Phylogenetic analysis of hepatitis C virus strains and risk factors associated with infection and viral subtypes among Iranian patients

Abstract

Hepatitis C virus (HCV) has infected approximately 170 million people worldwide. While the seroprevalence of anti-HCV antibody among Iranian blood donors is 0.13%, HCV infection is prevalent in 59-80% of Iranian injecting drug users. One hundred seventy-eight anti-HCV positive patients were referred to the Gastroenterology Department at the Taleghani Hospital (Tehran, Iran) between June 2007 and June 2012. Out of 178 samples, 142 were positive for HCV-RNA. HCV subtypes were determined using phylogenetic analysis of the NS5B or 5'UTR/core regions. Of 142 viremic patients, 71 (50%) were infected with HCV subtype 1a, 43 (30.3%) with subtype 3a, 20 (14.1%) with subtype 1b, 3 (2.1%) with subtype 4d, 2 (1.4%) with subtype 4a, 1 (0.7%) with subtype 2b, and 1 (0.7%) with subtype 6a. Interestingly, genetic analysis of a sub-genomic fragment from one patient identified a non-subtypeable HCV genotype-3 strain. There was a significant association between HCV subtype and a history of injecting drug use (P = 0.003). Subtype 3a was predominant among patients with such a history. Injecting drug use was associated with younger age (P < 0.001). HCV subtype was also significantly associated with a history of upper gastrointestinal endoscopy (P = 0.02). Subtype 1a was more frequent among patients with such a history. In addition, history of upper gastrointestinal endoscopy was significantly associated with older age (P = 0.002). In conclusion, while HCV subtype 1a is predominant among infected Iranian individuals, subtype 3a is predominant among Iranian injecting drug users.

Mixed HCV infection and reinfection in people who inject drugs—impact on therapy

“…61,62 The transfusion of contaminated blood products is particularly associated with HCV genotype 1b and 2a infections 61,63 and HCV genotypes 1a and 3a are most common among PWID. 61,[64][65][66][67][68][69][70][71][72][73] Blood product screening over the past two decades or more has led to a decrease in the prevalence of HCV genotypes 1b and 2a. During the same period, genotypes 1a and 3a have increased in prevalence, particularly among PWID.…”

“…During the same period, genotypes 1a and 3a have increased in prevalence, particularly among PWID. 61,64,[67][68][69][70][71][72][73] In addition, a group of endemic HCV strains exist, such as genotype 6 in southeast Asia and genotype 5 in Africa, which have a more restricted geographic distribution and are less prevalent than HCV genotypes 1, 2 or 3. 62 Finally, the last major group of strains reflect local epidemics and are highly prevalent in specific locations and risk groups, such as genotype 4d, which >10% of the Egyptian population are infected with (initially via contaminated medical devices) 74 and is also prevalent globally among HIV and HCV co-infected men who have sex with men.…”

“…60 For example, HCV genotype 3a infection is highly prevalent among populations of PWID globally and its prevalence has continued to increase over time. 64,65,[67][68][69][70][71][72][73] Interferon-free, pan-genotypic DAA combinations in development look very promising. 122,[137][138][139] The co-formulated sofosbuvir and GS-5816 single daily tablet, 12 week regimen (a nucleotide analogue and NS5A inhibitor, respectively), which is in phase II studies, has demonstrated a SVR rate of >90% for HCV genotypes 1, 2, 3, 4, and 6.…”

Molecular Tracing of Hepatitis C Virus Genotype 1 Isolates in Iran: A NS5B Phylogenetic Analysis with Systematic Review

“…We studied all available nucleotide sequences reported from Iran and other EMRO and Middle Eastern countries. Out of seven studies from Iran, four studies were published in 2004 - 2014 (33-36) and three were unpublished. Furthermore, 15 published and unpublished studies from EMRO and Middle Eastern countries including Afghanistan (37), Azerbaijan, Cyprus (38, 39), Egypt, Morocco (40), Pakistan (41), and Tunisia (42, 43) were collected.…”

Genetic Variations in Host Factors and their Critical Role on HCV Medication

“…Two important factors including cytokines and chemokines are the main players in the promotion of hepatitis C. These factors have been documented to have key roles in the regulation of innate and adaptive immune response to HCV infection (36)(37)(38). Multiple studies have found cytokines gene polymorphisms influence on the pathogenesis of HCV and outcome of response (39,40). In the literature review, the key roles of the most important host factors associated with HCV infection along with all related genes will be discussed.…”