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Histoire naturelle et diversité génétique des virus de la famille anelloviridae : étude de prélèvements biologiques contemporains et anciens / Natural History and genetic diversity of virus from the Anelloviridae family, study of old and contemporary biological samplesBedarida, Sandra 10 October 2014 (has links)
Les Anelloviridae sont de petits virus à ADN simple brin de découverte récente, très largement répandus chez les vertébrés. Chez l'homme, 3 genres distincts ont été caractérisés : Alphatorquevirus (TTV), Betatorquevirus (TTMV), Gammatorquevirus (TTMDV), engendrant une infection chronique mais dont le pouvoir pathogène potentiel demeure encore méconnu. Leur épidémiologie est en constante réévaluation du fait de leur extrême variabilité et diversité génétique. Au cours de cette recherche à l'interface entre virologie et paléomicrobiologie, nous avons exploré l'histoire naturelle de ces virus via 2 axes interconnectés. D'une part la diversité génétique a été analysée lors d'une étude transversale au sein de populations contemporaines (française et afghane) et de populations anciennes datant du néolithique à l'époque moderne. D'autre part, leur évolution a été étudiée à l'échelle individuelle par une étude longitudinale au sein de 2 corpus (suivis de patient transplanté et de patient hémodialysé). Dans le but de compléter les données concernant cette famille virale unique, un travail méthodologique a été mis en oeuvre afin d'apporter des améliorations et de standardiser les protocoles d'analyse existants. La comparaison de distribution des Anelloviridae parmi plusieurs populations contemporaines, nous a permis d'observer des différences significatives de profils, notamment dans la population afghane. Notre méthodologie d'analyse d'échantillons anciens a mis en évidence la présence de souches Anelloviridae, attestant ainsi leur ancestralité et révélant également l'existence de variabilités inter- et intra-individuelles, similaires à l'infection des populations modernes. / Anelloviridae are small single-stranded DNA viruses, recently discovered, and widely spread among vertebrates. In humans, three distinct genera were characterised: Alphatorquevirus (TTV), Betatorquevirus (TTMV), Gammatorquevirus (TTMDV), leading to a chronic infection whose pathogenicity remains unknown. Their epidemiology is constantly evolving due to their extreme variability and genetic diversity. In this multidisciplinary research, combining virology, bioanthropology and palaeomicrobiology, we have used genetic analysis to explore the natural history of those viruses via two linked issues. On the one hand, the genetic diversity was analysed by way of a cross-sectional study within contemporary populations (French and Afghan) and ancient populations from the Neolithic period to Modern times. On the other hand, their evolution was studied at the individual level through a longitudinal study in two corpora (follow-ups of a transplanted patient and haemodialysis patients). In order to complement data regarding this unique viral family, a methodological process was established to improve and standardize existing analysis protocols. Comparison of Anelloviridae's distributions among several healthy contemporary populations allowed us to notice significant differences of partitions, especially an almost complete absence of TTMDV in the Afghan sample. Our methodology dedicated to ancient remains displayed the presence of Anelloviridae strains, testifying their ancestral origin and highlighting inter- and intra-individual variations, similar to infections in modern populations.
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Torque Teno Virus em amostras fezes de pacientes com gastroenterite : prevalência, distribuição por genogrupos e carga viralNascimento, Carlos Augusto Pinho do January 2011 (has links)
Submitted by Anderson Silva (avargas@icict.fiocruz.br) on 2012-10-23T13:30:15Z
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Previous issue date: 2011 / CNPq
FAPERJ / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, Brasil. / O Torque teno virus (TTV) é um vírus de DNA do gênero Alphatorquevirus
da família Anelloviridae. O TTV é altamente prevalente em populações de todo
o mundo. Isolados foram classificados em cinco grupos filogenéticos (1-5) com
grande distância genética entre eles. A presença do TTV já foi detectada nas
fezes, porém, não se sabe se todos os cinco genogrupos do TTV são
excretados nas fezes, e qual a distribuição do TTV entre os genogrupos. A fim
de avaliar a presença, a diversidade genômica e a carga viral do TTV em fezes,
135 amostras de pacientes com gastroenterite foram analisadas. O DNA do
TTV foi extraído de suspensão fecal e três diferentes métodos de reação em
cadeia da polimerase (PCR), dois qualitativos e um quantitativo, foram
avaliados. Nas amostras de fezes estudadas, 123 (91,1%) foram positivas em
pelo menos um dos três métodos. O DNA do TTV pertencente aos genogrupos
de 1 a 5 foi detectado em 37 (27,4%), 27 (20,0%), 57 (42,2%), 29 (21,5%) e
33 (24,4%) amostras, respectivamente. Co-infecções com dois, três, quatro e
cinco genogrupos do TTV foram encontradas em 23 (17,0%), 15 (11,1%), 7
(5,2%) e 7 (5,2%) amostras fecais, respectivamente. Assim, 52 (38,5%)
amostras continham mais de um genogrupo de TTV. A carga viral variou de 2,6
a 6,5 log de genoma equivalentes por grama de fezes. No entanto, variações
de carga viral foram observadas em função do genogrupo detectado e do
número de genogrupos presentes simultaneamente. Os resultados encontrados
são os primeiros a mostrar a alta prevalência e a diversidade de TTV nas fezes
humanas. / Torque teno virus (TTV) is a DNA virus of the genus Alphatorquevirus of
Anelloviridae family. The TTV is highly prevalent in populations from around the
world. Isolates have been classified into at least five main phylogenetic groups
(1-5) showing a large genetic distance between them. The presence of TTV has
been detected in feces. However, are presently unknown whether all five TTV
genogroups are excreted in feces and the genogroup distribution. To evaluate
the presence and the genomic distribution of TTV DNA in feces, 135 samples of
patients with gastroenteritis were analyzed. The DNA was extracted of fecal
suspension and three different PCR methods, two qualitative and one
quantitative, were used. One hundred and twenty three (91.1%) samples were
positive with at least one method. The TTV DNA belonging to the genogroups 1
to 5 was detected in 37 (27.4%), 27 (20.0%), 57 (42.2%), 29 (21.5%) and 33
(24.4%) fecal samples, respectively. Coinfections with two, three, four and five
TTV genogroups were found in 23 (17.0%), 15 (11.1%), 7 (5.2%) and 7 (5.2%)
fecal samples, respectively. Thus, 52 (38.5%) samples contained more than
one TTV genogroup. Viral loads ranged from 2.6 to 6.5 log genome equivalents
per gram of feces. However, variations of viral load were noted depending on
genogroup and number of coinfecting TTV genogroups. These results are the
first to show high prevalence and the diversity of TTV isolates in human feces.
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