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Genetic analysis of the matrix and non-structural genes of equine influenza virus (H3N8) from epizootic of 2008-2009 in India.
Abstract: India faced an epizootic of equine influenza in 2008-2009. The isolated viruses were typed as H3N8 and grouped with the clade 2 viruses of Florida sublineage on the basis of haemagglutinin (HA) gene sequence analysis. This report describes the genetic analysis and selection pressure of matrix (M) and non-structural 1 (NS1) genes of the Indian isolates. All isolates shared 98.41% and 99.54% homology with other clade 2 viruses of Asian origin for M1 and M2 amino acid (aa) sequences, respectively. There were 3 and 4 unique aa residue changes respectively in M1 and M2 proteins in all Asian isolates. Phylogenetic analysis revealed clustering of Indian and Chinese isolates in a separate group designated here as Asian clade for M gene. Indian and Chinese isolates shared homology ranging from 98.17% to 99.08% at aa level. The M and NS1 genes were under negative selection pressure with estimated magnitude of pressure (ω) 0.054, 0.581 and 0.30 for M1, M2 and NS1, respectively.
Copyright © 2011 Elsevier B.V. All rights reserved.
Publication Date: 2011-04-22 PubMed ID: 21620592DOI: 10.1016/j.vetmic.2011.04.011Google Scholar: Lookup The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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The research in this paper focuses on the genetic analysis of the matrix (M) and non-structural (NS1) genes of the equine influenza virus (H3N8) that caused an epizootic in India in 2008-2009 to understand their relationship with other viruses and their evolutionary pressure.
Matrix and non-structural genes of H3N8
- For the epizootic in 2008-2009 in India, the culprit was the equine influenza virus H3N8. This virus was grouped with clade 2 viruses of Florida sublineage based on the analysis of its haemagglutinin (HA) gene sequence.
- The matrix (M) and non-structural 1 (NS1) genes of the virus isolates were analyzed for this study.
- The team discovered that all the isolates had a 98.41% and 99.54% homology with other clade 2 viruses of Asian origin based on M1 and M2 amino acid (aa) sequences. This means there was a strong genetic and evolutionary relationship between these viruses.
- The M1 and M2 proteins of all the Asian-origin isolates had respectively 3 and 4 unique amino acid changes, differentiating them somewhat from others in the clade.
Phylogenetic analysis and selection pressure of M and NS1 genes
- The phylogenetic analysis allowed the researchers to trace the evolutionary history and relationships of these Indian isolates of H3N8. This analysis showed that the Indian and Chinese isolates formed a separate group distinct from other clade 2 viruses and thus could be referred to as an Asian clade for the M gene.
- These Indian and Chinese isolates shared an amino acid level homology range of 98.17% to 99.08%. This close homology indicates a shared evolutionary origin and likely similar evolutionary pressures.
- Negative selection pressure was acting on M and NS1 genes as the estimated magnitude of pressure, denoted as ω, was calculated to be 0.054, 0.581 and 0.30 for M1, M2 and NS1, respectively. Negative selection pressure indicates that changes to these genes are generally detrimental, so the evolution of these genes is slow and conservative, retaining the original gene sequences.
Cite This Article
APA
Virmani N, Bera BC, Shanumugasundaram K, Singh BK, Gulati BR, Singh RK, Vaid RK.
(2011).
Genetic analysis of the matrix and non-structural genes of equine influenza virus (H3N8) from epizootic of 2008-2009 in India.
Vet Microbiol, 152(1-2), 169-175.
https://doi.org/10.1016/j.vetmic.2011.04.011 Publication
Researcher Affiliations
- National Research Centre on Equines, Sirsa Road, Hisar 125 001, Haryana, India.
MeSH Terms
- Amino Acid Sequence
- Amino Acid Substitution
- Animals
- Chick Embryo
- Hemagglutinin Glycoproteins, Influenza Virus / genetics
- India
- Influenza A Virus, H3N8 Subtype / classification
- Influenza A Virus, H3N8 Subtype / genetics
- Influenza A Virus, H3N8 Subtype / isolation & purification
- Molecular Sequence Data
- Orthomyxoviridae Infections / veterinary
- Orthomyxoviridae Infections / virology
- Phylogeny
- Selection, Genetic
- Sequence Analysis, RNA
- Viral Matrix Proteins / genetics
- Viral Nonstructural Proteins / genetics
Citations
This article has been cited 5 times.- Kwaśnik M, Góra IM, Żmudziński JF, Rola J, Polak MP, Rożek W. Genetic Analysis of the M Gene of Equine Influenza Virus Strains Isolated in Poland, in the Context of the Asian-like Group Formation. J Vet Res 2018 Dec;62(4):405-412.
- Singh RK, Dhama K, Karthik K, Khandia R, Munjal A, Khurana SK, Chakraborty S, Malik YS, Virmani N, Singh R, Tripathi BN, Munir M, van der Kolk JH. A Comprehensive Review on Equine Influenza Virus: Etiology, Epidemiology, Pathobiology, Advances in Developing Diagnostics, Vaccines, and Control Strategies. Front Microbiol 2018;9:1941.
- Favaro PF, Fernandes WR, Reischak D, Brandão PE, Silva SOS, Richtzenhain LJ. Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015. Braz J Microbiol 2018 Apr-Jun;49(2):336-346.
- Bera BC, Virmani N, Kumar N, Anand T, Pavulraj S, Rash A, Elton D, Rash N, Bhatia S, Sood R, Singh RK, Tripathi BN. Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution. BMC Genomics 2017 Aug 23;18(1):652.
- Bera BC, Virmani N, Shanmugasundaram K, Vaid RK, Singh BK, Gulati BR, Anand T, Barua S, Malik P, Singh RK. Genetic Analysis of the Neuraminidase (NA) Gene of Equine Influenza Virus (H3N8) from Epizootic of 2008-2009 in India. Indian J Virol 2013 Sep;24(2):256-64.
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