Recombination is a significant factor driving genomic evolution, but it is not well understood in Dengue virus.
We used phylogenetic methods to search for recombination in 636 Dengue virus type 3 (DENV-3) genomes and unveiled complex recombination patterns in two strains, which appear to be the outcome of recombination between genotype II and genotype I parental DENV-3 lineages.
Their genomes (∼11 kbp) encode a single open reading frame, flanked by highly structured 5′ and 3′ untranslated regions (UTRs) ( Lindenbach and Rice, 2003 and Rice et al., 1985).
The N-terminal of the polyprotein encodes the three structural proteins (C-pr M-E), followed by seven non-structural (NS) proteins (NS1–NS2A–NS2B–NS3-NS4A–NS4B–NS5) ( Chambers et al., 1990 and Rice et al., 1985).
Concomitant infection with two different strains (a prerequisite for DENV recombination) was demonstrated both in humans and in mosquitoes (Bharaj et al., 2008, Loroño-Pino et al., 1999, Laille et al., 1991, Montenegro et al., 2006 and Wang et al., 2003).
Recently, documented distinct lineages within the same host.
Genomic DENV-3 strains were retrieved from Gen Bank (, in the supplemental material) and their source feature inspected, as a caution required in obtaining data from a public database, to check each entry name and to exclude mutants and non-human/non-mosquitoes isolates.
Alignments were built with the Muscle 3.8.31 program (Edgar, 2004a and Edgar, 2004b), manually inspected, and trimmed to include only coding regions.
We used the automated algorithms contained within the recombination detection program 3.0 (RDP3) (-value cutoff according to the size of the dataset being examined) and set the analysis to report all hits detected by 6 or more algorithms.
Once a putative recombination event was detected, a smaller dataset was built from selected sequences that included the likely recombinant, surrogate parental taxa, and reference strains.
Evidence of recombination between diverse dengue strains has arisen (Aaskov et al., 2007, Abu Bakar et al., 2002, Carvalho et al., 2010, Chen et al., 2008, Craig et al., 2003, Lavergne et al., 2006, Uzcategui et al., 2001 and Worobey et al., 1999) since the first report of recombination in natural populations in 1999 ().
Also, recombination was shown in other [+] ss RNA viruses, (Becher and Tautz, 2011, Carney et al., 2011, Chuang and Chen, 2009, Gould et al., 2004, Kalinina et al., 2002 and Reiter et al., 2011), Retroviruses ().
Two main mechanisms have been proposed for viral RNA recombination: (i) non-replicative breakage and rejoining and (ii) replicative template switching (Cooper, 1974 and Nagy and Simon, 1997).