent of beach-cast events and their relationship with abiotic factors. A Redundancy Analysis (RDA) and a permutational analysis of variance (PERMANOVA) were carried out to explore the relationship between macroalgae accumulation level and the abiotic variables: sea surface temperature, wind speed, wind direction, currents, maximum sea level, significant wave height, salinity, nitrate, ammonium, phosphate, precipitation and radiation. The citizen science campaign showed great participation, resulting in 404 submissions between July 2021 and September 2023. The campaign revealed that three species of macroalgae accumulated on the beaches of Algarve, Ulva sp. (with the presence of Ectocarpales and Dyctiotales) along the sandy eastern coast, and the invasive species Asparagopsis armata and Rugulopteryx okamurae in the rocky central and western beaches, respectively. The accumulations of R. okamurae increased from 2021 to 2023, were registered throughout the year and were more abundant than those of Ulva sp. and A. armata, which were only observed in spring and summer. The highest levels of R. okamurae beach-cast depositions were related to strong wave conditions, and high sea surface temperature and salinity. The accumulation of Ulva sp. was related to high sea surface temperature and salinity whereas A. armata was also correlated with winds parallel to the shore (NW-W). PERMANOVA analysis revealed that sea surface temperature and wave conditions had a significant effect on the overall abundance of macroalgae beach-cast accumulations. Overall, our citizen science campaign effectively involved the public, leading to the collection of important data on monitoring macroalgae accumulations. Through these findings, we were able to pinpoint the environmental, atmospheric, and hydrodynamic factors that contribute to their development, movement, and buildup along the Algarve coastlines.NUTRISAFE project (AAC No. 41/ALG/2020—Project No. 072583—NUTRISAFE); LA/P/0101/2020info:eu-repo/semantics/publishedVersio

inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis

This deposit is composed by the main article plus the supplementary materials of the publication.Tuberculosis is currently the second highest cause of death from infectious diseases worldwide. The emergence of multi and extensive drug resistance is threatening to make tuberculosis incurable. There is growing evidence that the genetic diversity of Mycobacterium tuberculosis may have important clinical consequences. Therefore, combining genetic, clinical and socio-demographic data is critical to understand the epidemiology of this infectious disease, and how virulence and other phenotypic traits evolve over time. This requires dedicated bioinformatics platforms, capable of integrating and enabling analyses of this heterogeneous data.Instituto Gulbenkian de Ciência, Programa Nacional de Luta contra a Tuberculose, Instituto Nacional de Saúde Ricardo Jorge, Administração Regional de Saúde de Lisboa e Vale do Tejo

HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments

<p>Abstract</p> <p>Background</p> <p>N-linked glycosylation is a major mechanism for minimizing virus neutralizing antibody response and is present on the Human Immunodeficiency Virus (HIV) envelope glycoprotein. Although it is known that glycosylation changes can dramatically influence virus recognition by the host antibody, the actual contribution of compartmental differences in N-linked glycosylation patterns remains unclear.</p> <p>Methodology and Principal Findings</p> <p>We amplified the <it>env </it>gp120 C2-V5 region and analyzed 305 clones derived from plasma and other compartments from 15 HIV-1 patients. Bioinformatics and Bayesian network analyses were used to examine N-linked glycosylation differences between compartments. We found evidence for cellspecific single amino acid changes particular to monocytes, and significant variation was found in the total number of N-linked glycosylation sites between patients. Further, significant differences in the number of glycosylation sites were observed between plasma and cellular compartments. Bayesian network analyses showed an interdependency between N-linked glycosylation sites found in our study, which may have immense functional relevance.</p> <p>Conclusion</p> <p>Our analyses have identified single cell/compartment-specific amino acid changes and differences in N-linked glycosylation patterns between plasma and diverse blood leukocytes. Bayesian network analyses showed associations inferring alternative glycosylation pathways. We believe that these studies will provide crucial insights into the host immune response and its ability in controlling HIV replication <it>in vivo</it>. These findings could also have relevance in shielding and evasion of HIV-1 from neutralizing antibodies.</p

Are immigrants more vulnerable to the socioeconomic impact of COVID-19? A cross-sectional study in Amadora Municipality, Lisbon metropolitan area

Funding Information: The project was funded by a grant from the Portuguese Science and Technology Foundation (FCT), RESEARCH4COVID19, reference 065, co-financed by FAMI funds reference PT/2018/FAMI/350, and by Saúde Global e Medicina Tropical, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa, Portugal, ref. UID/04413/2020. Publisher Copyright: Copyright © 2022 O. Martins, Shaaban, Abecasis, Muggli, Amado, Vaz, Dias, Silva and Fronteira.Introduction: Immigrants carry an extra burden of morbidities and mortalities since the beginning of the coronavirus disease 2019 (COVID-19) pandemic. Pre-existing inequalities among immigrants may threaten their economic wellbeing during the pandemic. This study analyzed the socioeconomic impact of COVID-19 on immigrants and natives living in Amadora, Metropolitan Region of Lisbon and the extent to which preexisting inequalities had been exacerbated during the pandemic. Materials and methods: This cross-sectional study was conducted in Amadora Municipality, Lisbon Region, through phone interviews and using a structured questionnaire. Data collected in July 2020, included information on a cohort of 420 households, of which 51% were immigrants. To evaluate the socioeconomic position and economic wellbeing changes occurring during the pandemic we estimate crude and adjusted odds ratio (OR) and 95% CI, using Portuguese natives as the reference group. Results: Overall, 287 (70%) participants responded to the questionnaire, of which 47% are immigrants. Preexisting socioeconomic inequalities were exacerbated during the pandemic. Compared with natives, immigrants were more likely to experience job loss, temporary lay-off, and income loss during the COVID-19 pandemic. Immigrants were also more likely to face several kinds of financial hardship during the pandemic, such as difficulties in buying food, hygiene products, and paying bills. Conclusion: To the best of our knowledge, this study is the first to capture the direct socioeconomic impact of COVID-19 among immigrants and natives in Portugal. It highlights the bidirectional relation between inequalities deeply rooted among immigrants and COVID-19. Socioeconomic inequalities affect local patterns of COVID-19 burden, as confirmed in previous studies, but COVID-19 also has an impact on the economic wellbeing of Amadora immigrants during the pandemic. Urgent policies must be implemented to mitigate the economic burden of COVID-19 among immigrants, namely in Amadora, Lisbon Region.publishersversionpublishe