Genotype frequency and pattern of transmission and of Hepatitis C virus (HCV) from the Capital city and proximate areas of the Pakistan
Authors: Hashmi Asraf Hussain , Farooq Amjad , Kausar Mehran , Husnain Mehmod Ahmed , Imran Muhammad 
Published: February 2023

Background
Hepatitis C infection is pandemic public health problem in Pakistan and 71 million people carry the virus around the world. Pakistan is facing a gigantic challenge of hepatitis C infection. Pakistan was ranked 2nd in the world for the chronic hepatitis C infection. In Pakistan, around 10 million people were affected with HCV infection. Understanding of the transmission of the disease and its genotypes distribution were vital for prevention, treatment and eradication. This study aimed to determine the transmission risk factors, distribution and prevalence of HCV genotypes by sequence analysis of conserved regions and genotypic specific RT-PCR kit.
Methods
The analysis was carried out among 400 chronic HCV patients attending a tertiary care hospital from the Capital city and adjacent areas during period 2019–2022. The study subjects were carried out on those patients who were referred to the virology research laboratory from liver clinic in Islamabad. Baseline characteristics of the patients were collected including the possible transmission risk factor and different questionnaire options. Viral load was determined using Qiagen Quantitative PCR kit ((Lot No. 163042348) on Rotor Gene, ABI Quantstudion 3/5 and SLAN PCR systems. Genotyping of four hundred (n = 400) samples were performed by Sansure genotypic specific RT-PCR kit (Lot No. S3034E) and sequencing 5′ untranslated (5′ UTR) region. Analyzed sequences were manually read and compared with published database sequences to determine the genotypes using different bioinformatic tools. Thirty samples were also sequenced for Core/E1 and NS5B regions. The genotypes of other (n = 200) subjects were determined by Sansure HCV Real Time PCR genotyping kit.
Results
Four hundred samples were tested for all genotypes. Genotype 3 was found to be most foremost (93.75%). Other genotypes were detected in ratio of genotype 1 (3.25%), genotype 2 (1.25%), genotype 4 (1.25%). Genotype 5 and 6 were not detected in any samples. Two recombinant strains for Hepatitis C were observed (0.5%). One untyped sample was reported but it was a variant of genotype 3. Baseline parameters showed that the male gender (51.%%), mean age (43 years), mean ALTs (105 U/L) levels and viral load (2x103-1x107 U/mL) were observed during this analysis. Most of the Hepatitis C patients were used bad risky practices such injectable medical procedures and unsafe items of barber (major risk factors).
Conclusion
Sequence analysis and real time PCR methods indicated that a high percentage of HCV infected patients in North Pakistan and they were infected with 3a genotype. The patterns of HCV genotypes frequency distributions were almost similar to those of India but different from Iran and China. Healthcare related practices and barbers were the main drivers of HCV transmission. So, healthcare monitoring and sterilization of barber’s tools will be highly desired to control HCV and blood borne infections in Pakistan.