Inclusão de etapa de pós-processamento determinístico para aumento de performance do relacionamento (linkage) probabilístico

The objective of the present study was to demonstrate the application of a deterministic post-processing step, based on similarity measures, to increase the performance of the probabilistic relationship with and without the clerical review. The databases used in the study were the Information System of Notifiable Diseases and the Mortality Information System in the period from 2007 to 2015 of the municipality of Palmas, Tocantins, Brazil. The probabilistic software used was OpenRecLink; a deterministic post-processing step was developed and applied to the data obtained by three different probabilistic matching strategies. The three strategies were compared to each other and added to the deterministic post-processing step. The sensitivity of the probabilistic strategies without manual revision varied between 69.1% and 77.8%, while the same strategies, added to the deterministic post-processing step, ranged from 92.9% to 96.3%. The sensitivity of two probabilistic strategies with manual revision was similar to those obtained by the deterministic post-processing step. However, the number of pairs destined for manual revision by the two probabilistic strategies varied between 1,177 and 1,132 registers, against 149 and 145 after the post-processing step. Our results suggest that the deterministic postprocessing step is a promising option both to increase sensitivity and to reduce the number of pairs that need to be revised manually or even to eliminate their need.O objetivo do presente estudo foi demonstrar a aplicação de uma etapa de pós-processamento determinístico, baseada em medidas de similaridade, para aumentar a performance do relacionamento probabilístico com e sem a etapa de revisão manual. As bases de dados utilizadas no estudo foram o Sistema de Informações de Agravos de Notificação e o Sistema de Informação Sobre Mortalidade no período de 2007 a 2015 do município de Palmas, Tocantins. O software probabilístico utilizado foi o OpenRecLink; foi desenvolvida e aplicada uma etapa de pós-processamento determinístico aos dados obtidos por três diferentes estratégias de pareamento probabilístico. As três estratégias foram comparadas entre si e acrescidas da etapa de pós-processamento determinístico. A sensibilidade das estratégias probabilísticas sem revisão manual variou entre 69,1% e 77,8%, enquanto que as mesmas estratégias, acrescidas da etapa de pós-processamento determinístico, tiveram uma variação entre 92,9% e 96,3%. A sensibilidade de duas estratégias probabilísticas com revisão manual foi semelhante aos obtidos pela etapa de pós-processamento determinístico, no entanto o número de pares destinados a revisão manual pelas duas estratégias probabilísticas variou entre 1.177 e 1.132 registros, contra 149 e 145 após a etapa de pós-processamento determinístico. Nossos resultados sugerem que a etapa de pós-processamento determinístico é uma opção promissora, tanto para aumentar a sensibilidade quanto para reduzir o número de pares que precisam ser revisados manualmente, ou mesmo para eliminar sua necessidade

Repercussões da emergência do vírus Zika na saúde da população do estado do Tocantins, 2015 e 2016: estudo descritivo

Objective. To describe the occurrence of Zika and its complications in the state of Tocantins and in its capital, the city of Palmas. Methods. Descriptive study using data from Official Information Systems. Results. The incidence of reported cases of Zika in 2015 and 2016 was 295.2/100,000 and 411.1/100,000 inhabitants, respectively and 5.9/1000 and 27.8/1000 NV in pregnant women. Higher risks occurred in women, age 20-39 years, municipalities in the central and northwestern regions and hotter months (February and March). The incidence of Zika-related microcephaly at pregnancy was 0.06/1000 NV. One case of Guillain Barré Syndrome resulting from Zika virus infection has been confirmed. Conclusion. Zika virus fever has hit Tocantins intensely. However, their adverse outcomes have been less frequent than in others states.Objetivo. Descrever a ocorrência da febre pelo vírus Zika (ZIKV) e suas complicações no estado do Tocantins e em sua capital, Palmas. Métodos. Estudo descritivo, utilizando dados dos sistemas de informações em saúde. Resultados. A incidência de casos notificados de febre pelo ZIKV, em 2015 e 2016, foi de 295,2/100 mil e 411,1/100 mil habitantes na população geral, e de 5,9/1000 e 27,8/1000 nascidos vivos em gestantes, respectivamente. Maiores riscos ocorreram em mulheres, nas idades de 20-39 anos, nos municípios das regiões central e noroeste do estado, durante os meses mais quentes (fevereiro e março). A incidência de microcefalia relacionada à infecção pelo ZIKV na gestação foi de 0,06/1000 nascidos vivos. Foi confirmado um caso de síndrome de Guillain-Barré decorrente da infecção pelo ZIKV. Conclusão. A febre pelo ZIKV atingiu o Tocantins intensamente, embora seus desfechos adversos tenham sido menos frequentes que em outros estados

Inclusão de etapa de pós-processamento determinístico para o aumento de performance do relacionamento (linkage) probabilístico

O objetivo do presente estudo foi demonstrar a aplicação de uma etapa de pós-processamento determinístico, baseada em medidas de similaridade, para aumentar a performance do relacionamento probabilístico com e sem a etapa de revisão manual. As bases de dados utilizadas no estudo foram o Sistema de Informação de Agravos de Notificação e o Sistema de Informações sobre Mortalidade, no período de 2007 a 2015, do Município de Palmas, Tocantins, Brasil. O software probabilístico utilizado foi o OpenRecLink; foi desenvolvida e aplicada uma etapa de pós-processamento determinístico aos dados obtidos por três diferentes estratégias de pareamento probabilístico. As três estratégias foram comparadas entre si e acrescidas da etapa de pós-processamento determinístico. A sensibilidade das estratégias probabilísticas sem revisão manual variou entre 69,1% e 77,8%, já as mesmas estratégias, acrescidas da etapa de pós-processamento determinístico, apresentaram uma variação entre 92,9% e 96,3%. A sensibilidade de duas estratégias probabilísticas com revisão manual foi semelhante à obtida pela etapa de pós-processamento determinístico, no entanto, o número de pares destinados à revisão manual pelas duas estratégias probabilísticas variou entre 1.177 e 1.132 registros, contra 149 e 145 após a etapa de pós-processamento determinístico. Nossos resultados sugerem que a etapa de pós-processamento determinístico é uma opção promissora, tanto para aumentar a sensibilidade quanto para reduzir o número de pares que precisam ser revisados manualmente, ou mesmo para eliminar sua necessidade

Repercussions of Zika virus emergency on the health of the population of Tocantins state, Brazil, 2015 and 2016: a descriptive study

Objective To describe the occurrence of Zika virus disease and its complications in the state of Tocantins and in its capital, the city of Palmas. Methods This was a descriptive study using data from health information systems. Results Incidence of reported Zika virus disease cases in 2015 and 2016 was 295.2/100,000 inhabitants and 411.1/100,000 inhab. in the general population, and 5.9/1,000 and 27.8/1,000 live births, respectively. Higher risks occurred in women, the 20-39 year age group, municipalities in the central and northwestern regions of the state and in hotter months (February and March). Incidence of Zika-related microcephaly during pregnancy was 0.06/1,000 live births. One case of Guillain-Barré Syndrome resulting from Zika virus infection was confirmed. Conclusion Zika virus disease hit Tocantins intensely, although its adverse outcomes were less frequent than in other states

Wuhan large pig roundworm virus identified in human feces in Brazil

We report here the complete genome sequence of a bipartite virus, herein denoted WLPRV/human/BRA/TO-34/201, from a sample collected in 2015 from a two-year-old child in Brazil presenting acute gastroenteritis. The virus has 98-99% identity (segments 2 and 1, respectively) with the Wuhan large pig roundworm virus (unclassified RNA virus) that was recently discovered in the stomachs of pigs from China. This is the first report of a Wuhan large pig roundworm virus detected in human specimens, and the second genome described worldwide. However, the generation of more sequence data and further functional studies are required to fully understand the ecology, epidemiology, and evolution of this new unclassified virus.FAPESPCNPqAdolfo Lutz Inst, Virol Ctr, Enter Dis Lab, Av Dr Arnaldo 355, BR-01246902 Sao Paulo, SP, BrazilFed Univ Para, Inst Biol Sci, Belem, Para, BrazilFac Med ABC, Postgrad Program Hlth Sci, Santo Andre, BrazilUniv Fed Sao Paulo, Retrovirol Lab, Sao Paulo, SP, BrazilUniv Sao Paulo, Fac Med, LIM 46, Sao Paulo, BrazilFed Univ Tocantins, Palmas, Tocantins, BrazilPubl Hlth Lab Tocantins State LACEN TO, Palmas, BrazilUniv Sao Paulo, Inst Trop Med, Av Dr Eneas de Carvalho Aguiar 470, BR-05403000 Sao Paulo, SP, BrazilBlood Syst Res Inst, San Francisco, CA USAUniv Calif San Francisco, Dept Lab Med, San Francisco, CA 94143 USAUniv Fed Sao Paulo, Retrovirol Lab, Sao Paulo, SP, BrazilFAPESP: 2015/12944-9FAPESP: 2017/00021-9FAPESP: 2016/01735-2CNPq: 400354/2016-0Web of Scienc

Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus.

Plasma from patients with dengue-like symptoms was collected in 2013 to 2016 from the Brazilian states of Tocantins and Amapa. 781 samples testing negative for IgM against Dengue, Zika, and Chikungunya viruses and for flaviviruses, alphaviruses and enteroviruses RNA using RT-PCRs were analyzed using viral metagenomics. Viral particles-associated nucleic acids were enriched, randomly amplified, and deep sequenced in 102 mini-pools generating over 2 billion reads. Sequence data was analyzed for the presence of known and novel eukaryotic viral reads. Anelloviruses were detected in 80%, human pegivirus 1 in 19%, and parvovirus B19 in 17% of plasma pools. HIV and enteroviruses were detected in two pools each. Previously uncharacterized viral genomes were also identified, and their presence in single plasma samples confirmed by PCR. Chapparvovirus and ambidensovirus genomes, both in the Parvoviridae family, were partially characterized showing 33% and 34% identity in their NS1 sequences to their closest relative. Molecular surveillance using pre-existing plasma from febrile patients provides a readily scalable approach for the detection of novel, potentially emerging, viruses

Genomic constellation of human Rotavirus A strains identified in Northern Brazil: a 6-year follow-up (2010-2016)

Surveillance of Rotavirus A (RVA) throughout the national territory is important to establish a more complete epidemiological-molecular scenario of this virus circulation in Brazil. The aim of the present study was to investigate the genetic diversity of RVA strains circulating in Tocantins State (Northern Brazil) during six years of post-vaccination followup (2010-2016). A total of 248 stool samples were screened by next generation sequencing and 107 (43.1%) nearly full length RVA genome sequences were obtained; one sample was co-infected with two RVA strains (G2/G8P[4]). Six G and P genotypes combinations were detected: G12P[8] strains (78.6%), as well as the G3P[8] (9.3%) and G1P[8] (0.9%) were associated with a Wa-like genogroup backbone. All G2P[4] (5.6%) and G8P[4] (2.8%) strains, including the mixed G2/G8P[4] infection (0.9%) showed the DS-1-like genetic background. The two G12P[4] strains (1.9%) were associated with distinct genetic backbones: Wa-like and DS-1-like. The phylogenetic analysis revealed the circulation of lineages G1-I, G2-IV, G3-III, G8-I and G12-III, and P[4]-V and P[8]-III of the VP7 and VP4 genes, respectively. Conserved clustering pattern and low genetic diversity were observed regarding VP1-VP3 and VP6, as well as NSP1-5 segments. We identified the same RVA circulation pattern reported in other Brazilian regions in the period of 2010-2016, suggesting that rural and low-income areas may not have a different RVA genotypic distribution compared to other parts of the country. The unique presentation of whole-genome data of RVA strains detected in the Tocantins State provides a baseline for monitoring variations in the genetic composition of RVA in this area

Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis

Metagenomics based on the next-generation sequencing (NGS) technique is a target-independent assay that enables the simultaneous detection and genomic characterization of all viruses present in a sample. There is a limited amount of data about the virome of individuals with gastroenteritis (GI). In this study, the enteric virome of 250 individuals (92% were children under 5 years old) with GI living in the northeastern and northern regions of Brazil was characterized. Fecal samples were subjected to NGS, and the metagenomic analysis of virus-like particles (VLPs) identified 11 viral DNA families and 12 viral RNA families. As expected, the highest percentage of viral sequences detected were those commonly associated with GI, including rotavirus, adenovirus, norovirus (94.8%, 82% and 71.2%, respectively). The most common co-occurrences, in a single individual, were the combinations of rotavirus-adenovirus, rotavirus-norovirus, and norovirus-adenovirus (78%, 69%, and 62%, respectively). In the same way, common fecal-emerging human viruses were also detected, such as parechovirus, bocaporvirus, cosavirus, picobirnavirus, cardiovirus, salivirus, and Aichivirus. In addition, viruses that infect plants, nematodes, fungi, protists, animals, and arthropods could be identified. A large number of unclassified viral contigs were also identified. We show that the metagenomics approach is a powerful and promising tool for the detection and characterization of different viruses in clinical GI samples

New Variants of Squash Mosaic Viruses Detected in Human Fecal Samples

Squash mosaic virus (SqMV) is a phytovirus that infects great diversity of plants worldwide. In Brazil, the SqMV has been identified in the states of Ceará, Maranhão, Piauí, Rio Grande do Norte, and Tocantins. The presence of non-pathogenic viruses in animals, such as phytoviruses, may not be completely risk-free. Similarities in gene repertories between these viruses and viruses that affect animal species have been reported. The present study describes the fully sequenced genomes of SqMV found in human feces, collected in Tocantins, and analyzes the viral profile by metagenomics in the context of diarrhea symptomatology. The complete SqMV genome was obtained in 39 of 253 analyzed samples (15.5%); 97.4% of them belonged to children under 5 years old. There was no evidence that the observed symptoms were related to the presence of SqMV. Of the different virus species detected in these fecal samples, at least 4 (rotavirus, sapovirus, norovirus, parechovirus) are widely known to cause gastrointestinal symptoms. The presence of SqMV nucleic acid in fecal samples is likely due to recent dietary consumption and it is not evidence of viral replication in the human intestinal cells. Identifying the presence of SqMV in human feces and characterization of its genome is a relevant precursor to determining whether and how plant viruses interact with host cells or microorganisms in the human gastrointestinal tract

High Heterogeneity of Echoviruses in Brazilian Children with Acute Gastroenteritis

Echoviruses (E) are a diverse group of viruses responsible for various pathological conditions in humans including aseptic meningitis, myocarditis, and acute flaccid paralysis. The detection and identification of echovirus genotypes in clinical samples is challenging due to its high genetic diversity. Here, we report the complete genome sequences of nine echoviruses, obtained by next-generation sequencing of 238 fecal samples from individuals with gastroenteritis in regions of Brazil. Detected viruses were classified into six genotypes: Three E1 sequences (BRA/TO-028, BRA/TO-069 and BRA/TO-236), one E3 (BRA/TO-018), one E11 (BRA/TO-086), one E20 (BRA/TO-016), two E29 (BRA/TO-030 and BRA/TO-193), and one E30 sequence (BRA/TO-032). Phylogenetic analysis indicated that the echoviruses E1 and E29 circulating in Brazil are divergent from strains circulating worldwide. The genotype diversity identified in our study may under-represent the total echovirus diversity in Brazil because of the small sample size and the restricted geographical distribution covered by the survey