Skip to main content
SpringerLink
Log in

Virus-Host Evolution and Positive Selection

  • Reference work entry
  • First Online:
Encyclopedia of AIDS

  • 39 Accesses

Definition

Viruses, including HIV-like viruses, have been infecting primates and other hosts for millions of years. During this long-term common history, viruses and hosts have constantly put pressure on each other for survival. Over time, hosts have evolved first lines of defense against viruses, the cellular restriction factors, while pathogens have developed mechanisms of evasion and antagonism. These antagonistic relationships have set up genetic conflicts between viruses and hosts that drive their evolution and interactions. Therefore, over evolutionary time and as a result of virus-host arms races, host restriction factors have been rapidly evolving and display signatures of positive selection, in particular at the virus-host interface.

Introduction

Lentiviruses are retroviruses that have been infecting various mammals and in particular primates for millions of years (Gifford 2012). The virus responsible for the AIDS (acquired immune deficiency syndrome) pandemic in humans, HIV...

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 1,099.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 1,599.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Busnadiego I, Kane M, Rihn SJ, Preugschas HF, Hughes J, Blanco-Melo D, Strouvelle VP, Zang TM, Willett BJ, Boutell C, Bieniasz PD, Wilson SJ. Host and viral determinants of Mx2 antiretroviral activity. J Virol. 2014;88(14):7738–52.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Compton AA, Hirsch VM, Emerman M. The host restriction factor APOBEC3G and retroviral Vif protein coevolve due to ongoing genetic conflict. Cell Host Microbe. 2012;11(1):91–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Compton AA, Malik HS, Emerman M. Host gene evolution traces the evolutionary history of ancient primate lentiviruses. Philos Trans R Soc Lond B Biol Sci. 2013;368(1626):20120496.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Daugherty MD, Malik HS. Rules of engagement: molecular insights from host-virus arms races. Annu Rev Genet. 2012;46:677–700.

    Article  CAS  PubMed  Google Scholar 

  • Delport W, Poon AF, Frost SD, Kosakovsky Pond SL. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics. 2010;26(19):2455–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Demogines A, Abraham J, Choe H, Farzan M, Sawyer SL. Dual host-virus arms races shape an essential housekeeping protein. PLoS Biol. 2013;11(5):e1001571.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Desimmie BA, Delviks-Frankenberrry KA, Burdick RC, Qi D, Izumi T, Pathak VK. Multiple APOBEC3 restriction factors for HIV-1 and one Vif to rule them all. J Mol Biol. 2014;426(6):1220–45.

    Article  CAS  PubMed  Google Scholar 

  • Duggal NK, Emerman M. Evolutionary conflicts between viruses and restriction factors shape immunity. Nat Rev Immunol. 2012;12(10):687–95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Etienne L, Hahn BH, Sharp PM, Matsen FA, Emerman M. Gene loss and adaptation to hominids underlie the ancient origin of HIV-1. Cell Host Microbe. 2013;14(1):85–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fregoso OI, Ahn J, Wang C, Mehrens J, Skowronski J, Emerman M. Evolutionary toggling of Vpx/Vpr specificity results in divergent recognition of the restriction factor SAMHD1. PLoS Pathog. 2013;9(7):e1003496.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gifford RJ. Viral evolution in deep time: lentiviruses and mammals. Trends Genet. 2012;28(2):89–100.

    Article  CAS  PubMed  Google Scholar 

  • Goujon C, Moncorge O, Bauby H, Doyle T, Barclay WS, Malim MH. Transfer of the amino-terminal nuclear envelope targeting domain of human MX2 converts MX1 into an HIV-1 resistance factor. J Virol. 2014;88(16):9017–26.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hotter D, Sauter D, Kirchhoff F. Emerging role of the host restriction factor tetherin in viral immune sensing. J Mol Biol. 2013;425(24):4956–64.

    Article  CAS  PubMed  Google Scholar 

  • Hughes AL, Yeager M. Natural selection at major histocompatibility complex loci of vertebrates. Annu Rev Genet. 1998;32:415–35.

    Article  CAS  PubMed  Google Scholar 

  • Johnson WE. Rapid adversarial co-evolution of viruses and cellular restriction factors. Curr Top Microbiol Immunol. 2013;371:123–51.

    PubMed  Google Scholar 

  • Laguette N, Sobhian B, Casartelli N, Ringeard M, Chable-Bessia C, Segeral E, Yatim A, Emiliani S, Schwartz O, Benkirane M. SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx. Nature. 2011;474(7353):654–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Laguette N, Rahm N, Sobhian B, Chable-Bessia C, Munch J, Snoeck J, Sauter D, Switzer WM, Heneine W, Kirchhoff F, Delsuc F, Telenti A, Benkirane M. Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein. Cell Host Microbe. 2012;11(2):205–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lim ES, Malik HS, Emerman M. Ancient adaptive evolution of tetherin shaped the functions of Vpu and Nef in human immunodeficiency virus and primate lentiviruses. J Virol. 2010;84(14):7124–34.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lim ES, Fregoso OI, McCoy CO, Matsen FA, Malik HS, Emerman M. The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx. Cell Host Microbe. 2012;11(2):194–204.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Malfavon-Borja R, Wu LI, Emerman M, Malik HS. Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes. Proc Natl Acad Sci U S A. 2013;110(7):E583–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Malim MH, Bieniasz PD. HIV restriction factors and mechanisms of evasion. Cold Spring Harb Perspect Med. 2012;2(5):a006940.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Meyerson NR, Rowley PA, Swan CH, Le DT, Wilkerson GK, Sawyer SL. Positive selection of primate genes that promote HIV-1 replication. Virology. 2014;454–455:291–8.

    Article  PubMed  CAS  Google Scholar 

  • Pond SL, Frost SD, Muse SV. HyPhy: hypothesis testing using phylogenies. Bioinformatics. 2005;21(5):676–9.

    Article  CAS  PubMed  Google Scholar 

  • Quintana-Murci L, Clark AG. Population genetic tools for dissecting innate immunity in humans. Nat Rev Immunol. 2013;13(4):280–93.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sauter D, Schindler M, Specht A, Landford WN, Munch J, Kim KA, Votteler J, Schubert U, Bibollet-Ruche F, Keele BF, Takehisa J, Ogando Y, Ochsenbauer C, Kappes JC, Ayouba A, Peeters M, Learn GH, Shaw G, Sharp PM, Bieniasz P, Hahn BH, Hatziioannou T, Kirchhoff F. Tetherin-driven adaptation of Vpu and Nef function and the evolution of pandemic and nonpandemic HIV-1 strains. Cell Host Microbe. 2009;6(5):409–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sauter D, Specht A, Kirchhoff F. Tetherin: holding on and letting go. Cell. 2010;141(3):392–8.

    Article  CAS  PubMed  Google Scholar 

  • Sharp PM, Hahn BH. Origins of HIV and the AIDS pandemic. Cold Spring Harb Perspect Med. 2011;1(1):a006841.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sheehy AM, Gaddis NC, Choi JD, Malim MH. Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature. 2002;418(6898):646–50.

    Article  CAS  PubMed  Google Scholar 

  • Spragg CJ, Emerman M. Antagonism of SAMHD1 is actively maintained in natural infections of simian immunodeficiency virus. Proc Natl Acad Sci U S A. 2013;110(52):21136–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Van Valen L. A new evolutionary law. Evol Theory. 1973;1:1–30.

    Google Scholar 

  • Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586–91.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgment

LE is supported by an amfAR Mathilde Krim Fellowship in Basic Biomedical Research (108499-53-RKGN) and the Centre National de Recherche Scientifique (CNRS). Thank you to Molly Ohainle and Kevin Tartour for their comments on the manuscript, the members of the Emerman and Malik Labs for helpful discussions on these concepts.

Author information

Authors and Affiliations

  1. CIRI, Centre International de Recherche en Infectiologie, INSERM U1111 – CNRS UMR5308 – Université Lyon 1 – ENS de Lyon, 46, allée d’Italie, 69364, Lyon, France

    Lucie Etienne

Authors
  1. Lucie Etienne
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Lucie Etienne .

Editor information

Editors and Affiliations

  1. Department of Cell and Molecular Biology, Northwestern University, Robert H. Lurie Medical Research Center, Chicago, IL, USA

    Thomas J. Hope

  2. VA San Diego Healthcare System and University of California San Diego, La Jolla, CA, USA

    Douglas D. Richman

  3. Department of Medicine, University of Miami Leonard M. Miller School of Medicine, Miami, FL, USA

    Mario Stevenson

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media LLC

About this entry

Check for updates. Verify currency and authenticity via CrossMark

Cite this entry

Etienne, L. (2018). Virus-Host Evolution and Positive Selection. In: Hope, T.J., Richman, D.D., Stevenson, M. (eds) Encyclopedia of AIDS. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-7101-5_373

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7101-5_373

  • Published:

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4939-7100-8

  • Online ISBN: 978-1-4939-7101-5

  • eBook Packages: MedicineReference Module Medicine

Publish with us

Policies and ethics

Search

Navigation