<p>Despite high vaccination rates and effective adaptive immune responses from the part of infected individuals, influenza A viruses cause significant morbidity and mortality annually. This is due to influenza's rapid antigenic evolution, whereby continual mutations occurring in epitope regions of the virus's hemagglutinin protein result in the diminishment of long-term antibody recognition, in a process that has been termed `antigenic drift'. Although it is clear that antigenic drift enables previously infected individuals to become reinfected, the mechanism that is responsible for influenza's antigenic drift is still under debate. As recently as 2009, a new hypothesis of antigenic drift was put forward that argues that binding avidity changes in the viral hemagglutinin result in antigenic drift as a side effect. This hypothesis stands in contrast to the traditionally accepted hypothesis that mutations in epitope regions are positively selected for their ability to evade immune recognition. This thesis focuses on the use of epidemiological models and empirical data analysis to explore different hypotheses of antigenic drift. </p><p>In the first chapter, I am asking what effects on antigenic drift rate would be produced under the new hypothesis. I mathematically formulate the hypothesis that antigenic drift is simply a side effect of cellular receptor binding avidity changes that occur as the virus is transmitted between individuals of different immune status levels. I then use this formulation to explore how influenza's rate of antigenic drift depends on different epidemiological factors, including host contact rate, host lifespan, and the duration of infection. Finally, I use the model to assess alternative vaccination strategies by the impact they have on rates of antigenic drift and therewith rates of disease incidence/</p><p>In the second chapter, I critically evaluate the binding avidity hypothesis by comparing predictions of the hypothesis against empirical data. I first use a `phylodynamic' extension of the model presented in the first chapter to determine whether the hypothesis is consistent with the ladderlike phylogeny of influenza's hemagglutinin protein. I then use viral sequence data and metadata to determine whether older aged individuals (with a higher number of previous infections) harbor viruses with higher binding avidity than younger aged individuals (with a lower number of previous infections), a prediction made by the binding avidity hypothesis. Finally, I perform a phylogenetic analysis to determine how rapidly binding avidity changes occur. From these analyses, I conclude that the binding avidity hypothesis is not well supported by empirical data.</p><p>In the third chapter, I develop an integrated viral life cycle model, in which viral replication depends on three viral phenotypes: receptor binding avidity, neuraminidase activity, and antigenicity. This integrated model recognizes that receptor binding avidity changes will influence viral replication, but also allows for antigenic evolution to be brought about directly by epitope changes. I first use this model to show how the evolutionary dynamics of these phenotypes are dependent on one another and how antigenic drift can be interpreted within this framework. I then return to some of the questions addressed in the first chapter to ask how different epidemiological factors impact influenza's rate of antigenic drift.</p><p>Together, these three chapters highlight the importance of viral phenotypes other than antigenicity in contributing to influenza's antigenic evolution, and, more generally, the importance of computational and mathematical research in understanding constraints on viral adaptation.</p> / Dissertation

Thesis (Ph. D.)--Ohio State University, 2007. / Full text release at OhioLINK's ETD Center delayed at author's request.

Thesis (M.S.)--University of Texas Health Science Center at Houston, School of Public Health, 2007. / Source: Masters Abstracts International, Volume: 45-05, page: 2360. Adviser: Cynthia L. Chappell.

Thesis (M.S.)--University of Alabama at Birmingham, 2007. / Description based on contents viewed Oct. 3, 2008; title from PDF t.p. Includes bibliographical references (p. 64-67).

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (leaves 147-179).

A raiva é uma zoonose causada pelo vírus da raiva (VR), um membro do gênero Lyssavirus da família Rhabdoviridae. Apesar do VR ser considerado antigenicamente estável, amostras com variações antigênicas têm sido detectadas. Na busca de identificar possíveis variantes circulantes no Brasil, um dos objetivos do presente estudo foi identificar as características antigênicas de amostras de vírus rábico circulantes nas regiões Centro-Oeste e Norte do Brasil. Para tanto, amostras do VR coletadas naquelas regiões, isoladas de diferentes hospedeiros, tiveram seu perfil antigênico avaliado por imunofluorescência indireta frente a um painel de anticorpos monoclonais preparados contra antígenos de lissavírus. Foram identificados três perfís antigenicamente distintos: um característico de amostras de origem de cães domésticos, outro de amostras de morcegos hematófagos e outro de amostras de morcegos não hematófagos. O segundo objetivo deste estudo consistiu em avaliar a estabilidade antigênica e a patogenia de amostras com tais perfís antigênicos distintos. Para atingir este objetivo, três amostras de VR com diferentes perfís antigênicos foram submetidas a vinte inoculações sucessivas em camundongos. Á medida em que as passagens eram realizadas, o perfil antigênico das mesmas era monitorado. Os resultados obtidos revelaram que todas as amostras mantiveram-se relativamente estáveis e todas as amostras ao longo as 20 inoculações mantiveram altamente patogenicas. Duas delas (a amostra com perfil antigênico de cães e a amostra com perfil antigênico de morcegos hematófagos) mantiveram-se antigenicamente estáveis ao longo de todas as 20 inoculações. Por outro lado a amostra com perfil antigênico usualmente detectado em morcegos não hematófagos apresentou uma modificação antigênica após a sétima passagem sucessiva. Isto pode indicar diferenças no grau de adaptação do vírus à espécie hospedeira natural. Sumarizando os resultados desses estudos, conclui-se que as variantes do VR circulantes nas regiões Norte e Centro-Oeste do Brasil possuem características antigênicas comuns a amostras cujos hospedeiros naturais são cães domésticos, morcegos hematófagos e morcegos não hematófagos. As variantes detectadas apresentam um elevado grau de estabilidade antigênica; a variante cujo hospedeiro natural são morcegos não hematófagos parece menos estável antigenicamente. Essa menor estabilidade antigênica poderia ter relação com o grau de adaptação à espécie hospedeira natural, hipótese que será examinada mais profundamente em estudos futuros. / Rabies is caused by rabies virus (RV), a member of the genus Lyssavirus within the family Rhabdoviridae. Despite the acknowledged antigenic stability of RV, variants have been identified. In search for RV variants circulating in Brazil, one of the objectives of the present study was to identify the antigenic profile of RV isolates from different natural host species in North and Central West regions of Brazil. The isolates had its antigenic profiles determined by indirect immunofluorescence with a panel of monoclonal antibodies prepared to lyssavirus antigens. Three distinct antigenic profiles were detected: one characteristic of isolates from domestic dogs, another in isolates from vampire bats and another in non haematophagous bats. A second aim of the present study was to evaluate the degree of antigenic stability and patogeny of RV isolates with such distinct antigenic profiles. For that, three RV isolates were submitted to twenty successive inoculations in mice and periodically monitored in search for antigenic alterations. The results obtained revealed that in fact the three isolates were quite stable antigenically and all strains after 20 consecutive inoculations maintained higly patogenics. Two of the viruses (dog and vampire bat profiles) remained antigenically stable throughout the twenty successive passages in mice. On the other hand, the isolate with an antigenic profile commonly found in non haematophagous bat viruses revealed an antigenic modification after the seventh passage in mice. This could be indicative of differences in the degree of adaptation of the isolate to its natural host species. Summarizing the results of theses studies, it was concluded that RV variants circulating in the Centre-West and North regions of Brazil display antigenic profiles common to those usually detected in isolates whose natural hosts are domestic dogs, haematophagous and non hematophagous bats. Such variants display a relatively high degree of antigenic stability; however, the variant whose natural hosts are non haematophagous bats seem less antigenically stable. Such lesser degree of antigenic stability might be related to the degree of adaptation of the virus to its natural host species. Such hypothesis shall be examined more deeply in future studies.

Master of Science / Department of Diagnostic Medicine/Pathobiology / Richard Hesse / Bovine Coronavirus (BCoV) is known to cause enteric and respiratory diseases, such as calf diarrhea, winter dysentery, calf respiratory disease, and bovine respiratory disease complex (BRD). All of these diseases are believed to be caused by the same genotype of BCoV. BCoV exhibits tissue tropism for both the gastrointestinal and respiratory tracts. This tropism is due to 9-O-acetylated sialic acid receptor on both epithelial cells in the respiratory and enteric tract. Currently, the only vaccine available for BCoV targets the enteric form of the disease. This study addresses the hypothesis that antibodies from the enteric form of the disease can cross neutralize the respiratory form of the virus. Data from surveillance studies suggest that BCoV is one of the major contributors to BRD, for which there is no currently approved vaccine for the respiratory form of the disease. Our approach to answering this question is to sequence and analyze the complete genome of 11 respiratory and enteric coronavirus isolates using next generation sequencing (NGS). Following the NGS, viruses were selected based on phylogenetic analysis and ability to grow and be maintained in cell culture. These viruses were then be used as serum neutralization indicator viruses in SN assays. 147 bovine serums submitted to KSVDL were used to determine if there are any serological differences between the immune response to respiratory versus enteric viruses based on the antibodies produced by the animal. The overall results show that there are few differences between the enteric and respiratory isolates at the genomic level and the serological response from the animal to these viruses. The differences between enteric and respiratory virus will need to be further addressed and analyzed to conclude if there is a noteworthy difference between the viruses with different tropisms. Other factors, such as host immune response and environment, are believed to be involved in the virus tropism to certain areas of the body.

A raiva é uma zoonose causada pelo vírus da raiva (VR), um membro do gênero Lyssavirus da família Rhabdoviridae. Apesar do VR ser considerado antigenicamente estável, amostras com variações antigênicas têm sido detectadas. Na busca de identificar possíveis variantes circulantes no Brasil, um dos objetivos do presente estudo foi identificar as características antigênicas de amostras de vírus rábico circulantes nas regiões Centro-Oeste e Norte do Brasil. Para tanto, amostras do VR coletadas naquelas regiões, isoladas de diferentes hospedeiros, tiveram seu perfil antigênico avaliado por imunofluorescência indireta frente a um painel de anticorpos monoclonais preparados contra antígenos de lissavírus. Foram identificados três perfís antigenicamente distintos: um característico de amostras de origem de cães domésticos, outro de amostras de morcegos hematófagos e outro de amostras de morcegos não hematófagos. O segundo objetivo deste estudo consistiu em avaliar a estabilidade antigênica e a patogenia de amostras com tais perfís antigênicos distintos. Para atingir este objetivo, três amostras de VR com diferentes perfís antigênicos foram submetidas a vinte inoculações sucessivas em camundongos. Á medida em que as passagens eram realizadas, o perfil antigênico das mesmas era monitorado. Os resultados obtidos revelaram que todas as amostras mantiveram-se relativamente estáveis e todas as amostras ao longo as 20 inoculações mantiveram altamente patogenicas. Duas delas (a amostra com perfil antigênico de cães e a amostra com perfil antigênico de morcegos hematófagos) mantiveram-se antigenicamente estáveis ao longo de todas as 20 inoculações. Por outro lado a amostra com perfil antigênico usualmente detectado em morcegos não hematófagos apresentou uma modificação antigênica após a sétima passagem sucessiva. Isto pode indicar diferenças no grau de adaptação do vírus à espécie hospedeira natural. Sumarizando os resultados desses estudos, conclui-se que as variantes do VR circulantes nas regiões Norte e Centro-Oeste do Brasil possuem características antigênicas comuns a amostras cujos hospedeiros naturais são cães domésticos, morcegos hematófagos e morcegos não hematófagos. As variantes detectadas apresentam um elevado grau de estabilidade antigênica; a variante cujo hospedeiro natural são morcegos não hematófagos parece menos estável antigenicamente. Essa menor estabilidade antigênica poderia ter relação com o grau de adaptação à espécie hospedeira natural, hipótese que será examinada mais profundamente em estudos futuros. / Rabies is caused by rabies virus (RV), a member of the genus Lyssavirus within the family Rhabdoviridae. Despite the acknowledged antigenic stability of RV, variants have been identified. In search for RV variants circulating in Brazil, one of the objectives of the present study was to identify the antigenic profile of RV isolates from different natural host species in North and Central West regions of Brazil. The isolates had its antigenic profiles determined by indirect immunofluorescence with a panel of monoclonal antibodies prepared to lyssavirus antigens. Three distinct antigenic profiles were detected: one characteristic of isolates from domestic dogs, another in isolates from vampire bats and another in non haematophagous bats. A second aim of the present study was to evaluate the degree of antigenic stability and patogeny of RV isolates with such distinct antigenic profiles. For that, three RV isolates were submitted to twenty successive inoculations in mice and periodically monitored in search for antigenic alterations. The results obtained revealed that in fact the three isolates were quite stable antigenically and all strains after 20 consecutive inoculations maintained higly patogenics. Two of the viruses (dog and vampire bat profiles) remained antigenically stable throughout the twenty successive passages in mice. On the other hand, the isolate with an antigenic profile commonly found in non haematophagous bat viruses revealed an antigenic modification after the seventh passage in mice. This could be indicative of differences in the degree of adaptation of the isolate to its natural host species. Summarizing the results of theses studies, it was concluded that RV variants circulating in the Centre-West and North regions of Brazil display antigenic profiles common to those usually detected in isolates whose natural hosts are domestic dogs, haematophagous and non hematophagous bats. Such variants display a relatively high degree of antigenic stability; however, the variant whose natural hosts are non haematophagous bats seem less antigenically stable. Such lesser degree of antigenic stability might be related to the degree of adaptation of the virus to its natural host species. Such hypothesis shall be examined more deeply in future studies.

A partir de uma biblioteca de cDNA de glândulas de veneno de Micrurus corallinus (cobra-coral), uma serpente da Família Elapidae bastante representada no Brasil e muito comum em áreas florestais tropicais, foram gerados 1.438 Expressed Sequences Tags (ESTs), agrupados em 611 clusters. O banco representa os genes mais expressos na glândula de veneno de M. corallinus. Os transcritos relacionados às toxinas apresentaram ao redor de 46% de representação nesse banco de seqüências. A composição geral das toxinas inclui: toxinas de três dígitos (3FTx) (24%), fosfolipases A2 (PLA2) (16%), lectinas do tipo C (5%), entre outros. O banco permitiu não somente a identificação de possíveis toxinas, mas também de transcritos celulares, sendo a maioria envolvida nas funções fisiológicas de células da glândula de veneno. A maior parte dessas moléculas apresenta um envolvimento na expressão gênica e protéica, o que reflete uma alta especialização do tecido para a síntese de toxinas. A análise do transcriptoma de glândulas de veneno de M. corallinus possibilitou a identificação de alguns candidatos antigênicos para um anti-soro antielapídico alternativo. Cinco candidatos antigênicos foram selecionados por meio da análise do transcriptoma obtido: Atg1 (Grupo das neurotoxinas Homolog 8), Atg2 (Grupo das neurotoxinas Homolog 7/3/1), Atg3 (Outras neurotoxinas 1), Atg4 (Outras neurotoxinas 2) e Atg5 (fosfolipase do tipo A2). Avaliamos a viabilidade de imunização com o DNA desses candidatos. Para isso, os cinco grupos de antígenos foram clonados, primeiramente em pGEM-T e, posteriormente, em pSecTag2A, que é um vetor de expressão em células de mamíferos. As clonagens foram inicialmente testadas em células do tipo COS (transfecção transiente), entretanto não ficou clara a capacidade dessas células em expressar os antígenos. Para a análise da resposta imunológica da vacina de DNA, proteínas recombinantes produzidas em E. coli foram utilizadas para o coating de ELISA para detectar anticorpos presentes no soro primário proveniente da imunização com DNA. Os resultados mostraram que o soro dos animais imunizados foi capaz de reconhecer os antígenos recombinantes. Isso indica que a imunização por DNA em camundongos poderia ser uma boa alternativa em relação à imunização do veneno puro de serpente, que é custosa e muito depende da disponibilidade do veneno. Apesar da necessidade de testes complementares, esse é um resultado promissor, já que a produção de anticorpos pode ser alcançada por via de imunização intramuscular, mais prática para objetivos de produção. / Micrurus corallinus(coral snake) is a tropical forest snake belonging to the Elapidae Family, and is very common in Brazil. From the cDNA library of its venom glands, 1.438 Expressed Sequences Tags (ESTs) were generated and grouped into 611 clusters. This database contains the most expressed genes in the M. corallinus venom glands. The transcripts related to toxins represent approximately 46% of the total genes in this database. The toxin compound consists of: three finger toxins (24%), phospholipases A2 (PLA2s) (16%), type-C lectins (5%), among others. This database allowed not only the identification of possible toxins, but also the identification of cellular transcripts, most of which seems to be involved in physiological functions of venom gland cells. The majority of these molecules are involved in gene and protein expression, revealing the high level of specialization of the tissue for toxin synthesis. The analysis of the M. corallinus venom gland transcriptome allowed the identification of some antigenic candidates for an alternative antielapidic antiserum. Five antigenic candidates were selected after analysing the transcriptome: Atg1 (Homolog group 8), Atg2 (Homolog group 7/3/1), Atg3 (Other neurotoxins 1), Atg5 (A2-type phospholipase). These five antigenic groups were used for DNA immunization. Then they were first cloned in pGEM-T and, after, in pSecTag2A, which is an expression vector in mammal cells. The cloning was tested in COS-type cells (transient transfection), without signs of expression. To analyze the immunological response, recombinant proteins were produced in E. coli and used for ELISA coating to react with the primary serum deriving from the DNA immunization. The results showed that the serum from the immunized animals was able to recognize the recombinant antigens, indicating that the DNA immunization in mice could be a feasible alternative regarding the traditional immunization with crude snake venom, which is costly and heavily dependent on the availability of the venom. Regardless the need for additional tests, this is a promising result, because the antibody production can be achieved by intramuscular immunization, a more effective method when aiming for downstream production.

A raiva é uma zoonose causada pelo vírus da raiva (VR), um membro do gênero Lyssavirus da família Rhabdoviridae. Apesar do VR ser considerado antigenicamente estável, amostras com variações antigênicas têm sido detectadas. Na busca de identificar possíveis variantes circulantes no Brasil, um dos objetivos do presente estudo foi identificar as características antigênicas de amostras de vírus rábico circulantes nas regiões Centro-Oeste e Norte do Brasil. Para tanto, amostras do VR coletadas naquelas regiões, isoladas de diferentes hospedeiros, tiveram seu perfil antigênico avaliado por imunofluorescência indireta frente a um painel de anticorpos monoclonais preparados contra antígenos de lissavírus. Foram identificados três perfís antigenicamente distintos: um característico de amostras de origem de cães domésticos, outro de amostras de morcegos hematófagos e outro de amostras de morcegos não hematófagos. O segundo objetivo deste estudo consistiu em avaliar a estabilidade antigênica e a patogenia de amostras com tais perfís antigênicos distintos. Para atingir este objetivo, três amostras de VR com diferentes perfís antigênicos foram submetidas a vinte inoculações sucessivas em camundongos. Á medida em que as passagens eram realizadas, o perfil antigênico das mesmas era monitorado. Os resultados obtidos revelaram que todas as amostras mantiveram-se relativamente estáveis e todas as amostras ao longo as 20 inoculações mantiveram altamente patogenicas. Duas delas (a amostra com perfil antigênico de cães e a amostra com perfil antigênico de morcegos hematófagos) mantiveram-se antigenicamente estáveis ao longo de todas as 20 inoculações. Por outro lado a amostra com perfil antigênico usualmente detectado em morcegos não hematófagos apresentou uma modificação antigênica após a sétima passagem sucessiva. Isto pode indicar diferenças no grau de adaptação do vírus à espécie hospedeira natural. Sumarizando os resultados desses estudos, conclui-se que as variantes do VR circulantes nas regiões Norte e Centro-Oeste do Brasil possuem características antigênicas comuns a amostras cujos hospedeiros naturais são cães domésticos, morcegos hematófagos e morcegos não hematófagos. As variantes detectadas apresentam um elevado grau de estabilidade antigênica; a variante cujo hospedeiro natural são morcegos não hematófagos parece menos estável antigenicamente. Essa menor estabilidade antigênica poderia ter relação com o grau de adaptação à espécie hospedeira natural, hipótese que será examinada mais profundamente em estudos futuros. / Rabies is caused by rabies virus (RV), a member of the genus Lyssavirus within the family Rhabdoviridae. Despite the acknowledged antigenic stability of RV, variants have been identified. In search for RV variants circulating in Brazil, one of the objectives of the present study was to identify the antigenic profile of RV isolates from different natural host species in North and Central West regions of Brazil. The isolates had its antigenic profiles determined by indirect immunofluorescence with a panel of monoclonal antibodies prepared to lyssavirus antigens. Three distinct antigenic profiles were detected: one characteristic of isolates from domestic dogs, another in isolates from vampire bats and another in non haematophagous bats. A second aim of the present study was to evaluate the degree of antigenic stability and patogeny of RV isolates with such distinct antigenic profiles. For that, three RV isolates were submitted to twenty successive inoculations in mice and periodically monitored in search for antigenic alterations. The results obtained revealed that in fact the three isolates were quite stable antigenically and all strains after 20 consecutive inoculations maintained higly patogenics. Two of the viruses (dog and vampire bat profiles) remained antigenically stable throughout the twenty successive passages in mice. On the other hand, the isolate with an antigenic profile commonly found in non haematophagous bat viruses revealed an antigenic modification after the seventh passage in mice. This could be indicative of differences in the degree of adaptation of the isolate to its natural host species. Summarizing the results of theses studies, it was concluded that RV variants circulating in the Centre-West and North regions of Brazil display antigenic profiles common to those usually detected in isolates whose natural hosts are domestic dogs, haematophagous and non hematophagous bats. Such variants display a relatively high degree of antigenic stability; however, the variant whose natural hosts are non haematophagous bats seem less antigenically stable. Such lesser degree of antigenic stability might be related to the degree of adaptation of the virus to its natural host species. Such hypothesis shall be examined more deeply in future studies.