Complete genome sequencing and assessment of mutation-associated protein dynamics of the first Indian bovine ephemeral fever virus (BEFV) isolate

Background Bovine ephemeral fever (BEF) is a re-emerging disease caused by bovine ephemeral fever virus (BEFV). Although it poses a huge economic threat to the livestock sector, complete viral genome information from any South Asian country, including India, lacks. Aim Genome characterization of the...

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Autores principales:	Shruti Pyasi, Advika Gupta, Nagendra R. Hegde, Debasis Nayak
Formato:	article
Lenguaje:	EN
Publicado:	Taylor & Francis Group 2021
Materias:	bovine cattle bovine ephemeral fever virus complete genome befv ephemerovirus mutations protein dynamics phylogeny india Veterinary medicine SF600-1100
Acceso en línea:	https://doaj.org/article/23fe27d2891a465f86f69487637f3308
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spelling	oai:doaj.org-article:23fe27d2891a465f86f69487637f33082021-11-04T15:00:41ZComplete genome sequencing and assessment of mutation-associated protein dynamics of the first Indian bovine ephemeral fever virus (BEFV) isolate0165-21761875-594110.1080/01652176.2021.1995909https://doaj.org/article/23fe27d2891a465f86f69487637f33082021-01-01T00:00:00Zhttp://dx.doi.org/10.1080/01652176.2021.1995909https://doaj.org/toc/0165-2176https://doaj.org/toc/1875-5941Background Bovine ephemeral fever (BEF) is a re-emerging disease caused by bovine ephemeral fever virus (BEFV). Although it poses a huge economic threat to the livestock sector, complete viral genome information from any South Asian country, including India, lacks. Aim Genome characterization of the first Indian BEFV isolate and to evaluate its genetic diversity by characterizing genomic mutations and their associated protein dynamics. Materials and Methods Of the nineteen positive blood samples collected from BEF symptomatic animals during the 2018-19 outbreaks in India, one random sample was used to amplify the entire viral genome by RT-PCR. Utilizing Sanger sequencing and NGS technology, a complete genome was determined. Genome characterization, genetic diversity and phylogenetic analyses were explored by comparing the results with available global isolates. Additionally, unique genomic mutations within the Indian isolate were investigated, followed by in-silico assessment of non-synonymous (NS) mutations impacts on corresponding proteins’ secondary structure, solvent accessibility and dynamics. Results The complete genome of Indian BEFV has 14,903 nucleotides with 33% GC with considerable genetic diversity. Its sequence comparison and phylogenetic analysis revealed a close relatedness to the Middle Eastern lineage. Genome-wide scanning elucidated 30 unique mutations, including 10 NS mutations in the P, L and GNS proteins. The mutational impact evaluation confirmed alterations in protein structure and dynamics, with minimal effect on solvent accessibility. Additionally, alteration in the interatomic interactions was compared against the wild type. Conclusion These findings extend our understanding of the BEFV epidemiological and pathogenic potential, aiding in developing better therapeutic and preventive interventions.Shruti PyasiAdvika GuptaNagendra R. HegdeDebasis NayakTaylor & Francis Grouparticlebovinecattlebovine ephemeral fever viruscomplete genomebefvephemerovirusmutationsprotein dynamicsphylogenyindiaVeterinary medicineSF600-1100ENVeterinary Quarterly, Vol 41, Iss 1, Pp 308-319 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	bovine cattle bovine ephemeral fever virus complete genome befv ephemerovirus mutations protein dynamics phylogeny india Veterinary medicine SF600-1100
spellingShingle	bovine cattle bovine ephemeral fever virus complete genome befv ephemerovirus mutations protein dynamics phylogeny india Veterinary medicine SF600-1100 Shruti Pyasi Advika Gupta Nagendra R. Hegde Debasis Nayak Complete genome sequencing and assessment of mutation-associated protein dynamics of the first Indian bovine ephemeral fever virus (BEFV) isolate
description	Background Bovine ephemeral fever (BEF) is a re-emerging disease caused by bovine ephemeral fever virus (BEFV). Although it poses a huge economic threat to the livestock sector, complete viral genome information from any South Asian country, including India, lacks. Aim Genome characterization of the first Indian BEFV isolate and to evaluate its genetic diversity by characterizing genomic mutations and their associated protein dynamics. Materials and Methods Of the nineteen positive blood samples collected from BEF symptomatic animals during the 2018-19 outbreaks in India, one random sample was used to amplify the entire viral genome by RT-PCR. Utilizing Sanger sequencing and NGS technology, a complete genome was determined. Genome characterization, genetic diversity and phylogenetic analyses were explored by comparing the results with available global isolates. Additionally, unique genomic mutations within the Indian isolate were investigated, followed by in-silico assessment of non-synonymous (NS) mutations impacts on corresponding proteins’ secondary structure, solvent accessibility and dynamics. Results The complete genome of Indian BEFV has 14,903 nucleotides with 33% GC with considerable genetic diversity. Its sequence comparison and phylogenetic analysis revealed a close relatedness to the Middle Eastern lineage. Genome-wide scanning elucidated 30 unique mutations, including 10 NS mutations in the P, L and GNS proteins. The mutational impact evaluation confirmed alterations in protein structure and dynamics, with minimal effect on solvent accessibility. Additionally, alteration in the interatomic interactions was compared against the wild type. Conclusion These findings extend our understanding of the BEFV epidemiological and pathogenic potential, aiding in developing better therapeutic and preventive interventions.
format	article
author	Shruti Pyasi Advika Gupta Nagendra R. Hegde Debasis Nayak
author_facet	Shruti Pyasi Advika Gupta Nagendra R. Hegde Debasis Nayak
author_sort	Shruti Pyasi
title	Complete genome sequencing and assessment of mutation-associated protein dynamics of the first Indian bovine ephemeral fever virus (BEFV) isolate
title_short	Complete genome sequencing and assessment of mutation-associated protein dynamics of the first Indian bovine ephemeral fever virus (BEFV) isolate
title_full	Complete genome sequencing and assessment of mutation-associated protein dynamics of the first Indian bovine ephemeral fever virus (BEFV) isolate
title_fullStr	Complete genome sequencing and assessment of mutation-associated protein dynamics of the first Indian bovine ephemeral fever virus (BEFV) isolate
title_full_unstemmed	Complete genome sequencing and assessment of mutation-associated protein dynamics of the first Indian bovine ephemeral fever virus (BEFV) isolate
title_sort	complete genome sequencing and assessment of mutation-associated protein dynamics of the first indian bovine ephemeral fever virus (befv) isolate
publisher	Taylor & Francis Group
publishDate	2021
url	https://doaj.org/article/23fe27d2891a465f86f69487637f3308
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Complete genome sequencing and assessment of mutation-associated protein dynamics of the first Indian bovine ephemeral fever virus (BEFV) isolate

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