REVIEW Hepatitis C genotype 4: A report on resistance-associated substitutions in NS3, NS5A, and NS5B genes Nahla Fadl 1 | Tamer Z. Salem 1,2 1 Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt 2 Department of Microbial Genetics, AGERI, ARC, Giza, Egypt Correspondence Tamer Z. Salem, Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza 12578, Egypt. Email: tsalem@zewailcity.edu.eg Funding information Science and Technology Development Fund, Grant/Award Number: ID 22976 Summary Author Contribution: FN performed the literature review and wrote the manuscript; STZ coauthored, edited, and reviewed the manuscript. Abstract: Treatment response in Hepatitis C virus (HCV) has generated varied effects in patients. Recently, nonresponsive and relapse patients related to host and geno- type variabilities have been reported in clinical trials. However, these trials included minimal sample sizes of patients with genotype 4, the most prevalent genotype in Egypt and the Middle East, compared with genotypes 1 and 2. The genetic variabil- ities that have been detected within the HCV genes, especially the ones associated with genotype 4, and are linked to treatment response, will be the focus of this review with emphasis on direct acting antiviral agents. In addition, the major studies and clinical trials performed globally and their inclusivity of genotype 4 are reported. This review also delineates future study areas and missing data that need further investigation when it comes to genotype 4. KEYWORDS direct acting antivirals, genetic variability, genotype 4, HCV, resistance-associated substitutions, viral response 1 | INTRODUCTION Hepatitis C virus (HCV) is a member of the Flaviviridae family with dis- tinct structural characteristics. Its genome is a single-stranded RNA of approximately 9.6 kb, in which a single-open reading frame (ORF) is flanked by two untranslated regions (UTRs) at the 5 0 and 3 0 ends (around 340 and 230 nucleotides, respectively). 1 The 5 0 UTR and 3 0 UTR regions have conserved RNA structures that function in pro- tein translation through internal ribosomal entry site and RNA replica- tion, respectively. 2 The ORF encodes a minimum of 10 proteins divided into structural and nonstructural regions. The structural region consists of three genes called core, E1, and E2 forming the capsid and the glycoprotein envelope of the virus, respectively. There is a small hydrophobic p7 protein (viroporin), whose function has been charac- terized as an ion channel. The p7 protein is known to be important for the virus assembly but not part of its structure. 3 The rest of the genome consists of the nonstructural region, which is made up of six genes (NS2, NS3, NS4A, NS4B, NS5A, and NS5B) encoding important viral proteins such as helicase, protease, and RNA-dependent RNA polymerase (RdRp). 4 Ever since its identification back in 1989, HCV remains a global health challenge. In 2017, around 71 million people have chronic HCV worldwide. 5 As of April 2020, there are 8 major genotypes and around 90 subtypes with sequence variation of 15% to 30%. 6 Additionally, HCV circulates as “quasi-species” within each infected individual, which makes it easier for the virus to evade immunity. 7 The largest number of patients infected with genotype 4 worldwide belongs to the Middle East and Africa (32.3% and 65.3%, excluding and including Egypt, respectively). 8 Egypt used to have the highest frequency of HCV occurrence worldwide, with a rate of ~14.7% of the Egyptian Abbreviations: BT, breakthrough response; DAAs, direct acting antivirals; EVR, early virological response; HVR, hypervariable region; LDV, ledipasvir; NI, nucleoside inhibitor; NGS, next-generation sequencing; NNI, nonnucleoside inhibitors; OBV, ombitasvir; ORF, open reading frame; PePHD, PKR-eIF2 phosphorylation homology domain; PKR, protein kinase R; RAS, resistance-associated substitutions; RAV, resistant variants; RdRp, RNA- dependent RNA polymerase; SOF, sofosbuvir; SVR, sustained virological response; UTR, untranslated region; VF, viral failure. Received: 14 March 2020 Revised: 4 May 2020 Accepted: 6 May 2020 DOI: 10.1002/rmv.2120 Rev Med Virol. 2020;30:e2120. wileyonlinelibrary.com/journal/rmv © 2020 John Wiley & Sons, Ltd 1 of 11 https://doi.org/10.1002/rmv.2120