Positive selection results in frequent reversible amino acid replacements in the G protein gene of human respiratory syncytial virus

Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a flipflop phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites.

Avaliação da patogenicidade e da imunidade cruzada de estirpe variante do vírus da bronquite infecciosa aviária isolada no Brasil

Pós-graduação em Medicina Veterinária - FCAV

Caracterização molecular de cepas do vírus respiratório sincicial isoladas de casos de infecção respiratória aguda na cidade de Belém, Pará, Brasil nos anos de 2000 a 2006

As doenças do trato respiratório são as principais queixas nos serviços de atendimento médico, sendo as infecções respiratórias agudas (IRA) as manifestações mais comuns, principalmente em crianças menores de cinco anos de idade. Em países em desenvolvimento as IRA constituem um sério problema de saúde pública. Em todo mundo estima-se que ocorram cerca de dois milhões de mortes devido as IRA a cada ano. Dentre os agentes causais das mesmas, destaca-se o Vírus Respiratório Sincicial (VRS), especialmente por causar doença grave em crianças menores de dois anos. Com o objetivo de gerar dados sobre a epidemiologia molecular deste vírus, foram analisadas amostras colhidas de pacientes com IRA no período de 2000 a 2006 na cidade de Belém, Pará. Foram utilizados testes de imunofluorescência indireta (IFI) para caracterização antigênica dos vírus isolados e RT-PCR para os genes codificadores das proteínas G e F, que foram em seguida parcialmente seqüenciados. Dentro do período estudado, 153 amostras positivas para VRS foram detectadas. A faixa etária de 0-4 anos foi a que concentrou maior número de casos (n=138; 90,19%). Em relação ao perfil sazonal, o pico de atividade do VRS ocorreu nos primeiros seis meses do ano, estando associado principalmente ao período de troca da estação chuvosa para um período de menor pluviosidade. Houve co-circulação dos subgrupos A e B nos anos de 2001 e 2003. Em 2000, 2005 e 2006 somente o subgrupo A circulou. Entretanto no ano de 2004 foi registrada a ocorrência somente do subgrupo B. Dentro do período estudado, genótipos distintos da proteína G do subgrupo A (GA2 e GA5) e do subgrupo B (SAB1 e SAB3) foram detectados, indicando o primeiro relato da circulação do genótipo SAB1 na América do Sul. Em 2004, um cluster diferenciado dos demais genótipos circulantes foi encontrado, sendo este denominado BRB1. A análise do gene codificador da proteína F permitiu a identificação de mutações na sequência nucleotídica resultando em trocas na cadeia aminoacídica da mesma. Este estudo representa o primeiro relato sobre dados da epidemiologia molecular do Vírus Respiratório Sincicial na região Norte do Brasil.

Estudo da ocorrência e perfil de suscetibilidade aos antimicrobianos de Staphylococcus aureus isolados de pacientes e profissionais de saúde na Unidade de Terapia Intensiva de hospital público de Rio Branco-AC

A infecção hospitalar (IH) é um grave problema de saúde pública, principalmente em pacientes internados em Unidade de Terapia Intensiva (UTI), devido à gravidade do quadro clínico, uso constante de antimicrobianos e frequência do emprego de procedimentos invasivos. O Staphylococcus aureus (S. aureus) é um dos principais patógenos que coloniza indivíduos saudáveis e responde também, por infecções em pacientes hospitalizados. O presente estudo objetivou a identificação do perfil de suscetibilidade, principais sítios acometidos por infecção e possíveis fatores de risco associados à infecção ou colonização por S. aureus isolados de pacientes e profissionais de saúde da UTI de Hospital de Urgência e Emergência de Rio Branco (HUERB) – Acre. Foi desenvolvido um estudo transversal no período de janeiro a agosto de 2009. Para pesquisa de portadores, foram coletadas amostras biológicas da microbiota dos pacientes e profissionais de saúde. Para o levantamento de casos de pacientes com IH, foram coletadas amostras biológicas dos sítios suspeitos de estarem acometidos, a partir de 72 horas da data de sua admissão, até alta, transferência ou óbito. Dos 62 pacientes inseridos nos estudo, 19,3% foram portadores e 6,4% desenvolveram IH por S. aureus; e dos 35 profissionais, 28,6% foram portadores de S. aureus. Foi a segunda espécie bacteriana mais isolada de pacientes portadores e a quinta mais isolada de casos de IH. Não houve comprovação estatística para as variáveis abordadas no estudo serem consideradas fatores de risco para aquisição de IH por S. aureus. Os sítios anatômicos acometidos por IH por S. aureus foram o trato respiratório (n=2), seguido de corrente sanguínea (n=1). A amostra ponta de cateter foi responsável por 1 isolado. Um (1,6%) paciente desenvolveu IH por MRSA; e 5 (8,1%) pacientes e 2 (5,7%) profissionais foram portadores de MRSA, ocorrência baixa quando se relaciona com os resultados do restante do Brasil e do mundo. Destaca-se ainda, a incidência do MSSA sobre o MRSA e a baixa resistência dos MRSA aos antimicrobianos, demonstrando que na UTI do HUERB, as IH por S. aureus ainda não se constituem um problema de saúde pública. Não houve isolados de S. aureus resistentes à vancomicina, podendo ser considerada uma opção terapêutica para os casos de IH por MRSA. Vale ressaltar a importância desse estudo no Estado do Acre, por constituir o primeiro desta natureza em UTI, envolvendo S. aureus e MRSA.

Ocorrência do metapneumovírus humano nas infecções respiratórias agudas em estados da região nordeste do Brasil

As doenças do trato respiratório são responsáveis por uma significativa taxa de absenteísmo laboral bem como por elevados índices de morbidade e morte, entre as quais as infecções respiratórias aguda (IRA) representam as maiores queixas nos serviços de atendimento médico-ambulatorial em todo o mundo. Os vírus são considerados os principais agentes etiológicos das IRA, atuando seja como patógeno principal ou predispondo às infecções bacterianas secundárias, entre eles encontra-se o Metapneumovirus Humano (HMPV). Este vírus foi identificado em 2001 apresentando-se como um importante agente causador de IRA adquirida na comunidade. É um vírus cosmopolita que causa doenças respiratórias semelhantes ao Vírus Respiratório Sincicial. No Brasil, são relativamente escassos os relatos da ocorrência do HMPV na população. O objetivo deste estudo é investigar a ocorrência de Metapneumovírus Humano (HMPV) em pacientes com diagnóstico clínico de infecção respiratória aguda (IRA) na Região Nordeste do Brasil. Entre o período de Junho de 2009 a Setembro de 2010, pacientes oriundos de atendimentos em unidades de atenção básica ou hospitalar de cinco estados da Região Nordeste, foram submetidos a coleta de espécimes para detecção a partir de técnicas de biologia molecular. Análises estatísticas foram utilizadas para escolha do tamanho amostral (545) e tratamento dos resultados obtidos. O estudo mostrou uma positividade de 4.7% para HMPV, sem a existência de uma faixa etária específica para a ocorrência da infecção. Ocorreu uma prevalência do sexo feminino entre os casos positivos, entretanto, sem significado estatístico. O pico de positividade para o vírus (n=16) mostrou existir no terceiro trimestre do ano em todos os Estados investigados. Neste estudo, foi possível descrever a ocorrência de HMPV na Região Nordeste, afetando pacientes portadores de infecção respiratória aguda, tanto acompanhados ambulatorialmente como hospitalizados, que preencheram critério clínico para Síndrome Respiratória Aguda Grave.

Detection of an untyped strain of bovine respiratory syncytial virus in a dairy herd

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Pathology and virus tissue distribution of Turkey Coronavirus (TCoV) in experimentally infected chicks and turkey poults

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Diversity and Adaptation of Human Respiratory Syncytial Virus Genotypes Circulating in Two Distinct Communities: Public Hospital and Day Care Center

HRSV is one of the most important pathogens causing acute respiratory tract diseases as bronchiolitis and pneumonia among infants. HRSV was isolated from two distinct communities, a public day care center and a public hospital in Sao Jose do Rio Preto - SP, Brazil. We obtained partial sequences from G gene that were used on phylogenetic and selection pressure analysis. HRSV accounted for 29% of respiratory infections in hospitalized children and 7.7% in day care center children. On phylogenetic analysis of 60 HRSV strains, 48 (80%) clustered within or adjacent to the GA1 genotype; GA5, NA1, NA2, BA-IV and SAB1 were also observed. SJRP GA1 strains presented variations among deduced amino acids composition and lost the potential O-glycosilation site at amino acid position 295, nevertheless this resulted in an insertion of two potential O-glycosilation sites at positions 296 and 297. Furthermore, a potential O-glycosilation site insertion, at position 293, was only observed for hospital strains. Using SLAC and MEME methods, only amino acid 274 was identified to be under positive selection. This is the first report on HRSV circulation and genotypes classification derived from a day care center community in Brazil.

The therapeutic journey of families of children with respiratory diseases in the public health service

This study's purpose was to identify the therapeutic journey of families seeking health care for their children with respiratory diseases. This qualitative study had the participation of parents of children younger than five years old who were hospitalized with respiratory diseases. Path mapping was used as an instrument to collect data, which was analyzed through thematic analysis. The finding indicate that families sought the health services as soon as they perceived symptoms and had access to medical care, however such care was not decisive in resolving their health issues. Even though the families returned to the service at least another three times, the children had to be hospitalized. The attributes of primary health care were not observed in the public health services, while therapeutic encounters had no practical success.

Respiratory diseases and associated factors: population-based study in Sao Paulo, Brazil, 2008-2009

OBJECTIVE: To assess the prevalence of acute bronchitis, rhinitis, and sinusitis among children and adolescents and identify associated factors. METHODS: This is a population-based, cross-sectional study. A household survey was conducted with 1,185 children and adolescents from the city of Sao Paulo (Southeastern Brazil), from 2008 to 2009. The participants were selected by means of probability sampling, stratified by sex and age, and by two-stage cluster sampling. For the adjusted analysis, multiple Poisson regression was used. RESULTS: Of the respondents, 7.3% reported acute bronchitis, 22.6% rhinitis and 15.3% sinusitis. After the adjusted analysis, the following characteristics were associated with self;reported acute bronchitis: age 0 to 4 years (PR=17.86; 95%Cl: 3.65;90.91), 5 to 9 years (PR=37.04; 95%CI: 8.13;166.67), 10 to 14 years (PR.=20,83; 95%Cl: 4.93;90.91), allergy (PR=3.12; 95%Cl: 1.70;5.73), black and mixed-ethnicity (black and white) skin color (PR=2.29; 95%Cl: 1.21;4.35), and living in a household with 1 to 3 rooms (PR=1.85; 95%Cl: 1.17;2.94). As to self-reported rhinitis, the following characteristics were associated: age 10 to 14 years (PR=2.77; 95%Cl: 1.60;4.78), 15 to 19 years (P.R=2.58; 95%Cl: 1.52;4.39), allergy (PR=4.32; 95%Cl: 2.79;6.70), asthma (PR=2.30; 95%CI: 1.30;4.10) and living in flats (PR=1.70; 95%Cl: 1.06;2.73). Concerning self-reported sinusitis, the following characteristics were associated: age 5 to 9 years (PR=2.44; 95%Cl: 1.09;5.43), 10 to 14 years (PR=2.99; 95%CI: 1.36;6.58), 15 to 19 years (PR=3.62; 95%Cl: 1.68;7.81), allergy (PR=2.23 (95%CI: 1.41;3.52) and obesity (PR=4.42; 95%Cl: 1.56;12.50). CONCLUSIONS: Respiratory diseases were more prevalent in population groups with defined characteristics, such as age group, self-reported diseases, type of household and obesity.

SEASONALITY OF VIRAL RESPIRATORY INFECTIONS IN SOUTHEAST OF BRAZIL: THE INFLUENCE OF TEMPERATURE AND AIR HUMIDITY

Viruses are the major cause of lower respiratory tract infections in childhood and the main viruses involved are Human Respiratory Syncytial Virus (HRSV), Human Metapneumovirus (HMPV), Influenzavirus A and B (FLUA and FLUB), Human Parainfluenza Virus 1, 2 and 3 (HPIV1, 2 and 3) and Human Rhinovirus (HRV). The purposes of this study were to detect respiratory viruses in hospitalized children younger than six years and identify the influence of temperature and relative air humidity on the detected viruses. Samples of nasopharyngeal washes were collected from hospitalized children between May/2004 and September/2005. Methods of viral detection were RT-PCR, PCR and HRV amplicons were confirmed by hybridization. Results showed 54% (148/272) of viral positivity. HRSV was detected in 29% (79/272) of the samples; HRV in 23.1% (63/272); HPIV3 in 5.1% (14/272); HMPV in 3.3% (9/272); HPIV1 in 2.9% (8/272); FLUB in 1.4% (4/272), FLUA in 1.1% (3/272), and HPIV2 in 0.3% (1/272). The highest detection rates occurred mainly in the spring 2004 and in the autumn 2005. It was observed that viral respiratory infections tend to increase as the relative air humidity decreases, showing significant association with monthly averages of minimal temperature and minimal relative air humidity. In conclusion, viral respiratory infections vary according to temperature and relative air humidity and viral respiratory infections present major incidences it coldest and driest periods.

Virulence and molecular aspects of Bordetella avium isolated from cockatiel chicks (Nymphicus hollandicus) in Brazil

Bordetella avium is an opportunistic pathogen that presents tropism for ciliated epithelia, leading to upper respiratory tract disease in turkeys. This agent has also been associated with Lockjaw Syndrome in psittacine birds, but literatures describing the importance of this agent in such species are rare. The purpose of the present study was to report the first outbreak of B. avium infection in juvenile cockatiels demonstrating the Lockjaw Syndrome in Brazil and to investigate the antimicrobial resistance profile and phenotypic and genotypic characteristics of these strains. Surprising, the strains obtained from five infected cockatiel chicks from three different breeders from different Brazilian states showed a clonal relationship using the Pulsed Field Gel Electrophoresis and Single Enzyme Amplified Fragment Length Polymorphism techniques. The virulence potentials of the B. avium strains were assessed using tracheal adherence and cytotoxic effects on a VERO cell monolayer. (C) 2012 Elsevier B.V. All rights reserved.

Crowding: risk factor or protective factor for lower respiratory disease in young children?

Abstract Background To study the effects of household crowding upon the respiratory health of young children living in the city of São Paulo, Brazil. Methods Case-control study with children aged from 2 to 59 months living within the boundaries of the city of São Paulo. Cases were children recruited from 5 public hospitals in central São Paulo with an acute episode of lower respiratory disease. Children were classified into the following diagnostic categories: acute bronchitis, acute bronchiolitis, pneumonia, asthma, post-bronchiolitis wheezing and wheezing of uncertain aetiology. One control, crudely matched to each case with regard to age (<2, 2 years old or more), was selected among healthy children living in the neighborhood of the case. All buildings were surveyed for the presence of environmental contaminants, type of construction and building material. Plans of all homes, including measurements of floor area, height of walls, windows and solar orientation, was performed. Data were analysed using conditional logistic regression. Results A total of 313 pairs of children were studied. Over 70% of the cases had a primary or an associated diagnosis of a wheezing illness. Compared with controls, cases tended to live in smaller houses with less adequate sewage disposal. Cases and controls were similar with respect to the number of people and the number of children under five living in the household, as well the number of people sharing the child's bedroom. After controlling for potential confounders, no evidence of an association between number of persons sharing the child's bedroom and lower respiratory disease was identified when all cases were compared with their controls. However, when two categories of cases were distinguished (infections, asthma) and each category compared separately with their controls, crowding appeared to be associated with a 60% reduction in the incidence of asthma but with 2 1/2-fold increase in the incidence of lower respiratory tract infections (p = 0.001). Conclusion Our findings suggest that household crowding places young children at risk of acute lower respiratory infection but may protect against asthma. This result is consistent with the hygiene hypothesis.

Seasonality of viral respiratory infections in Southeast of Brazil: the influence of temperature and air humidity

Viruses are the major cause of lower respiratory tract infections in childhood and the main viruses involved are Human Respiratory Syncytial Virus (HRSV), Human Metapneumovirus (HMPV), Influenzavirus A and B (FLUA and FLUB), Human Parainfluenza Virus 1, 2 and 3 (HPIV1, 2 and 3) and Human Rhinovirus (HRV). The purposes of this study were to detect respiratory viruses in hospitalized children younger than six years and identify the influence of temperature and relative air humidity on the detected viruses. Samples of nasopharyngeal washes were collected from hospitalized children between May/2004 and September/2005. Methods of viral detection were RT-PCR, PCR and HRV amplicons were confirmed by hybridization. Results showed 54% (148/272) of viral positivity. HRSV was detected in 29% (79/272) of the samples; HRV in 23.1% (63/272); HPIV3 in 5.1% (14/272); HMPV in 3.3% (9/272); HPIV1 in 2.9% (8/272); FLUB in 1.4% (4/272), FLUA in 1.1% (3/272), and HPIV2 in 0.3% (1/272). The highest detection rates occurred mainly in the spring 2004 and in the autumn 2005. It was observed that viral respiratory infections tend to increase as the relative air humidity decreases, showing significant association with monthly averages of minimal temperature and minimal relative air humidity. In conclusion, viral respiratory infections vary according to temperature and relative air humidity and viral respiratory infections present major incidences it coldest and driest periods.

Study of two novel streptococcus pneumoniae operons: pilus islet 2 and the lantibiotic operon

Analysis of publicly available genomes of Streptococcus pneumoniae has led to the identification of a new genomic element resembling gram-positive pilus islets (PIs). Here, we demonstrate that this genomic region, herein referred to as PI-2 (containing the genes pitA, sipA, pitB, srtG1, and srtG2) codes for a novel functional pilus in pneumococcus. Therefore, there are two pilus islets identified so far in this pathogen (PI-1 and PI-2). Polymerization of the PI-2 pilus requires the backbone protein PitB as well as the sortase SrtG1 and the signal peptidase-like protein SipA. PI-2 is associated with serotypes 1, 2, 7F, 19A, and 19F, considered to be emerging in both industrialized and developing countries. Interestingly, strains belonging to clonal complex 271 (CC271) contain both PI-1 and PI-2, as revealed by genome analyses. In these strains both pili are surface exposed and independently assembled. Furthermore, in vitro experiments provide evidence that the pilus encoded by PI-2 of S. pneumoniae is involved in adherence. Thus, pneumococci encode at least two types of pili that may play a role in the initial host cell contact to the respiratory tract. In addition, the pilus proteins are potential antigens for inclusion in a new generation of pneumococcal vaccines. Adherence by pili could represent important factor in bacterial community formation, since it has been demonstrated that bacterial community formation plays an important role in pneumococcal otitis media. In vitro quantification of bacterial community formation by S. pneumoniae was performed in order to investigate the possible role of pneumococcal pili to form communities. By using different growth media we were not able to see clear association between pili and community formation. But our findings revealed that strains belonging to MLST clonal complex CC15 efficiently form bacterial communities in vitro in a glucose dependent manner. We compared the genome of forty-four pneumococcal isolates discovering four open reading frames specifically associated with CC15. These four genes are annotated as members of an operon responsible for the biosynthesis of a putative lanctibiotic peptide, described to be involved in bacterial community formation. Our experiments show that the lanctibiotic operon deletion affects glucose mediated community formation in CC 15 strain INV200. Moreover, since glucose consumption during bacterial growth produce an acidic environment, we tested bacterial community formation at different pH and we showed that the lanctibiotic operon deletion affected pH mediated community formation in CC 15 strain INV200. In conclusion, these data demonstrate that the putative lanctibiotic operon is associated with pneumococcal CC 15 strains in vitro bacterial community formation.