Phylogenetic analysis of hepatitis C virus isolates from Tunisian patients.

International audienceThere is little information on the epidemiology characterisation of HCV isolates in Tunisia. Previous report showed predominance of genotype 1b. In this study, 32 HCV isolates from genotypes 1a (n = 10), 1b (n = 14), 2 (n = 4), 3a (n = 3) and 4 (n = 1) were genotyped by sequencing and phylogenetic analysis on the non-structural 5b (NS5b) region. The isolates originated from 14 patients with chronic hepatitis, 10 haemophiliacs and eight healthy blood donors. NS5b sequence grouping was concordant with previous 5' untranslated region (5'UTR) genotyping results in 91% of cases. Most of the Tunisian isolates were closely related to the European ones, except for genotype 4 which seems to be related mostly to isolates from Egypt. Isolates from genotype 1a obtained from haemophiliacs showed distinct clustering and nucleic divergence from those obtained from non-haemophiliac patients, this underlines the particular mode of contamination of this group of patients

Identification of measles virus genotypes from recent outbreaks in countries from the Eastern Mediterranean Region

International audienceBackground: Molecular characterization of measles viruses (MV) helps to identify transmission pathways of the virus and to document persistence or interruption of endemic virus circulation. In the Eastern Mediterranean Region, measles genotypes from only few countries have been documented.Objectives: This study reports the genetic characteristics of virus strains from recent measles outbreaks in Tunisia, Libya, Syria and Iran in 2002–2003.Study design: Virus sequences in the nucleoprotein gene were obtained by PCR amplification of virus isolates or serum samples. The sequences were compared to the reference ones for genotype identification and to other published sequences within the same genotype.Results and conclusions: The Tunisian and Libyan epidemic strains belonged to genotype B3, they were closely related to each other and to isolates from Western Africa. The Syrian and Iranian viruses belonged to genotype D4, and differed from each other and from the other published sequences within this genotype. Our results provide valuable baseline and new tools for improved virological measles surveillance in the future, at country, regional and global levels

Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa.

HCV genotype 2 (HCV-2) has a worldwide distribution with prevalence rates that vary from country to country. High genetic diversity and long-term endemicity were suggested in West African countries. A global dispersal of HCV-2 would have occurred during the 20th century, especially in European countries. In Tunisia, genotype 2 was the second prevalent genotype after genotype 1 and most isolates belong to subtypes 2c and 2k. In this study, phylogenetic analyses based on the NS5B genomic sequences of 113 Tunisian HCV isolates from subtypes 2c and 2k were carried out. A Bayesian coalescent-based framework was used to estimate the origin and the spread of these subtypes circulating in Tunisia. Phylogenetic analyses of HCV-2c sequences suggest the absence of country-specific or time-specific variants. In contrast, the phylogenetic grouping of HCV-2k sequences shows the existence of two major genetic clusters that may represent two distinct circulating variants. Coalescent analysis indicated a most recent common ancestor (tMRCA) of Tunisian HCV-2c around 1886 (1869-1902) before the introduction of HCV-2k in 1901 (1867-1931). Our findings suggest that the introduction of HCV-2c in Tunisia is possibly a result of population movements between Tunisia and European population following the French colonization

Phylogenetic analysis of isolates from Subtype 2k.

<p>Phylogenetic analyses were performed using the Maximum Composite Likelihood method included in the MEGA package (version 5.1). The reliability of the phylogenetic constructions was estimated by bootstrap analysis with 1000 pseudo replicate data sets. The tree is based on the analysis of a 222-nucleotide long fragment in the NS5B region (nucleotides 8346 to 8568 according to the H77-1a prototype strain, AF009606). It includes the 11 studied Tunisian sequences (in red) and 39 HCV-2k field sequences from other countries (in black). All the sequences were indicated by their Accession Numbers followed by the country code and the collection date. The country codes according to the standard abbreviation are: France (FRA), Martinique (MTQ), Canada (CAN), Russia (RUS), United Kingdom (GBR), Uzbekistan (UZB), Azerbaijan (AZE), Morocco (MAR), Iran (IRN) and Moldova (MDA).</p

The timeline of HCV subtype 2c introduction in Tunisia.

<p>The timeline of HCV subtype 2c introduction in Tunisia.</p

Bayesian Skyline Plots for Demographic Reconstruction using NS5B sequences.

<p>A) subtype 2c, B) subtype 2k; X-axis: Date in Years; Y-axis: Estimated effective number of infections; Bold Line: Mean Effective Number of viral population. Upper and lower Lines: Upper and Lower HPD95% (High Population Density) of Effective Number of viral population.</p

Phylogenetic analysis of isolates from subtype 2c.

<p>Phylogenetic analyses were performed using the Maximum Composite Likelihood method included in the MEGA package (version 5.1). The reliability of the phylogenetic constructions was estimated by bootstrap analysis with 1000 pseudo replicate data sets. The tree is based on the analysis of a 222-nucleotide-long fragment in the NS5B region (nucleotides 8316 to 8537 according to the H77-1a prototype strain, AF009606). It includes the 102 studied Tunisian sequences (in red) and 53 HCV-2c field sequences from other countries (in black). All the sequences were indicated by their Accession Numbers followed by the country code and the collection date. The country codes according to the standard abbreviation are: France (FRA), Martinique (MTQ), Canada (CAN), Italy (ITA), Venezuela (VEN), Ghana (GHA), Russia (RUS), Netherlands (NLD), Spain (ESP), Japan (JPN), Germany (DEU), Argentina (ARG) and United Kingdom (GBR).</p

_tMRCA estimations using the NS5B region for the HCV- 2c and HCV-2k in Tunisia.

<p>_tMRCA estimations using the NS5B region for the HCV- 2c and HCV-2k in Tunisia.</p