Genomic Diversity, Phylogenetic Structure, and In Silico Diagnostic Primer Compatibility of Available DENV-1 Genotype V from Mexico.
- 1Laboratory of Conservation Medicine, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88700, Tamaulipas, Mexico.
- 2UAM Reynosa-Aztlán, Universidad Autónoma de Tamaulipas, Reynosa 88740, Tamaulipas, Mexico.
Abstract
Background: Dengue virus serotype 1 (DENV-1) is prevalent across the Americas, yet its genomic diversity in Mexico is poorly characterized. Methods: We analyzed 119 public Mexican DENV-1 genomes (polyprotein CDS, 10,179 nt) alongside 111 from 19 other American countries and territories. The Mexican panel was temporally and geographically uneven (91% from 2006 to 2009), representing available sequences, not nationwide diversity. We assessed diversity, phylogeny, dating, selection, recombination, and compatibility with three primer sets. Results: The Mexican genotype V sequences formed 115 haplotypes (Hd = 0.9994; π = 0.00831), resolving into clades A (n = 6) and B (n = 112) plus one independent introduction in Jalisco. These sequences were not monophyletic: both clades grouped with Nicaraguan and United States viruses. Their common ancestor dated to 1977.5 and clade divergence to 1984.2. Selection appeared to be predominantly purifying (ω = 0.037); no site showed concordant evidence of diversifying selection, and no recombination was detected. In silico, 84% of Mexican sequences were compatible with all three CDC real-time oligonucleotides; none matched every oligonucleotide in either conventional set. Conclusions: This historical panel shows substantial haplotype diversity and multiple introductions. The compatibility results are computational and were not validated experimentally. We recommend periodic in silico primer revalidation.
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BibTeX
@article{cabrerasantos2026genomic,
title = {{Genomic Diversity, Phylogenetic Structure, and In Silico Diagnostic Primer Compatibility of Available DENV-1 Genotype V from Mexico.}},
author = {Francisco Joel Cabrera-Santos and Fátima Yedith Camacho-Sánchez and Sorayda Leonela González-Trujillo and Miguel Angel Reyes-López and Erick de Jesús De Luna-Santillana},
journal = {Tropical medicine and infectious disease},
year = {2026},
month = oct,
doi = {10.3390/tropicalmed11100287},
url = {https://europepmc.org/article/MED/42931472},
note = {CC BY},
}
RIS
TY - JOUR
TI - Genomic Diversity, Phylogenetic Structure, and In Silico Diagnostic Primer Compatibility of Available DENV-1 Genotype V from Mexico.
AU - Francisco Joel Cabrera-Santos
AU - Fátima Yedith Camacho-Sánchez
AU - Sorayda Leonela González-Trujillo
AU - Miguel Angel Reyes-López
AU - Erick de Jesús De Luna-Santillana
PY - 2026
DA - 2026/10/12
JO - Tropical medicine and infectious disease
DO - 10.3390/tropicalmed11100287
UR - https://europepmc.org/article/MED/42931472
AB - Background: Dengue virus serotype 1 (DENV-1) is prevalent across the Americas, yet its genomic diversity in Mexico is poorly characterized. Methods: We analyzed 119 public Mexican DENV-1 genomes (polyprotein CDS, 10,179 nt) alongside 111 from 19 other American countries and territories. The Mexican panel was temporally and geographically uneven (91% from 2006 to 2009), representing available sequences, not nationwide diversity. We assessed diversity, phylogeny, dating, selection, recombination, and compatibility with three primer sets. Results: The Mexican genotype V sequences formed 115 haplotypes (Hd = 0.9994; π = 0.00831), resolving into clades A (n = 6) and B (n = 112) plus one independent introduction in Jalisco. These sequences were not monophyletic: both clades grouped with Nicaraguan and United States viruses. Their common ancestor dated to 1977.5 and clade divergence to 1984.2. Selection appeared to be predominantly purifying (ω = 0.037); no site showed concordant evidence of diversifying selection, and no recombination was detected. In silico, 84% of Mexican sequences were compatible with all three CDC real-time oligonucleotides; none matched every oligonucleotide in either conventional set. Conclusions: This historical panel shows substantial haplotype diversity and multiple introductions. The compatibility results are computational and were not validated experimentally. We recommend periodic in silico primer revalidation.
SN - 2414-6366
ER -