Decline in hepatitis B and C prevalence among hemodialysis patients in Tocantins, Northern Brazil

Infection control measures have been responsible for a decline in the prevalence of hepatitis B virus (HBV) and hepatitis C virus (HCV) infections in hemodialysis patients. In Brazil, these measures have been in place since 1996. The aim of this study was to evaluate the current HBV and HCV epidemiology among hemodialysis patients in the State of Tocantins comparing them with those found 14 years ago. There was a significant decline in hepatitis B surface antigen (HBsAg) and anti-HCV prevalence from 4% and 13% in 2001 to 0.8% and 2.8% in 2014-2015, respectively (p < 0.05). Variables related to hemodialysis environment such as working shift and length of time on hemodialysis treatment were no longer associated to HCV and HBV exposure in 2014-2015. A high prevalence of self-reported hepatitis B vaccination was observed in both periods, but only 30% of the individuals showed serological profile of effective previous immunization, suggesting a low compliance with surveillance of hepatitis B immunization in hemodialysis centers. The significant decline in viral hepatitis B and C prevalence in hemodialysis patients in Tocantins underscores the importance of infection control measures, but the low frequency of protective serological profile after immunization against hepatitis B points to the need for greater vigilance of the patients’ vaccination

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

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

ATLANTIC EPIPHYTES: a data set of vascular and non-vascular epiphyte plants and lichens from the Atlantic Forest

Epiphytes are hyper-diverse and one of the frequently undervalued life forms in plant surveys and biodiversity inventories. Epiphytes of the Atlantic Forest, one of the most endangered ecosystems in the world, have high endemism and radiated recently in the Pliocene. We aimed to (1) compile an extensive Atlantic Forest data set on vascular, non-vascular plants (including hemiepiphytes), and lichen epiphyte species occurrence and abundance; (2) describe the epiphyte distribution in the Atlantic Forest, in order to indicate future sampling efforts. Our work presents the first epiphyte data set with information on abundance and occurrence of epiphyte phorophyte species. All data compiled here come from three main sources provided by the authors: published sources (comprising peer-reviewed articles, books, and theses), unpublished data, and herbarium data. We compiled a data set composed of 2,095 species, from 89,270 holo/hemiepiphyte records, in the Atlantic Forest of Brazil, Argentina, Paraguay, and Uruguay, recorded from 1824 to early 2018. Most of the records were from qualitative data (occurrence only, 88%), well distributed throughout the Atlantic Forest. For quantitative records, the most common sampling method was individual trees (71%), followed by plot sampling (19%), and transect sampling (10%). Angiosperms (81%) were the most frequently registered group, and Bromeliaceae and Orchidaceae were the families with the greatest number of records (27,272 and 21,945, respectively). Ferns and Lycophytes presented fewer records than Angiosperms, and Polypodiaceae were the most recorded family, and more concentrated in the Southern and Southeastern regions. Data on non-vascular plants and lichens were scarce, with a few disjunct records concentrated in the Northeastern region of the Atlantic Forest. For all non-vascular plant records, Lejeuneaceae, a family of liverworts, was the most recorded family. We hope that our effort to organize scattered epiphyte data help advance the knowledge of epiphyte ecology, as well as our understanding of macroecological and biogeographical patterns in the Atlantic Forest. No copyright restrictions are associated with the data set. Please cite this Ecology Data Paper if the data are used in publication and teaching events. © 2019 The Authors. Ecology © 2019 The Ecological Society of Americ

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

EPIDEMIOLOGICAL AND MOLECULAR STUDY OF HEPATITIS B VIRUS INFECTION IN AFRO-DESCENDANTS FROM ISOLATED COMMUNITY IN GOIÁS STATE (KALUNGAS)

Made available in DSpace on 2014-07-29T15:26:23Z (GMT). No. of bitstreams: 1 Tese Marcia Alves Dias Matos.pdf: 1405580 bytes, checksum: cff6253aff8dbc7e48a7a6c687cebfa0 (MD5) Previous issue date: 2007-12-18Hepatitis B virus (HBV) infection occurs throughout the world. In Africa, this infection is highly endemic, with the majority of individuals becoming infected during childhood. Although Brazil has been globally considered a country of HBV intermediate endemicity, variable rates have been found in all five Brazilian regions and even inside the same region. This study aimed to investigate the epidemiological and molecular profile of the HBV infection among the Kalunga population in Goiás, Central Brazil, which is considered the largest Afro-Brazilian isolated community. A total of 878 individuals were interviewed about sociodemographic characteristics, risk factors and HBV vaccination. Blood samples were collected from all participants and serum samples were screened by enzyme-linked immunosorbent assay for the presence of HBsAg, anti-HBc and anti-HBs serological markers. HBsAg-positive samples were submitted to HBeAg and anti-HBe detection. HBsAg and anti-HBc positive samples were tested for HBV DNA detection by polymerase chain reaction and genotyping by subsequent restriction fragment length polymorphism (RFLP) analysis and nucleotide sequencing of preS/S region. The overall prevalence of HBV infection was 35.4% (95% CI: 32.3-38.7). HBsAg carrier rate was 1.8% (95% CI: 1.1- 3.0). Multivariate analysis of risk factors showed that increased age, male gender, illiteracy and history of multiple sexual partners were associated with this infection. Isolated anti-HBs was found in 301 (34.3%) individuals who were immune for hepatitis B. HBV DNA was detected in 75% (12/16) of the HBsAg positive samples, in 100% (2/2) of the HBeAg and in 83.3% (10/12) of the anti-HBe positive samples. An occult HBV infection rate of 1.7% (5/295) was found among anti-HBc positive individuals. All genotyped isolates belonged to genotype A by RFLP analysis. Nucleotide sequencing of preS/S region confirmed the circulation of genotype A (subgenotype Aa) in this community. The epidemiological findings indicate that preventive measures, such as additional health education and HBV vaccination programs, are needed to control HBV infection in this population. In addition, the molecular results suggest the introduction of genotype A, subgenotype Aa in Brazil from Africa during the slave trade.infecção pelo vírus da hepatite B (HBV) apresenta distribuição mundial. Na África, é altamente endêmica, sendo a maioria dos indivíduos infectada durante a infância. Embora o Brasil seja considerado um país de endemicidade intermediária, taxas variadas de prevalência têm sido encontradas nas cinco regiões geográficas e mesmo dentro de uma mesma região. Este estudo teve como objetivo investigar o perfil epidemiológico e molecular da infecção pelo HBV na população Kalunga em Goiás, Brasil Central, que é considerada a maior comunidade afro-descendente isolada no Brasil. Um total de 878 indivíduos foi entrevistado sobre características sócio-demográficas, fatores de risco e vacinação contra hepatite B. Amostras sanguíneas foram coletadas de todos os participantes e os soros triados para detecção dos marcadores HBsAg, anti-HBc total e anti-HBs por ensaio imunoenzimático. As amostras HBsAg positivas foram submetidos à detecção dos marcadores HBeAg e anti-HBe. O DNA viral foi detectado nas amostras HBsAg e anti-HBc reagentes pela reação da polimerase em cadeia, sendo as amostras HBV DNA positivas genotipadas pela análise do polimorfismo de comprimento dos fragmentos de restrição (RFLP) e sequenciamento da região Pré-S/S. A prevalência global da infecção pelo HBV foi de 35,4% (IC 95% 32,3-38,7), sendo de 1,8% (IC 95% 1,1-3,0) para o HBsAg. A análise multivariada mostrou que aumento da idade, gênero masculino, analfabetismo e história de múltiplos parceiros sexuais foram fatores associados a esta infecção. Em 301 (34,3%) indivíduos, verificou-se positividade isolada ao marcador anti-HBs, sugerindo imunidade ao HBV. O HBV DNA foi detectado em 75% (12/16) das amostras HBsAg reagentes, em 100% (2/2) das HBeAg e 83,3% (10/12) das anti-HBe positivas. Um índice de 1,7% (5/295) para infecção oculta pelo HBV foi encontrado nos indivíduos anti-HBc reagentes. Todas as amostras genotipadas por RFLP foram do genótipo A. O sequenciamento da região Pré-S/S confirmou a circulação do genótipo A (subgenótipo Aa) nesta comunidade. Os achados epidemiológicos indicam que medidas preventivas, como programas de educação em saúde e de vacinação contra hepatite B, são necessárias para o controle da infecção pelo HBV nesta população. Além disso, os resultados moleculares sugerem que o genótipo A, subgenótipo Aa foi introduzido no Brasil durante o tráfico de escravos da África