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

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 5ʹ untranslated region (UTR) is usually used for HCV genotyping, but it is less important in numerous subtypes due to its scarce sequence v...

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Autores principales:	Amin Ullah, Irshad Ur Rehman, Jamshaid Ahmad, Margaret Odenthal, Saad Ahmad, Tariq Nadeem, Qurban Ali, Muhammad Rizwan, Muhammad Ajmal Khan, Said Hassan, Hina Ahsan, Bashir Ahmad
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/61c22d022b5540a68292c89166b2f165
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spelling	oai:doaj.org-article:61c22d022b5540a68292c89166b2f1652021-12-02T16:17:34ZPhylogenetic analysis of the 5ʹ untranslated region of HCV from cirrhotic patients in Khyber Pakhtunkhwa, Pakistan10.1038/s41598-021-94063-12045-2322https://doaj.org/article/61c22d022b5540a68292c89166b2f1652021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-94063-1https://doaj.org/toc/2045-2322Abstract 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 5ʹ 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 5ʹ 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 5ʹ UTR. The HCV 5′ UTR was sequenced using the Sanger method. MEGA-7 software was used to analyze evolutionary relatedness. After 5ʹ 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 5ʹ 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.Amin UllahIrshad Ur RehmanJamshaid AhmadMargaret OdenthalSaad AhmadTariq NadeemQurban AliMuhammad RizwanMuhammad Ajmal KhanSaid HassanHina AhsanBashir AhmadNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Amin Ullah Irshad Ur Rehman Jamshaid Ahmad Margaret Odenthal Saad Ahmad Tariq Nadeem Qurban Ali Muhammad Rizwan Muhammad Ajmal Khan Said Hassan Hina Ahsan Bashir Ahmad Phylogenetic analysis of the 5ʹ untranslated region of HCV from cirrhotic patients in Khyber Pakhtunkhwa, Pakistan
description	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 5ʹ 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 5ʹ 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 5ʹ UTR. The HCV 5′ UTR was sequenced using the Sanger method. MEGA-7 software was used to analyze evolutionary relatedness. After 5ʹ 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 5ʹ 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.
format	article
author	Amin Ullah Irshad Ur Rehman Jamshaid Ahmad Margaret Odenthal Saad Ahmad Tariq Nadeem Qurban Ali Muhammad Rizwan Muhammad Ajmal Khan Said Hassan Hina Ahsan Bashir Ahmad
author_facet	Amin Ullah Irshad Ur Rehman Jamshaid Ahmad Margaret Odenthal Saad Ahmad Tariq Nadeem Qurban Ali Muhammad Rizwan Muhammad Ajmal Khan Said Hassan Hina Ahsan Bashir Ahmad
author_sort	Amin Ullah
title	Phylogenetic analysis of the 5ʹ untranslated region of HCV from cirrhotic patients in Khyber Pakhtunkhwa, Pakistan
title_short	Phylogenetic analysis of the 5ʹ untranslated region of HCV from cirrhotic patients in Khyber Pakhtunkhwa, Pakistan
title_full	Phylogenetic analysis of the 5ʹ untranslated region of HCV from cirrhotic patients in Khyber Pakhtunkhwa, Pakistan
title_fullStr	Phylogenetic analysis of the 5ʹ untranslated region of HCV from cirrhotic patients in Khyber Pakhtunkhwa, Pakistan
title_full_unstemmed	Phylogenetic analysis of the 5ʹ untranslated region of HCV from cirrhotic patients in Khyber Pakhtunkhwa, Pakistan
title_sort	phylogenetic analysis of the 5ʹ untranslated region of hcv from cirrhotic patients in khyber pakhtunkhwa, pakistan
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/61c22d022b5540a68292c89166b2f165
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Phylogenetic analysis of the 5ʹ untranslated region of HCV from cirrhotic patients in Khyber Pakhtunkhwa, Pakistan

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