The Core/E1 domain of hepatitis C virus genotype 4a in Egypt does not contain viral mutations or strains specific for hepatocellular carcinoma

https://doi.org/10.1016/j.jcv.2011.08.022Get rights and content

Abstract

Background

Hepatitis C virus (HCV) infection is a well-documented etiological factor for hepatocellular carcinoma (HCC). As HCV shows remarkable genetic diversity, an interesting and important issue is whether such a high viral genetic diversity plays a role in the incidence of HCC. Prior data on this subject are conflicting.

Objectives

Potential association between HCV genetic mutations or strain variability and HCC incidence has been examined through a comparative genetic analysis merely focused on a single HCV subtype (genotype 4a) in a single country (Egypt).

Study design

The study focused on three HCV sequence datasets with explicit sampling dates and disease patterns. An overlapping HCV Core/E1 domain from three datasets was used as the target for comparative analysis through genetic and phylogenetic approaches.

Results

Based on partial Core/E1 domain (387 bp), genetic and phylogenetic analysis did not identify any HCC-specific viral mutations and strains, respectively.

Conclusions

The Core/E1 domain of HCV genotype 4a in Egypt does not contain HCC-specific mutations or strains. Additionally, sequence errors resulting from the polymerase chain reaction, together with a strong evolutionary pressure on HCV in patients with end-stage liver disease, have significant potential to bias data generation and interpretation.

Section snippets

Background

The causal relationship between hepatitis C virus (HCV) infection and hepatocellular carcinoma (HCC) is well documented.1, 2 About 1–3% patients with chronic HCV infection will develop HCC in the United States.3 HCV-related tumorigenesis has been studied extensively and almost all HCV-encoded viral proteins, especially Core protein, can cause cellular transformation through multiple mechanisms.4 As a positive, single-strand RNA virus, a remarkable feature of HCV genome is the high genetic

Objectives

In the present study, the potential association between HCV genetic mutations or strain variability and HCC incidence has been examined through a comparative genetic analysis merely focused on a single HCV subtype (genotype 4a) in a single country (Egypt).

HCV sequence data collection

Three HCV sequence datasets were included in this study. The first HCV dataset was derived from a nationwide epidemiological study designed to evaluate the prevalence of HCV in Egyptian blood donors.18 The dataset consists of 49 HCV genotype 4a E1/Core sequences with assigned GenBank accession numbers from AF271825 to AF271873, representing a subset of blood donors from 15 geographically diverse governorates in Egypt.19 The second dataset was generated in our laboratory in a study to

Lack of amplification bias by different primer sets

The potential effect of different primer sets on the amplification of HCV Core/E1 domain was tested in five serum samples. Direct sequencing of amplicons with the primer sets from either dataset 2 or 3 showed the complete identity. Over 1935 bp amplicon sequence (387 bp 5×), the primer set from dataset 1 generated one silent mutation (A → T), indicating a 99.95% match in comparison with the primer sets from datasets 2 and 3. Therefore, the use of different primer sets did not result in noticeable

Discussion

Identification of HCC-specific mutations is a challenging endeavor. HCV's great diversity makes it difficult to perform a comparative analysis among different HCV genotypes or subtypes. The existence of ethnically or geographically specific mutations is also a concern.8 More importantly, even if putative HCC-associated mutations are observed, it is not known if these mutations are responsible for the HCC incidence or a simple result of evolutionary adaptation. The current study was designed to

Funding

This work was supported by NIH grants R01 DK80711 (Dr. Xiaofeng Fan), R21 AI076834 (Dr. Adrian M. Di Bisceglie) and USA and Egypt Science and Technology Joint Fund BIO6-002-004 (Dr. Adrian M. Di Bisceglie).

Competing interest

All authors with this manuscript have no conflict of interests.

Ethical approval

This study is purely a genetic analysis with sequence data from published studies and thus does not involve any ethical issues.

Acknowledgments

This work was supported by NIH grants R01 DK80711 (XF), R21 AI076834 (AMD) and USA and Egypt Science and Technology Joint Fund BIO6-002-004 (AMD).

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