Genomic Diversity, Phylogenetic Structure, and In Silico Diagnostic Primer Compatibility of Available DENV-1 Genotype...

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.