Background: The development of direct-acting antiviral agents (DAAs) has
revolutionized the treatment of HCV infection. The main challenge to HCV effective
treatment with daas is the emergence of HCV drug-resistant variants. Detection of
resistance associated variants is of importance in clinical settings in order to optimize
DAA regimens, maximize success rates and reduce the impact of treatment failure.
Objectives: The prevalence of possible mutations expected to induce potential directly
acting antiviral agent (DAA) resistance was investigated in twenty DAAs naïve HCV
infected patients. Methodology: The twenty HCV isolates were genotyped using the full
length NS3/4A, NS5B, and two third of the carboxy terminal region (including ISDR) of
NS5A gene sequences. Results: Eighteen (90%) out of 20 strains were diagnosed as
subgenotype 4a while 2 (10%) were of subgenotype 4n, Amino acid frequencies at each
position in the NS3 protease sequence were determined with the VESPA software
program. Twenty four Genotype4-specific amino acid signatures were present in almost
all of our sequences, but were absent from all other genotypes. Among the twenty four
amino acid signatures only one mutation at position 41 (T/S) reported to be associated
with resistance to protease inhibitors. Compared to the wild type HCV GT-4; nine
mutations were detected among our isolates at a frequency ranging from 27% to 100%.
None of these mutations were associated with resistance to protease inhibitors. Forty
three mutations were detected among our isolates at a much lower frequency ranging
from 5.5% to 16.6%. Only 5 out of them were associated with protease inhibitor
resistance. Amplification of domain II and III including the interferon sensitivitydetermining
region and the interferon/ribavirin resistance-determining region of the
NS5a region showed a number of mutations exceeding 4 in all isolates and 82.3% of
them had from 10-30 mutations. Thirty two Genotype 4-specific amino acid signatures
were present in almost all of our sequences and absent from all other genotypes. The
primary NS5B nucleoside polymerase inhibitors (NPIs) resistance variant 282T was not
detected in our isolates. Conclusion: The large number of natural polymorphism of HCV
4 isolates as well as the large number of mutations detected in this study and different
from those associated with DAA resistance makes it more practical to detect resistance
associated mutations in DAA treatment failure then to look for these mutations in naïve
patients