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Research Article

volume 40 issue 4 (december 2019) : 329-333,   Doi: 10.18805/ag.R-1786

Paleovirology: Blessing or Curse of Ancient Viruses - A Review

S
Shubhangi Warke
P
Prabhakar Tembhurne
S
Sumedha Bobade
V
V.C. Ingle
1Nagpur Veterinary College, Maharashtra Animal and Fishery Sciences University, Nagpur-440 006, Maharashtra, India.
Cite article:- Warke Shubhangi, Tembhurne Prabhakar, Bobade Sumedha, Ingle V.C. (2019). Paleovirology: Blessing or Curse of Ancient Viruses - A Review. Agricultural Reviews. 40(4): 329-333. doi: 10.18805/ag.R-1786.

ABSTRACT

Ancient virus genomes preserved as fossils and carried by host within their genome. Although viral genomes evolve rapidly, their rate of change slows to the same pace as that of the host’s DNA after insertion, making it possible to study viral DNA sequences that are many millions of years old. Paleovirology is the study of viral fossil records typically over prehistoric or geological timescales and the effects that these agents have had on the evolution of their hosts. Viruses sometimes heritably integrate into the genomes of their hosts, resulting in genomic features known as endogenous viral elements (EVEs). Using EVEs, the field of paleovirology investigates the long term evolution of viruses and their impact on hosts. One of the fruitful outcomes of high throughput genomics is the widespread availability of whole genome data, offering the unprecedented opportunity to investigate EVEs at a large scale. This review, highlights the utility of antiviral gene evolution for the study of paleovirology, the consequent surge in paleovirology and the main methodological techniques used to study them. EVEs can only be understood within an evolutionary framework and we outline a generalized workflow for conducting paleovirology studies.

REFERENCES

  1. Andersson, A., Svensson, A., Rolny, C., et al, (1998). Expression of human endogenous retrovirus ERV3 (HERV-R) mRNA in normal and neoplastic tissues. Int J Oncol. 12:309–13.
  2. Aswad, A. and Katzourakis, A. (2012). Paleovirology and virally derived immunity. Trends in Ecology and Evolution. DOI 10.1016/j.tree.2012.07.007. 
  3. Bannert, N. and Kurth, R. (2006). The evolutionary dynamics of human endogenous retroviral families. Annu Rev Genomics Hum Genet. 7: 149–173.
  4. Belshaw, R., Pereira, V., Katzourakis, A., Talbot, G, Paces, J., et al, (2004). Long-term reinfection of the human genome by endogenous retroviruses. Proc Natl Acad Sci USA. 101: 4894–4899. 
  5. Boyd, M.T., Bax, C.M.R., Bax, B.E., et al., (1993). The human endogenous retrovirus ERV-3 is upregulated in differentiating placental trophoblast cells. Virology. 196: 905–9.
  6. Daugherty, M.D. and Malik, H.S. (2012). Rules of engagement: molecular insights from host-virus arms races. Annu. Rev. Genet. 46: 677–700. 
  7. DeMartini, J. C., Carlson, J. O., Leroux, C., Spencer, T., Palmarini, M. (2003). Endogenous retroviruses related to jaagsiekte sheep retrovirus. Curr Top Microbiol Immunol, 275:117–137.
  8. Duggal, N.K. and Emerman, M. (2012). Evolutionary conflicts between viruses and restriction factors shape immunity. Nat. Rev. Immunol. 12:687–695. 
  9. Emerman, M. and Malik, H.S. (2010). Paleovirology—Modern Consequences of Ancient Viruses. PLoS Biol. 8(2): e1000301. doi:10.1371/journal.pbio.1000301.
  10. Feschotte, C. and Gilbert, C. (2012). Endogenous viruses: insights into viral evolution and impact on host biology. Nat. Rev. Genet. 13: U283–U288. (doi:10.1038/nrg3199)
  11. Garry, R.F., Fermin, C.D., Darenn, J.H., et al., (1990). Detection of a human intracisternal particle antigenically related to HIV. Science. 250: 1127–9.
  12. Horie, M., Honda, T., Suzuki, Y., Kobayashi, Y., Daito, T., et al., (2010). Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature. 463: 84–87.
  13. Katzourakis, A., Rambaut, A. and Pybus, O.G. (2005).The evolutionary dynamics of endogenous retroviruses. Trends Microbiol. 13: 463–468. 
  14. Katzourakis, A. (2013). Paleovirology: inferring viral evolution from host genome sequence data. Philos Trans R Soc Lond B Biol Sci. 368(1626): 20120493.
  15. Katzourakis, A. and Gifford, R.J. (2010). Endogenous viral elements in animal genomes. PLoS Genet. 6, e1001191. (doi:10.1371/journal.pgen.1001191).
  16. Larsson, E. andersson, G. (1998). Beneficial role of human endogenous retroviruses: facts and hypotheses. Scand J Immunol. 48: 329–38.
  17. Lower, R., Lower, J., Tondera-Koch, C., et al., (1993). A general method for identification of transcribed retrovirus sequences (R-U5 PCR) reveals the expression of the human endogenous retrovirus loci HERV-H and HERV-    K in teratocarcinoma cells. Virology. 192: 501–11. 
  18. Mallet, F., Bouton, O., Prudhomme, S., Cheynet, V., Oriol, G., Bonnaud, B., Lucotte, G., Duret, L., Mandrand, B. (2004). The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology. Proc Natl Acad Sci USA. 101:1731–1736. 
  19. Mi, S., Lee, X., Li X., Veldman, G.M., Finnerty, H., Racie, L., LaVallie, E., Tang, X.Y., Edouard, P., Howes, S., et al.,(2000). Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature. 403:785–789. 
  20. Nelson, P. N ., Carnegie, P. R., Martin, J., Davari Ejtehadi, H., Hooley, P., Roden, D., Rowland-Jones, S., Warren, P., Astley, J ., Murray P. G. (2003). Demystified. Human endogenous retroviruses. Mol Pathol, 56:11–18.
  21. OhAinle, M., Kerns, J.A., Li, M.M., Malik, H.S., Emerman, M. (2008). Antiretroelement activity of APOBEC3H was lost twice in recent human evolution. Cell Host Microbe. 4: 249–259.
  22. Patel, M.R., Emerman, M. and Malik, H.S. (2011). Paleovirology –Ghosts and gifts of viruses past. Curr Opin Virol, 1(4): 304–309. doi:10.1016/j.coviro.2011.06.007.
  23. Sauter, M., Roemer, K., Best, B., et al., (1996). Specificity of antibodies directed against Env protein of human endogenous retroviruses in patients with germ cell tumours. Cancer Res, 56:4362–5. 
  24. Sauter, M., Schommer, S., and Kremmer, E., et al., (1995). Human endogenous retrovirus K10: expression of gag protein and detection of antibodies in patients with seminomas. J Virol. 69: 414–21.
  25. Schulte, A.M., Shoupeng, L. and Kurtz, A., et al., (1996). Human trophoblast and choriocarcinoma expression of the growth factor pleiotrophin attributable to germ-line insertion of an endogenous retrovirus. Proc Natl Acad Sci USA. 93: 14759–64. 
  26. Speek, M. (2001). Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes. Mol Biol Cell. 21:1973–85.
  27. Stocking, C. and Kozak, C. A. (2008). Murine endogenous retroviruses. Cell Mol Life Sci. 65(21): 3383–3398. Doi:10.1007/    s00018-008-8497-0.
  28. Venkataraman, N., Cole, A.L., Ruchala, P., Waring, A.J., Lehrer, R.I., et al., (2009). Reawakening retrocyclins: ancestral human defensins active against HIV-1. PLoS Biol. 7: e95.
  29. Weiss, R.A. (2013). On the concept and elucidation of endogenous retroviruses. Phil. Trans. R. Soc. B. 368: 20120494. (doi:10.1098/rstb.2012.0494).
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    Research Article

    volume 40 issue 4 (december 2019) : 329-333,   Doi: 10.18805/ag.R-1786

    Paleovirology: Blessing or Curse of Ancient Viruses - A Review

    S
    Shubhangi Warke
    P
    Prabhakar Tembhurne
    S
    Sumedha Bobade
    V
    V.C. Ingle
    1Nagpur Veterinary College, Maharashtra Animal and Fishery Sciences University, Nagpur-440 006, Maharashtra, India.
    Cite article:- Warke Shubhangi, Tembhurne Prabhakar, Bobade Sumedha, Ingle V.C. (2019). Paleovirology: Blessing or Curse of Ancient Viruses - A Review. Agricultural Reviews. 40(4): 329-333. doi: 10.18805/ag.R-1786.

    ABSTRACT

    Ancient virus genomes preserved as fossils and carried by host within their genome. Although viral genomes evolve rapidly, their rate of change slows to the same pace as that of the host’s DNA after insertion, making it possible to study viral DNA sequences that are many millions of years old. Paleovirology is the study of viral fossil records typically over prehistoric or geological timescales and the effects that these agents have had on the evolution of their hosts. Viruses sometimes heritably integrate into the genomes of their hosts, resulting in genomic features known as endogenous viral elements (EVEs). Using EVEs, the field of paleovirology investigates the long term evolution of viruses and their impact on hosts. One of the fruitful outcomes of high throughput genomics is the widespread availability of whole genome data, offering the unprecedented opportunity to investigate EVEs at a large scale. This review, highlights the utility of antiviral gene evolution for the study of paleovirology, the consequent surge in paleovirology and the main methodological techniques used to study them. EVEs can only be understood within an evolutionary framework and we outline a generalized workflow for conducting paleovirology studies.

    REFERENCES

    1. Andersson, A., Svensson, A., Rolny, C., et al, (1998). Expression of human endogenous retrovirus ERV3 (HERV-R) mRNA in normal and neoplastic tissues. Int J Oncol. 12:309–13.
    2. Aswad, A. and Katzourakis, A. (2012). Paleovirology and virally derived immunity. Trends in Ecology and Evolution. DOI 10.1016/j.tree.2012.07.007. 
    3. Bannert, N. and Kurth, R. (2006). The evolutionary dynamics of human endogenous retroviral families. Annu Rev Genomics Hum Genet. 7: 149–173.
    4. Belshaw, R., Pereira, V., Katzourakis, A., Talbot, G, Paces, J., et al, (2004). Long-term reinfection of the human genome by endogenous retroviruses. Proc Natl Acad Sci USA. 101: 4894–4899. 
    5. Boyd, M.T., Bax, C.M.R., Bax, B.E., et al., (1993). The human endogenous retrovirus ERV-3 is upregulated in differentiating placental trophoblast cells. Virology. 196: 905–9.
    6. Daugherty, M.D. and Malik, H.S. (2012). Rules of engagement: molecular insights from host-virus arms races. Annu. Rev. Genet. 46: 677–700. 
    7. DeMartini, J. C., Carlson, J. O., Leroux, C., Spencer, T., Palmarini, M. (2003). Endogenous retroviruses related to jaagsiekte sheep retrovirus. Curr Top Microbiol Immunol, 275:117–137.
    8. Duggal, N.K. and Emerman, M. (2012). Evolutionary conflicts between viruses and restriction factors shape immunity. Nat. Rev. Immunol. 12:687–695. 
    9. Emerman, M. and Malik, H.S. (2010). Paleovirology—Modern Consequences of Ancient Viruses. PLoS Biol. 8(2): e1000301. doi:10.1371/journal.pbio.1000301.
    10. Feschotte, C. and Gilbert, C. (2012). Endogenous viruses: insights into viral evolution and impact on host biology. Nat. Rev. Genet. 13: U283–U288. (doi:10.1038/nrg3199)
    11. Garry, R.F., Fermin, C.D., Darenn, J.H., et al., (1990). Detection of a human intracisternal particle antigenically related to HIV. Science. 250: 1127–9.
    12. Horie, M., Honda, T., Suzuki, Y., Kobayashi, Y., Daito, T., et al., (2010). Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature. 463: 84–87.
    13. Katzourakis, A., Rambaut, A. and Pybus, O.G. (2005).The evolutionary dynamics of endogenous retroviruses. Trends Microbiol. 13: 463–468. 
    14. Katzourakis, A. (2013). Paleovirology: inferring viral evolution from host genome sequence data. Philos Trans R Soc Lond B Biol Sci. 368(1626): 20120493.
    15. Katzourakis, A. and Gifford, R.J. (2010). Endogenous viral elements in animal genomes. PLoS Genet. 6, e1001191. (doi:10.1371/journal.pgen.1001191).
    16. Larsson, E. andersson, G. (1998). Beneficial role of human endogenous retroviruses: facts and hypotheses. Scand J Immunol. 48: 329–38.
    17. Lower, R., Lower, J., Tondera-Koch, C., et al., (1993). A general method for identification of transcribed retrovirus sequences (R-U5 PCR) reveals the expression of the human endogenous retrovirus loci HERV-H and HERV-    K in teratocarcinoma cells. Virology. 192: 501–11. 
    18. Mallet, F., Bouton, O., Prudhomme, S., Cheynet, V., Oriol, G., Bonnaud, B., Lucotte, G., Duret, L., Mandrand, B. (2004). The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology. Proc Natl Acad Sci USA. 101:1731–1736. 
    19. Mi, S., Lee, X., Li X., Veldman, G.M., Finnerty, H., Racie, L., LaVallie, E., Tang, X.Y., Edouard, P., Howes, S., et al.,(2000). Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature. 403:785–789. 
    20. Nelson, P. N ., Carnegie, P. R., Martin, J., Davari Ejtehadi, H., Hooley, P., Roden, D., Rowland-Jones, S., Warren, P., Astley, J ., Murray P. G. (2003). Demystified. Human endogenous retroviruses. Mol Pathol, 56:11–18.
    21. OhAinle, M., Kerns, J.A., Li, M.M., Malik, H.S., Emerman, M. (2008). Antiretroelement activity of APOBEC3H was lost twice in recent human evolution. Cell Host Microbe. 4: 249–259.
    22. Patel, M.R., Emerman, M. and Malik, H.S. (2011). Paleovirology –Ghosts and gifts of viruses past. Curr Opin Virol, 1(4): 304–309. doi:10.1016/j.coviro.2011.06.007.
    23. Sauter, M., Roemer, K., Best, B., et al., (1996). Specificity of antibodies directed against Env protein of human endogenous retroviruses in patients with germ cell tumours. Cancer Res, 56:4362–5. 
    24. Sauter, M., Schommer, S., and Kremmer, E., et al., (1995). Human endogenous retrovirus K10: expression of gag protein and detection of antibodies in patients with seminomas. J Virol. 69: 414–21.
    25. Schulte, A.M., Shoupeng, L. and Kurtz, A., et al., (1996). Human trophoblast and choriocarcinoma expression of the growth factor pleiotrophin attributable to germ-line insertion of an endogenous retrovirus. Proc Natl Acad Sci USA. 93: 14759–64. 
    26. Speek, M. (2001). Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes. Mol Biol Cell. 21:1973–85.
    27. Stocking, C. and Kozak, C. A. (2008). Murine endogenous retroviruses. Cell Mol Life Sci. 65(21): 3383–3398. Doi:10.1007/    s00018-008-8497-0.
    28. Venkataraman, N., Cole, A.L., Ruchala, P., Waring, A.J., Lehrer, R.I., et al., (2009). Reawakening retrocyclins: ancestral human defensins active against HIV-1. PLoS Biol. 7: e95.
    29. Weiss, R.A. (2013). On the concept and elucidation of endogenous retroviruses. Phil. Trans. R. Soc. B. 368: 20120494. (doi:10.1098/rstb.2012.0494).
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