Restricted Genetic Diversity of Plasmodium falciparum and Plasmodium vivax During the 2025 Phase of a Malaria Outbreak in the Bay Islands of Honduras

Honduras is progressing toward malaria elimination as part of the Mesoamerican goal for 2030. As transmission declines, malaria increasingly occurs in focal outbreaks, particularly in geographically confined settings such as islands. Following an increase in cases beginning in 2024, the Bay Islands Department experienced continued outbreak transmission during 2025. This study characterized the genetic diversity and multilocus haplotype patterns of Plasmodium falciparum and P. vivax lineages circulating during this outbreak. Cases were confirmed by photo-induced electron transfer PCR (PET-PCR). Genetic diversity was assessed by Sanger sequencing of pfmsp1 for P. falciparum, and pvcsp and pvmsp3α for P. vivax; pfmdr1 was analysed separately as a drug-resistance marker. Diversity indices and multilocus profiles were analysed using DnaSP. Forty-nine samples were analysed: 18 P. falciparum and 31 P. vivax infections from three municipalities. All P. falciparum isolates carried a single pfmsp1 haplotype of the K1 allelic family. In P. vivax, two concordant multilocus haplotypes were detected: A/A predominated, whereas B/B was observed in five samples, mainly early in the outbreak. The outbreak showed marked P. falciparum homogeneity and restricted P. vivax multilocus diversity, consistent with focal amplification of limited parasite lineages. However, multiple introductions of genetically similar parasites cannot be excluded.