Identification of novel E6-E7 sequence variants of human papillomavirus 16

Identification of novel E6-E7 sequence variants of human papillomavirus 16 The rate of evolution of the human papillomavirus 16 (HPV16) genome is low. However, the ability of the E6 oncoprotein to interact with distinct p53 variants causes selective pressure on the E6 gene. In addition, intratypic recombination events in the HPV16 E6 and E7 genes have been characterized as extraordinary phenomena during the evolutionary history of virus. In the present study, we identified two new sequence variants through nucleotide analysis of the E6-E7 region of the HPV16 genome. Maximum-likelihood and empirical Bayesian methods were used in order to identify positive selection at particular residues of the E6 and E7 genes. Using the single recombination breakpoint (SBP) method, we found evidence of recombination events in the E6 ORF. Nucleotide sequence analysis showed that the new sequence variants are phylogenetically distant from the other members of the population. Our results indicate that new evolutionary intermediates of HPV16 might be formed either though positive selective pressure or through recombination events by multiple infections with distinct HPV16 variants. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Archives of Virology Springer Journals

Identification of novel E6-E7 sequence variants of human papillomavirus 16

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Publisher
Springer Vienna
Copyright
Copyright © 2013 by Springer-Verlag Wien
Subject
Biomedicine; Virology; Medical Microbiology; Infectious Diseases
ISSN
0304-8608
eISSN
1432-8798
D.O.I.
10.1007/s00705-012-1555-9
Publisher site
See Article on Publisher Site

Abstract

The rate of evolution of the human papillomavirus 16 (HPV16) genome is low. However, the ability of the E6 oncoprotein to interact with distinct p53 variants causes selective pressure on the E6 gene. In addition, intratypic recombination events in the HPV16 E6 and E7 genes have been characterized as extraordinary phenomena during the evolutionary history of virus. In the present study, we identified two new sequence variants through nucleotide analysis of the E6-E7 region of the HPV16 genome. Maximum-likelihood and empirical Bayesian methods were used in order to identify positive selection at particular residues of the E6 and E7 genes. Using the single recombination breakpoint (SBP) method, we found evidence of recombination events in the E6 ORF. Nucleotide sequence analysis showed that the new sequence variants are phylogenetically distant from the other members of the population. Our results indicate that new evolutionary intermediates of HPV16 might be formed either though positive selective pressure or through recombination events by multiple infections with distinct HPV16 variants.

Journal

Archives of VirologySpringer Journals

Published: Apr 1, 2013

References

  • Human papillomavirus type 16 E2 and E6/E7 variants
    Swan, DC; Rajeevan, M; Tortolero-Luna, G; Follen, M; Tucker, RA; Unger, ER
  • New method for the extraction of viral RNA and DNA from cerebrospinal fluid for use in the polymerase chain reaction assay
    Casas, I; Powell, L; Klapper, PE; Cleator, GM
  • Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
    Pond, SL; Frost, SD
  • Human papillomavirus 16 E6, L1, L2 and E2 gene variants in cervical lesion progression
    Lee, K; Magalhaes, I; Clavel, C; Briolat, J; Birembaut, P; Tommasino, M; Zehbe, I
  • Molecular and phylogenetic analysis of the HPV 16 E4 gene in cervical lesions from women in Greece
    Tsakogiannis, D; Ruether, IG; Kyriakopoulou, Z; Pliaka, V; Skordas, V; Gartzonika, C; Levidiotou-Stefanou, S; Markoulatos, P
  • Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome
    Kosiol, C; Bofkin, L; Whelan, S
  • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    Yang, Z; Nielsen, R; Goldman, N; Pedersen, AM

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