Fig 1.
Geographical origin of the sampling site in Colombia and the process of sample collection.
(A). The blue area indicates the Norte de Santander region, and the pink area indicates Villa del Rosario City. The map was created using DIVA-GIS software (V.7.5.0 for Windows™ and mapchart.net (https://mapchart.net/americas.html). (B). Process of sample collection. The samples were collected during two periods. The first period was between August 2015 and April 2016 and the second was between November 2018 and July 2019. For DENV identification, conventional PCR was performed; multiplex RT–qPCR was performed for serotyping. Finally, the envelope (E) gene was amplified and sequenced and the phylogenetic and phylogeographic analyses were conducted.
Table 1.
Demographic information of patients from whom the DENV E protein genes were sequenced.
Fig 2.
Phylogenetic analysis of DENV-1 strains.
The analysis was conducted using the maximum likelihood method based on the Envelope gene using 6 sequences of 945 nt length and 131 sequences that have been previously deposited in GenBank. The tree was reconstructed using the nucleotide replacement model TN93 + G + I. The red circles represent the sequences from Norte de Santander identified as NDS-VDR. G: Genotype, BR: Brazil and VE: Venezuela. Color Code: Red: Colombia, red wine color: Venezuela, Blue: Argentina, Light Blue: Dominican Republic, green: Brazil, yellow: British Virgin Islands, and purple: Asian sequences.
Table 2.
Diversity of nucleotides in genotype V of DENV-1.
Fig 3.
Phylogenetic analysis of DENV-2 strains.
The analysis was performed using the maximum likelihood method based on the E gene, using 8 sequences of 1178 nt in length and 142 sequences that have been previously deposited in GenBank. The tree was reconstructed using the nucleotide replacement model TN93 + G + I. The red circles represent the sequences from Norte de Santander and identified as NDS-VDR. G: Genotype, C: Cosmopolitan, As: Asian, Am: American, SA: South America and CA: Central America. Color Code: Red: Colombia, Light Blue: Venezuela Light green: Mexico, Blue: Argentina, Green: Brazil, Orange: Ecuador, and purple: Asian sequences.
Table 3.
Diversity of nucleotides in Asian–American genotype of DENV-2.
Fig 4.
Maximum clade credibility tree of DENV-1 corresponding to the genotype V.
Branches are coloured according to the most probable location of their parental node and legends shown on the left side. All horizontal branch lengths are drawn according to a scale of years. Two clades (I-II) and subclade of the clade I (VE: Venezuela, BR: Brazil) are identified on the right side and the gray frame represented our sequences isolated from Villa del Rosario, Norte de Santander. ■: virus strains isolated in 1985 (AF425616) and 1996 (AF425617) available in Genbank. PSP: posterior state probability, PP: posterior probability, TMRCA: the mean estimated time to the most recent common ancestor and 95% HPD: 95% highest posterior density interval. ABW: Aruba, CRI: Costa Rica, ECU: Ecuador, GRD: Grenada, COL: Colombia, GUY: Guyana, NIC: Nicaragua, MTQ: Martinique, MEX: Mexico, URU: Uruguay, PRY: Paraguay, PRI: Puerto Rico, JAM: Jamaica, PER: Peru, BRA: Brazil, TTO: Trinidad and Tobago, HTI: Haiti, VGB: British Virgin Islands, VEN: Venezuela, IND: India, SGP:Singapure and REU:Reunion.
Fig 5.
Maximum clade credibility tree of DENV-2 corresponding to Asian–American genotype.
Branches are coloured according to the most probable location of their parental node and legend shown on the left side. All horizontal branch lengths are drawn to a scale of years. Three clades (I–III) and subclade of the clade III are identified on the right side and the gray frame represents our sequences isolated from Villa del Rosario, Norte de Santander. ■: virus strains isolated in 1993 (AY484644) and 1997 (DQ364497) available in Genbank. PSP: posterior state probability, PP: posterior probability, TMRCA: the mean estimated time to the most recent common ancestor and 95% HPD: 95% highest posterior density interval. ABW: Aruba, BHS: Bahamas, BLZ: Belize, BOL: Bolivia, BRB: Barbados, CRI: Costa Rica, CUB: Cuba, CUW: Curacao, DOM: Dominica, ECU: Ecuador, GRD: Grenada, GTM: Guatemala, GUY: Guyana, COL: Colombia, GUF: French Guiana, LCA: Santa Lucia, NIC: Nicaragua, MTQ: Martinique, MEX: Mexico, PRY: Paraguay, PRI: Puerto Rico, JAM: Jamaica, PER: Peru, BRA: Brazil, TTO: Trinidad and Tobago, HND: Honduras, SLV: Salvador, SUR: Surinam, VCT: Saint Vincent and the Grenadines,VIR: United States Virgin Islands, VEN: Venezuela, TWN:Taiwan, KHM:Cambodia, VNM:Vietman.