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BMC genomics2017; 18(1); 652; doi: 10.1186/s12864-017-4063-1

Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution.

Abstract: Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) were analyzed to elucidate the genetic and evolutionary relationships in a novel perspective. Results: The group - specific consensus amino acid substitutions were identified in all polymerase genes of EIVs that led to divergence of EIVs into various clades. The consistent amino acid changes were also detected in the Florida clade 2 EIVs circulating in Europe and Asia since 2007. To study the codon usage patterns, a total of 281,324 codons of polymerase genes of EIV H3N8 isolates from 1963 to 2015 were systemically analyzed. The polymerase genes of EIVs exhibit a weak codon usage bias. The ENc-GC3s and Neutrality plots indicated that natural selection is the major influencing factor of codon usage bias, and that the impact of mutation pressure is comparatively minor. The methods for estimating host imposed translation pressure suggested that the polymerase acidic (PA) gene seems to be under less translational pressure compared to polymerase basic 1 (PB1) and polymerase basic 2 (PB2) genes. The multivariate statistical analysis of polymerase genes divided EIVs into four evolutionary diverged clusters - Pre-divergent, Eurasian, Florida sub-lineage 1 and 2. Conclusions: Various lineage specific amino acid substitutions observed in all polymerase genes of EIVs and especially, clade 2 EIVs underwent major variations which led to the emergence of a phylogenetically distinct group of EIVs originating from Richmond/1/07. The codon usage bias was low in all the polymerase genes of EIVs that was influenced by the multiple factors such as the nucleotide compositions, mutation pressure, aromaticity and hydropathicity. However, natural selection was the major influencing factor in defining the codon usage patterns and evolution of polymerase genes of EIVs.
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Publication Date: 2017-08-23 PubMed ID: 28830350PubMed Central: PMC5568313DOI: 10.1186/s12864-017-4063-1Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research article delves into the complex genetic interactions of the polymerase genes in the Equine Influenza Virus (EIV), focusing on the factors that have influenced the evolution of these genes. Key findings indicate natural selection as a major driver of these genes’ evolution and the role of various mutations leading to diverse EIV clades.

Understanding Polymerase Genes in EIV

  • The research examined in-depth the polymerase genes present within the EIV. These genes have vital roles in the virus’s replication, transcription, and transmission between hosts. They also play a significant role in the pathogenesis of the virus.
  • By analyzing the genetic sequences and codon usage bias of these genes, the researchers aimed to build a better understanding of the genetic relationships and the evolution of the EIV.
  • Through their research, they managed to identify group-specific consensus amino acid substitutions in all polymerase genes of EIV, leading to divergence into different clades, which are groups of organisms with a common ancestor.

Nature and Evolution of Codon Usage

  • A total of 281,324 codons of polymerase genes of EIV H3N8 isolates from 1963 to 2015 were analyzed to study codon usage patterns.
  • The polymerase genes in EIV exhibited a weak codon usage bias, indicating a lack of preference for specific codons in gene sequences.
  • The influencing factors of this bias were found to be a mixture of natural selection and mutation pressure, with natural selection playing a greater role.
  • Additional influences such as nucleotide compositions, aromaticity, and hydropathicity also played a part in shaping the codon usage patterns.

Impact on EIV Evolution

  • The polymerase acidic (PA) gene was found to be under less translational pressure compared to polymerase basic 1 (PB1) and polymerase basic 2 (PB2) genes. This difference suggests varying rates of mutation and evolution among these genes.
  • The EIVs were divided into four evolutionary diverged clusters based on multivariate statistical analysis of these polymerase genes.
  • Lineage-specific amino acid substitutions were observed across all polymerase genes. Particularly notable were major variations in the clade 2 EIVs, which have given rise to a distinctly different group of EIVs originating from Richmond/1/07.

Cite This Article

APA
Bera BC, Virmani N, Kumar N, Anand T, Pavulraj S, Rash A, Elton D, Rash N, Bhatia S, Sood R, Singh RK, Tripathi BN. (2017). Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution. BMC Genomics, 18(1), 652. https://doi.org/10.1186/s12864-017-4063-1

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 18
Issue: 1
Pages: 652
PII: 652

Researcher Affiliations

Bera, Bidhan Ch
  • National Research Centre on Equines, Sirsa Road, Hisar, Haryana, India.
Virmani, Nitin
  • National Research Centre on Equines, Sirsa Road, Hisar, Haryana, India. nvirmani@gmail.com.
Kumar, Naveen
  • National Institute of High Security Animal Diseases, Hathai Kheda Dam Road, Anand Nagar, Bhopal, Madhya Pradesh, India.
Anand, Taruna
  • National Research Centre on Equines, Sirsa Road, Hisar, Haryana, India.
Pavulraj, S
  • National Research Centre on Equines, Sirsa Road, Hisar, Haryana, India.
Rash, Adam
  • Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, CB8 7UU, UK.
Elton, Debra
  • Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, CB8 7UU, UK.
Rash, Nicola
  • Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, CB8 7UU, UK.
Bhatia, Sandeep
  • National Institute of High Security Animal Diseases, Hathai Kheda Dam Road, Anand Nagar, Bhopal, Madhya Pradesh, India.
Sood, Richa
  • National Institute of High Security Animal Diseases, Hathai Kheda Dam Road, Anand Nagar, Bhopal, Madhya Pradesh, India.
Singh, Raj Kumar
  • Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India.
Tripathi, Bhupendra Nath
  • National Research Centre on Equines, Sirsa Road, Hisar, Haryana, India.

MeSH Terms

  • Codon / genetics
  • DNA-Directed DNA Polymerase / genetics
  • Evolution, Molecular
  • Influenza A Virus, H3N8 Subtype / enzymology
  • Influenza A Virus, H3N8 Subtype / genetics
  • Phylogeny
  • Selection, Genetic

Conflict of Interest Statement

ETHICS APPROVAL AND CONSENT TO PARTICIPATE: Not applicable. CONSENT FOR PUBLICATION: Not applicable. COMPETING INTERESTS: The authors declare that they have no competing interests. PUBLISHER’S NOTE: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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