Skip to main content

Advertisement

SpringerLink
Log in

Viral species, viral genomes and HIV vaccine design: is the rational design of biological complexity a utopia?

  • In honor of Marc van Regenmortel
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

A common logical confusion is prevalent in the whole of biology, namely that biological species are viewed both as an abstract category in an hierarchical classification and as a concrete kind of organism. This is partly due to the fact that the vast majority of living organisms do not have common names that differ from the Latin name of the species to which the organism belongs. However, it is somewhat astonishing that the same confusion exists in virology since every virus has a common name, different from the species name to which the virus belongs, which could be used to refer to the infectious viral entity as a concrete material object. The original 1991 ICTV definition of virus species stated that a virus species is a polythetic class of viruses and thus that a species is a class, namely a conceptual construction of the mind and not a physical, real object located in space and time. In 2013, the ICTV redefined a virus species no longer as a class but as a material object consisting of a monophyletic group of viruses that were all physically part of the species. This new definition is reminiscent of an earlier school of thought known as bionominalism which considered species to be concrete individuals rather than classes. Both bionominalism and the new ICTV definition are based on the logical fallacy of reification which treats abstractions such as classes as if they were concrete physical entities. The implications of this new ontology of virus species for virus taxonomy and for the possibility of incorporating nucleotide metagenomic sequences in the current ICTV classification is discussed.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Quine WV (1990) Classes versus properties. In: Quiddities: an intermittently philosophical dictionary. Penguin Books, London, pp 22–26

    Google Scholar 

  2. Pringle CR (1991) The 20th meeting of the executive committee of the ICTV. Virus species, higher taxa, a universal database and other matters. Arch Virol 119:303–304

    Article  Google Scholar 

  3. Fauquet CM, Fargette D (2005) International Committee on Taxonomy of Viruses and the 3, 142 unassigned species. Virol J 2:64–73

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  4. Ereshefsky M (2011) Mystery of mysteries: Darwin and the species problem. Cladistics 27:67–79

    Article  Google Scholar 

  5. Simmonds P (2018) A clash of ideas - the varying uses of the ‘species’ term in virology and their utility for classifying viruses in metagenomic datasets. J Gen Virol 99:277–287

    Article  Google Scholar 

  6. Van Regenmortel MHV, Fauquet CM (2002) Only italicized species names of viruses have a taxonomic meaning. Arch Virol 147:2247–2250

    Article  PubMed  Google Scholar 

  7. Calisher CH, Mahy BWJ (2003) Taxonomy: get it right or leave it alone. Am J Trop Med Hyg 68:505–506

    Article  PubMed  Google Scholar 

  8. Van Regenmortel MHV (2007) Virus species and virus identification: past and current controversies. Infect Genet Evol 7:133–144

    Article  PubMed  CAS  Google Scholar 

  9. Van Regenmortel MHV (2011) Virus species. In: Tibayrenc M (ed) Genetics and evolution of infectious diseases. Elsevier, Amsterdam, pp 3–19

    Chapter  Google Scholar 

  10. Van Regenmortel MHV (2017) Recent developments in the definition and official names of virus species. In: Tibayrenc M (ed) Genetics and evolution of infectious diseases. Elsevier, Amsterdam, pp 1–23

    Google Scholar 

  11. Van Regenmortel MHV, Ackermann H-W, Calisher CH, Dietzgen RG, Horzinek M, Keil GM et al (2013) Virus species polemics: 14 senior virologists oppose a proposed change to the ICTV definition of virus species. Arch Virol 158:1115–1119

    Article  PubMed  CAS  Google Scholar 

  12. Van Regenmortel MHV (2000) On the relative merits of italics, Latin and binomial nomenclature in virus taxonomy. Arch Virol 145:433–441

    Article  PubMed  Google Scholar 

  13. Amarasinghe GK, Bào Y, Basler CF et al (2017) Taxonomy of the order Mononegavirales: update 2017. Arch Virol 162:2493–2504

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  14. Beckner M (1959) The biological way of thought. Columbia University Press, New York

    Google Scholar 

  15. Hull DL (1976) Are species really individuals? Syst Zool 25:174–191

    Article  Google Scholar 

  16. Van Regenmortel MHV, Maniloff J, Calisher CH (1991) The concept of virus species. Arch Virol 120:313–314

    Article  PubMed  Google Scholar 

  17. Van Regenmortel MHV, Bishop DHL, Fauquet CM, Mayo MA, Maniloff J, Calisher CH (1997) Guidelines to the demarcation of virus species. Arch Virol 142:1505–1518

    Article  PubMed  Google Scholar 

  18. Van Regenmortel MHV (2000) Introduction to the species concept in virus taxonomy. In: Van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens EB, Estes MK, Lemon SM, McGeogh DJ, Maniloff J, Mayo MA, Pringle CR, Wickner RB (eds) Virus taxonomy. Seventh ICTV Report. Academic Press, San Diego, pp 3–16

    Google Scholar 

  19. Van Regenmortel MHV (2010) The nature of viruses. In: Mahy BWJ, Van Regenmortel MHV (eds) Desk encyclopedia of general virology. Academic Press, Elsevier, Oxford, pp 23–29

    Google Scholar 

  20. Gibbs AJ, Gibbs MJ (2006) A broader definition of the ‘virus species’. Arch Virol 151:1419–1422

    Article  PubMed  CAS  Google Scholar 

  21. King A. (2012) Comments to proposed modification to code rule 3.21 (defining virus species). ICTV Discussions. https://talk.ictvonline.org/ictv1/f/general_ictv_discussions-20/3930/comments-to-proposed-modification-to-code-rule-3-21-defining-virus-species. Accessed 23 July 2018

  22. Schaefer JA, Wilson CC (2002) The fuzzy structure of populations. Can J Zool 80:2235–2241

    Article  Google Scholar 

  23. McNeill D, Freiberger P (1993) Fuzzy logic. Simon and Schuster, New York

    Google Scholar 

  24. Bunge M (2016) Modes of existence. Rev Metaphys 70:225

    Google Scholar 

  25. Ghiselin MT (1984) ‘‘Definition’’ ‘‘character’’ and other equivocal terms. Syst Zool 33:104–110

    Article  Google Scholar 

  26. Mahner M, Bunge M (1997) Foundations of biophilosophy. Springer, Berlin

    Book  Google Scholar 

  27. Gibbs AJ, Armstrong JS, Gibbs MJ (2004) A type of nucleotide motif that distinguishes tobamovirus species more efficiently than nucleotide signatures. Arch Virol 149:1941–1954

    PubMed  CAS  Google Scholar 

  28. Adams MJ, Lefkowitz EJ, King AM, Carstens EB (2013) Recently agreed changes to the International Code of Virus Classification and Nomenclature. Arch Virol 158:2633–2639

    Article  PubMed  CAS  Google Scholar 

  29. Calisher CH, Horzinek MC, Mayo MA, Ackermann HW, Maniloff J (1995) Sequence analyses and a unifying system of virus taxonomy: consensus via consent. Arch Virol 140:2093–2099

    Article  PubMed  CAS  Google Scholar 

  30. Ball LA (2005) The universal taxonomy of viruses in theory and practice. In: Fauquet CM et al (eds) Eighth ICTV Report. Elsevier, Amsterdam, pp 11–16

    Google Scholar 

  31. Buck RC, Hull DL (1966) The logical structure of the Linnaean hierarchy. Syst Zool 15:97–111

    Article  Google Scholar 

  32. Baldwin JT, Lessmann O (1998) What is Russell’s paradox?. Scientific American. http://www.scientificamerican.com/article/what-is-russells-paradox/. Accessed 23 July 2018

  33. King AMQ, Lefkowitz EJ, Mushegian AR, Adams MJ, Dutilh BE et al (2018) Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses. Arch Virol. https://doi.org/10.1007/s00705-018-3847-1

    Article  PubMed  Google Scholar 

  34. Van Regenmortel MHV (2018) The species problem in virology. Adv Virus Res 100:1–18

    Article  PubMed  Google Scholar 

  35. Van Regenmortel MHV (2016) Only viruses, but not their genome sequences, can be classified into hierarchical species and genus classes. Curr Top Virol 13:59–68

    Google Scholar 

  36. Dupré J (2001) In defence of classification. Stud Hist Philos Biol Biomed Sci 32:203

    Article  Google Scholar 

  37. Hey J (2001) The mind problem. Trends Ecol Evol 12:326–329

    Article  Google Scholar 

  38. Ruse M (1998) All my love is for individuals. Evolution 52:283–288

    Article  Google Scholar 

  39. Fauquet CM (2010) Taxonomy, classification and nomenclature of viruses. In: Mahy BWJ, Van Regenmortel MHV (eds) Desk Encyclopedia of General Virology. Elsevier, San Diego, pp 80–95

    Google Scholar 

  40. Brüssow H (2009) The not so universal tree of life or the place of viruses in the living world. Philos Trans R Soc Lond B Biol Sci 364:2263–2274

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Daszak P, Carroll D, Wolfe N et al (2016) The global virome project. Int J Infect Dis 535:4–163

    Google Scholar 

  42. Geoghegan JL, Holmes EC (2017) Predicting virus emergence amid evolutionary noise. Open Biol 7:170189

    Article  PubMed  PubMed Central  Google Scholar 

  43. Simmonds P, Adams MJ, Benkő M et al (2017) Consensus statement: virus taxonomy in the age of metagenomics. Nat Rev Microbiol 15:161–168

    Article  PubMed  CAS  Google Scholar 

  44. Finlay BJ, Esteban GF (2009) Can Biological complexity be rationalized ? Bioscience 59:333–340

    Article  Google Scholar 

  45. Brito AF, Braconi CT, Weidmann M, Dilcher M, Alves JM, Gruber A, Zanotto PM (2015) The pangenome of the Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV). Genome Biol Evol 8:94–108

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  46. Van Regenmortel MHV (2012) Basic research in HIV vaccinology is hampered by reductionist thinking. Front Immunol 3:194

    PubMed  PubMed Central  Google Scholar 

  47. Pulendran B (2014) Systems vaccinology: probing humanity’s diverse immune systems with vaccines. Proc Natl Acad Sci USA 111:12300–12306

    Article  PubMed  CAS  Google Scholar 

  48. Van Regenmortel MHV (2018) Development of a preventive HIV vaccine requires solving inverse problems which is unattainable by rational vaccine design. Front Immunol 8:2009

    Article  PubMed  PubMed Central  Google Scholar 

  49. Zeder-Lutz G, Benito A, Van Regenmortel MHV (2009) Active concentration measurements of recombinant biomolecules using biosensor technology. J Mol Recognit 12:300–309

    Article  Google Scholar 

  50. Richalet-Sécordel PM, Rauffer-Bruyère N, Christensen LL, Ofenloch-Haehnle B, Seidel C, Van Regenmortel MH (1997) Concentration measurement of unpurified proteins using biosensor technology under conditions of partial mass transport limitation. Anal Biochem 249:165–173

    Article  PubMed  Google Scholar 

  51. Zeder-Lutz G, Benito A, Van Regenmortel MHV (1999) Active concentration measurements of recombinant biomolecules using biosensor technology. J Mol Recognit 12:300–309

    Article  PubMed  CAS  Google Scholar 

  52. Azimzadeh A, Van Regenmortel MHV (1991) Measurement of affinity of viral monoclonal antibodies by ELISA titration of free antibody in equilibrium mixtures. J Immunol Methods 141:199–208

    Article  PubMed  CAS  Google Scholar 

  53. Van Regenmortel MHV (2014) An outdated notion of antibody specificity is one of the major detrimental assumptions of the structure-based reverse vaccinology paradigm, which prevented it from helping to develop an effective HIV-1 vaccine. Front Immunol 5:593

    PubMed  PubMed Central  Google Scholar 

  54. Van Regenmortel MHV (2017) Immune systems rather than antigenic epitopes elicit and produce protective antibodies against HIV. Vaccine 35:1985–1986

    Article  PubMed  CAS  Google Scholar 

  55. Du Sautoy M (2016) What we cannot know. Harper Collins Publishers, New York, pp 36–73

    Google Scholar 

  56. Green S (2015) Can biological complexity be reverse engineered? Stud Hist Philos Biol Biomed Sci 53:73–83

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Biotechnology, CNRS, University of Strasbourg, 67412, Illkirch, France

    Marc H. V. van Regenmortel

Authors
  1. Marc H. V. van Regenmortel
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Marc H. V. van Regenmortel.

Ethics declarations

Conflict of interest

The author declares that he has no conflict of interest.

Additional information

Handling Editor: Tim Skern.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

van Regenmortel, M.H.V. Viral species, viral genomes and HIV vaccine design: is the rational design of biological complexity a utopia?. Arch Virol 163, 2047–2054 (2018). https://doi.org/10.1007/s00705-018-3955-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-018-3955-y

Search

Navigation