New insight into HCV E1/E2 region of genotype 4a

Nehal Hussein, Abdel-Rahman N Zekri, Mohamed Abouelhoda, Hanaa M Alam El-din, Ahmed Abdelwahab Ghamry, Mahmoud A Amer, Ghada M sherif, Abeer A Bahnassy

IntroductionHepatitis C virus (HCV) is a public health problem in many countries, especially in Egypt which has the highest prevalence worldwide. Molecular characterization of the HCV genome is crucial for understanding the natural history of the virus, disease progression, and response to therapy. The HCV genome contains two envelope proteins (E1 and E2) responsible for the virus entry into the cell. They are characterized by a high rate of mutation during replication, which enables HCV to evade immune system. Therefore, understanding the variability of these two proteins and their evolutionary dynamics is essential to develop effective HCV vaccines and treatment plans, and hence reduce the spread of the virus.Although many studies have focused on the E1/E2 regions, there is a substantial lack of sequences covering the full length of E1/E2 region for genotype 4 in general and for subtype 4a in particular. Our study aims at providing new sequences. It also aims at characterizing the genetic divergence of the E1/E2 region of HCV genotype 4a using our new sequences along with all publicly available datasets.MethodsThe genomic segments covering the whole E1/E2 (genotype 4a) region were isolated from five Egyptian HCV patients and sequenced. The resulting sequences, which are 36 ones, were then analyzed using sequence analysis techniques to study their variability within and among hosts in the same time point. Furthermore, all previously published HCV E1/E2 sequence datasets for genotype 4a have been retrieved and categorized according to the geographical location and date of isolation. Using the retrieved data and our new sequences, we studied the variability among Egyptian sequences over a period of about 15 years. We also compared variability among Egyptian and non-Egyptian sequences to figure out region-specific variability.ResultsPhylogenetic analysis of the new 36 HCV genotype 4a sequences has shown variability within the host and among different individuals in the same time point. Analysis of the 36 sequences along with the Egyptian public sequences (254 sequences in E1 in the period from 1997 to 2010 and 8 E2 sequences in the period from 2006 to 2010) has shown temporal change over time. Analysis of the new HCV sequences with the non-Egyptian public sequences (182 sequences in E1 region and 155 sequences in the E2 sequences) has shown region specific variability. The molecular clock rate of E1 was estimated to be 5E-3 per site per year for Egyptian sequences and 5.38E-3 for non-Egyptian sequences. The clock rate of E2 was estimated to be 8.48E per site per year for Egyptian sequences and 6.3E-3 for non-Egyptian sequences.ConclusionThe results of this study support the high rate of evolution of the Egyptian HCV genotype 4a. It has also revealed significant level of genetic variability among sequences from different regions in the world.