Reliable timescale inference of HBV genotype A origin and phylodynamics.

The worldwide distributed Hepatitis B virus (HBV) genotype A is classified into three subgenotypes, and one quasi-subgenotype. The majority of HBV-A subgenotypes are widespread in Africa and in ethnic groups that have relatively recently emigrated from African countries, whereas HBV-A2 is highly prevalent among subjects at high risk for sexual exposure to HBV in north-western Europe and the USA. The aim of this study was to reconstruct the origin and dispersion of HBV-A subgenotypes on a reliable timescale using short-term calibration based on heterochronous sampling for HBV-A2, and long-term calibration based on historical data for the other subgenotypes.

Enigmatic origin of hepatitis B virus: an ancient travelling companion or a recent encounter?

Hepatitis B virus (HBV) is the leading cause of liver disease and infects an estimated 240 million people worldwide. It is characterised by a high degree of genetic heterogeneity because of the use of a reverse transcriptase during viral replication. The ten genotypes (A-J) that have been described so far further segregate into a number of subgenotypes which have distinct ethno-geographic distribution.

Different evolutionary trends of swine H1N2 influenza viruses in Italy compared to European viruses.

European H1N2 swine influenza viruses (EU H1N2SIVs) arose from multiple reassortment events among human H1N1, human H3N2, and avian influenza viruses. We investigated the evolutionary dynamics of 53 Italian H1N2 strains by comparing them with EU H1N2 SIVs. Hemagglutinin (HA) phylogeny revealed Italian strains fell into four groups: Group A and B (41 strains) had a human H1 similar to EU H1N2SIVs, which probably originated in 1986.

Evolutionary dynamics of HBV-D1 genotype epidemic in Turkey.

Hepatitis B virus (HBV), is the leading cause of liver diseases infecting an estimated 240 million persons worldwide. The HBV prevalence rates are variables between different countries, with an high level of endemicity in the south-eastern part of Europe. Seven main HBV-D subgenotypes have been described until now (D1-D7).

Bayesian phylogeography of Crimean-Congo hemorrhagic fever virus in Europe.

Crimean-Congo hemorrhagic fever (CCHF) is a zoonosis mainly transmitted by ticks that causes severe hemorrhagic fever and has a mortality rate of 5-60%. The first outbreak of CCHF occurred in the Crimean peninsula in 1944-45 and it has recently emerged in the Balkans and eastern Mediterranean. In order to reconstruct the origin and pathway of the worldwide dispersion of the virus at global and regional (eastern European) level, we investigated the phylogeography of the infection by analysing 121 publicly available CCHFV S gene sequences including two recently characterised Albanian isolates.

Recurrence of another hepatitis B virus escape mutant comes back in a patient infected with HIV and low CD4+ count.

The case of an HIV-positive patient who cleared formerly acute HBV infection and experienced HBV exacerbation before starting antiretroviral therapy (ART) followed by a severe elevation of liver enzymes one month after the introduction of ART is reported. Laboratory tests revealed the presence of a subgenotype A2 carrying at least seven different mutations within the S protein and high lopinavir plasma concentrations. Irrespectively of the many possible mechanisms of HBV reactivation in patients infected with HIV (escape mutants selection, host immune deficiency progression, antiretroviral-related immune reconstitution, glucocorticosteroids, chemotherapy), the message is that HIV patients should be monitored strictly not only by serological and virological assays to recognize early HBV reactivation, but also for drug over-exposure.

Reconstruction of the evolutionary dynamics of hepatitis C virus subtypes in Montenegro and the Balkan region.

More than 20 million hepatitis C virus (HCV) carriers live in the countries of the Eastern Mediterranean. We determined HCV genotype distribution among chronically infected patients in Montenegro and investigated the phylodynamics and phylogeography of the most represented HCV subtypes. The HCV-NS5b sequences of the Montenegrin patients were compared with sequences isolated in different known localities of the Mediterranean area, Europe and Asia.

Epidemiological history and phylogeography of West Nile virus lineage 2.

West Nile virus (WNV) was first isolated in Uganda. In Europe WNV was sporadically detected until 1996, since then the virus has been regularly isolated from birds and mosquitoes and caused several outbreaks in horses and humans. Phylogenetic analysis showed two main different WNV lineages.

Molecular analysis of hepatitis B virus in Bulgaria.

Hepatitis B virus infection is a global health problem. Based on the sequence divergence of the entire genome, hepatitis B virus has been classified into eight genotypes which have a characteristic geographic distribution. To date, no data are available on the molecular epidemiology of hepatitis B virus in Bulgaria.

Reconstruction of the evolutionary dynamics of the A(H1N1)pdm09 influenza virus in Italy during the pandemic and post-pandemic phases.

The aim of this study was to reconstruct the evolutionary dynamics of the A(H1N1)pdm09 influenza virus in Italy during two epidemic seasons (2009/2010 and 2010/2011) in the light of the forces driving the evolution of the virus. Nearly six thousands respiratory specimens were collected from patients with influenza-like illness within the framework of the Italian Influenza Surveillance Network, and the A(H1N1)pdm09 hemagglutinin (HA) gene was amplified and directly sequenced from 227 of these. Phylodynamic and phylogeographical analyses were made using a Bayesian Markov Chain Monte Carlo method, and codon-specific positive selection acting on the HA coding sequence was evaluated.

Spatial and temporal dynamics of hepatitis B virus D genotype in Europe and the Mediterranean Basin.

Hepatitis B virus genotype D can be found in many parts of the world and is the most prevalent strain in south-eastern Europe, the Mediterranean Basin, the Middle East, and the Indian sub-continent. The epidemiological history of the D genotype and its subgenotypes is still obscure because of the scarcity of appropriate studies. We retrieved from public databases a total of 312 gene P sequences of HBV genotype D isolated in various countries throughout the world, and reconstructed the spatio-temporal evolutionary dynamics of the HBV-D epidemic using a bayesian framework.

Phylogeographic reconstruction of HIV type 1B in Montenegro and the Balkan region.

Human immunodeficiency virus (HIV) is one of the most genetically variable human viruses as it is characterized by high rates of mutation, viral replication, and recombination. Phylodynamics is a powerful means of describing the behavior of an infection as a combination of evolutionary and ecological processes. Only a few studies of HIV-1 molecular epidemiology have so far been carried out in the Balkans.

Spatial and temporal reconstruction of bovine viral diarrhea virus genotype 1 dispersion in Italy.

Bovine viral diarrhea virus (BVDV) is a widespread and economically important pathogen of cattle; genetic typing of BVDV isolates distinguished two species, namely BVDV-1 and BVDV-2. BVDV-1 is the most widespread worldwide and it includes at least 11 subtypes. With the aim of clarifying the routes of circulation of BVDV-1 subtypes in an endemic area and in order to investigate the relationships between the genetic diversity of BVDV and its geographic distribution, a phylogenetic analysis of 5' untranslated region of Italian sequences was performed using a new Bayesian framework allowing the spatial-temporal reconstruction of the evolutionary dynamics of highly variable viruses.

Reconstruction of the epidemic history of hepatitis B virus genotype D in Albania.

Despite a recent decrease in the prevalence of HBsAg in the general population, Albania is still highly endemic for HBV infection. Genotype D is the most prevalent HBV strain in the Mediterranean area. We studied the prevalence and distribution of HBV genotypes and subgenotypes in a total of 73 HBsAg-positive patients living in Albania, and reconstructed the epidemiological history of the most prevalent HBV D subgenotype using a "phylodynamic" framework.