A wastewater-based epidemiology tool for COVID-19 surveillance in Portugal

Funding: Strategic funding of Fundação para a Ciência e a Tecnologia (FCT), Portugal, to cE3c and BioISI Research Units ( UIDB/00329/2020 and UIDB/04046/2020 ] is also gratefully acknowledged. This work was supported by Programa Operacional de Competitividade e Internacionalização (POCI) (FEDER component), Programa Operacional Regional de Lisboa , and Programa Operacional Regional do Norte (Project COVIDETECT, ref. 048467 ).The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater produced interest in its use for sentinel surveillance at a community level and as a complementary approach to syndromic surveillance. With this work, we set the foundations for wastewater-based epidemiology (WBE) in Portugal by monitoring the trends of SARS-CoV-2 RNA circulation in the community, on a nationwide perspective during different epidemiological phases of the pandemic. The Charité assays (E_Sarbecco, RdRP, and N_Sarbecco) were applied to monitor, over 32-weeks (April to December 2020), the dynamics of SARS-CoV-2 RNA at the inlet of five wastewater treatment plants (WWTP), which together serve more than two million people in Portugal. Raw wastewater from three Coronavirus disease 2019 (COVID-19) reference hospitals was also analyzed during this period. In total, more than 600 samples were tested. For the first weeks, detection of SARS-CoV-2 RNA was sporadic, with concentrations varying from 103 to 105 genome copies per liter (GC/L). Prevalence of SARS-CoV-2 RNA increased steeply by the end of May into late June, mainly in Lisboa e Vale do Tejo region (LVT), during the reopening phase. After the summer, with the reopening of schools in mid-September and return to partial face-to-face work, a pronounced increase of SARS-CoV-2 RNA in wastewater was detected. In the LVT area, SARS-CoV-2 RNA load agreed with reported trends in hotspots of infection. Synchrony between trends of SARS-CoV-2 RNA in raw wastewater and daily new COVID-19 cases highlights the value of WBE as a surveillance tool, particularly after the phasing out of the epidemiological curve and when hotspots of disease re-emerge in the population which might be difficult to spot based solely on syndromic surveillance and contact tracing. This is the first study crossing several epidemiological stages highlighting the long-term use of WBE for SARS-CoV-2.PostprintPeer reviewe

Investigation of 15q11-q13, 16p11.2 and 22q13 CNVs in Autism Spectrum Disorder Brazilian Individuals with and without Epilepsy

Copy number variations (CNVs) are an important cause of ASD and those located at 15q11-q13, 16p11.2 and 22q13 have been reported as the most frequent. These CNVs exhibit variable clinical expressivity and those at 15q11-q13 and 16p11.2 also show incomplete penetrance. In the present work, through multiplex ligation-dependent probe amplification (MLPA) analysis of 531 ethnically admixed ASD-affected Brazilian individuals, we found that the combined prevalence of the 15q11-q13, 16p11.2 and 22q13 CNVs is 2.1% (11/531). Parental origin could be determined in 8 of the affected individuals, and revealed that 4 of the CNVs represent de novo events. Based on CNV prediction analysis from genome-wide SNP arrays, the size of those CNVs ranged from 206 kb to 2.27 Mb and those at 15q11-q13 were limited to the 15q13.3 region. In addition, this analysis also revealed 6 additional CNVs in 5 out of 11 affected individuals. Finally, we observed that the combined prevalence of CNVs at 15q13.3 and 22q13 in ASD-affected individuals with epilepsy (6.4%) was higher than that in ASD-affected individuals without epilepsy (1.3%; p<0.014). Therefore, our data show that the prevalence of CNVs at 15q13.3, 16p11.2 and 22q13 in Brazilian ASD-affected individuals is comparable to that estimated for ASD-affected individuals of pure or predominant European ancestry. Also, it suggests that the likelihood of a greater number of positive MLPA results might be found for the 15q13.3 and 22q13 regions by prioritizing ASD-affected individuals with epilepsy.Support was provided by FAPESP-INCT - grant number: 2008/57899-7; FAPESP-CEPID - grant number: 2013/08028-1; CNPq [http://www.fapesp.br/]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Analysis of distributed algorithms for scheduling in Data Grids

É um resultado conhecido que em Data Grids, onde o processamento envolve grandes quantidades de dados, pode ser mais eficaz escalonar os processos para execução nos sites que já dispõem dos dados do que transferir os dados para um site onde o processo que irá necessitar deles foi escalonado. Os estudos existentes se baseiam em pequenas quantidades de sites, com conhecimento centralizado sobre o estado dos diversos sites. Essa opção não é escalável para Grids com grande número de participantes. Este trabalho analisa versões distribuídas com informação local para os algoritmos de escalonamento de processo e replicação de dados, mostrando o efeito das topologias de interconexão de sites no desempenho desses. É observado que, considerando a existência apenas de informações locais devido às restrições topologicas, resultados diferentes quanto aos melhores algoritmos de escalonamento de processos e replicação de dados são encontrados.It is a known result that in Data Grids, where the processing involves large amounts of data, can be more effective schedule processes to run on sites that already have the data than transfering data to a site where the process that will require them was installed. The existing studies are based on small numbers of sites, with centralized knowledge about the state of the various sites. This option is not scalable for grids with large numbers of participants. This paper will propose distributed versions with local information for process scheduling algorithms and data replication, showing the effect of interconnect topologies on the performance of these sites. It is observed that, considering the existence of only local information due to topological constraints, different results related to the best scheduling algorithms and data replication processes are found

Avaliação de citocinas pró e anti-inflamatórias e de fatores pró e anti-angiogênicos em placenta de gestantes com pré-eclâmpsia

A pré-eclâmpsia é uma síndrome específica da gestação humana, caracterizada por hipertensão arterial e proteinúria após a 20ª. semana de gestação. É aceito que esta patologia tem origem na placenta. O fator de crescimento placentário (PlGF) tem importante papel no desenvolvimento vascular durante a invasão trofoblástica e, citocinas de perfil Th2 podem estar envolvidas na manutenção da gestação durante a interação materno-fetal.O presente trabalho avaliou a concentração de citocinas e de fatores pró e anti-angiogênicos em homogenato de placenta, obtido de gestantes normais e com pré-eclâmpsia, correlacionando esses parâmetros com a gravidade da doença e com a idade gestacional.Foram estudadas 70 gestantes, sendo 30 normotensas e 40 portadoras de pré-eclâmpsia. As gestantes com pré-eclâmpsia foram classificadas de acordo com o aparecimento das manifestações clínicas em pré-eclâmpsia precoce (< 34 semanas de gestação, n=13) e pré-eclâmpsia tardia (≥ 34 semanas de gestação, n=27). Um fragmento de placenta foi obtido imediatamente após o parto, homogeneizado em solução salina tamponada com fosfatos e submetido à centrifugação. O sobrenadante obtido foi empregado para determinação de fator de necrose tumoral-alfa (TNF-a), fator estimulador de colônias de granulócitos e macrófagos (GM-CSF), interleucina-10 (IL-10), fator de crescimento e transformação beta (TGF-b1), fator de crescimento placentário (PlGF) e Endostatina por ensaio imunoenzimático (ELISA). Outro fragmento placentário foi obtido para análise histopatológica. As diferenças entre os grupos de gestantes normais e com préeclâmpsia foram avaliadas por teste t de Student, com nível de significância de 5%.Os níveis de TNF-a, Endostatina e GM-CSF detectados na placenta de gestantes com pré-eclâmpsia foram significativamente maiores em relação às gestantes...Preeclampsia is a human pregnancy-specific syndrome characterized by the onset of hypertension and proteinuria after the 20th gestational week. It is widely accepted that this disorder is placental in origin. Placental growth factor (PlGF) plays an important role in the vascular development during trophoblast invasion and cytokines with Th2 profile may be involved in gestation maintenance and promoting a balance in maternal– fetal interaction. This study investigated the concentration of cytokines, angiogenic and anti-angiogenic factors in placental homogenate obtained from normotensive and preeclamptic pregnant women, and correlated these parameters with disease severity and gestational age.The subjects were 70 pregnant women of whom 30 were normotensive pregnant, and 40 were pregnant women with preeclampsia. The preeclamptic pregnant women were classified according to the onset of clinical manifestations in early-onset (< 34 weeks of gestation, n=13) and late-onset (≥ 34 weeks of gestation, n=27) preeclampsia. A tissue fragment of the placenta was obtained immediately after delivery, homogenized with phosphate-buffered saline solution and centrifuged. Separated supernatant was employed for determination of tumor necrosis factor alpha (TNF-a), granulocyte-macrophage colony-stimulating factor (GM-CSF) Interleukin-10 (IL-10), transforming growth factor beta (TGF-b1), placental growth factor (PlGF), and Endostatin, by enzyme-linked immunosorbent assay (ELISA). Another placental tissue segment was prepared for histopathological analysis. Differences between groups were evaluated by Student t unpaired test with significance set at p < 0.05.The levels of TNF-a, Endostatin and GM-CSF detected in placenta of preeclamptic women were significantly increased when compared with the normotensive pregnant women. On the other hand, the concentration of IL-10, TGF-b1 and PlGF have shown... (Complete abstract click electronic access below)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Newborn Screening for 5q Spinal Muscular Atrophy: Comparisons between Real-Time PCR Methodologies and Cost Estimations for Future Implementation Programs

Since the approval of modifying therapies for Spinal Muscular Atrophy (SMA), several protocols aiming to screen SMN1 homozygous deletion in a neonatal context have been published. However, no work has compared different methodologies along with detailed implementation costs for centers where the neonatal screening of SMA has not yet been implemented. Therefore, our work compared different qualitative real-time PCR approaches for SMA screening and the estimated costs of test implementation. Using Brazilian blood samples, the presence and absence (P/A) and melt curve protocols were analyzed. MLPA was used as a confirmatory test. The costs were calculated for the simplex and multiplex tests plus equipment. The test workflow was based on the present experience and literature report. The accuracy of the P/A protocol was 1 (95% CI 0.8677−1) using dried blood spots (DBS). The melt curve protocol also achieved 100% concordance. The consumable costs ranged from USD 1.68 to 4.42 and from USD 2.04 to 12.76 per reaction, for the simplex and multiplex tests, respectively. The equipment acquisition costs ranged from USD 44,817.07 to 467,253.10, with several factors influencing this value presented. Our work presents a framework for decision-making, with a project demonstration of the different assays that will be useful in dealing with the issues of cost and availability of reagents. Moreover, we present a literature review and discussion of important concerns regarding treatment policies. We take the first step towards a future SMA NBS pilot program where it is not yet a reality

CONEXÃO HÍDRICA ENTRE AS CAVERNAS QUARTZÍTICAS BROMÉLIAS e MARTIMIANO II, NA SERRA DE IBITIPOCA, MG: HYDRIC CONNECTION BETWEEN THE BROMELIA AND MARTIMIANO II QUARTZITE CAVES, IN THE IBITIPOCA MOUNTAIN RANGE, MG

Defining cave systems and underground water flows when human passage is impossible requires the use of specific techniques such as hydrochemistry and fluorescent dye tracers application, which are widely used methodologies in karst environments. The Ibitipoca State Park (Parque Estadual do Ibitipoca PEIB) is in a speleological district with a high number of registered siliciclastic rock caves in a relatively small area (1,488 ha), the highest density of large siliciclastic rock caves in Brazil. Therefore, this work aims to determine the possible water connection of the two largest caves in the PEIB waterflows, the Martimiano II Cave (the country's largest quartzite cave) and the Bromélias Cave. This was done by hydrogeochemical analysis and the fluorescent tracer technique, consequently defining the probable largest quartzite system in Brazil, with approximately 7.5 km of underground conduits.Definir sistemas de cavernas e fluxos hídricos subterrâneos quando a passagem humana é impossibilitada faz-se necessário o uso de técnicas específicas como hidroquímica e a aplicação de corantes traçadores fluorescentes, que são metodologias amplamente usadas em ambientes cársticos. O Parque Estadual do Ibitipoca (PEIB) está em um distrito espeleológico com elevado número de cavidades em rochas siliciclásticas cadastradas em uma área relativamente pequena (1.488 ha), a maior densidade de cavernas em rochas siliciclásticas de grande porte do Brasil. Sendo assim, este trabalho busca determinar a possível conexão hídrica das drenagens das duas maiores cavernas do PEIB, a Gruta Martimiano II (a maior caverna em quartzito do país) e a Gruta das Bromélias, por meio da análise hidrogeoquímica e da técnica de traçadores fluorescentes, consequentemente definindo o provável maior sistema quartzítico do Brasil, com aproximadamente 7,5 km de condutos subterrâneos

A wastewater-based epidemiology tool for COVID-19 surveillance in Portugal

The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater produced interest in its use for sentinel surveillance at a community level and as a complementary approach to syndromic surveillance. With this work, we set the foundations for wastewater-based epidemiology (WBE) in Portugal by monitoring the trends of SARS-CoV-2 RNA circulation in the community, on a nationwide perspective during different epidemiological phases of the pandemic. The Charité assays (E_Sarbecco, RdRP, and N_Sarbecco) were applied to monitor, over 32-weeks (April to December 2020), the dynamics of SARS-CoV-2 RNA at the inlet of five wastewater treatment plants (WWTP), which together serve more than two million people in Portugal. Raw wastewater from three Coronavirus disease 2019 (COVID-19) reference hospitals was also analyzed during this period. In total, more than 600 samples were tested. For the first weeks, detection of SARS-CoV-2 RNA was sporadic, with concentrations varying from 103 to 105 genome copies per liter (GC/L). Prevalence of SARS-CoV-2 RNA increased steeply by the end of May into late June, mainly in Lisboa e Vale do Tejo region (LVT), during the reopening phase. After the summer, with the reopening of schools in mid-September and return to partial face-to-face work, a pronounced increase of SARS-CoV-2 RNA in wastewater was detected. In the LVT area, SARS-CoV-2 RNA load agreed with reported trends in hotspots of infection. Synchrony between trends of SARS-CoV-2 RNA in raw wastewater and daily new COVID-19 cases highlights the value of WBE as a surveillance tool, particularly after the phasing out of the epidemiological curve and when hotspots of disease re-emerge in the population which might be difficult to spot based solely on syndromic surveillance and contact tracing. This is the first study crossing several epidemiological stages highlighting the long-term use of WBE for SARS-CoV-2.info:eu-repo/semantics/publishedVersio

A wastewater-based epidemiology tool for COVID-19 surveillance in Portugal

The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater produced interest in its use for sentinel surveillance at a community level and as a complementary approach to syndromic surveillance. With this work, we set the foundations for wastewater-based epidemiology (WBE) in Portugal by monitoring the trends of SARS-CoV-2 RNA circulation in the community, on a nationwide perspective during different epidemiological phases of the pandemic. The Charité assays (E_Sarbecco, RdRP, and N_Sarbecco) were applied to monitor, over 32-weeks (April to December 2020), the dynamics of SARS-CoV-2 RNA at the inlet of five wastewater treatment plants (WWTP), which together serve more than two million people in Portugal. Raw wastewater from three Coronavirus disease 2019 (COVID-19) reference hospitals was also analyzed during this period. In total, more than 600 samples were tested. For the first weeks, detection of SARS-CoV-2 RNA was sporadic, with concentrations varying from 103 to 105 genome copies per liter (GC/L). Prevalence of SARS-CoV-2 RNA increased steeply by the end of May into late June, mainly in Lisboa e Vale do Tejo region (LVT), during the reopening phase. After the summer, with the reopening of schools in mid-September and return to partial face-to-face work, a pronounced increase of SARS-CoV-2 RNA in wastewater was detected. In the LVT area, SARS-CoV-2 RNA load agreed with reported trends in hotspots of infection. Synchrony between trends of SARS-CoV-2 RNA in raw wastewater and daily new COVID-19 cases highlights the value of WBE as a surveillance tool, particularly after the phasing out of the epidemiological curve and when hotspots of disease re-emerge in the population which might be difficult to spot based solely on syndromic surveillance and contact tracing. This is the first study crossing several epidemiological stages highlighting the long-term use of WBE for SARS-CoV-2