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Dissertations / Theses on the topic 'Viral diversity'

Author: Grafiati

Published: 4 June 2021

Last updated: 26 July 2025

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1

Wikramaratna, Paul Silva. "The evolution of viral diversity." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:1d718b15-af79-4567-84ef-f97f61f75369.

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This thesis focuses on the population dynamics of three antigenically diverse RNA viruses: dengue, influenza and HIV-1. It comprises a set of studies highlighting the roles of structural constraints on critical antigenic determinants, interactions between immune responses to different antigenic types, host lifespan, and the degree of mixing between different host populations in determining the epidemiology and within-host dynamics of these pathogen systems. Dengue exists in humans as a collection of four antigenically related serotypes. Although infection by one serotype appears to convey life

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2

Goldsmith, Dawn. "Marine Viral Diversity and Spatiotemporal Variability." Scholar Commons, 2014. https://scholarcommons.usf.edu/etd/5227.

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Marine viruses are the most numerous biological entities in the ocean, with an estimated abundance of 4 x 1030. They merit study not only because of their sheer abundance, but also because of the role they play in the Earth's biogeochemical cycles. Viral lysis of bacteria redirects the flow of nutrients among marine microbes, which ultimately affects the efficiency of the biological pump. Viral diversity is important because most viruses are host-specific. In preying on a certain type of bacteria, viruses affect the diversity and structure of the bacterial community, leading to changes in carb

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3

Smith, Jennifer. "Viral diversity and dynamics of hepatitis C virus." Thesis, University of Oxford, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.559853.

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Complex patterns of HCV infection are increasingly reported, particularly in highly exposed individuals, with multiple and variable subtype profiles seen in many chronic patients. This study aims to address some of the questions arising from this increasingly diverse and dynamic picture, both within hosts and at a population level. In Chapter 2 I find evidence for a highly dynamic infection profile in acute HCV, both in terms of viral load and the dominant subtype. I extrapolate these observations from individual patients to formulate a model of HCV transmission across a high-risk population i

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4

Rollman, Erik. "Concepts in DNA immunization : overcoming viral diversity and enhancing plasmid immunogenicity /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-943-9/.

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5

Souza, Richards Rosineide. "Searching for plant viral diversity by using 454-pyrosequencing." Thesis, University of Nottingham, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.594740.

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Genetic variability in populations of RNA viruses are a very important trait, which can result on the emergence of new more powerful and destructive strains for many plant viruses, e.g. Potato virus Y. Genomic sequencing has been greatly improved due to the generation of new sequencing technologies, such as the 4S4-GS-FLX Titanium series. Different methods of viral RNA extraction and sample preparation were evaluated for their capacity to generate the whole genome of a plant virus. Partial virus purification as a method of viral RNA extraction combined with a double-stranded cDNA sample prepar

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6

Bull, Rowena Biotechnology &amp Biomolecular Sciences Faculty of Science UNSW. "Mechanisms of replication and genomic diversity in human caliciviruses." Awarded by:University of New South Wales. Biotechnology & Biomolecular Sciences, 2007. http://handle.unsw.edu.au/1959.4/40657.

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Norovirus (NoV) and Sapovirus (SaV) are major causes of outbreak gastroenteritis worldwide. NoV and SaV are highly infectious, have multiple transmission routes and have a short incubation period, thereby facilitating rapid intercontinental spread of new variants. Consequently, a treatment would be advantageous for controlling them. However, currently little is known about the replication cycle and evolution of human NoV or SaV as neither are culturable. NoV and SaV are RNA viruses of the Caliciviridae family and have great genetic diversity which is thought to facilitate irnmune evasion. Cons

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7

Anderson, Jon Paul. "Molecular diversity and evolution of human immunodeficiency virus type 1 /." Thesis, Connect to this title online; UW restricted, 1999. http://hdl.handle.net/1773/8049.

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8

Ribeiro, Ruy Miguel. "Models of viral diversity and disease development in HIV infection." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302403.

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9

Ignacio, Espinoza Julio C. "Functional and Population Based Viral Ecology." Diss., The University of Arizona, 2015. http://hdl.handle.net/10150/347118.

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Viruses represent the most abundant biological entities on earth where, they are able to interact with all kingdoms of life. Yet their diversity, ecology and evolutionary aspects are only beginning to be fully elucidated, mainly due to technical limitations. The vast majority of the microbial world remains elusive to culture; more than 90% of genome sequenced viral isolates infect only 5 of the 54 prokaryotic phyla that are currently recognized. In contrast, viral metagenomics bypasses the need for cultures by directly sequencing fragmented genetic material of environmental viral communities.

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10

Stevens, Kim. "Multiplicity of viral infection in brown algae." Thesis, University of Plymouth, 2014. http://hdl.handle.net/10026.1/3156.

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Brown algae are important primary producers and habitat formers in coastal environments and are believed to have evolved multicellularity independently of the other eukaryotes. The phaeoviruses that infect them form a stable lysogenic relationship with their host via genome integration, but have only been extensively studied in two genera: Ectocarpus and Feldmannia. In this study I aim to improve our understanding of the genetic diversity, host range and distribution of phaeoviruses. Sequencing and phylogenetic analysis of amplified fragments of three core phaeoviral genes (encoding major caps

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11

Fancello, Laura. "A viral metagenomic approach to study taxonomic and functional diversity of viral communities from the environment to humans." Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM5046/document.

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Les virus sont les entités biologiques les plus abondantes et diversifiées sur Terre et leur diversité est encore très peu connue. Récemment, la métagénomique virale a facilité l'exploration de cette diversité. Néanmoins, la plupart des viromes environnementaux générés à ce jour proviennent de régions tempérées et la plupart des viromes humains proviennent d’échantillons de selles, sang ou de prélèvements oro-naso-pharyngés. L'objectif de mon travail de thèse était d’apporter de nouvelles connaissances sur les communautés virales d’environnements et d’échantillons humains les moins étudiés en

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12

Madrieres, Sarah. "Etude des interactions entre l'orthohantavirus Puumala et son réservoir dans l'épidémiologie de la néphropathie épidémique." Electronic Thesis or Diss., Montpellier, SupAgro, 2020. http://www.theses.fr/2020NSAM0022.

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Afin de mieux prévenir l'émergence des maladies infectieuses, il est important d'étudier et de mieux comprendre les interactions qui régissent entre les différents acteurs (humain, virus, hôtes/réservoirs, environnement) intervenant dans ce processus. Nous nous sommes intéressés à la néphropathie épidémique (NE) et plus particulièrement à sa situation épidémiologique en France où une extension de la distribution géographique des cas humains a pu être observée au cours de ces dernières années. La France propose une situation particulière avec des zones dites endémiques (nombreux cas humains de

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13

Gnädig, Nina Franziska. "Role of genetic diversity of RNA viruses in viral evolution and pathogenicity." Paris 7, 2012. http://www.theses.fr/2012PA077095.

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Le taux de fréquence de mutation des virus à ARN est très élevé, en raison des erreurs commises par TARN polymerase dépendante de TARN. Par conséquent, une population virale génétiquement diverse est générée, sur la base d'une séquence consensus. Cette population, ou quasi-espèce, se comportent comme une entité unique en terme d'évolution et de sélection. Cet aspect permet aux virus de s'adapter rapidement à de nouveaux environnements. Pendant le première partie de mon travail, je me suis concentrée sur l'étude d'un variant haute fidélité (A372V) et d'un variant basse fidélité (S299T) de la po

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14

Leoz, Marie. "HIV-1 Group O Genetic Diversity : Characterization, Evolution and Associated Viral Properties." Rouen, 2016. http://www.theses.fr/2016ROUENR14.

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Les VIH-1 de groupe 0 (VIH-1/0) sont des variants rares, essentiellement retrouvés au Cameroun où ils représenteraient plusieurs milliers de cas. Les causes de leur faible diffusion restent méconnues: leur émergence serait aussi ancienne que les VIH-1 de groupe M, pourtant devenus pandémiques. En près d'un siècle, les VIII-1/0 ont développé une importante diversité génétique, dont la description reste ambiguë du fait de l'existence de plusieurs nomenclatures basées sur un nombre restreint de séquences génétiques. Peu de données sont disponibles quant aux causes de cette diversité et à son impa

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15

French, Rebecca. "Using Metagenomics to Reveal the Drivers of Viral Diversity in New Zealand Ecological Communities." Thesis, The University of Sydney, 2022. https://hdl.handle.net/2123/29881.

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Viruses are commonly viewed as pathogens. However, recent studies using large-scale metagenomic and metatranscriptomic sequencing have shown that viruses are highly diverse, abundant and often found in apparently healthy hosts. This suggests a change in perspective is needed, in which viruses are viewed as integral parts of ecosystems rather than solely as agents of disease. My thesis aims to build on this new perspective and contribute to understanding the role of viruses at the ecosystem scale. Accordingly, I investigated the drivers of viral diversity and abundance in ecological communities

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16

Boussier, Jeremy. "Chikungunya Virus Superinfection Exclusion and Defective Viral Genomes : Insights into Alphavirus Regulation of Genetic Diversity." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC181/document.

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Les arbovirus (dont le virus chikungunya, CHIKV) sont responsables de millions d'infections chaque année ; aucun vaccin n'est encore approuvé, et les traitements disponibles restent limités. De part leur circulation constante entre le moustique et l'humain, leur adaptation rapide à différents hôtes est un facteur clé pour leur pathogenèse. Le taux d'erreur particulièrement élevé de leur polymérase ARN permet une rapide diversification génique qui conduit à la génération d'un nuages de mutants, appelée quasi espèce. Les quasi espèces contiennent non seulement des génomes mutés, mais aussi des A

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17

Bandawe, Gama Petulo. "Understanding the interplay between HIV-1 diversity, humoral immune responses and viral fitness." Doctoral thesis, University of Cape Town, 2014. http://hdl.handle.net/11427/8689.

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Includes bibliographical references.<br>HIV-1 antibody dependent cell cytotoxicity (ADCC) and neutralizing antibody (nAb) responses are both thought to be important responses to elicit through vaccination. This thesis characterises neutralizing response in two cohorts in Africa, and in a detailed study of one individual, elucidates the interplay between ADCC and nAb responses in early infection, and the impact of humoral escape on viral fitness. It remains an open question whether different geographically distinct population groups vary in their neutralization responses to HIV-1. We compared n

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18

Bollyky, Paul Laszlo. "Viral genetic diversity and clinical disease in Hepatitis B virus infection : a phylogenetic approach." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301179.

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19

Telford, Marco 1984. "Genetic diversity and geographic patterns of human herpesvirus 4 and 6." Doctoral thesis, Universitat Pompeu Fabra, 2017. http://hdl.handle.net/10803/664509.

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This thesis focuses on Human herpesvirus 4 and 6, two ubiquitous viruses with a long list of putative disease associations, ranging from malignancies such as lymphomas and carcinomas to multiple sclerosis. To date, the relatively limited genetic data on these organisms hinders the understanding of their variability and their genetic structure at a population level. We here explore wet lab techniques for the production of genetic data in a cost-effective manner in order to reach the order of magnitude that is required to unravel the genetics these viruses. After successfully identifying indiv

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20

Lymer, David. "Significance and Diversity of Lake Bacteriophages." Doctoral thesis, Uppsala : Uppsala universitet, Universitetsbiblioteket, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9499.

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21

Noune, Christopher. "Dynamics, diversity and evolution of Baculoviruses." Thesis, Queensland University of Technology, 2017. https://eprints.qut.edu.au/113154/2/Christopher_Noune_Thesis.pdf.

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This thesis describes an innovative application of leading-edge bioinformatics and sequencing technology to analyse strain diversity, dynamics, and evolution in Baculoviruses under selection in vivo and in vitro. It provides evidence for the first time that these double-stranded DNA viruses are quasispecies. It develops and demonstrates a novel application of high-throughput sequencing and new computational techniques to analyse strain variants in non-model organisms, with potential applications in health, biosecurity and microbial ecology.

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22

Félez, Sánchez-Ocaña Marta. "Connection between viral genetic diversity and clinical manifestation of Papillomavirus infection = Connexió entre la diversitat de genotips virals i les manifestacions clíniques de la infecció pel virus del Papil·loma." Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/404669.

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Papillomaviruses (PVs) are a numerous family of small dsDNA viruses infecting virtually all mammals. PVs cause infections without triggering a strong immune response, and natural infection provides only limited protection against reinfection. Most PVs are part and parcel of the skin microbiota. In some cases, infections by certain PVs take diverse clinical presentations, from highly productive self-limited warts to invasive cancers. The main aim of this thesis is explore the link between HPV genotypic diversity and the phenotypic, clinical diversity of the diseases associated with HPV infecti

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23

MANEA, ELISABETTA. "Microbial biodiversity and viral impact in benthic deep-sea ecosystems." Doctoral thesis, Università Politecnica delle Marche, 2017. http://hdl.handle.net/11566/245403.

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Gli ambienti marini profondi ricoprono il 95% del globo terrestre e sono caratterizzati da basse temperature, assenza di luce ed elevate pressioni. Tra i sistemi marini profondi i più remoti e inesplorati sono le fosse adali, sistemi che possono superare gli 11000 m di profondità. Lo studio di questi ambienti estremi rappresenta una delle più grandi sfide della ricerca scientifica a causa delle difficoltà che si presentano nel raggiungerli. Questo studio fornisce i primi dati riguardanti l’impatto dei virus sui procarioti che abitano i sedimenti di tre tra le più profonde fosse oceaniche conos

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24

Long, Elizabeth Michelle. "Genetic and co-receptor characterization of viral diversity early in human immunodeficiency virus type 1 infection /." Thesis, Connect to this title online; UW restricted, 2001. http://hdl.handle.net/1773/4997.

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25

Droillard, Clément. "Origine de la pathogénicité des lagovirus : avancées sur la diversité génétique virale et le développement d’un système de génétique inverse." Thesis, Rennes 1, 2020. http://www.theses.fr/2020REN1B016.

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Les lagovirus infectent les léporidés (lapins et lièvres). Les lagovirus pathogènes tels que le Rabbit haemorragic disease virus (RHDV) et l’European Brown Hare Syndrome virus (EBHSV) provoquent des hépatites virales souvent mortelles ayant de graves conséquences économiques et écologiques. Les lagovirus non-pathogènes tels que les European Rabbit Calicivirus 1 et 2 (RCV-E1 et RCV-E2) et les Hare Calicivirus (HaCV) ne provoquent aucune maladie chez les lapins et les lièvres, respectivement. L’émergence d’un nouveau lagovirus pathogène en 2010, nommé RHDV2, capable d’infecter à la fois les lapi

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26

Olonade, Israel Temiloluwa. "Development of a novel high throughput method for identifying phage-host pairs in an extreme environment." University of the Western Cape, 2017. http://hdl.handle.net/11394/5664.

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Philosophiae Doctor - PhD<br>There are approximately 10³¹ bacteriophages in the biosphere, outnumbering bacteria 10:1, hence, the dynamic and specific nature of phage-host interactions exerts significant influence on microbial communities. Bacteriophages also represent the reservoir of the highest known genetic diversity making them a potential source of novel biotechnological products. However, the isolation of novel bacteriophages is limited by the observation that less than 1% of bacterial hosts have been cultured. This study aimed to bypass this problem by developing novel culture independ

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27

Gustavsen, Julia Anne. "Drivers of viral diversity and community compositional change over spatial and temporal scales in coastal British Columbia." Thesis, University of British Columbia, 2016. http://hdl.handle.net/2429/58045.

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Marine viruses are ubiquitous, abundant, and genetically diverse in natural waters. They play key roles in nutrient and carbon cycles. The composition of marine viral communities changes seasonally and repeats annually, and such patterns can be driven by their hosts in response to environmental changes. Moreover, environmental parameters can also directly affect the viral community through the decay of viruses, and differences in viral infectivity under different conditions. Marine viral communities show changes over time and space, but the mechanisms that drive compositional changes and maint

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28

Gantner, Pierre. "Impact des inhibiteurs de l'intégrase sur la constitution et la compartimentalisation du réservoir viral." Thesis, Strasbourg, 2018. http://www.theses.fr/2018STRAJ018.

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L’étude de stratégies visant à diminuer la taille du reservoir viral, et notamment l’impact des traitements antirétroviraux, permettront peut-être de s’approcher des objectifs de guérison de l’infection à VIH. Nous avons analysé la dynamique de ce réservoir chez des personnes vivant avec le VIH débutant un traitement comprenant du dolutegravir (TCD) à différents stades de l’infection. L’étude DRONE a inclus des personnes débutant et répondant à un TCD et suivies pendant 48 semaines. L’ADN-VIH dans les cellules mononucléées du sang périophérique (CMSP), l’ADN-VIH dans les sous-populations lymph

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Kelly, Christabel. "Novel adenoviral vectored vaccines and the implications of viral diversity in therapeutic strategies against Hepatitis C Virus infection." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:8991c349-7096-4643-ae6a-2e36902c8056.

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Hepatitis C virus (HCV) is a major global pathogen estimated to infect over 170 million people worldwide. A recent study has shown that vaccination with adenoviral vectors, based on rare human and simian serotypes encoding the non-structural (NS) proteins of HCV, induces highly potent, multi-specific and durable T cell responses in healthy human volunteers. In this thesis I assess the safety and immunogenicity of these vaccines (ChAd3–NSmut and Ad6-NSmut), for the first time in HCV infected patients. This work also explores whether vaccine-induced T cell responses target in vivo circulating HC

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30

Rademeyer, Cecilia. "An investigation of HIV-1 diversity in Southern Africans, and characterisation of viral populations in recently infected women." Master's thesis, University of Cape Town, 2003. http://hdl.handle.net/11427/2736.

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31

Volle, Romain. "Pathogénie des entérovirus : étude de la charge virale au cours de méningites et de la permissivité des cellules endothéliales microvasculaires cérébrales humaines." Thesis, Clermont-Ferrand 1, 2014. http://www.theses.fr/2014CLF1MM05/document.

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Les entérovirus humains (EV) constituent un groupe de virus à ARN d'une grande diversité génétique. Ils sont responsables d'infections cérébrales graves mais rares et de méningites bénignes mais fréquentes. Les évènements conduisant à l'entrée des EVs dans le système nerveux central (SNC), l'importance de la charge virale dans le liquide céphalo rachidien (LCR) et sa corrélation éventuelle avec l'intensité du processus inflammatoire réactionnel restent peu explorés. Comme de nombreux génotypes d'EV sont associés à des manifestations neurologiques semblables, des processus pathologiques communs

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Ferté, Suzanne. "Exploring the diversity of cyclic electron flow around photosystem I in microalgae species." Electronic Thesis or Diss., Sorbonne université, 2019. http://www.theses.fr/2019SORUS615.

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Les micro-algues sont à l’origine de l’immense majorité des chaines trophiques océaniques et participent à presque la moitié de la photosynthèse sur Terre. Si leur diversité génétique est aujourd’hui bien connue, leur diversité fonctionnelle reste encore peu explorée. La voie principale de la photosynthèse, le flux linéaire d’électrons depuis l’eau vers le CO2 semble bien conservé dans la phylogénie. Il fait intervenir deux photosystèmes en série, les photosystèmes II (PSII) et I (PSI). Chez les plantes et les algues vertes, il existe un flux cyclique d’électrons qui ne fait intervenir que le

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Kuča, Adam. "Determination of the prevalence and diversity of viral gastroenteritis infections and secretor status in the elderly population of the Tshwane region in South Africa." Diss., University of Pretoria, 2019. http://hdl.handle.net/2263/73858.

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Diarrhoeal disease is considered the second most common cause of morbidity and fourth most common cause of mortality, worldwide. Low-income countries such as those in Africa and Asia bear the greatest burden of gastroenteritis. Diarrhoeal disease affects individuals of all ages, however, children <5 years of age, the immunocompromised and the elderly population ≥65 years of age are most severely affected. The elderly population, particularly immunocompromised patients residing in long-term care facilities represent high-risk groups for gastroenteritis and su

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Barbosa, Filho Roberto Alexandre Alves. "Clonagem, sequenciamento e estudos moleculares do genoma de HPV 16 isolado na Amazônia." Universidade Federal do Amazonas, 2010. http://tede.ufam.edu.br/handle/tede/3630.

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Made available in DSpace on 2015-04-22T22:12:45Z (GMT). No. of bitstreams: 1 Roberto Alexandre.pdf: 1763581 bytes, checksum: c0c0eb448d286d60be56fecd5eb291e0 (MD5) Previous issue date: 2010-08-03<br>CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior<br>The Human papillomavirus is responsible for lesions in the oral mucosa, anal and urogenital tract of male and female, transmitted by direct or indirect contact with infected skin or through sexual intercourse. In women these infections can progress to cervical cancer, which is estimated incidence for the Northern region in 2

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Graillot, Benoït. "Analyse de la durabilité de la lutte biologique à l'aide de Baculovirus dans les conditions de protection des cultures." Thesis, Saint-Etienne, EMSE, 2015. http://www.theses.fr/2015EMSE0782.

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La résistance aux agents de biocontrôle est un problème majeur dans les cultures du monde entier. Ainsi, le carpocapse du pommier, Cydia pomonella, a développé des résistances contre des traitements répétés au Cydia pomonella granulovirus (CpGV) dans plusieurs pays d’Europe. Ces résistances posent la question de la durabilité de ce type de lutte contre les ravageurs. Ce travail porte sur l’étude de plusieurs aspects des interactions granulovirus/hôtes : en premier lieu, sur l’étude des différences de sensibilité au CpGV entre des colonies d’insectes de laboratoire afin de mieux cerner les méca

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Thiberville, Simon-Djamel. "Investigations épidémiologiques, cliniques et thérapeutiques du chikungunya." Thesis, Aix-Marseille, 2016. http://www.theses.fr/2016AIXM5016.

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Le virus chikungunya est un arbovirus, transmis par les moustiques du genre Aedes, qui provoque des arthralgies invalidantes et parfois des rhumatismes chroniques. Dans une première partie nous avons décrit les aspects ambulatoires cliniques, biologiques et virologiques du chikungunya (CHIK) de la phase aiguë jusqu'au 300ème jour lors de l’épidémie de la Réunion en 2006. Des scores d’aide au diagnostic ont été élaboré et une étude de la diversité virale intra-hôte a été réalisée. Pour compléter nos premiers résultats nous avons étudié une épidémie survenue en République du Congo en 2011. La de

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Kauffman, Robert Clark. "Genetic Diversity of RT-SHIV Viremia and Viral Reservoirs in a Non-human Primate Model of Human HIV-1 Highly Active Antiretroviral Therapy." Thesis, University of California, Davis, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3626762.

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<p> In most human immunodeficiency virus type 1 (HIV−1) infected individuals, highly active antiretroviral therapy (HAART) suppresses viremia to levels below standard clinical detection limits and delays the progression to AIDS. More sensitive assays have demonstrated that low−level residual viremia is present during HAART. Furthermore, viremia rebounds upon cessation of therapy and thus, life−long treatment is required to prevent the progression to AIDS. This is presumably due to viral persistence within anatomical and cellular viral reservoirs that are not eliminated during

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Zhang, Chunquan. "GENETIC DIVERSITY OF BEAN POD MOTTLE VIRUS (BPMV) AND DEVELOPMENT OF BPMV AS A VECTOR FOR GENE EXPRESSION IN SOYBEAN." UKnowledge, 2005. http://uknowledge.uky.edu/gradschool_diss/437.

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Bean pod mottle virus (BPMV), a member of the genus Comovirus in the family Comoviridae, is widespread in the major soybean-growing areas in the United States. The complete nucleotide sequences of the genomic RNAs of the naturally occurring partial diploid strain IL-Cb1 were determined. Intermolecular RNA1 recombinants were isolated from strain IL-Cb1 and characterized at the molecular level. Structurally similar recombinant RNA1 was also generated after four passages in soybean derived from plants previously inoculated with a mixture of infectious RNA1 transcripts from two distinct strains. B

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Amgarten, Deyvid Emanuel. "Análise computacional da diversidade viral presente na comunidade microbiana do processo de compostagem do Zoológico de São Paulo." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/95/95131/tde-14072017-161226/.

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O estudo da diversidade viral em amostras ambientais tem se tornado cada vez mais importante devido a funções-chave desempenhadas por esses organismos. Estudos recentes têm fornecido evidências de que vírus de bactérias (bacteriófagos) podem ser os principais determinantes em ciclos biogeoquímicos de grandes ecossistemas, além de atuarem no fluxo de genes entre comunidades ambientais e na plasticidade funcional das mesmas frente a estresses ambientais. Neste trabalho, propomos a investigação e caracterização da diversidade viral presente em amostras de compostagem através de abordagens não dep

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El, Ayoubi Miriam Diala. "Human rhinoviruses : development of new reverse genetics methods dedicated to the improvement of the conservation of viral heterogeneity." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0392.

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Les systèmes de génétique inverse permettent de manipuler les génomes viraux et se sont révélés essentiels pour étudier les virus à ARN. Récemment, une méthode basée sur la PCR, la méthode ISA (Infectious Subgenomic Amplicons), a été développée. La première partie de cette thèse se concentre sur la simplification de la méthode ISA. La principale contrainte d'ISA est l'exigence de produire des fragments génomiques modifiés qui nécessite un promoteur de transcription à l’extrémité 5’ du premier fragment et un ribozyme du virus de l'hépatite delta, suivi du signal de polyadénylation du virus simi

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Phan, Ngoc Minh Hien. "Perusing peripatetic pathogenic viruses: Hepatitis B virus and severe acute respiratory syndrome coronavirus 2." Thesis, Queensland University of Technology, 2021. https://eprints.qut.edu.au/226107/1/Ngoc%20Minh%20Hien_Phan_Thesis.pdf.

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This project characterised the genetic diversity of hepatitis B virus (HBV) and SARS-CoV-2, which reflects viral evolution, and drives transmission, viral pathogenesis, and clinical outcomes. Genomes and coding genes of these viruses were analysed using next-generation sequencing, bioinformatic tools and publicly available viral sequences. HBV nucleotide diversity was identified amongst HBV sequences from Australian and non-Australian blood donors. In addition, the frequency of HBV mutants circulating in Southeast Asia, Australia and New Zealand was identified. Europe and East Asia were shown

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Symonds, Erin M. "Viruses Found in Raw Sewage and Their Potential to Indicate Fecal Pollution in Coastal Environments." [Tampa, Fla] : University of South Florida, 2008. http://purl.fcla.edu/usf/dc/et/SFE0002528.

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Pichon, Maxime. "Caractérisation du microbiome respiratoire et de la diversité génomique virale au cours des formes de grippes sévères." Thesis, Lyon, 2018. http://www.theses.fr/2018LYSE1271.

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La grippe est une infection respiratoire responsable de complications respiratoires ou neurologiques nécessitant une prise en charge rapide et adaptée. L’émergence des technologies de séquençage à haut débit (NGS) permet l’étude des communautés microbiennes résidentes ainsi qu’une étude approfondie du génome des pathogènes impliqués. Cette thèse a pour objectif de caractériser le microbiome respiratoire et la diversité génomique virale des patients infectés par les virus grippaux, en corrélant les données clinicobiologiques recueillies. Après recueil des prélèvements respiratoires d’enfants ho

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Costa, Antonio Charlys da. "Caracterização molecular do vírus da dengue pela análise do genoma completo viral em amostras de doadores e receptores de sangue nos estados de Pernambuco e Rio de Janeiro." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/99/99131/tde-13112017-090100/.

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O dengue vírus é o responsável por uma das mais importantes doenças transmitidas por vetores em todo o mundo, causando cerca de 390 milhões de infecções anualmente em mais de 100 países. Estima-se que mais de 3,51 bilhões de pessoas (40% da população mundial) estejam vivendo em regiões de risco. A distribuição geográfica dos tipos de dengue aumentou drasticamente nas últimas décadas, impulsionada pela expansão de sua principal espécie de vetor, o Aedes aegypti, o crescimento da população humana, as viagens, o comércio internacional e a crescente urbanização nos trópicos e subtrópicos. Objetivo

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Chéret, Antoine. "Etude de l’établissement des réservoirs VIH lors de la primo-infection et de l’impact des traitements antirétroviraux très précoces sur ces réservoirs." Thesis, Paris 5, 2014. http://www.theses.fr/2014PA05T013/document.

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La primo-infection est un moment critique de l’établissement du réservoir justifiant de l’initiation d’un traitement précoce. Nous avons initié un essai randomisé évaluant l’impact de deux ans d’un traitement antirétroviral intense (essai ANRS147 OPTIPRIM, trithérapie versus pentathérapie) sur le réservoir et avons initié des études physiopathologiques au cours de cet essai. Nous montrons ainsi la faible diversité génétique des virus en primo-infection dans les compartiments sanguins et rectaux. Le réservoir s’établit dès le premier mois de l’infection par diffusion d’un cluster viral homogène

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Sassi, Mohamed. "La diversité des espèces du groupe Mycobacterium abscessus et leurs mycobactériophages." Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM5041/document.

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Premièrement, nous avons analysé 14 génomes publiés de M. abscessus montrant quece taxon comprend au moins cinq taxons différents spécifiés par des caractéristiques microbiologiques d’intérêt médical. Au cours d'un deuxième travail, nous avons développé une technique d’identification et de génotypage de M. abscessus qui a permis de distinguer sans ambiguïté M. massiliense de M. bolletii et M. abscessus.Nous avons ensuite analysé le bactériophage de M. bolletii que nous avons nommé Araucaria. La résolution de sa structure 3D a montré une capside et un connecteur similaires à ceux de plusieurs b

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Diouara, Abou Abdallah Malick. "Réponse virologique au traitement antirétroviral chez les patients infectés par le VIH-1, suivis en milieux décentralisés en Afrique de l’Ouest (Sénégal, Mali et Guinée Conakry)." Thesis, Montpellier 1, 2014. http://www.theses.fr/2014MON1T013/document.

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L'une des principales barrières à la prise en charge optimale des patients sous traitement antirétroviral est l'accès limité aux tests de charge virale (CV) et de génotypage particulièrement en milieu décentralisé. Ces tests ne sont généralement disponibles qu'au niveau des structures sanitaires centrales de grandes villes et le plasma en est l'échantillon de référence. Or, son transfert des régions périphériques vers les laboratoires de références est difficile, voire impossible. Pour rapprocher les patients du laboratoire, nous avons démontré la possibilité d'assurer un suivi virologique com

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Ballaud, Flore. "Dynamique spatio-temporelle des communautés virales et microbiennes des tourbières à Sphagnum." Thesis, Rennes 1, 2015. http://www.theses.fr/2015REN1S166/document.

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Les tourbières couvrent 3 % des surfaces continentales et jouent un rôle important dans le cycle du carbone en stockant le tiers du carbone des sols. L'accumulation de tourbe est liée au déséquilibre production primaire/décomposition du à une activité microbienne limitée par les conditions environnementales. L'infection et la lyse virale ont un impact sur la diversité et l'activité des communautés microbiennes, et influent sur le cycle du carbone. Cependant, le fonctionnement de ce compartiment viral n'avait jamais été pris en compte dans les études de fonctionnement des tourbières. Le but de

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Mahasha, Phetole Walter. "Compartmentalization, adaptive evolution and therapeutic response of HIV-1 in the gastrointestinal tract (GIT) of African patients infected with Subtype C: implications for the enhancement of therapeutic efficacy." Thesis, University of Pretoria, 2014. http://hdl.handle.net/2263/43156.

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Background: Due to its continuous exposure to food antigens and microbes, the gastrointestinal tract (GIT) is in a constant state of low level immune activation and contains an abundance of activated CCR5+CD4+ T lymphocytes, the primary target HIV-1. As a result, the GIT is a site of intense viral replication and severe CD4+ T cell depletion, a process that begins during primary HIV-1 infection and continues at a reduced rate during chronic infection in association with increased production of pro-inflammatory cytokines, a breakdown in the epithelial barrier, microbial translocation, systemic

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Frange, Pierre. "Caractérisation virologique des virus VIH-1 isolés en primo-infection en France." Thesis, Paris 5, 2013. http://www.theses.fr/2013PA05T022.

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L’épidémiologie moléculaire des virus VIH-1 en France est caractérisée par une augmentation constante de la diversité virologique et de la fréquence des virus de sous-types non-B chez les patients en primo-infection. Entre 1997 et 2007, 28.4% des 591 patients suivis étaient infectés par des virus de sous-types non-B. De plus, 49 patients (8.3%) étaient infectés par des souches de sous-types différents sur les gènes pol et env, témoignant d’évènements de recombinaisons entre ces gènes. Ces virus recombinants étaient isolés à la fois chez des patients originaires d’Afrique sub-saharienne (28.3%)

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