As diarréias neonatais constituem-se em um dos mais importantes fatores econômico e sanitário nas granjas suínas, quer pela mortalidade, quer pelas perdas agregadas ao atraso no desenvolvimento dos leitões, à profilaxia e ao manejo. Os rotavírus ocupam lugar de destaque pela rápida disseminação dentro do plantel, bem como pelo potencial zoonótico, dada a probabilidade de rearranjo ou recombinação genética entre amostras humanas e animais O objetivo deste trabalho foi detectar a presença de rotavírus a partir de 277 amostras fecais de leitões com quadro clínico de diarréia, provenientes dos Estados do Rio Grande do Sul (RS), Santa Catarina (SC), Paraná (PR), Mato Grosso do Sul (MS), Mato Grosso (MT), São Paulo (SP), Rio de Janeiro (RJ) e Minas Gerais (MG) entre os anos de 2009 e 2011 e analisar o perfil eletroforético de migração dos segmentos genômicos bem como diferenças de eletroferótipos nas amostras positivas, pela técnica de eletroforese em gel de poliacrilamida (PAGE). Das 277 amostras fecais diarréicas de leitões analisadas, 25 foram positivas (25/277= 9%). De conformidade com os Estados de origem, foram verificadas as frequências de 20% (1/5) no RS, 11,1% (1/9) em SC, 12,5% (1/8) no PR, 15,3% (6/39) em MS, 14,2% (3/21) em MT, 6,7% (5/74) em SP, 0% (0/7) no RJ e 7% (8/114) em MG. Pela análise da migração eletroforética dos segmentos genômicos, todas as 25 amostras positivas apresentaram perfil eletroforético compatível com o RV-A, tal como a amostra padrão NCDV com migração característica em quatro classes ou agregados [4-2-3- 2]. Foram observadas pequenas diferenças na velocidade de migração de um ou mais segmentos dentro da mesma classe. Estes resultados evidenciam a importância da PAGE como metodologia de diagnóstico e de investigações epidemiológicas nas rotaviroses suínas. / The neonatal diarrhea constitute one of the most important economic and health factors in pig farms either by death or by the aggregate losses to the delay in the development of piglets, prophylaxis and management. Rotaviruses have a prominent role by the rapid spread within the herd, as well as the zoonotic potential, given the likelihood of genetic reassortment or recombination between human and animal samples. The objective of this study was to detect the presence of rotavirus from fecal samples from 277 piglets with clinical cases of diarrhea, from the states of Rio Grande do Sul (RS), Santa Catarina (SC), Paraná (PR), Mato Grosso do Sul (MS), Mato Grosso (MT), São Paulo (SP), Rio de Janeiro (RJ) e Minas Gerais (MG) between the years 2009 and 2011 and to analyze the electrophoretic migration of genomic segments and electropherotype differences in positive samples, by polyacrylamide gel electrophoresis (PAGE) technique. From 277 piglets diarrheal stool samples analyzed, 25 were positive (25/277 = 9%). In accordance with the States of origin, were observed frequencies of 20% (1/5) in the RS, 11.1% (1/9) in SC, 12.5% (1/8) in PR, 15.3 % (6/39) in MS, 14.2% (3/21) in MT, 6.7% (5/74) in SP, 0% (0/7) in Rio de Janeiro and 7% (8/114) in MG. For the analysis of the electrophoretic migration of genome segments, all 25 positive samples showed electrophoretic profile compatible with the RV-A as a standard sample NCDV, showing characteristic fourth class or aggregates [4-2-3-2]. We observed small differences in the migration speed of one or more segments within the same class. These results highlight the importance of PAGE as a method of diagnosis and epidemiological investigations in the porcine rotavirus.

Os rotavírus, membros da família Reoviridae, são uma importante causa de diarreia em mamíferos e aves. São partículas icosaédricas não envelopadas e seu genoma é formado por 11 segmentos de RNA fita dupla que codificam seis proteínas estruturais e seis proteínas não estruturais. O objetivo deste estudo foi caracterizar os genes codificadores das proteínas não estruturais (NSP1-5) e estruturais (VP1-4, VP6-7) dos rotavírus do grupo A em aves de criações comerciais (corte, postura, matrizeiros e avozeiros) localizadas em 12 estados brasileiros, seguido de análises de recombinação e pressão de seleção das amostras definidas. Um total de 226 amostras fecais foram triadas através de reações de RT-PCR tendo como alvo a amplificação da VP6 e NSP5. A frequência de ocorrência, baseada em cada uma destas provas, variou de 9,7% a 18,14%, respectivamente. Em seguida, 10 das amostras positivas foram processadas com primers específicos visando a amplificação dos demais genes, seguido do sequenciamento nucleotídico e filogenia baseada no método de maximum likelihood, tendo como modelos de substituição GTR (NSP1-3, VP1-3, VP4, VP6, VP7) e HKY (NSP4, NSP5) e 1.000 repetições de bootstrap. Foram definidas sequências parciais para os genes codificadores da VP1-4, VP6-7 e NSP1-4 e sequências completas para NSP5. As respectivas árvores demonstraram que as dez amostras definidas se agruparam em clados aviários previamente descritos. Duas constelações genotípicas foram caracterizadas: G19-P[31]-I11-R6-C6-M7-A16-N6-T8-E10-H8 e G19-P[31]-I4-R4-C4-M4-A16-N4-T4-E4-H4. Estes genotipos são tipicamente encontrados em aves, mas quando analisados em conjunto, esta é a primeira descrição destas constelações. Eventos de recombinação foram observados nos genes NSP2, VP1, VP3 e VP7. Pelo menos um códon com pressão de seleção positiva foi encontrado nos genes codificadores das proteínas NSP1, VP2 e VP3. Este estudo propicia um melhor entendimento acerca da epidemiologia e diversidade viral circulante nas criações aviárias brasileiras, servindo de base para o estabelecimento de medidas profiláticas mais eficazes. / Rotaviruses are members of the Reoviridae family and they are a common cause of acute diarrhea in several mammalian and avian species. They are non-enveloped icosahedral particles and its genome comprises 11 segments of double-stranded RNA, which encodes six structural proteins (VP1-4, VP6-7) and six nonstructural proteins (NSP1-6). The objective of this study was to characterize the RVA nonstructural and structural proteins coding genes (NSP1-NSP5, VP1-VP4, VP6 and VP7) from fecal samples from avian farms (broiler breeders, poultry, laying hens, and grandparents) raised in Brazilian commercial farms from 12 states, followed by recombination and selection pressure analysis from samples defined here. A total of 226 fecal samples were screened using a RT-PCR technique targeting the amplification of the VP6 and NSP5. The frequency of occurrence, using these techniques, ranging from 9.7% to 18,14%, respectively; and from these, ten samples were further processed with specific primers to amplify the remaining genes, followed by respective nucleotide sequencing of the amplicons and phylogeny based on method maximum likelihood, as substitutions models GTR (NSP1-3, VP1-3, VP4, VP6, VP7) and HKY (NSP4, NSP5) and 1.000 bootstrap repetitions. Partial nucleotide sequences of VP1-4, VP6-7, and NSP1-4, and complete from NSP5, were obtained in this study. The phylogenetic trees depicted that the ten Brazilian rotavirus strains segregated with previous avian RVA described elsewhere. Two avian genotype constellations have been characterized here: G19-P[31]-I11-R6-C6-M7-A16-N6-T8-E10-H8, and G19-P[31]-I4-R4-C4-M4-A16-N4-T4-E4-H4. These genotypes are typically found in avian species, although when analyzed together, this is the first report of such constellations. Recombination events were observed in NSP2, VP1, VP3, and VP7 coding genes. At least on positive selected site was observed in NSP1, VP2, and VP3 genes. This study provides a better understanding of rotavirus epidemiology, by the definition of genetic variability of circulating strains.

Rotavirus is the most common cause of severe gastroenteritis among children <5 years of age worldwide and is responsible for 453,000 deaths among children in this age group. More than half of these deaths occur in sub-Saharan Africa. Because of the tremendous global burden of rotavirus, vaccine development and introduction has been a high priority for several international agencies, including the World Health Organization (WHO) and GAVI. Two live, attenuated, orally administered rotavirus vaccines, a pentavalent bovine-human reassortant vaccine (RV5; RotaTeq® (Merck and Co, Inc, Pennsylvania)) and a monovalent vaccine (RV1; Rotarix™ (GSK Biologicals, Rixensart, Belgium)) based on a human rotavirus strain, are licensed and available for use in many countries worldwide. Pre-licensure clinical trials of each of these vaccines in high and middle-income countries demonstrated high efficacy (85-98%) against severe rotavirus disease. Further studies conducted in low-income countries of Asia and Africa found modest efficacy (50%-70%) of these vaccines against severe rotavirus disease. However, the public health impact of vaccination (in terms of burden of severe rotavirus disease prevented by vaccinating a given number of children) is greater in developing countries because of the substantially higher baseline rotavirus disease burden in these settings. In 2009, the World Health Organization recommended the inclusion of rotavirus vaccine in the national immunization programs of all countries globally and particularly in those countries with high child mortality due to diarrhea. Of the 16 countries recently approved by GAVI for rotavirus vaccine introduction, 12 countries are located in Africa. As rotavirus vaccines are introduced into national immunization programs, monitoring their impact is a high priority for several reasons. There is a need to assess the effectiveness of these vaccines in routine use to ensure it parallels that of pre-licensure trials, particularly when used in developing countries. Assessing the impact of vaccination on disease burden in countries such as Rwanda will be vital to understanding the full public health benefit of the vaccine. The primary purpose of this program evaluation is to determine the impact of pentavalent rotavirus vaccine on rotavirus and all-cause diarrhea morbidity following introduction into the national immunization program in Rwanda in May 2012. Additionally, this evaluation will document changes in circulating strains over time pre- and post-vaccine introduction. It will also strengthen support for economic evaluation of treating diarrhea versus introduction of new vaccine in routine immunization. Methodology Various studies have been implemented since 2011 in the health sector in Rwanda to reach the goal of this thesis. First, we analyzed data for all-cause, non-bloody diarrheal disease among children <5 years of age from the routine health management information system (HMIS) in Rwanda from January 2008 through December 2011, The objective of this analysis was to determine whether routinely collected health information on national diarrhea hospitalizations, in-hospital deaths, and outpatient visits can be used to monitor the impact of rotavirus vaccine. We used data from the health management information system (HMIS) in Rwanda to describe trends in all-cause, non-bloody diarrhea hospitalizations and outpatient visits among children <5 years of age from 2008 to 2011 prior to vaccine introduction. Second, we evaluated the economic burden attributable to hospitalization for diarrhea among children aged less than 5 years in Rwanda. This was a prospective costing study where medical records and hospital bills for children admitted with diarrhea at 3 hospitals were collected to estimate costs. Interviews with the child’s caregivers provided medical costs incurred before and after hospitalization and the household costs. Third, we analyzed and tried to understand the introduction and delivery cost per dose or per child of the three new vaccines in Rwanda including the rotavirus vaccine for domestic and external financial resource mobilization. Fourth, we determined the rotavirus prevalence rates and circulating genotypes directly pre- and post-introduction of the RotaTeq rotavirus vaccine in May 2012. Stool samples were collected from 1,847 children <5 admitted to 8 surveillance sites for acute gastroenteritis (AGE) and tested for rotavirus antigens by enzyme immunoassay. Fifth, to monitor the effect of rotavirus vaccine in Rwanda, we studied trends in the number of hospital admissions for diarrhea and rotavirus before and after the introduction of the rotavirus vaccine. We conducted a time-series analysis to examine trends in admissions to hospital for non-bloody diarrhea in children younger than 5 years in Rwanda between Jan 1, 2009, and Dec 31, 2014, using monthly discharge data from the HMIS.Result All-cause, non bloody diarrheal hospitalizations and outpatient visits among children <5 years of age in Rwanda from 2008 to 2011 peaked during the June to August dry season, coinciding with the rotavirus season. The bulk of the diarrheal disease burden occurred in children <1 year of age. Average medical costs for each child for the hospitalization were $44.22 ± $23.74 and the total economic burden per hospitalization was $101, of which 65% was borne by the household. The unit cost of introducing rotavirus vaccines 2012 was 22.69 US. Among the 397 stool samples that were genotyped, 5 G types (G1, G4, G8, G9, and G12) and 3 P types (P[4], P[6], and P[8]) were identified. G8 (30.3%), G9 (28.0%), and G1 (19.7%) were the most prevalent G types, while P[8] (52.0%) and P[4] (32.6%) were the most prevalent P types. There was a significant amount of mixed G genotypes (12.1%), while mixed P types were less common (5.1%). G8P[4], G9P[8], and G1P[8] were the most prevalent strains, accounting for 27.8%, 24.3%, and 15.3% of all specimens, respectively.Compared with the 2009–11 pre vaccine baseline, hospital admissions for non-bloody diarrhea captured by the HMIS fell by 17–29% from a pre-vaccine median of 4051 to 2881 in 2013 and 3371 in 2014, admissions for AGE captured in pediatric ward registries decreased by 48–49%, and admissions specific to rotavirus captured by active surveillance fell by 61–70%. The greatest effect was recorded in children age-eligible to be vaccinated, but we noted a decrease in the proportion of children with diarrhea testing positive for rotavirus in almost every age group.ConclusionGiven the stable and consistent trends and the prominent seasonality consistent with that of rotavirus, HMIS data should provide a useful baseline to monitor rotavirus vaccine impact on the overall diarrheal disease burden in Rwanda. Active, sentinel surveillance for rotavirus diarrhea will help interpret changes in diarrheal disease trends following vaccine introduction. Other countries planning rotavirus vaccine introduction should explore the availability and quality of their HMIS data.Households often bear the largest share of the economic burden attributable to diarrhea hospitalization and the burden can be substantial, especially for households in the lowest income quintile.The cost of introduction of new vaccines (rotavirus) is less than the cost of treating the diarrhea diseases. The number of admissions to hospital for diarrhea and rotavirus in Rwanda fell substantially after rotavirus vaccine implementation, including among older children age-ineligible for vaccination, suggesting indirect protection through reduced transmission of rotavirus. These data highlight the benefits of routine vaccination against rotavirus in low-income settings. / Doctorat en Santé Publique / info:eu-repo/semantics/nonPublished

Gastrenterites virais em cães são doenças transmissíveis infecciosas com importância para a saúde animal, como as causadas por Parvovírus canino e Coronavírus canino (CCoV) e saúde pública, como no caso dos rotavírus. Rotavírus em cães são encontrados com baixa freqüência, tanto em cães com diarréia quanto sadios, mas sua importância como reservatório para a rotavirose humana já é conhecido. O CCoV, pertencente ao grupo 1 do gênero Coronavirus, ocorre sob a forma dos genótipos I e II, amplamente distribuídos mundialmente e implicados em diarréia moderada, mas podendo levar a elevada letalidade no caso de patótipos altamente patogênicos. No Brasil, a ocorrência de rotavírus do sorogrupo A em cães é um fato conhecido, mas, no caso do CCoV, existe, até o momento, apenas uma investigação relatando sua ocorrência, sem dados de diversidade molecular. A presente investigação teve por objetivos avaliar o papel de cães jovens com enterite sintomática, bem como sadios, como reservatórios de rotavírus, estudar a freqüência de ocorrência de Coronavírus canino (CCoV) em amostras fecais destes animais e estudar a diversidade molecular das amostras de CCoV encontradas. Para tato foram colhidas 100 amostras fecais de cães não vacinados, entre 1 e 180 dias de idade entre 2007 e 2008, sendo 50 com diarréia e 50 sem diarréia no momento da colheita, nos Municípios de São Paulo, São Bernardo do Campo, Santo André, São Caetano do Sul, Taboão da Serra, Itapecerica da Serra e uma aldeia indígena em Parelheiros. Às amostras foi aplicada a técnica de eletroforese em gel de poliacrilamida (PAGE) para a detecção de rotavírus e uma RT-PCR dirigida ao gene da proteína de membrana M do CCoV (nucleotídeos 337 a 746) para a detecção deste vírus, sendo os fragmentos detectados submetidos a seqüenciamento de DNA. As seqüencias obtidas, traduzidas em aminoácidos, foram utilizadas para a construção de uma árvore genealógica enraizada de distância com o algoritmo Neighbor-Joning e modelo de Poisson com 100 repetições de bootstrap. Nenhuma das amostras resultou positiva para rotavirus, enquanto que 47 foram positivas para CCoV, com freqüência significativamente superior nos animais com diarréia. Vinte e dois dos 47 fragmentos de DNA obtidos resultaram em seqüências viáveis de DNA, sendo 12 classificadas como CCoV Tipo I e 10 como Tipo II, tendo sido encontrada uma sublinhagem exclusivamente brasileira para o Tipo II. Em relação à amostra vacinal de CCoV submetida ao seqüenciamento de DNA, a maior identidade ocorreu com o grupo Tipo II sublinhagem 01, com um valor de 100%, seguido de 97,2% para o Tipo II sublinhagem 02 (a linhagem brasileira) e 93,2% para o Tipo I. Sugere-se que a diversidade de CCoV encontrada seja derivada da elevada freqüência de ocorrência deste vírus, o que pode aumentar a probabilidade de divergências e de possíveis falhas vacinais por diferenças entre a amostra vacinal (Tipo II) e as amostras de campo (Tipos I e II), e, dessa forma, a vacina não diminuiria a transmissão e novas linhagens de CCoV emergiriam. Conclui-se que cães jovens com enterite sintomática, bem como sadios, não tiveram papel como reservatório para rotavírus, considerando-se a região geográfica e o período de colheita de amostras. O CCoV ocorreu com uma freqüência de 47% na população canina estudada, com freqüência estatisticamente significativamente superior naqueles com diarréia do que naqueles sem diarréia. Finalmente, amostras brasileiras de CCoV, com base em seqüenciamento parcial do gene codificador da proteína de membrana M, ocorrem tanto como tipo I quanto II, sendo que, para o tipo II, há uma lihangem tipicamente brasileira. / Viral canine gastroenteritis is infectious transmissible diseases with importance for animal health, as those caused by Canine parvovirus and Canine coronavirus (CCoV) and public health, as in the case of rotavirus. Canine rotavirus occurs at low frequencies, both in diarrheic and health dogs, but the importance of dog as reservoirs for human rotaviruses is known. CCoV belongs to group 1 of the genus Coronavirus and occurs as genotypes I and II, worldwide distributed and implicated in mild diarrhea, but high pathogenic types might lead to high lethality. In Brazil, the occurrence of serogroup A rotavirus in dogs is already known but, in the case of CCoV, theres a single report on the occurrence of this virus, with no data on its molecular diversity. The aims of the present investigation were to evaluate the roles of diarrheic and health young dogs as reservoirs of rotavirus, to study the occurrence of CCoV in these animals and to assess the molecular diversity of the strains found. One hundred fecal samples were collected from unvaccinated dogs between 2007 and 2008 (50 with diarrhea and 50 health dogs) in the Municipalities of São Paulo, São Bernardo do Campo, Santo André, São Caetano do Sul, Taboão da Serra, Itapecerica da Serra and in an indian community in Parelheiros. The samples were submitted to polyacrilamide gel electrophoresis (PAGE) for rotavirus detection and to an RT-PCR targeted to the membrane M protein gene (nucleotides 337 to 746) of CCoV for the detection of this virus; amplicons were then submitted to DNA sequencing and the putative amino acids sequences were used to build a rooted distance genealogic tree with the Neighbor-Joinng algorithm and he Poisson correction with 1,000 bootstrap replicates. No sample was positive to rotavirus, while 47 out of the 100 samples were positive for CCoV, with a statistically significative higher frequency for the dogs with diarrhea. Twenty-two out of the 47 ampicons resulted in viable sequences, being 12 classified as CCoV Type II and 10 as Type I; besides, and exclusively Brazilian sub lineage was found for Type II. Regarding the vaccine strain, the highest identity was found to Type II sub linage 02 (10%), followed by 97.2% for Type II sub linage II (the Brazilian sub linage) and 93.2% for Type I. Its suggested that the high diversity for CCoV detected is a consequence of the high frequency of occurrence of this virus, what might increase the probability of the emergence of divergence and possible vaccine failures due to differences amongst the vaccine strain (Type II) and field strains (Types I and II) and thus vaccination would not decrease the transmission and new lineages would emerge. It can be concluded that both health and diarrheic young dogs have played no role as reservoirs for rotavirus taking into account the geographic area and the time of samples collection. CCoV ocurred at a frequecy of 47%, with a higher frequency in the diarreic animals. Finally, Brazilian strains of CCoV, based on partial M gene sequences, occur as both type I and II, while, for Type II, a typical Brazilian lineage was described.

O coronavírus bovino (BCoV) e rotavírus (RV) são importantes agentes da diarréia neonatal bovina, causando grandes perdas econômicas. O BCoV é também responsável pela disenteria de inverno em vacas adultas e por desordens respiratórias e o RV possui um aspecto zoonótico de importância na saúde pública. Este estudo teve o objetivo de desenvolver uma multiplex hemi-nested RT-PCR para detecção simultânea de BCoV e RV do grupo A com a utilização de um controle interno. Para tanto, foram desenhados três primers dirigidos ao gene N de BCoV (306pb) e três primers dirigidos ao gene VP1 do RV do grupo A (228pb); para o controle interno, foram utilizados dois primers dirigidos ao mRNA do gene mitocondrial bovino ND5 (191pb). Foram utilizados como controles positivos a amostra Kakegawa de BCoV (título HA de 256), a amostra 8209 de rotavírus do grupo A (título viral de 101.66TCID50%/200µL) e suspensão de células MDBK para o controle interno. A extração de RNA foi realizada com o reagente comercial TRIzol, de acordo com as recomendações do fabricante. Foram realizados gradientes de temperatura para a determinação da temperatura ótima de hibridação para cada par de primers, resultando em 50ºC para PCR e 55ºC para a hemi-nested. Doze protocolos com diferentes concentrações de Taq DNA polymerase, MgCl2, primers e DNA-alvo foram testados. Para determinação do limiar de detecção, o protocolo final foi utilizado em diluições dos dois vírus em suspensão de amostras fecais negativas para BCoV e RV adicionadas de 10% de suspensão de células MDBK, obtendo o limiar de detecção de 10-8 para os dois vírus e aplicado em amostras fecais de bezerros (53) e vacas adultas (22). Todas as amostras foram previamente testadas para BCoV por uma nested RT-PCR dirigida ao gene RdPd, sendo 15 positivas, e para rotavírus pela PAGE, sendo 3 positivas. Para a multiplex, 15 amostras foram positivas para BCoV e 6 para rotavírus. O seqüenciamento de DNA das amostras positivas para multiplex demonstrou a especificidade do teste. Uma concordância ótima foi encontrada para BCoV (0,833) e substancial para rotavírus (0,648) calculada pela estatística kappa, comparando-se com os testes de referência. Estes resultados demonstram que a padronização da multiplex foi eficiente para a detecção de BCoV e RV, com elevadas sensibilidade e especificidade. Além disso, o diagnóstico simultâneo dos dois agentes permite um diagnóstico rápido e a um menor custo devido à utilização de reduzidas quantidades de reagentes e mão de obra, fornecendo uma importante ferramenta para o diagnóstico e estudo da etiologia da diarréia em bovinos. / Bovine coronavirus (BCoV) and rotavirus (RV) are important agents of neonatal diarrhea in cattle, causing large economic losses. BCoV is also responsible for winter dysentery in adult cattle and respiratory disorders and RV has a zoonotic aspect of importance in public health. This study aimed to develop a multiplex hemi-nested RT-PCR for simultaneous detection of BCoV and RV of group A with an internal control. For this purpose, three primers were designed targeting the N gene of BCoV (306pb) and three primers targeting to the VP1 gene of group A RV (228pb); for internal control, two primers targeting to the mRNA of ND5 bovine mitochondrial gene (191pb) were used. Positive controls were BCoV Kakegawa strain (HA titer 256), group A bovine rotavirus strain 8209 (viral titer of 101.66TCID50%/200µL), and MDBK cells suspension for internal control. The RNA extraction was performed with the commercial reagent TRIzol. Temperature gradients were carried out for each primers pair for the determination of the optimal hybridization temperatures, resulting in 50°C for PCR and 55°C for the hemi-nested. Twelve protocols were tested with different concentrations of Taq DNA polymerase, MgCl2, primers and target DNA. The final protocol was used in 10-fold dilutions of the two viruses in suspension of fecal sample negative for BCoV and RV added to 10% of MDBK cells suspension, obtaining the detection limit of 10-8 for the two viruses, and applied to 75 fecal samples from calves (53) and cows (22). All samples were previously tested for BCoV by a nested RT-PCR to RdPd gene, being 15 positive; and for rotavirus by PAGE, being 3 positive. For multiplex, 15 samples were positive for BCoV and 6 for RV. The DNA sequencing of multiplex-positive samples substantiates the specificity of the test. A great agreement was found for BCoV (0.833) and substantial for RV (0.648) by calculating the kappa statistic in comparison to the reference tests. These results demonstrate that the multiplex standard was effective in the detection of BCoV and RV, with high sensitivity and specificity. In addition, simultaneous diagnosis of both agents allows a faster and at lower cost diagnosis due to use of smaller quantities of reagents and labor, providing an important tool for the diagnosis and study on the etiology of diarrhea in cattle.

Previous multi-strain mathematical models have elucidated that the degree of cross-protective responses between similar strains, acting as a form of immune selection, generates different behavioural states of the pathogen population. This thesis explores these multi-strain dynamic states, to examine their robustness and stability in the face of pathogenic intrinsic phenotypic variation, and the extrinsic force of immune selection. This is achieved in two main ways: Chapter 2 introduces phenotypic variation in pathogen transmissibility, testing the robustness of a stable pathogen population to the emergence of an introduced strain of higher transmission potential; and Chapter 3 introduces a new model with a possibility of immunity to both strain-specific and cross-strain (conserved) determinants, to investigate how heterogeneity in the specificity of a host immune response alters the pathogen population structure. A final investigation in Chapter 4 develops a method of reverse-pattern oriented modelling using a machine learning algorithm to determine which intrinsic properties of the pathogen, and their combinations, lead to particular disease-like population patterns. This research offers novel techniques to complement previous and ongoing work on multi-strain modelling, with direct applications to a range of infectious agents such as Plasmodium falciparum, influenza A, and rotavirus, but also with a wider potential for other multi-strain systems.

Os rotavírus, membros da família Reoviridae, são uma importante causa de diarreia em mamíferos e aves. São partículas icosaédricas não envelopadas e seu genoma é formado por 11 segmentos de RNA fita dupla que codificam seis proteínas estruturais e seis proteínas não estruturais. O objetivo deste estudo foi caracterizar os genes codificadores das proteínas não estruturais (NSP1-5) e estruturais (VP1-4, VP6-7) dos rotavírus do grupo A em aves de criações comerciais (corte, postura, matrizeiros e avozeiros) localizadas em 12 estados brasileiros, seguido de análises de recombinação e pressão de seleção das amostras definidas. Um total de 226 amostras fecais foram triadas através de reações de RT-PCR tendo como alvo a amplificação da VP6 e NSP5. A frequência de ocorrência, baseada em cada uma destas provas, variou de 9,7% a 18,14%, respectivamente. Em seguida, 10 das amostras positivas foram processadas com primers específicos visando a amplificação dos demais genes, seguido do sequenciamento nucleotídico e filogenia baseada no método de maximum likelihood, tendo como modelos de substituição GTR (NSP1-3, VP1-3, VP4, VP6, VP7) e HKY (NSP4, NSP5) e 1.000 repetições de bootstrap. Foram definidas sequências parciais para os genes codificadores da VP1-4, VP6-7 e NSP1-4 e sequências completas para NSP5. As respectivas árvores demonstraram que as dez amostras definidas se agruparam em clados aviários previamente descritos. Duas constelações genotípicas foram caracterizadas: G19-P[31]-I11-R6-C6-M7-A16-N6-T8-E10-H8 e G19-P[31]-I4-R4-C4-M4-A16-N4-T4-E4-H4. Estes genotipos são tipicamente encontrados em aves, mas quando analisados em conjunto, esta é a primeira descrição destas constelações. Eventos de recombinação foram observados nos genes NSP2, VP1, VP3 e VP7. Pelo menos um códon com pressão de seleção positiva foi encontrado nos genes codificadores das proteínas NSP1, VP2 e VP3. Este estudo propicia um melhor entendimento acerca da epidemiologia e diversidade viral circulante nas criações aviárias brasileiras, servindo de base para o estabelecimento de medidas profiláticas mais eficazes. / Rotaviruses are members of the Reoviridae family and they are a common cause of acute diarrhea in several mammalian and avian species. They are non-enveloped icosahedral particles and its genome comprises 11 segments of double-stranded RNA, which encodes six structural proteins (VP1-4, VP6-7) and six nonstructural proteins (NSP1-6). The objective of this study was to characterize the RVA nonstructural and structural proteins coding genes (NSP1-NSP5, VP1-VP4, VP6 and VP7) from fecal samples from avian farms (broiler breeders, poultry, laying hens, and grandparents) raised in Brazilian commercial farms from 12 states, followed by recombination and selection pressure analysis from samples defined here. A total of 226 fecal samples were screened using a RT-PCR technique targeting the amplification of the VP6 and NSP5. The frequency of occurrence, using these techniques, ranging from 9.7% to 18,14%, respectively; and from these, ten samples were further processed with specific primers to amplify the remaining genes, followed by respective nucleotide sequencing of the amplicons and phylogeny based on method maximum likelihood, as substitutions models GTR (NSP1-3, VP1-3, VP4, VP6, VP7) and HKY (NSP4, NSP5) and 1.000 bootstrap repetitions. Partial nucleotide sequences of VP1-4, VP6-7, and NSP1-4, and complete from NSP5, were obtained in this study. The phylogenetic trees depicted that the ten Brazilian rotavirus strains segregated with previous avian RVA described elsewhere. Two avian genotype constellations have been characterized here: G19-P[31]-I11-R6-C6-M7-A16-N6-T8-E10-H8, and G19-P[31]-I4-R4-C4-M4-A16-N4-T4-E4-H4. These genotypes are typically found in avian species, although when analyzed together, this is the first report of such constellations. Recombination events were observed in NSP2, VP1, VP3, and VP7 coding genes. At least on positive selected site was observed in NSP1, VP2, and VP3 genes. This study provides a better understanding of rotavirus epidemiology, by the definition of genetic variability of circulating strains.

Made available in DSpace on 2015-04-22T22:14:05Z (GMT). No. of bitstreams: 1 Dissertacao Final Giane Zupellari.pdf: 1538567 bytes, checksum: 99734d4093e76fed6d05c37113c7903d (MD5) Previous issue date: 2008-08-01 / Fundação de Amparo à Pesquisa do Estado do Amazonas / Human rotavirus constitutes one of the most important causes of diarrheic disease in children less than five years in the whole world. With the objective of verifying the occurrence of genotypes of human rotavirus in children of 1 the 36 months residents in the city of Manaus in Amazon, had been analyzed during the years from 2004 to 2006, a total of 607 the feces diarrheic samples that had been collected of children attended hospital of children in the city of Manaus. This analyzes was carried through by the detention of the viral genome through the techniques of EGPA (electrophoresis in gel of polyacrylamide), and RT-PCR (reaction in chain of polymerases associated to the reaction of reversal transcriptase). Through the EGPA method can be observed a positivity of 25% of the human rotavirus samples. All of the positive samples for rotavirus had been genotyped by the method of RT-PCR with use of specific primers for genotypes G (G1, G2, G3, G4 and G9) and genotypes P (P[8], P[4], P[6], P[9] and P[10]). By the genotyping, it was detected genotype G in 30,7% of the positive samples for rotavirus, with predominance of the G2 genotypes (17%), followed of G1 (14.9%) and G9 (10.6%) and genotype P in 44,7% of the positive samples for rotavirus, with predominance of genotypes P[8] in 66,2% of samples and P[4] in 13,2% of the samples. The combinations of genotypes G and P had been responsible for 53,3% of the positive samples for rotavirus, being that P[8]G1 and P[4]G2 had been found with 12,5% and 10% consecutively, followed of P[8]G3 (5%). Other combinations as P[4]G1, P[8]G9 and P[10]G1 had been also found in less expressive numbers. It was observed that 38.3% of the positive samples for genotype G and 11.7% of the positive samples for genotype P had not presented characteristics for none of searched genotypes G and P. The number positive samples for human rotavirus, as well as for genotypes G and genotypes P had been similar in such a way in children of the masculine sex, how much in children of the feminine sex, being that these samples had predominated in children less than 18 months. The positive samples for human rotavirus, as well as for genotypes G and genotype P had been found in every month of the years of had lasted the study. The east zone of the city of Manaus was where they had been found the biggest number of positive samples for rotavirus, as well as for genotype G and genotype P. The children with positive samples for rotavirus had presented on average of 10 episodes of diarrhea for child per day with predominance for the feces of liquid aspect (86.2%), this profile also was observed in the children with positive samples for genotypes G and genotypes P. With exception of the hyperthermia, other signals and characteristic symptoms of the diarrheic disease for rotavirus as vomit, dehydration and abdominal pain, had been presents in the biggest parcel of the children with positive samples in such a way for human rotavirus as for genotype G, as for genotype P. The high number of samples that had not been tipadas with use of specific primers for genotypes G and P, suggest the circulation of uncommon genotypes in the region, however so that this situation is defined, new studies of the epidemiological molecular of rotavirus circulating in Manaus, Amazon, must be developed, enclosed specific primers also for detention of rotavirus of animal origin. / Os rotavírus humano constituem uma das mais importantes causas de doença diarréica em crianças menores de cinco anos em todo o mundo. Com o objetivo de verificar a ocorrência de genótipos de rotavírus humano em crianças de 1 a 36 meses residentes no município de Manaus no Amazonas, foram analisadas durante os anos de 2004 a 2006, um total de 607 amostras de fezes diarréica que foram coletadas de crianças atendidas em prontos socorros infantis do município de Manaus. Esta análise foi realizada pela detecção do genoma viral através das técnicas de EGPA (eletroforese em gel de poliacrilamida) e RT-PCR (reação de polimerase em cadeia com transcriptase reversa). Através do método de EGPA pode-se observar uma positividade de 25% das amostras para rotavírus humano. Todas as amostras positivas para rotavírus foram genotipadas pelo método de RT-PCR com utilização de primers específicos para os genótipos G (G1, G2, G3, G4 e G9) e genótipos P (P[8], P[4], P[6], P[9] e P[10]). Pela genotipagem foi detectado o genótipo G em 30,7% das amostras positivas para rotavírus, com predominância dos genótipos G2 (17%), seguidos de G1 (14,9%) e G9 (10,6%) e o genótipo P em 44,7% das amostras positivas para os rotavírus, com predominância dos genótipos P[8] em 66,2% das amostras e P[4] em 13,2% das amostras. As combinações dos genótipos G e P foram responsáveis por 53,3% das amostras positivas para rotavírus, sendo que P[8]G1 e P[4]G2 foram as mais encontradas com 12,5% e 10% consecutivamente, seguidas de P[8]G3 (5%). Outras combinações como P[4]G1, P[8]G9 e P[10]G1 também foram encontradas em números menos expressivos. Foi observado que 38,3% das amostras positivas para o genótipo G e 11,7% das amostras positivas para o genótipo P não apresentaram características para nenhum dos genótipos G e P pesquisados. O número amostras positivas para rotavírus humano, bem como para os genótipos G e para os genótipos P foram semelhantes tanto em crianças do sexo masculino, quanto em crianças do sexo feminino, sendo que estas amostras predominaram em crianças menores de 18 meses. As amostras positivas para rotavírus humano, assim como para os genótipos G e para o genótipo P foram encontradas em todos os meses do estudo. A zona leste da cidade de Manaus foi onde foram encontradas o maior número de amostras positivas para rotavírus, assim como para o genótipo G e para o genótipo P. As crianças com amostras positivas para rotavírus apresentaram em média de 10 episódios de diarréia por criança por dia com predominância para os fezes de aspecto líquido (86,2%). Este perfil também foi observado nas crianças com amostras positivas para os genótipos G e para os genótipos P. Com exceção da hipertermia, outros sinais e sintomas característicos da doença diarréica por rotavírus como vômito, desidratação e dor abdominal, estiveram presentes na maior parcela das crianças com amostras positivas para os rotavírus humano, para o genótipo G e para o genótipo P. O número elevado de amostras que não foram tipadas com utilização de primers específicos para os genótipos G e P sugerem a circulação de genótipos incomuns na região, porém para que esta situação seja definida, novos estudos da epidemiologia molecular dos rotavírus circulantes em Manaus, Amazonas, devem ser desenvolvidos, incluindo inclusive primers específicos para detecção de rotavírus de origem animal.

Um total de 144 amostras fecais colhidas de leitões com diarréia provenientes de diversas granjas distribuídas por 10 municípios do Estado de São Paulo, Brasil, foram examinadas para a presença de rotavírus através de eletroforese em gel de poliacrilamida e ELISA, num esquema de triagem em paralelo. Destas, 24 e 39 amostras foram, respectivamente, positivas por estes testes e a caracterização dos genotipos P e G foi realizada em 43 amostras por nested RT-PCR, usando diferentes conjuntos de primers. Utilizando-se primers animais, o genotipo P[6] foi o mais freqüente, detectado em 25,58% das amostras, seguido pelo P[1] (11,62%) e P[7] (9,3%). Infecção concomitante de genotipos P[6]+P[7] (9,3%), P[1]+P[6] (4,65%), P[1]+P[6]+P[7] (2,32%) foi também observada. O genotipo G[5] foi o mais freqüente, detectado em 30,23% das amostras, seguido pelo G[10] (20,93%) e G[6] (4,65%). Infecção concomitante de genotipos G[5]+G[10] (18,6%) foi também observada. Utilizando-se primers humanos, somente o genotipo P[6] (65,11%) foi encontrado. Foram detectados os genotipos G[4] (27,9%), G[3] (13,95%) nas amostras, e as infecções concomitantes G[3]+G[4] (9,3%), G[2]+G[3]+G[4] (4,65%) e G[2]+G[3] (2,32%). A combinação mais freqüente foi G[5]P[6] e G[4]P[6], porém foram encontradas também infecções mistas, genotipos atípicos e reassortants. O seqüenciamento do gene a partir dos produtos de nested PCR dos genotipos animais P e G mostrou diversidade de nucleotídeos e aminoácidos dentro de um mesmo genotipo. As árvores filogenéticas utilizando o critério de maxima parcimônia e o algoritmo branch-and-bound, tiveram topologias nas quais as seqüências de nucleotídeos geradas neste trabalho concordam com as outras descritas anteriormente e pertencentes a um mesmo genotipo, suportadas por índices aceitáveis de \"bootstrap\". Os resultados deste estudo, além de contribuir para um melhor entendimento da epidemiologia dos rotavírus suínos, é relevante ao mostrar que além de haver uma diversidade de genotipos circulantes no campo, há também dentro dos mesmos genotipos, e isto deve ser considerado ao se utilizar e desenvolver métodos de diagnóstico, bem como ao se adotarem medidas preventivas específicas contra esta doença. / A total of 144 fecal specimens collected from piglets with diarrhea from many swine-producing units distributed among 10 municipalities of São Paulo State, Brazil, were examined for rotavirus by polyacrylamide gel electrophoresis and ELISA, in a parallel screening scheme. Twenty-four and thirty-nine samples, respectively, were positive by these tests and the characterization of the P and G genotypes was performed on 43 samples by a nested reverse transcription-PCR typing assay, using different sets of primers. Using the animal set of primers, the P[6] genotype was the most frequent, accounting for viruses in 25.58% of the samples, followed by P[1] (11.62%) and P[7] (9.3%). Concomitant infection of P[6]+P[7] (9.3%), P[1]+P[6] (4.65%), P[1]+P[6]+P[7] (2.32%) genotypes was also observed. The G[5] genotype was the most frequent, accounting for viruses in 30.23% of the samples, followed by G[10] (20.93%) and G[6] (4.65%). Concomitant infection of G[5]+G[10] (18.6%) genotypes was observed. Using human set of primers, only the P[6] (65.11%) genotype was found. It was detected the genotypes G[4] (27.9%), G[3] (13.95%) on the samples. Concomitant infection of the genotypes G[3]+G[4] (9.3%), G[2]+G[3]+G[4] (4.65%) and G[2]+G[3] (2.32%) was also observed. The more frequent combination were G[5]P[6] and G[4]P[6], but it was found mixed infections, atypical genotypes and reassortants. Gene sequencing of nested products of G and P animal genotypes showed a diversity of nucleotides and aminoacids under the same genotype. The phylogenetic trees for P and G genotypes under the maximum parsimony criterion, using the branch-and-bound algorithm, had topologies in which the nucleotide sequences generated by this work agree to others described elsewhere that have the same genotypes, supported by acceptable scores of bootstrapping. The results of the present study, while contributing to a better understanding of epidemiology of porcine rotaviruses, address the relevance that there is not only a diversity of genotypes circulating on the field, but inside the same genotypes, and this must be considered when using and developing diagnostic tests, as well when carrying out specific preventive measures against this disease.

Au niveau de la santé publique, l'impact meurtrier des infections au rotavirus humain (RVH) et les limites d'application des vaccins disponibles déterminent l'urgence et la nécessité de développer de nouvelles approches pour immuniser une grande partie de la population mondiale sans effets secondaires néfastes. Pour pallier à l'énorme demande en médicaments et en vaccins, plusieurs groupes de recherche tentent de développer de nouvelles méthodes de production à base de plantes transgéniques. La production de médicaments et vaccins chez les végétaux possèdent des avantages inhérents dont une absence de pathogènes humain, une inoculation facile, de faibles coûts de production à grande échelle et la production d'inocula bruts stockables. Le succès des systèmes d'expression à base de plantes justifie le développement de plants qui produisent beaucoup de biomasse et se transforment génétiquement de façon courante. Le travail présenté ici démontre le potentiel du système d'expression transitoire par agroinfiltration de Nicotiana benthamiana pour produire les antigènes VP7 et VP4∆ du RVH ainsi que l'adjuvant protéinique fljB de Salmonella typhimurium. Le clonage des séquences codantes des antigènes VP7, VP4∆ et fljB a permis de générer de multiples constructions simple, double et triple. Toutes les contructions ont été exprimées dans les feuilles agroinfiltrées à l'exception de VP4∆::VP7 qui n'a pas été détectée par immunobuvardage. Le rendement de protéines d'intérêt dans les extraits végétaux se situe entre 0,85 et 31,97 µg de protéine recombinante par gramme de feuilles fraîches. Plusieurs facteurs dont la toxicité et la stabilité des différentes constructions dans les plantes peuvent expliquer cet écart. Dans nos conditions expérimentales, toutes les constructions contenant le fragment fljB ont permis la production d'anticorps spécifiques à fljB dans les souris immunisées avec les extraits végétaux. Par contre, aucune construction n'as permis la production d'anticorps spécifiques à VP7 ou VP4. Ces résultats montrent que l'expression transitoire dans Nicotiana benthaminana permet de produire rapidement de multiples antigènes et que les protéines fortement immunogéniques dans les extraits végétaux induisent une réponse humorale chez les souris. Plusieurs applications de cette technologie sont envisageables dans la cadre du contrôle endémique du RVH ou de Salmonella typhimurium. ______________________________________________________________________________ MOTS-CLÉS DE L’AUTEUR : Rotavirus humain, VP7, VP4, Salmonella typhimurium, fljB, Expression transitoire, Vaccins à base de plantes, Nicotiana benthaminana.