Insights into synonymous codon usage bias in hepatitis c virus and Its adaptation to hosts

Khandia, Rekha; Ali Khan, Azmat; Karuvantevida, Noushad; Gurjar, Pankaj; Vladimirovich Rzhepakovsky, Igor; Legaz Pérez, Isabel

Publication:
Insights into synonymous codon usage bias in hepatitis c virus and Its adaptation to hosts

dc.contributor.author	Khandia, Rekha
dc.contributor.author	Ali Khan, Azmat
dc.contributor.author	Karuvantevida, Noushad
dc.contributor.author	Gurjar, Pankaj
dc.contributor.author	Vladimirovich Rzhepakovsky, Igor
dc.contributor.author	Legaz Pérez, Isabel
dc.contributor.department	Ciencias Sociosanitarias
dc.date.accessioned	2024-07-08T11:41:30Z
dc.date.available	2024-07-08T11:41:30Z
dc.date.issued	2023-02-15
dc.description	© 2023 by the authors. This manuscript version is made available under the CC-BY 4.0 license http://creativecommons.org/licenses/by/4.0/. This document is the Published version of a Published Work that appeared in final form in Pathogens. To access the final edited and published work see https://doi.org/10.3390/pathogens12020325
dc.description.abstract	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.	es
dc.format	application/pdf	es
dc.format.extent	20	es
dc.identifier.citation	Pathogens 2023, 12(2), 325
dc.identifier.doi	https://doi.org/10.3390/pathogens12020325
dc.identifier.issn	Electronic: 2076-0817
dc.identifier.uri	http://hdl.handle.net/10201/142912
dc.language	eng	es
dc.publisher	MDPI
dc.relation	This work was funded by the Researchers Supporting Project Number (RSP2023R339) King Saud University, Riyadh, Saudi Arabia and project R-1007/2018, University of Murcia, Spain.	es
dc.relation.publisherversion	https://www.mdpi.com/2076-0817/12/2/325
dc.rights	info:eu-repo/semantics/openAccess	es
dc.rights	Atribución 4.0 Internacional	*
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	*
dc.subject	Hepatitis C virus (HCV)	es
dc.subject	Codon usage	es
dc.subject	Liver cirrhosis	es
dc.subject	Hepatocellular carcinoma	es
dc.subject	Similarity index	es
dc.subject	Relative codon deoptimization index	es
dc.subject	Allograft rejection	es
dc.subject	Liver transplantation	es
dc.title	Insights into synonymous codon usage bias in hepatitis c virus and Its adaptation to hosts	es
dc.type	info:eu-repo/semantics/article	es
dspace.entity.type	Publication	es
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