Group A rotavirus genotypes and the ongoing Brazilian experience: a review

Brazil was the first Latin American country to introduce universal group A rotavirus (RV-A) vaccination in March 2006, resulting in a unique epidemiological scenario. Since RV-A first identification in Brazil, 2,691 RV-A-positive stool samples, collected between 1982- 2007, were typed by independent research groups throughout the country. In the pre-vaccination era, 2,492 RV-A-positive samples collected from 1982-2005 were successfully typed, while 199 samples were analyzed from 2006-2007. According to the reviewed studies, there were two important times in the pre-vaccination era: (i) the period from 1982-1995, during which the detection of G5P[8] RV-A, in addition to the classical genotypes G1-4, challenged vaccine development programs; and (ii) the period from 1996-2005, during which genotype G9P[8] emerged, following a global trend. The rate of G2P[4] RV-A detection decreased from 26% (173/653) during 1982-1995 to 2% (43/1,839) during 1996-2005. The overall detection rate of RV-A genotypes from 1982-2005 was as follows: 43% (n = 1,079) G1P[8]/G1P[not typed (NT)]; 20% (n = 488) G9P[8]/G9P[NT]; 9% (n = 216) G2P[4]/G2P[NT]; 6% (n = 151) G3P[8]/G3P[NT]; 4% (n = 103) G4P[8]/G4P[NT]; and 4% (n = 94) G5P[8]/G5P[NT]. Mixed infections accounted for 189 (7%) of the positive samples, while atypical G/P combinations or other genotypes, including G6, G8, G10 and G12, were identified in 172 (7%) samples. The initial surveillance studies carried out in several Brazilian states with RV-A-positive samples collected in 2006 and 2007 show a predominance of G2P[4] strains (148/199 or 74%). Herein, we review RV-A typing studies carried out since the 1980s in Brazil, highlighting the dynamics of RV-A strain circulation profiles before and early after universal use of RV-A vaccine in Brazil.

Molecular detection of human astrovirus in an urban sewage treatment plant in Rio de Janeiro, Brazil

The objective of this study was to evaluate the prevalence and dissemination of human astroviruses (HAstV) in the environment by analyzing urban sewage samples from a wastewater treatment plant in the city of Rio de Janeiro, Brazil. A one-year study was performed with a total of 48 raw and treated sewage composite samples, which were collected biweekly from an activated sludge plant. Virus particles were concentrated by the adsorption-elution method using negatively charged membranes associated to a Centriprep Concentrator® 50 (Nihon Millipore). HAstV were detected in 16.7% of the samples in raw and treated sewage by using both qualitative and quantitative reverse transcriptase-polymerase chain reactions (RT-PCR and qPCR, respectively). Positive untreated sewage sample exhibited mean values of 1.1 x 10(4) gEq/mL. The qPCR sensitivity was 18 gEq/reaction. Through utilization of qPCR, a HAstV recovery efficiency of 4.2% and 4.3% was demonstrated for raw and treated sewage samples, respectively. The presence of HAstV in both the raw and treated sewage samples demonstrated the dissemination of these viruses in the environment as well as viral permanence after sewage treatment. There was a reduction in the total and faecal coliform levels, indicating efficiency of the wastewater treatment plant.

The circulation of human astrovirus genotypes in the Central West Region of Brazil

Out of 1,588 faecal samples of children taken from three locations of the Central West Region of Brazil, 57 were positive for astroviruses (HAstVs) using reverse transcription-polymerase chain reaction (RT-PCR). They were genotyped by nested RT-PCR and/or genomic sequencing. HAstV-1 (42.8%), HAstV-2 (23.2%), HAstV-3 (3.6%), HAstV-4 (14.3%) and HAstVs -5, -6, -7 and -8 (1.8% each) were detected. In Goiânia and Campo Grande, HAstV-1 was the most frequently detected genotype while in Brasília (DF) it was HAstV-2. Shifts in the circulation of astrovirus genotypes were observed in DF and Campo Grande. All samples collected by rectal swabs were viral negative. The astrovirus genotypes were detected in all age groups and there was no correlation between genotype and age group.

Molecular characterization of adenoviruses from children presenting with acute respiratory disease in Uberlândia, Minas Gerais, Brazil, and detection of an isolate genetically related to feline adenovirus

Human adenoviruses (HAdV) are a major cause of acute respiratory diseases (ARD), gastroenteritis, conjunctivitis and urinary infections. Between November 2000-April 2007, a total of 468 nasopharyngeal aspirate samples were collected from children with ARD at the Clinics Hospital of Uberlândia. These samples were tested by immunofluorescence assay (IFA) and 3% (14/468) tested positive for the presence of HAdV. By performing polymerase chain reaction (PCR) to detect HAdV DNA in samples that tested negative or inconclusive for all viruses identifiable by IFA (respiratory syncytial virus, parainfluenza viruses 1, 2 and 3, influenza viruses A and B and HAdV), as well as negative for rhinoviruses by reverse transcription-PCR, additional 19 cases were detected, for a total of 33 (7.1%) HAdV-positive samples. Nucleotide sequences of 13 HAdV samples were analyzed, revealing that they belonged to species B, C and E. Further analyses showed that species C (HAdV-2) was the most prevalent among the sequenced samples. To our knowledge, this is the first report describing the presence of HAdV-4 in Brazil. We also detected an isolate that was 100% identical to a part of the feline adenovirus hexon gene sequence.

Rotavirus A genotype G1P[8]: a novel method to distinguish wild-type strains from the Rotarix® vaccine strain

Rotaviruses are important enteric pathogens for humans and animals. Group A rotaviruses (RV-A) are the most common agents of severe gastroenteritis in infants and young children and vaccination is the most effective method to reduce RV-A-associated diseases. G1P[8], the most prevalent RV-A genotype worldwide, is included in the RV-A vaccine Rotarix®. The discrimination between wild-type G1P[8] and vaccine G1P[8] strains is an important topic in the study of RV-A epidemiology to manage outbreaks and to define control measures for vaccinated children. In this study, we developed a novel method to segregate the wild-type and vaccine strains using restriction endonucleases. The dsRNA from the Rotarix® vaccine was sequenced and the NSP3 gene was selected as the target gene. The vaccine strain has a restriction pattern that is different than that of wild-type RV-A G1P[8] isolates after digestion with the restriction endonuclease BspHI. This pattern could be used as a marker for the differentiation of wild-type G1P[8] strains from the vaccine strain.

Genetic diversity of noroviruses in Brazil

Norovirus (NoV) infections are a major cause of acute gastroenteritis outbreaks around the world. In Brazil, the surveillance system for acute diarrhoea does not include the diagnosis of NoV, precluding the ability to assess its impact on public health. The present study assessed the circulation of NoV genotypes in different Brazilian states by partial nucleotide sequencing analysis of the genomic region coding for the major capsid viral protein. NoV genogroup II genotype 4 (GII.4) was the prevalent (78%) followed by GII.6, GII.7, GII.12, GII.16 and GII.17, demonstrating the great diversity of NoV genotypes circulating in Brazil. Thus, this paper highlights the importance of a virological surveillance system to detect and characterize emerging strains of NoV and their spreading potential.

Detection of enteric viruses in recreational waters of an urban lagoon in the city of Rio de Janeiro, Brazil

The aim of this study was to determine the occurrences of the group A rotavirus (RVA), norovirus (NoV) and human adenovirus (HAdV) in the surface waters of an urban lagoon (Rodrigo de Freitas Lagoon) in the city of Rio de Janeiro, Brazil. During one year of surveillance, water samples were obtained from the lagoon and other interconnected ecosystems (river and beach). The samples were concentrated using an adsorption-elution method with a negatively charged membrane and tested by qualitative and quantitative polymerase chain reaction assays. RVA was the most prevalent virus detected (24.3%) with a viral load ranging from 3.0 x 10¹-5.6 x 10(4) genome copies/L, followed by NoV (18.8%) and HAdV (16.7%). Considering water samples suitable for bathing, according to Escherichia coli criterion (< 2,000 most probable number/100 mL), viruses were detected in 50% (57/114) of them. Physicochemical parameters were also measured and showed possible correlations between turbidity and RVA presence and between pH and NoV presence. These data demonstrate the importance of considering viral parameters to ensure water quality and the utilisation of these parameters as additional tools for the characterisation of environmental contamination.

Genotyping of gastroenteric viruses in hospitalised children: first report of norovirus GII.21 in Brazil

This retrospective study (April-September 2003) was designed to investigate the roles of the main viruses responsible for cases of acute infantile gastroenteritis in hospitalised children up to two years of age. The viruses were identified in 64.7% (88/136) of the cases and the detection rates of rotavirus A (RVA), norovirus (NoV) and astrovirus were 41.9% (57/136), 30.3% (24/79) and 12.7% (7/55), respectively. RVA and NoV were detected in 20 of the 24 reported nosocomial infection cases. This study identified the first circulation of the genotype NoV GII.21 in Brazil and highlights the need to establish differential diagnoses through active laboratorial surveillance.

A non-enteric adenovirus A12 gastroenteritis outbreak in Rio de Janeiro, Brazil

A gastroenteritis outbreak that occurred in 2013 in a low-income community in Rio de Janeiro was investigated for the presence of enteric viruses, including species A rotavirus (RVA), norovirus (NoV), astrovirus (HAstV), bocavirus (HBoV), aichivirus (AiV), and adenovirus (HAdV). Five of nine stool samples (83%) from patients were positive for HAdV, and no other enteric viruses were detected. Polymerase chain reaction products were sequenced and subjected to phylogenetic analysis, which revealed four strains and one strain of non-enteric HAdV-A12 and HAdV-F41, respectively. The HAdV-A12 nucleotide sequences shared 100% nucleotide similarity. Viral load was assessed using a TaqMan real-time PCR assay. Stool samples that were positive for HAdV-A12 had high viral loads (mean 1.9 X 107 DNA copies/g stool). All four patients with HAdV-A12 were < 25 months of age and had symptoms of fever and diarrhoea. Evaluation of enteric virus outbreaks allows the characterisation of novel or unique diarrhoea-associated viruses in regions where RVA vaccination is routinely performed.

Estruturas de governança e recursos estratégicos em destilarias do estado do Paraná: uma análise a partir da complementaridade da ECT e da VBR

Neste artigo, apresenta-se como objetivo compreender como se configuram as estruturas de governança, ao se considerarem custos de transação (ECT) e recursos estratégicos (VBR), nas relações envolvendo produtores e processadores em destilarias no estado do Paraná. Sua compreensão justifica-se quando se tem em vista a forte interdependência produtiva dessas partes. Para tanto, realizou-se uma pesquisa qualitativa, descritiva e de corte transversal, com perspectiva longitudinal. O estudo envolveu entrevistas semiestruturadas com gerentes agrícolas e produtores contratados de cinco, das sete, destilarias presentes no estado do Paraná. Os resultados demonstraram forte tendência para estruturas tendendo à integração vertical, que se dão, em sua expressiva maioria, por meio de parceria do tipo arrendamento. A segunda opção de arranjo organizacional tem sido o contrato de parceria agrícola, seguido pelo contrato de fornecimento. A integração vertical e o mercado não são normalmente empregados. Em relação aos recursos estratégicos capazes de gerar vantagens competitivas para as destilarias, a localização e a distância média das propriedades contratadas foram os mais citados. Além desses, a capacidade de expansão (devido a fertilidade do solo, abundância de áreas mecanizáveis e ausência de competidores), a transparência, bem como a reputação, a fidelidade, a tradição e o conhecimento foram outros recursos estratégicos identificados. A complementaridade é ratificada a partir da consideração de que os recursos e capacidades internos das destilarias, tais como localização, distância, conhecimento, entre outros, influenciam na escolha de estruturas de governança mais integradas verticalmente. Essas, por sua vez, são escolhidas para explorar, proteger e obter vantagens competitivas por meio do controle obtido sobre esses recursos.

Colêmbolos (Hexapoda: Collembola) como bioindicadores de qualidade do solo em áreas com Araucaria angustifolia

Não existem informações sobre a diversidade de colêmbolos associados às florestas com Araucaria angustifolia (Bert.) O. Kuntze no Brasil. Este estudo teve o objetivo de avaliar o potencial da diversidade de famílias de colêmbolos como bioindicadores da qualidade do solo e para separar diferentes áreas com araucária, utilizando atributos químicos e microbiológicos do solo como variáveis explicativas. O estudo foi realizado em quatro áreas: 1. floresta nativa com predominância de araucária (NF); 2. reflorestamento de araucária (R); 3. reflorestamento de araucária submetido a incêndio acidental (RF); e 4. pastagem natural com araucárias nativas e ocorrência de incêndio acidental (NPF). Na captura dos organismos, utilizaram-se dez armadilhas, distribuídas ao acaso em cada área, nos mesmos pontos de coleta dos atributos químicos e microbiológicos do solo. O número de colêmbolos de cada família, extraído por armadilhas (abundância), o índice de diversidade de Shannon (H) e a riqueza de famílias foram submetidos à Análise de Variância (ANOVA). A abundância de cada família de Collembola foi submetida à Análise de Componentes Principais (ACP). Considerando as quatro áreas, foram identificadas oito famílias de colêmbolos (Brachystomellidae, Entomobryidae, Hypogastruridae, Isotomidae, Katiannidae, Paronellidae, Sminthuridae e Tomoceridae). A diversidade de famílias de colêmbolos foi maior nas áreas NF e R, em comparação com as áreas RF e NPF. Os atributos químicos e microbiológicos do solo foram eficientes como variáveis explicativas, pois auxiliaram na interpretação das modificações das famílias de colêmbolos. A ACP mostrou que a identificação ao nível de família de Collembola é suficiente para separar as áreas estudadas, além de indicar quais foram as famílias de colêmbolos mais associadas a cada área, o que possibilita sua utilização como bioindicadores de intervenções antrópicas, bem como da qualidade do solo.

Behavioral avoidance tests to evaluate effects of cattle slurry and dairy sludge application to soil¹

The application of organic wastes to agricultural soils is not risk-free and can affect soil invertebrates. Ecotoxicological tests based on the behavioral avoidance of earthworms and springtails were performed to evaluate effects of different fertilization strategies on soil quality and habitat function for soil organisms. These tests were performed in soils treated with: i) slurry and chemical fertilizers, according to the conventional fertilization management of the region, ii) conventional fertilization + sludge and iii) unfertilized reference soil. Both fertilization strategies contributed to soil acidity mitigation and caused no increase in soil heavy metal content. Avoidance test results showed no negative effects of these strategies on soil organisms, compared with the reference soil. However, results of the two fertilization managements differed: Springtails did not avoid soils fertilized with dairy sludge in any of the tested combinations. Earthworms avoided soils treated with sludge as of May 2004 (DS1), when compared with conventional fertilization. Possibly, the behavioral avoidance of earthworms is more sensitive to soil properties (other than texture, organic matter and heavy metal content) than springtails

Macrofauna Edáfica e Atributos Físicos e Químicos em Sistemas de Uso do Solo no Planalto Catarinense

RESUMO O uso do solo pode alterar processos como decomposição da matéria orgânica, ciclagem de nutrientes e agregação das partículas e, com isso, influenciar a ocorrência da macrofauna. Objetivou-se com este estudo relacionar os sistemas de uso do solo e os efeitos deles sobre a distribuição de grupos da macrofauna do solo, bem como a relação desses com os atributos físicos e químicos do solo. Os sistemas de uso do solo avaliados foram: floresta nativa, reflorestamento de eucalipto, pastagem, integração lavoura-pecuária e lavoura com sistema plantio direto. As amostras foram coletadas em uma grade de amostragem de 3 × 3, totalizando nove pontos, distanciados entre si em 30 m, no inverno e verão, em três municípios do Planalto Sul-catarinense, considerados réplicas verdadeiras. As avaliações foram de atributos físicos e químicos do solo e da abundância e diversidade da macrofauna, coletada pelo método Tropical Soil Biology and Fertility (TSBF). Os organismos do solo são pertencentes a 16 grupos taxonômicos, com 4.702 indivíduos m-2 no inverno e 7.438 indivíduos m-2 no verão. Houve interação entre época e sistemas de uso do solo, com flutuação populacional dos organismos dependente do uso e com relação aos atributos físicos e químicos do solo, evidenciada pela análise de redundância, que apresentou alta correlação entre variáveis ambientais e fauna do solo. As mudanças na composição da macrofauna do solo foram observadas nos seus sistemas de uso, que tiveram maior intervenção antrópica. Floresta nativa, reflorestamento de eucalipto e pastagem são mais estáveis em termos de biodiversidade da macrofauna do solo, quando comparados com áreas agrícolas com plantio direto e integração lavoura-pecuária.

Mapeamento da condutividade elétrica e relação com a argila de Latossolo sob plantio direto

O objetivo deste trabalho foi mapear e avaliar a variabilidade espacial da condutividade elétrica do solo (CE), obtida por meio de sensor de contato de campo, num Latossolo Vermelho distroférrico, sob plantio direto de grãos, e relacionar a CE com os teores de argila medidos pelo método do densímetro, em amostras georreferenciadas de solo. As amostras foram coletadas numa área de 13 ha, por meio de uma grade de 40x40 m e de grades de 20x20 m, 10x10 m e 5x5 m. A continuidade espacial da CE e do teor de argila foi modelada com o uso de semivariogramas. A CE variou de 1,9 a 13,7 mS m-1, com valor médio de 5,2 mS m-1 e coeficiente de variação de 48%. O mapa interpolado mostrou tendência de aumento da CE com o aumento dos teores de argila. Os coeficientes de determinação foram de 0,78 e 0,77 entre CE e teor de argila, camadas 0-5 e 5-10 cm, respectivamente. O mapa da CE reflete suficientemente a variação espacial dos teores de argila para uso na delimitação de zonas de manejo.

Comportamento do NDVI obtido por sensor ótico ativo em cereais

O objetivo deste trabalho foi avaliar, com um sensor ótico ativo, o comportamento do índice de vegetação por diferença normalizada (NDVI - "normalized difference vegetation index"), nas culturas de trigo, triticale, cevada e milho. Cinco experimentos foram conduzidos no Paraná e São Paulo, com variação de classes de solo, doses e fontes de N, e variedades de trigo. As seguintes variáveis foram avaliadas: NDVI, teor de N foliar, matéria seca e produtividade das culturas. Análises de regressões foram realizadas entre as doses de N aplicadas e NDVI, teor de N foliar, matéria seca e produtividade. Análises de correlação entre as variáveis foram realizadas. O trigo, triticale e cevada apresentaram resposta às aplicações de doses crescentes de N, pelo aumento nas leituras do NDVI, no teor de N foliar e na produtividade. Medido pelo sensor ótico ativo utilizado, o NDVI apresenta alto potencial para manejo do N nas culturas do trigo, triticale e cevada, e baixo potencial para a cultura do milho. Há interferência das variedades de trigo nas leituras do sensor ótico ativo.