A case of a patient infected with a hepatitis C virus genotype 3a multidrug resistant variant in Pakistan

Abstract

Background: Approximately 10 million people in Pakistan are infected with the hepatitis C virus (HCV). Most patients develop chronic hepatitis, with rare cases of spontaneous clearance. However, little is known about multidrug resistant viral variants in Pakistan.

Findings: This case study describes a 47-year-old male diagnosed with chronic HCV genotype 3a infection in 2003. After an initial diagnosis of viral infection, the patient remained treatment naïve for 5 years. He received two therapy cycles of interferon (IFN) plus ribavirin (RBV) in 2007 and 2010, however, he was non-responsive to the therapy. The patient then received an additional two treatment cycles of pegylated IFN α-2b plus RBV (in 2011 and 2013); he was still non-responsive. In 2016, the patient underwent sofosbuvir plus RBV combination therapy, however, the sustained virological response was still not achieved. The host genetic factor was found to be heterozygous guanine and thymine (GT) and cytosine and thymine (CT) genotypes of rs8099917 and rs12979860 polymorphism of IL28B, respectively. Phylogenetic analysis suggests that the resistant variant belong to an out-group and may require triple therapy.

Conclusions: This is the first case that reports on a HCV-infected individual who was a non-responder to multiple IFN therapies in Pakistan. Further studies are needed to understand multidrug-resistant HCV variants in the Pakistani population.

Fig. 1

a IL-28B polymorphism showing host genotype CT (rs12978960) and TG (rs8099917) in the patient. Line 1: DNA ladder; Line 2: Amplified uncut product of rs12978960; Line 3: CT genotype by RFLP; Line 4: Amplified uncut product of rs8099917; Line 5: GT genotype by Restriction Fragment Length Polymorphism (RFLP). b Chromatogram showing (a) heterozygous G/T (rs8099917) and (b) heterozygous C/T (rs12979860) polymorphism of IL28b

Fig. 2

Nucleotide sequence-based genotyping of HCV. The resistant variant is labeled as Pk1-RV (GenBank accession no. KY971494) and clustered with genotype 3a reference sequences. The fragment length of target sequence is 353 nucleotides of NS5B gene. Analysis was carried out using 14 reference viral genome sequences. Sequences included genotype 3a (accession no. AB44523, AB44525, AB44527, PP3, PP39, and KPK2); 3b (accession no. AB444466); 3 k (accession no. AB444470); 1a (KPK1, PP5, PP7); and 1b (KPK6, accession no. AB330344, AB330346)