Genomic and epidemiological characterisation of a dengue virus outbreak among blood donors in Brazil.

Outbreaks caused by Dengue, Zika and Chikungunya viruses can spread rapidly in immunologically naïve populations. By analysing 92 newly generated viral genome sequences from blood donors and recipients, we assess the dynamics of dengue virus serotype 4 during the 2012 outbreak in Rio de Janeiro. Phylogenetic analysis indicates that the outbreak was caused by genotype II, although two isolates of genotype I were also detected for the first time in Rio de Janeiro. Evolutionary analysis and modelling estimates are congruent, indicating a reproduction number above 1 between January and June, and at least two thirds of infections being unnoticed. Modelling analysis suggests that viral transmission started in early January, which is consistent with multiple introductions, most likely from the northern states of Brazil, and with an increase in within-country air travel to Rio de Janeiro. The combination of genetic and epidemiological data from blood donor banks may be useful to anticipate epidemic spread of arboviruses

Genótipos e resistência transmitida aos medicamentos do HIV entre doadores de sangue soropositivos no Brasil: papel dos doadores infectados como populações sentinelas para vigilância molecular do HIV

Background: There are few surveillance studies analyzing genotypes or primary (transmitted) drug resistance in HIV-infected blood donors in Brazil. The aim of this study was to characterize patterns of HIV genotypes and primary resistance among HIV seropositive donors identified at 4 geographically dispersed blood centers in Brazil. Methods: All HIV-infected donors who returned for counseling at the 4 REDS-II Hemocenters in Brazil from January 2007 to March 2011 were invited to participate in a case–control study involving a questionnaire on risk factors. Viral sequencing was also offered to positive cases to assign genotypes and to detect and characterize primary resistance to reverse transcriptase and protease inhibitors according to World Health Organization guidelines. Results: Of the 341 HIV seropositive donors who consented to participate in the risk factor and genetics study, pol sequences were obtained for 331 (97%). Clade B was predominant (76%) followed by F (15%) and C (5%). Primary resistance was present in 36[12.2%, 95% confidence interval (CI) 8.2 to 15.5] of the 303 individuals not exposed to antiretroviral therapy, varying from 8.2 %( 95% CI: 2.7 to 13.6) in Recife to 19.4% in São Paulo (95% CI: 9.5 to 29.2); there were no significant correlations with other demographics or risk factors. Conclusions: Although subtype B remains the most prevalent genotype in all 4 areas, increasing rates of subtype C in Sao Paulo and F in Recife were documented relative to earlier reports. Transmitted drug resistance was relatively frequent, particularly in the city of Sao Paulo which showed an increase compared with previous HIV-seropositive donor data from 10 years.Há poucos estudos de vigilância que analisam genótipos ou resistência primária (transmitida) aos medicamentos em doadores de sangue infectados pelo HIV no Brasil. O objetivo deste estudo foi caracterizar os padrões de genótipos de HIV e resistência primária entre os doadores HIV positivos identificados em quatro hemocentros geograficamente dispersos no Brasil. Métodos: todos os doadores infectados pelo HIV que retornaram para o aconselhamento nos quatro hemocentros REDS-II no Brasil, a partir de janeiro de 2007 a Março de 2011, foram convidados a participar de um estudo caso-controle, envolvendo um questionário sobre fatores de risco. Também foi oferecido o sequenciamento viral para os casos positivos para definir genótipos e para detectar e caracterizar a resistência primária (transmitida) aos inibidores da transcriptase reversa e protease de acordo com as diretrizes da Organização Mundial de Saúde (OMS). Resultados: 341 doadores HIV soropositivos consentiram em participar do estudo fatores de risco e genética. As sequências pol foram obtidas para 331 (97%). A Classe B foi predominante (76%), seguido por F (15%) e C (5%). A resistência primária estava presente em 36 [12,2%, intervalo de confiança de 95% (IC) 8,2-15,5] dos 303 indivíduos não expostos à terapia antirretroviral, variando de 8,2% (IC 95%: 2,7-13,6), em Recife para 19,4%, em São Paulo (IC 95%: 9,5-29,2); não houve correlações significativas e outros fatores de risco demográficos. Conclusões: embora o subtipo B continue a ser o genótipo mais prevalente em todas as quatro áreas, aumentando as taxas de subtipo C, em São Paulo e F, em Recife, que foram documentados em relação a relatórios anteriores. Resistência transmitida aos medicamentos foi relativamente frequente, particularmente na cidade de São Paulo, que apresentou um aumento em comparação aos dados anteriores de doadores soropositivos para o HIV há 10 anos.Dados abertos - Sucupira - Teses e dissertações (2013 a 2016

Use of an automated pyrosequencing technique for confirmation of sickle cell disease.

BackgroundThe diagnosis of sickle cell disease (SCD) is made by hemoglobin assays such as high-performance liquid chromatography (HPLC), isoelectric focusing and cellulose acetate or citrate agar electrophoresis. These assays are easy to perform and used in large-scale newborn screening in many countries. These tests however may not easily differentiate Sβ0 thalassemia from SS or identify other hemoglobin variants, and in this case, hemoglobin (HBB) gene sequencing may be necessary.ObjectivesTo develop a high throughput DNA based confirmatory assay for SCD and to detect mutations in the HBB gene.MethodsWe developed an automated pyrosequencing technique (PyS) based on QIAGEN technology (Hilden, Germany) to detect homozygous or heterozygous hemoglobin S mutations as well as hemoglobin C mutations. The technique was tested on 2,748 samples from patients enrolled in a multi-center SCD cohort in Brazil. Patients were previously tested using HPLC to diagnose SCD as part of routine clinical care. Any subjects with discrepant results between HPLC and PyS or with heterozygous hemoglobin S detected had Sanger sequencing of the HBB gene.ResultsWe identified 168 samples with discrepant results between HPLC and PyS and 100 with concordant PyS = heterozygous S and HPLC, which would suggest SB-thalassemia or other heterozygous S variants. The PyS assay correctly identified 1906 (98.7%) of the 1930 HbSS and 628 (98.7%) of the 636 HbSC samples. Of the 179 remaining samples, PyS correctly indicated S heterozygosis in 165 (92.2%). Of the 165 heterozygous S samples confirmed by Sanger as consistent with Sβ thalassemia genotype, 84 samples were classified as Sβ0 thalassemia and 81 as Sβ+ thalassemia. The most frequent beta thalassemia mutations of Sβ0 and Sβ+ were HBB: c.118C>T (Gln40Stop) and HBB c.92 + 6T> C, respectively.DiscussionThe PyS proved to be satisfactory for large-scale confirmatory testing of hemoglobin mutation. Moreover, with this study we were able to describe the most common β+ and β0 mutations in SCD patients with Sβ-thalassemia in a large multi-institutional SCD cohort in Brazil

Genomic Analyses of Potential Novel Recombinant Human Adenovirus C in Brazil

Human Adenovirus species C (HAdV-C) is the most common etiologic agent of respiratory disease. In the present study, we characterized the nearly full-length genome of one potential new HAdV-C recombinant strain constituted by Penton and Fiber proteins belonging to type 89 and a chimeric Hexon protein of types 1 and 89. By using viral metagenomics techniques, we screened out, in the states of Tocantins and Pará, Northern and North regions of Brazil, from 2010 to 2016, 251 fecal samples of children between 0.5 to 2.5 years old. These children were presenting acute diarrhea not associated with common pathogens (i.e., rotavirus, norovirus). We identified two HAdV-C strains in two distinct patients. Phylogenetic analysis performed using all complete genomes available at GenBank database indicated that one strain (HAdV-C BR-245) belonged to type 1. The phylogenetic analysis also indicated that the second strain (HAdV-C BR-211) was located at the base of the clade formed by the newly HAdV-C strains type 89. Recombination analysis revealed that strain HAdV-C BR-211 is a chimera in which the variable regions of Hexon gene combined HAdV-C1 and HAdV-C89 sequences. Therefore, HAdV-C BR-211 strain possesses a genomic backbone of type HAdV-C89 and a unique insertion of HAdV-C1 in the Hexon sequence. Recombination may play an important driving force in HAdV-C diversity and evolution. Studies employing complete genomic sequencing on circulating HAdV-C strains in Brazil are needed to understand the clinical significance of the presented data

Antiretroviral Drug Resistance in a Respondent-Driven Sample of HIV-Infected Men Who Have Sex With Men in Brazil

Background: There are few studies on HIV subtypes and primary and secondary antiretroviral drug resistance (ADR) in community-recruited samples in Brazil. We analyzed HIV clade diversity and prevalence of mutations associated with ADR in men who have sex with men in all five regions of Brazil.Methods: Using respondent-driven sampling, we recruited 3515 men who have sex with men in nine cities: 299 (9.5%) were HIV-positive; 143 subjects had adequate genotyping and epidemiologic data. Forty-four (30.8%) subjects were antiretroviral therapy-experienced (AE) and 99 (69.2%) antiretroviral therapy-naive (AN). We sequenced the reverse transcriptase and protease regions of the virus and analyzed them for drug resistant mutations using World Health Organization guidelines.Results: the most common subtypes were B (81.8%), C (7.7%), and recombinant forms (6.9%). the overall prevalence of primary ADR resistance was 21.4% (i.e. among the AN) and secondary ADR was 35.8% (i.e. among the AE). the prevalence of resistance to protease inhibitors was 3.9% (AN) and 4.4% (AE); to nucleoside reverse transcriptase inhibitors 15.0% (AN) and 31.0% (AE) and to nonnucleoside reverse transcriptase inhibitors 5.5% (AN) and 13.2% (AE). the most common resistance mutation for nucleoside reverse transcriptase inhibitors was 184V (17 cases) and for nonnucleoside reverse transcriptase inhibitors 103N (16 cases).Conclusions: Our data suggest a high level of both primary and secondary ADR in men who have sex with men in Brazil. Additional studies are needed to identify the correlates and causes of antiretroviral therapy resistance to limit the development of resistance among those in care and the transmission of resistant strains in the wider epidemic.Ministry of Health/Secretariat of Health Surveillance/Department of STD, AIDS and Viral Hepatitis through Brazilian GovernmentMinistry of Health/Secretariat of Health Surveillance/Department of STD, AIDS and Viral Hepatitis through United Nations Office on Drugs and Crime-UNODCDepartment of STD, AIDS and Viral Hepatitis of the Ministry of HealthFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Univ Fed Ceara, Dept Saude Comunitaria, BR-60430971 Fortaleza, Ceara, BrazilUniversidade Federal de São Paulo, São Paulo, BrazilTulane Univ, Sch Publ Hlth & Trop Med, New Orleans, LA USAUniv Fed Minas Gerais, Belo Horizonte, MG, BrazilUniv Fed Bahia, Inst Saude Colet, BR-41170290 Salvador, BA, BrazilUniv Fed Rio de Janeiro, Rio de Janeiro, BrazilUniv Brasilia, BR-70910900 Brasilia, DF, BrazilUniv Calif San Francisco, San Francisco, CA 94143 USAUniv São Paulo, LIM 03, São Paulo, BrazilUniversidade Federal de São Paulo, São Paulo, BrazilMinistry of Health/Secretariat of Health Surveillance/Department of STD, AIDS and Viral Hepatitis through Brazilian Government: AD/BRA/03/H34Ministry of Health/Secretariat of Health Surveillance/Department of STD, AIDS and Viral Hepatitis through United Nations Office on Drugs and Crime-UNODC: AD/BRA/03/H34Department of STD, AIDS and Viral Hepatitis of the Ministry of Health: CSV 234/07FAPESP: 2004/15856-9CAPES: BEX 3495/06-0Web of Scienc

NEOTROPICAL ALIEN MAMMALS: a data set of occurrence and abundance of alien mammals in the Neotropics

Biological invasion is one of the main threats to native biodiversity. For a species to become invasive, it must be voluntarily or involuntarily introduced by humans into a nonnative habitat. Mammals were among first taxa to be introduced worldwide for game, meat, and labor, yet the number of species introduced in the Neotropics remains unknown. In this data set, we make available occurrence and abundance data on mammal species that (1) transposed a geographical barrier and (2) were voluntarily or involuntarily introduced by humans into the Neotropics. Our data set is composed of 73,738 historical and current georeferenced records on alien mammal species of which around 96% correspond to occurrence data on 77 species belonging to eight orders and 26 families. Data cover 26 continental countries in the Neotropics, ranging from Mexico and its frontier regions (southern Florida and coastal-central Florida in the southeast United States) to Argentina, Paraguay, Chile, and Uruguay, and the 13 countries of Caribbean islands. Our data set also includes neotropical species (e.g., Callithrix sp., Myocastor coypus, Nasua nasua) considered alien in particular areas of Neotropics. The most numerous species in terms of records are from Bos sp. (n = 37,782), Sus scrofa (n = 6,730), and Canis familiaris (n = 10,084); 17 species were represented by only one record (e.g., Syncerus caffer, Cervus timorensis, Cervus unicolor, Canis latrans). Primates have the highest number of species in the data set (n = 20 species), partly because of uncertainties regarding taxonomic identification of the genera Callithrix, which includes the species Callithrix aurita, Callithrix flaviceps, Callithrix geoffroyi, Callithrix jacchus, Callithrix kuhlii, Callithrix penicillata, and their hybrids. This unique data set will be a valuable source of information on invasion risk assessments, biodiversity redistribution and conservation-related research. There are no copyright restrictions. Please cite this data paper when using the data in publications. We also request that researchers and teachers inform us on how they are using the data