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

Abstract

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.

5′ UTR and NS5B-based genotyping of hepatitis C virus in patients from Damietta governorate, Egypt

“…Combination of Elbasvir (NS5A inhibitor) and Grazoprevir (NS3/4A protease inhibitor) for treating genotypes 1 and 4 produced high SVR rates [23] . HCV genotyping is clinically important in predicting the efficiency of antiviral therapy, in determining the duration of treatment [24] and, also, in detecting HCV molecular epidemiology [25] . This study aims to genotype HCV strains circulating in Damietta Governorate and to investigate the variation in HCV NS5B region that is targeted by the newly approved antiviral drugs.…”

Presence of rare hepatitis C virus subtypes, 2j, 2k, and 2r in Mexico City as identified by sequencing

“…Currently, 15 subtypes have been confirmed for GT‐2 (2a‐2u), with frequencies varying among countries . The spread of GT‐2 is thought to have started at the beginning of the 20th century due to slave trade . GTs 2a, 2b, and 2c have been identified worldwide.…”

“…In this study, we found two patients (4%) had GT‐2j and one (2%) had a mixed infection with GT‐2k + 2j. We believe that European populations migrating to the Americas may have helped spread GT‐2j …”

“…Mexico is a migration route between South and North America, and population movement spreads HCV, generating new subtypes . Mexico City is the most populous city in the country as well as the most important international business centre.…”

Identification of two novel hepatitis C virus subtype 2 from Tunisia (2v and 2w)

“…Genotype 1 is the most common, especially subtype 1b, with prevalence of around 80% followed by genotype 2 with prevalence of 10% approximatively [ 12 – 14 ]. HCV genotype 2 has been poorly studied in Tunisia and until now only two studies have investigated its genetic diversity and molecular epidemiology [ 15 , 16 ]. The study conducted in 2014 showed that the major circulating subtype is subtype 2c (75.5%).…”