Phylogenetic analysis of the 5ʹ untranslated region of HCV from cirrhotic patients in Khyber Pakhtunkhwa, Pakistan

Ullah, Amin; Rehman, Iqra; Ahmad, Jamshaid; Odenthal, M; Ahmad, Saad; Nadeem, Tariq; Ali, Qurban; Rizwan, Muhammad; Khan, Muhammad Ajmal; Hassan, Said; Ahsan, Hina; Ahmad, Bashir

doi:10.1038/s41598-021-94063-1

Cited by 3 publications

(3 citation statements)

References 28 publications

(23 reference statements)

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“…The 5ʹ UTR is commonly used for the identification of genotype because of the 90% sequence identity in its 341 nucleotides. The rate of mutations is rare in 5-UTR, and sometimes compensatory mutations are developed to preserve the base-pairing shape and conserve the structural characteristics associated with translation efficiency 26 . This study indicates that genotype 3 is most prevalent, so therapies should be directed against this genotype in clinical settings.…”

Section: Discussionmentioning

confidence: 99%

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Determination of hepatitis C virus subtype prevalent in Sindh, Pakistan: a phylogenetic analysis

Farooq,

Faiz,

Wahab

et al. 2024

Sci Rep

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Hepatitis is a major public health issue, affecting 10–17 million people worldwide, with its prevalence continuously increasing. The Hepatitis C virus (HCV) is responsible for liver related diseases, which include liver cirrhosis, hepatocellular carcinoma, and chronic hepatitis. Pakistan is experiencing a serious rise in HCV cases. This study aimed to assess the prevalence and distribution of HCV genotypes in Sindh, Pakistan. Serum samples from HCV-positive patients were collected from various local hospitals in Sindh. These samples were first screened for HCV antibodies using ELISA. Samples that tested positive for HCV RNA underwent further genotyping through sequencing using the standard Sanger method. The genotypes were identified by comparing the sequences with those available in the National Center for Biotechnology Information (NCBI) database, and a phylogenetic tree was constructed. The phylogenetic analysis showed that all isolates in this study were clustered with genotypes 3a and 3b, except for one sequence that was clustered with genotype 1a. No isolates were found to be clustered with reference genomes of genotypes 2, 4, 5, 6, and 7 suggesting that genotype 3a is endemic in this region. The analyzed sequences demonstrated a 98% similarity with reference and isolated sequences. In summary, sequencing of the HCV 5′ UTR essential for identifying the predominant genotype of HCV RNA in the Sindh region Further research on the distribution of HCV genotypes in other regions of Pakistan could aid in improving screening processes, identifying more effective treatment options, and developing suitable prevention strategies.

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Section: Discussionmentioning

confidence: 99%

“…This also reflects the increased rate of oncogenicity 25 . Direct sequencing of the 5ʹ UTR is a valuable method for clinical detection of different HCV genotypes 26 . The current study was conducted to assess the identification, confirmation, and characterization of most predominant genotype of HCV in Sindh province.…”

Section: Introductionmentioning

confidence: 99%

Determination of hepatitis C virus subtype prevalent in Sindh, Pakistan: a phylogenetic analysis

Farooq,

Faiz,

Wahab

et al. 2024

Sci Rep

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“…Due to the lack of proof-reading activity by RNA polymerase, the HCV genome displays a high-level degree of genetic variability, characterized by a non-uniform distribution across the genome [ 10 , 11 ]. Although the Core, E1, and NS5B regions were routinely utilized for HCV genotyping and subtyping, the 5’-UTR fragment, the most conserved region in the HCV genome, has recently emerged as an important target for the determination of HCV genotype and subtype across diverse populations [ 12 – 16 ]. To date, eight major HCV genotypes designated GT1 through GT8 have been identified worldwide, with further classification into up to one hundred subtypes [ 17 , 18 ].…”

Section: Introductionmentioning

confidence: 99%

Hepatitis C virus subtype diversity and transmission clusters characteristics among drug users in Zhuhai, South China

Li,

Huang,

Huang

et al. 2024

BMC Infect Dis

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Background Hepatitis C virus (HCV) infection poses a major public health challenge globally, especially among injecting drug users. China has the world’s largest burden of HCV infections. However, little is known about the characteristics of transmission networks among drug user populations. This study aims to investigate the molecular epidemiology and transmission characteristics of HCV infections among drug users in Zhuhai, a bustling port city connecting Mainland China and its Special Administrative Regions. Methods Participants enrolled in this study were drug users incarcerated at Zhuhai’s drug rehabilitation center in 2015. Their sociodemographic and behavioral information, including gender, promiscuity, drug use method, and so forth, was collected using a standardized questionnaire. Plasmas separated from venous blood were analyzed for HCV infection through ELISA and RT-PCR methods to detect anti-HCV antibodies and HCV RNA. The 5’UTR fragment of the HCV genome was amplified and further sequenced for subtype identifications and phylogenetic analysis. The phylogenetic tree was inferred using the Maximum Likelihood method based on the Tamura-Nei model, and the transmission cluster network was constructed using Cytoscape3.8.0 software with a threshold of 0.015. Binary logistic regression models were employed to assess the factors associated with HCV infection. Results The overall prevalence of HCV infection among drug users was 44.37%, with approximately 19.69% appearing to clear the HCV virus successfully. Binary logistic regression analysis revealed that those aged over 40, engaging in injecting drug use, and being native residents were at heightened risk for HCV infection among drug user cohorts. The predominant HCV subtypes circulating among those drug users were 6a (60.26%), followed by 3b (16.7%), 3a (12.8%), 1b (6.41%) and 1a (3.85%), respectively. Molecular transmission network analysis unveiled the presence of six transmission clusters, with the largest propagation cluster consisting of 41 individuals infected with HCV subtype 6a. Furthermore, distinct transmission clusters involved eight individuals infected with subtype 3b and seven with subtype 3a were also observed. Conclusion The genetic transmission networks revealed a complex transmission pattern among drug users in Zhuhai, emphasizing the imperative for a targeted and effective intervention strategy to mitigate HCV dissemination. These insights are pivotal for shaping future national policies on HCV screening, treatment, and prevention in port cities.

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An Overview of Hepatitis C Virus and Liver Cirrhosis in Pakistan

ULLAH,

BIBI,

ULLAH

et al. 2024

Bull. Biol. All. Sci. Res.

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Liver cirrhosis is a medical condition characterized by atrophy, fibrosis and physiological malfunctioning of the liver. This ailment may or may not be associated with liver carcinoma, which can be diagnosed via alphafetoprotein (AFP) blood test. The liver is a multi-tasking organ responsible for enzyme synthesis and toxin degradation; the patient with cirrhosis falls prone to various health issues such as jaundice, malaise, nausea, fatigue, swellings, loss of appetite, accumulation of fluid in the abdominal spaces, weight loss etc. This hepatic pathology, in later stages, is fatal. This disease leads to the annual mortality of 4000 lives in the UK and is the 12th major life-threatening disease in the USA. Chronic infection with HCV (hepatitis C virus), HBV (hepatitis B virus), and alcohol consumption are major factors of liver cirrhosis. Due to its slower progression (as it develops over months), liver cirrhosis can be detected earlier via diagnostic tools like CT (Computed Tomography) scan, MRI (Magnetic Resonance Imaging) scan, liver biopsy etc. Liver cirrhosis is the major reason for liver transplants around the world. It is more common in males than females and is prevalent in developing countries. Pakistan has an enormous burden of liver cirrhosis. This article briefly discusses the recent developments in the understanding of the pathogenesis, diagnosis and frequency of liver cirrhosis in the Pakistani population.

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Phylogenetic analysis of the 5ʹ untranslated region of HCV from cirrhotic patients in Khyber Pakhtunkhwa, Pakistan

Cited by 3 publications

References 28 publications

Determination of hepatitis C virus subtype prevalent in Sindh, Pakistan: a phylogenetic analysis

Determination of hepatitis C virus subtype prevalent in Sindh, Pakistan: a phylogenetic analysis

Hepatitis C virus subtype diversity and transmission clusters characteristics among drug users in Zhuhai, South China

An Overview of Hepatitis C Virus and Liver Cirrhosis in Pakistan

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