Evaluation of genetic recombination on phylogenetics relationships in Dengue virus

A. Susana Ortiz Bae

Laboratorio de Sistematica y Biogeografia

Introduction

Genetic recombination in RNA viruses is an evolutionary process defined as the exchange of genetic information from two or more nucleotide sequences into recombinant progeny virus (Mahy, 2009). This mechanism apparently plays a significant role in the generation of genetic diversity especially important under adverse conditions (Worobey et al. 1999). Despite above, the process is a rare event in natural populations of Dengue virus in which through a copy-choice mechanism, the polymerase switches between parental viral molecules during replication (Lai, 1992). However, the approximate inference of recombination can be based regarding their effect on genealogy as events that can change or not the final topology or branch lengths and therefore can disrupt the pattern of phylogenetic relationships between viral sequences (Wiuf et al. 2000). Given that many recombinant sequences are mosaics comprising regions with quite different phylogenetic histories, this study evaluated the effect of genetic recombination on phylogenetics relationships in Dengue virus type 1 sequence, based on the detection of conflicting phylogenic signals under parsimony criterion.

Methods

Viral recombinants , parental and no recombinants sequences from dengue strains used in this study were provide from the analysis reported by Chen et al. (2008) and Worobey et al. (1999). Prior to the analysis of these sequences was constructed a data set and recombination events were simulated between regions of the serotypes with the aim to detect sensitivity to genetic recombination in the inter-serotype level. The sequences from literature, was partitioned in specific coding regions corresponding to recombination breakpoints and were aligned, then the the phylogenetic relationships were reconstructed under phylogenetic inference criteria such as parsimony implementing heuristic method and finally the pattern of relationships were summarized on a strict consensus. Representative sequences from Denv-2, Denv-3 and Denv4 were used as outgroups to root the tree.

Results and Discussion

Based on phylogenies inferred from the structural and non-structural regions, the results pointed differential levels of resolution and rearrangement of the parental sequences as recombinant sequences were eliminated depending on the analyzed partition. This was clearly seen given the pattern of phylogenetic relationships between Philippines84 with Nauru74 and ARG992 strains which are closely related in the region encoding the capside. On the other hand, from the region encoding the membrane (prM/M) protein the Philippines84 strain diverges to associate with Thailand80 strain while the region coding for envelope (E) protein and at the junction with the membrane protein (preM/E), Phylippines84 is reassociated with both viral sequences Nauru74 and Thailand80 which indicates these sequences as parental of Philippines84 in a higher or lower component depending on the partition analyzed and corroborates Philippines84 as descendant of one ancestor that derived independently.

Moreover, despite the reassociations between Thailand80 strains with Philippines84, this was never dissociated from its parental sequence Jamaica77 which indicates an important contribution of this sequence to the genetic diversity of Thailand80. Concerning the strain BR 90, although suggested by Woorobey et al. (1999) no clearly evidenced the pattern of relationships with its parental sequences Jamaica77 and Singapore90 when new sequences are incorporated into the analysis, however seems that Jamaica77 classified as genotype VI represent a significant component in the C and preM regions while Singapore90 classified as genotype I, contributes most notably to E and junction preM/E regions. Such discordant relationships and different topologies between regions within the same sequence may suggest the existence of intra-serotype mosaic genomes produced by recombination between divergent parent lineages (Worebey and Holmes, 1999).

Similarly for GD23_95 strain, phylogenetic trees based on recombinants and non-recombinants regions showed that the variation in the sequence on the topology generated under Parsimony criterion is nor a strong indication of its recombinant condition, opposite to that found by Chen et al. (2008) by the neighbor-joining method, then such a definition could be an artifact. Additionally, given the elimination of the putative recombinant sequences on the topology, we often observe an improvement in the resolution of phylogenetic relationships, except in the preM region where three sequences were localizated in the same clade. Nonetheless this response was nor evident on topologies where the GD23_95 strain was eliminated, which could promote a false positive. Finally, it is important to note that although not recover a general pattern of phylogenetic relationships, each partition reflects a hypothesis that despite being different between these may be clouded by the presence of recombinant sequences which may contain regions with very different evolutionary histories within individual strains present.

Conclusions

Phylogenetic approaches can provide a method for detecting and characterizing recombination events among conflicting phylogenetic signals in gene sequence data with different patterns of relationship for different sequence regions in Dengue viruses, however, is necessary be careful in the some affirmations about recombinant events given that different regions pointed different patterns of phylogenetic relationships and regions non-recombinants don’t imply resolution on this relationships.

References

Lai, M.M.C., 1992. RNA recombination in animal and plant viruses. Microbiol. Rev. 56, 61–79.
Mahy, B., 2009. The Dictionary of virology. Elsevier, 4ed. 518p.
Wiuf, C. & Hein, J., 2000. Genetics 155, 451–462.
Worobey, M., Rambaut, A., Holmes, E.C., 1999. Widespread intraserotype recombination in natural populations of dengue virus. Proc. Natl. Acad. Sci. U.S.A. 96, 7352–7357.
Worobey, M., Holmes, E.C., 1999. Evolutionary aspects of recombination in RNA viruses. Mol. Journal of General Virology , 80, 2535±2543