Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

Hepatitis C virus (HCV) is enveloped RNA virus, encoding for a polyprotein that is processed by cellular proteases. The virus is responsible for liver cirrhosis, allograft rejection, and human hepatocellular carcinoma. Based on studies including compositional analysis, odds ratio analysis, parity an...

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Главные авторы:	Rzhepakovsky, I. V., Ржепаковский, И. В.
Формат:	Статья
Язык:	English
Опубликовано:	2023
Темы:	Allograft rejection Liver transplantation Codon usage Liver cirrhosis Hepatitis C virus (HCV) Hepatocellular carcinoma Similarity index Relative codon deoptimization index
Online-ссылка:	https://dspace.ncfu.ru/handle/20.500.12258/23498
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spelling	ir-20.500.12258-234982025-02-11T09:15:27Z Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts Rzhepakovsky, I. V. Ржепаковский, И. В. Allograft rejection Liver transplantation Codon usage Liver cirrhosis Hepatitis C virus (HCV) Hepatocellular carcinoma Similarity index Relative codon deoptimization index Hepatitis C virus (HCV) is enveloped RNA virus, encoding for a polyprotein that is processed by cellular proteases. The virus is responsible for liver cirrhosis, allograft rejection, and human hepatocellular carcinoma. Based on studies including compositional analysis, odds ratio analysis, parity analysis, skew analysis, relative synonymous codon usage, codon bias, and protein properties, it was evident that codon usage bias in HCV is dependent upon the nucleotide composition. Codon context analysis revealed CTC-CTG as a preferred codon pair. While CGA and CGT codons were rare, none of the codons were rare in HCV-like viruses envisaged in the present study. Many of the preferred codon pairs were valine amino acid-initiated, which possibly infers viral infectivity; hence the role of selection forces appears to act on the HCV genome, which was further validated by neutrality analysis where selection accounted for 87.28%, while mutation accounted for 12.72% force shaping codon usage. Furthermore, codon usage was correlated with the length of the genome. HCV viruses prefer valine-initiated codon pairs, while HCV-like viruses prefer alanine-initiated codon pairs. The HCV host range is very narrow and is confined to only humans and chimpanzees. Based on indices including codon usage correlation analysis, similarity index, and relative codon deoptimization index, it is evident in the study that the chimpanzee is the primary host of the virus. The present study helped elucidate the preferred host for HCV. The information presented in the study paved the way for generating an attenuated vaccine candidate through viral recoding, with finely tuned nucleotide composition and a perfect balance of preferred and rare codons. 2023-05-24T14:02:23Z 2023-05-24T14:02:23Z 2023 Статья Khandia, R., Khan, A.A., Karuvantevida, N., Gurjar, P., Rzhepakovsky, I.V., Legaz, I. Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts // Pathogens. - 2023. - 12(2), art. no. 325. - DOI: 10.3390/pathogens12020325 http://hdl.handle.net/20.500.12258/23498 en Pathogens application/pdf application/pdf
institution	СКФУ
collection	Репозиторий
language	English
topic	Allograft rejection Liver transplantation Codon usage Liver cirrhosis Hepatitis C virus (HCV) Hepatocellular carcinoma Similarity index Relative codon deoptimization index
spellingShingle	Allograft rejection Liver transplantation Codon usage Liver cirrhosis Hepatitis C virus (HCV) Hepatocellular carcinoma Similarity index Relative codon deoptimization index Rzhepakovsky, I. V. Ржепаковский, И. В. Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts
description	Hepatitis C virus (HCV) is enveloped RNA virus, encoding for a polyprotein that is processed by cellular proteases. The virus is responsible for liver cirrhosis, allograft rejection, and human hepatocellular carcinoma. Based on studies including compositional analysis, odds ratio analysis, parity analysis, skew analysis, relative synonymous codon usage, codon bias, and protein properties, it was evident that codon usage bias in HCV is dependent upon the nucleotide composition. Codon context analysis revealed CTC-CTG as a preferred codon pair. While CGA and CGT codons were rare, none of the codons were rare in HCV-like viruses envisaged in the present study. Many of the preferred codon pairs were valine amino acid-initiated, which possibly infers viral infectivity; hence the role of selection forces appears to act on the HCV genome, which was further validated by neutrality analysis where selection accounted for 87.28%, while mutation accounted for 12.72% force shaping codon usage. Furthermore, codon usage was correlated with the length of the genome. HCV viruses prefer valine-initiated codon pairs, while HCV-like viruses prefer alanine-initiated codon pairs. The HCV host range is very narrow and is confined to only humans and chimpanzees. Based on indices including codon usage correlation analysis, similarity index, and relative codon deoptimization index, it is evident in the study that the chimpanzee is the primary host of the virus. The present study helped elucidate the preferred host for HCV. The information presented in the study paved the way for generating an attenuated vaccine candidate through viral recoding, with finely tuned nucleotide composition and a perfect balance of preferred and rare codons.
format	Статья
author	Rzhepakovsky, I. V. Ржепаковский, И. В.
author_facet	Rzhepakovsky, I. V. Ржепаковский, И. В.
author_sort	Rzhepakovsky, I. V.
title	Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts
title_short	Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts
title_full	Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts
title_fullStr	Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts
title_full_unstemmed	Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts
title_sort	insights into synonymous codon usage bias in hepatitis c virus and its adaptation to hosts
publishDate	2023
url	https://dspace.ncfu.ru/handle/20.500.12258/23498
work_keys_str_mv	AT rzhepakovskyiv insightsintosynonymouscodonusagebiasinhepatitiscvirusanditsadaptationtohosts AT ržepakovskijiv insightsintosynonymouscodonusagebiasinhepatitiscvirusanditsadaptationtohosts
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Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

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