Besides, there is a number of reasons for believing that

recombination can occur in DENV and this process is being described with increasing frequency in DENV-1 [13, 18] and other members of the family Flaviviridae [19–22]. The recombination in DENV was reported in the structural HSP inhibitor genes region and particularly in E gene sequence through the use of the BOOTSCAN, DIVERSE PLOTS, and LARD software [14]. The co-circulation of multiple DENV populations increases the opportunities for a mosquito vector to ingest several variants by feeding on a number of diverse infected hosts, or for a host to be infected by vectors infected with distinct DENV variants. These conditions exist in Mexico, the Caribbean Area and South-East Asia [23]. This is supported by the fact that there are many reports of multiple serotypes

of DENV from single hosts [3, 23–25]. Furthermore, it is likely that mixed infections with different genotypes of the same serotype may also occur where they co-circulate [26, 27]. Oaxaca, Mexico is one of the states where DENV is endemic and serotypes -1, -2 and -3 of DENV are co-circulating [23]. DENV-2 was reported as the serotype with higher frequency compared with DENV-1, -3 or -4. Six partial sequences of the genes encoding proteins: capsid (C), pre-membrane-membrane (prM-M), envelop (E), and non-structural 1 (NS1) represented as C(91)-prM-E-NS1(2400) from six different isolates Cyclin-dependent kinase 3 of DENV-2 from the Oaxaca outbreaks 2005-2006 Tucidinostat ic50 were obtained. In addition, the RT-PCR products of C(91)-prM-E-NS1(2400) and E genes obtained from the MEX_OAX_1656_05 isolate were cloned and sequenced. MEX_OAX_1656_05 and MEX_OAX_1038_05 isolates displayed recombination in the prM-E and E-NS1 genes

and the parental strains were the Asian/American and Cosmopolitan genotypes. In addition, the E gene sequences from the clone 7 (MEX_OAX_1656_05_C07) showed recombination between the nucleotides 906 to 1047 and the parental strains were Asian/American and American genotypes. Results To determine recombinant sequences in DENV-2, the nucleotide sequences of the partial C(91)-prM-E-NS1(2400) genome from six isolates and 90 representative sequences of the different genotypes were aligned and analyzed by RDP3 and GARD. In addition, the RT-PCR product of the partial C(91)-prM-E-NS1(2400) genome from the MEX_OAX_1656_05 isolate was cloned in pGEM-3Z. The sequences of 9 clones were aligned with all of the above sequences (Figure 1A). We also sequenced 10 clones of the E structural gene from the isolate MEX_OAX_1656_05 and aligned with 180 representative sequences containing different genotypes by the programs mentioned above (Figure 1B). Figure 1 Experimental strategy. A) The flow chart shows the experimental strategy that we followed to detect the recombinants in DENV-2 isolates.