SPATIAL AND TEMPORAL DYNAMICS OF PESTIVIRUS, CRIMEAN-CONGO HEMORRHAGIC FEVER AND HEPATITIS E VIRUS: A PHYLOGENETIC APPROACH
Tesi di Dottorato
Data di Pubblicazione:
2015
Citazione:
SPATIAL AND TEMPORAL DYNAMICS OF PESTIVIRUS, CRIMEAN-CONGO HEMORRHAGIC FEVER AND HEPATITIS E VIRUS: A PHYLOGENETIC APPROACH / C. Luzzago ; tutor: V. Bronzo ; co-tutor: G. Zehender ; coordinatore: F. Gandolfi. DIPARTIMENTO DI SCIENZE VETERINARIE E SANITA' PUBBLICA, 2015 Dec 15. 28. ciclo, Anno Accademico 2015. [10.13130/c-luzzago_phd2015-12-15].
Abstract:
The general aim of the PhD project was to apply phylogenetic analysis to viral sequences obtained in different geographic areas at different times, in order to reconstruct the most probable places of origin and pathways of dispersion of infections. Viral population growth and evolution leave a measurable imprint on the genome of viruses over the course of years, months or even days and occur simultaneously with geographic dispersal (Holmes, 2008; Pybus & Rambaut, 2009). This interaction characterizes a spatial phylodynamic process that can be recovered from genomic data using phylogeographic analyses (Faria et al., 2011). The research activity has been focused on Pestivirus genus, that includes pathogens of livestock (Bovine viral diarrhea virus - BDV) and wildlife (Border disease virus - BDV), and on zoonotic emerging diseases, involving in their epidemiological cycle both livestock and wildlife (Crimean-Congo hemorrhagic fever - CCHF, Hepatitis E virus- HEV).
Concerning BDV, since 2001 several outbreaks of disease have been reported in Pyrenean chamois in Spain, France and Andorra. These outbreaks have decimated several Pyrenean chamois populations, with mortalities ranging from 40% to 85%. The infection has become endemic in the Central and Eastern Pyrenees. The aim of this study was to clarify the origin and dispersion of the Pyrenean chamois BDV genetic variant by reconstructing the spatial and temporal dynamics of BDV 5’ UTR sequences of Pyrenean chamois, 10 novel sequences and 41 retrieved from public databases and Sheep BDV sequences (n=44) from Spain and France were also retrieved. The phylogenetic analysis was performed using a Bayesian Markov chain Monte Carlo (MCMC) method implemented in the BEAST v.1.74 package. The chamois clade originated from sheep BDV genotype 4, generating a founder effect due to intra-species spread and spatial dispersion. The time of the most recent common ancestor estimates for the chamois clade dated back to a time span between 1974 and 1996, with a mean estimation falling in 1988. The pathway of dispersion of isolates suggests a complex exchange between neighboring Pyrenean chamois populations, still going on such as Western direction.
Genetic typing of bovine viral diarrhea virus (BVDV) has distinguished BVDV-1 and BVDV-2 species and an emerging putative third species (HoBi-like virus), recently detected in southern Italy, signaling the occurrence of natural infection in Europe. Recognizing the need to update the data on BVDV genetic variability in Italy for mounting local and European alerts, a wide collection of 5’ UTR sequences (n = 371) was selected to identify the frequency of genotypes and subtypes at the herd level. BVDV-1 had the highest frequency, followed by sporadic BVDV-2. No novel HoBi-like viruses were identified. Four distribution patterns of BVDV-1 subtypes were observed: highly prevalent subtypes with a wide temporal-spatial distribution (1b and 1e), low prevalent subtypes with a widespread geographic distribution (1a, 1d, 1g, 1h, and 1k) or a restricted geographic distribution (1f), and sporadic subtypes detected only in single herds (1c, 1j, and 1l). BVDV-1c, k, and l are reported for the first time in Italy. Italy is one of the countries with the highest genetic diversity of BVDV worldwide. Northern Italy ranked first for BVDV introduction, prevalence, and dispersion. Nevertheless, the presence of sporadic variants in other restricted areas suggests the risk of different routes of BVDV introduction.
CCHF is a zoonosis mainly transmitted by ticks that causes sporadic cases and severe hemorrhagic fever of acute human disease with a mortality rate of 5-60% and it has recently emerged in the Balkans and eastern Mediterranean areas. In order to reconstruct the or
Tipologia IRIS:
Tesi di dottorato
Keywords:
RNA virus; phylogenetic analysis; molecular evolution; phylogeography; phylodynamics; zoonoses; Crimean-Congo Hemorrhagic Fever; Pestivirus; Chamois; Cattle; Border disease virus; Bovine viral diarrhea virus; epidemiology; Hepatitis E virus; HEV genotype 3
Elenco autori:
C. Luzzago
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