lunes, 10 de septiembre de 2007

Applying the species concepts to dengue viruses

Villabona-Arenas, C. J.
Laboratorio de Sistemática y Biogeografía, Escuela de Biología
Universidad Industrial de Santander

In 1991, the international Committee on taxonomy of viruses (ICTV) endorsed the following definition of virus species: a virus species is a polythetic class of viruses that constitutes a lineage of replication and occupies a particular ecological niche [1]; the virologists adopted its own species concept because they assumed that the only legitimate species concept was that of biological species [2]. The species problem has been discussed in different publications and diverse species concepts have been proposed [3, 4]. The dengue viruses are an ICTV approved species of the genus flavivirus, family flaviviridae and comprise four antigenically related but distinct serotypes (DENV-1 to DENV-4) [5, 6]. In this work I explored the change in the number of species within the dengue viruses applying different applicable concepts and I proposed one of them to be used in the virology field.

The Table 1 presents the different species concepts applied in this work. The data set included 47 published E gene sequences from worldwide isolates of each serotype deposited in Genbank (See appendix 1). The nucleotide sequences were aligned using multiple alignment with Muscle 3.6 software package (7) and optimal alignment with Poy 4.0 software package (8). The former alignment was used to reconstruct an UPGMA tree with the Muscle 3.6 software package and the latter alignment was used to reconstruct a Parsimony tree with the TNT 1.1 software package (9) using the Yellow Fever virus to root the tree. A bootstrapping with 100 replicates was used to place confidence values on groupings within the parsimony tree and a value ≥ 99% was used as the criterion by which a taxon was ranked as a species according to phylogenetic species concept (PSC) sensu Mishler and Theriot. The Parsimony tree was use also as a guide to differentiate groups within the DENV-1 and then the characters were mapped to identify species in this serotype following the PSC sensu Wheeler and Platnick

The UPGMA tree is presented in Figure 1; three different cut points are shown representing different percentage of genome sequence similarity. The number of recognized species was 37, 41 and 45 for 73, 75 and 77% respectively. A parsimony tree is presented in Figure 2; the sixhighlighted groups represent the identified species using the  ranking decision mentioned above. The Figure 3 shows and scheme of the diagnosed groups for the DENV-1 sequences: each line represents a position in which the respective group fixed a unique nucleotide; the diagnose groups are highlighted and a summary of the same analysis for each one serotypes is presented in Table 2.

Figure 1
Figure 2

Figure 3

Figura 4


It has been shown in Figure 1 that minor differences in the percentages used to discriminate species lead to changes in the number of encountered species. The determination of such percentages is subjective and there is indeed no simple relationship between the extent of genome sequence similarity and the affiliation of a single virus to a particular species: the imaginary data matrix presented in Figure 4 shows a problematic case in which the sequence number 4 has the same similarity value with both of the other two set of sequences which are clearly different between them, therefore a level of genome similarity fails to identify the members of species. Mishler and Theriot (3) have proposed that organisms are grouped into taxa using as grouping criterion the evidence for monophyly and at the same time they have suggested to use as criterion by which a taxon is ranked as a species the amount of character support for putative groups or involve biological criteria in better known organisms. The application of ranking decisions, as in the percentage rules, is arbitrary to some extent and suggests that species are artificial constructs in the minds of researchers. On the other hand the PSC sensu Mishler and Theriot raise the idea that species are the result of phylogenetic analyses of the organisms. Hennig (10) described phylogenetic analysis as a means of reconstructing hierarchic descent relationships among species; the phylogenetic history is retrievable above the level of species, in part because of the emergence of hierarchical relations marked by character transformations; and consequently using a phylogenetic analysis to determine species is rather circular. The PSC sensu Wheeler and Platnick (3) shows that it is possible to have a species concept that avoids rampant subjectivity and furthermore applicable to viruses. The identified species in the Figure 4 are just based on characters and such species can be diagnosed by a unique combination of character states. While is some cases The PSC sensu Mishler and Theriot sometimes present a putative group as one species (the case of Dengue Virus type 1 in Figure 2) in which according to the PSC sensu Wheeler and Platnick is possible to identify multiple species, diagnosed even by a unique fixed mutation. This point highlights a particular aspect of the PSC sensu Wheeler and Platnick: it may result in an enormous number of species. In the other hand it looks that the recognizable groups that have been called genotypes (6) inside each one of the dengue virus serotypes somehow could be equated with the diagnosable species reported here using PSC sense Wheeler and Platnick. In this respect is possible that the dengue virologists misinterpret their study units because they often use as classification guides epidemiology and/or disease clinical presentations. As thousands of sequences of viral genomes are continuously added to databases, there is an increasing tendency to rely almost exclusively on molecular data for virus classification (11). Here I introduced PSC that represents a unit species concept that also can be applied to the virology field using molecular data: a concept that aims to recognize the lineages that perpetuate more in the nature avoiding the arbitrary in the decisions for their identification and recognizing species like real entities, as diagnosable lineages by their characters.

1. Van Regenmortel, M.H.V. and Mahy, B.W.J., 2004. Emerging issues in virus taxonomy. Emerg. Infect. Dis. 10, 8–13.Van Regenmortel, M.H.V., 2006. Virologists, taxonomy and the demands of logic. Arch. Virol. 151, in press.
2. Van-Regenmortel, M.H.V., 2007. Virus species and virus identification: Past and current controversies. Infection Genetics and Evolution 7(1): 133-144
3. Wheeler, Q. D. and Meier, R. (Editors). 2000. Species Concepts and Phylogenetic Theory: A Debate. New York: Columbia University Press
4. Goldstein, P.Z. and DeSalle, R. 2000. Phylogenetic species, nested hierarchies, and character fixation. Cladistics 16: 364-384.
5. Henchal, E. and Putnak, R. 1990. The Dengue Viruses. Clinical Microbiology Reviews, 3 (4), 376-396
6. Rico-Hesse, R. 2003. Microevolution and virulence of dengue viruses. Adv Virus Res 59: 315-341.
7. Edgar, Robert C., 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.
8. Varón A., Vinh L.S., Bomash I., Wheeler W.C., 2007. POY 4.0 Beta 1665. American Museum of Natural History.
9. Goloboff, P., Farris J. S., and Nixon K. T.N.T.: Tree Analysis Using New Technology. Program and Documentation, available from the authors, and at
10. Hennig, W. 1966. Phylogenetic systematics. University of Illinois, Urbana, Illinois. 263 p.
Calisher, C.H., Horzinek, M.C., Mayo, M.A., Ackermann, H.W., Maniloff, J., 1995. Sequence analyses and a unifying system of virus taxonomy: consensus via consent. Arch. Virol. 140, 2093–2099