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Updated: Aug 1, 2026
11:10
Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
Published on: December 27, 2010
Identification, phylogeny, and evolution of retroviral elements based on their envelope genes
L Bénit1, P Dessen, T Heidmann
1Unité des Rétrovirus Endogènes et Eléments Rétroïdes des Eucaryotes Supérieurs, CNRS UMR 1573, Institut Gustave Roussy, 94805 Villejuif Cedex, France.
Journal of Virology
|November 2, 2001
Summary
This study reveals conserved features in the transmembrane (TM) protein of retroviruses, including human endogenous retroviruses (HERVs). Phylogenetic analysis of TM proteins provides new insights into retroviral evolution and recombination.
Area of Science:
- Virology
- Molecular Biology
- Genetics
Background:
- Phylogenetic analysis of retroviral elements typically uses the reverse transcriptase (pol gene).
- The transmembrane (TM) subunit of the envelope gene, crucial for viral entry, possesses a conserved immunosuppressive domain essential for virus spread.
- This immunosuppressive domain's conservation suggests its utility in phylogenetic studies.
Purpose of the Study:
- To explore phylogenetic links between retroviral elements using the immunosuppressive domain of the TM protein.
- To identify novel human endogenous retroviruses (HERVs) and analyze conserved TM domain organization.
- To compare TM-based phylogenies with traditional pol-based trees for a comprehensive retroelement survey.
Main Methods:
- Tentative alignment of the immunosuppressive domain and adjacent sequences from retroviral elements.
- Phylogenetic analysis of TM proteins from various retroelements, including those with and without identified immunosuppressive domains.
- Comparison of TM-based phylogenetic trees with pol-based trees.
Main Results:
- Unraveled conserved organization among TM domains, also present in filoviruses (Ebola, Marburg).
- Identified numerous HERVs, including new families, from sequence databases.
- TM-based phylogenetic analysis provided a comprehensive survey of retroelements and evidence for recombination.
Conclusions:
- The TM protein, particularly its immunosuppressive domain, is a valuable marker for retroviral phylogeny.
- This approach expands the identification of HERVs and refines understanding of retroviral evolution.
- TM-based phylogenetics offers a complementary view to pol-based analyses, revealing recombination events.
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