Genetic diversity of hepatitis C virus in Ethiopia

Abstract

Hepatitis C virus (HCV) is genetically highly divergent and classified in seven major genotypes and approximately hundred subtypes. These genotypes/subtypes have different geographic distribution and response to antiviral therapy. In Ethiopia, however, little is known about their molecular epidemiology and genetic diversity. The aim of this study was to investigate the distribution and genetic diversity of HCV genotypes/subtypes in Ethiopia, using 49 HCV RNA positive samples. HCV genotypes and subtypes were determined based on the sequences of the core and the nonstructural protein 5B (NS5B) genomic regions. Phylogenetic analysis revealed that the predominant was genotype 4 (77.6%) followed by 2 (12.2%), 1 (8.2%), and 5 (2.0%). Seven subtypes were identified (1b, 1c, 2c, 4d, 4l, 4r and 4v), with 4d (34.7%), 4r (34.7%) and 2c (12.2%) as the most frequent subtypes. Consistent with the presence of these subtypes was the identification of a potential recombinant virus. One strain was typed as genotype 2c in the NS5B region sequence and genotype 4d in the core region. In conclusion, genotype 4 HCV viruses, subtypes 4d and 4r, are most prevalent in Ethiopia. This genotype is considered to be difficult to treat, thus, our finding has an important impact on the development of treatment strategies and patient management in Ethiopia.

Fig 1. Bayesian inference phylogenetic tree of the NS5B region.

A phylogenetic tree was constructed based on the NS5B region (356 nucleotides), corresponding to nucleotide numbering of 8288–8643 in the H77 genome, using the GTR+I+G model of evolution. Numbers on branches are posterior probabilities from the Bayesian inference analysis. Reference sequences are labeled to the right of each branch in the order of subtype hyphen GenBank accession number. Ethiopian sequences are shown in color (color corresponding to their geographic origin: Red = Addis Ababa; Blue = Adama; Green = Mekelle; Pink = Gondar; Light blue = Jimma), a potential recombinant MK32ETH highlighted in yellow.

Fig 2. Bayesian inference phylogenetic tree of the core region.

A phylogenetic tree was constructed based on the core region (418 nucleotides), corresponding to nucleotide numbering of 300–717 in the H77 genome, using the GTR+I+G model of evolution. Numbers on branches are posterior probabilities from the Bayesian inference analysis. Reference sequences are labeled to the right of each branch in the order of subtype hyphen GenBank accession number. Ethiopian sequences are shown in color (color corresponding to their geographic origin: Red = Addis Ababa; Blue = Adama; Green = Mekelle; Pink = Gondar; Light blue = Jimma), a potential recombinant MK32ETH highlighted in yellow.