Universität zu Köln

Ullah, Amin, Rehman, Irshad Ur, Ahmad, Jamshaid ORCID: 0000-0003-2105-1918, Odenthal, Margaret, Ahmad, Saad, Nadeem, Tariq, Ali, Qurban ORCID: 0000-0002-3160-4830, Rizwan, Muhammad, Khan, Muhammad Ajmal, Hassan, Said ORCID: 0000-0001-9612-4048, Ahsan, Hina and Ahmad, Bashir (2021). Phylogenetic analysis of the 5' untranslated region of HCV from cirrhotic patients in Khyber Pakhtunkhwa, Pakistan. Sci Rep, 11 (1). BERLIN: NATURE PORTFOLIO. ISSN 2045-2322

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Abstract

Hepatitis C virus (HCV), a small, single-stranded RNA virus with a 9.6 kb genome, is one of the most common causes of liver diseases. Sequencing of the 5' untranslated region (UTR) is usually used for HCV genotyping, but it is less important in numerous subtypes due to its scarce sequence variations. This study aimed to identify genotypes using the 5' UTR of HCV from cirrhotic patients of Khyber Pakhtunkhwa (KP). Serum RNA samples (44) were screened by real time PCR to determine the HCV viral load. Nested PCR was performed to identify cDNA and the 5' UTR. The HCV 5 ' UTR was sequenced using the Sanger method. MEGA-7 software was used to analyze evolutionary relatedness. After 5' UTR sequencing, 26 samples (59%) were identified as genotype 3, and 2 samples (6%) were identified as genotypes 1, 2 and 4. The most predominant genotype was 3a, and genotype 4 was rarely reported in the phylogenetic tree. Analysis of the HCV 5' UTR is an efficient alternative method for confirmation of various genotypes. Phylogenetic analysis showed that genotype 3 was dominant in the area of KP, Pakistan.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Ullah, Amin UNSPECIFIED UNSPECIFIED UNSPECIFIED Rehman, Irshad Ur UNSPECIFIED UNSPECIFIED UNSPECIFIED Ahmad, Jamshaid UNSPECIFIED orcid.org/0000-0003-2105-1918 UNSPECIFIED Odenthal, Margaret UNSPECIFIED UNSPECIFIED UNSPECIFIED Ahmad, Saad UNSPECIFIED UNSPECIFIED UNSPECIFIED Nadeem, Tariq UNSPECIFIED UNSPECIFIED UNSPECIFIED Ali, Qurban UNSPECIFIED orcid.org/0000-0002-3160-4830 UNSPECIFIED Rizwan, Muhammad UNSPECIFIED UNSPECIFIED UNSPECIFIED Khan, Muhammad Ajmal UNSPECIFIED UNSPECIFIED UNSPECIFIED Hassan, Said UNSPECIFIED orcid.org/0000-0001-9612-4048 UNSPECIFIED Ahsan, Hina UNSPECIFIED UNSPECIFIED UNSPECIFIED Ahmad, Bashir UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-595073
DOI:	10.1038/s41598-021-94063-1
Journal or Publication Title:	Sci Rep
Volume:	11
Number:	1
Date:	2021
Publisher:	NATURE PORTFOLIO
Place of Publication:	BERLIN
ISSN:	2045-2322
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language HEPATITIS-C-VIRUS; SEQUENCE-ANALYSIS; EPIDEMIOLOGY; GENOTYPE; INTERFERON; EVOLUTION; RIBAVIRIN; RNA Multiple languages Multidisciplinary Sciences Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/59507