Tracing the Origin of the 2022 Dengue Virus Epidemic in Karachi, Pakistan, Through Genome Analyses

Abstract Background The 2022 dengue outbreak in Karachi, Pakistan, posed a severe threat to the region, yet no study has investigated the origins of the causal strain. Methods This study aimed to trace the origins and transmission route of the dengue virus serotype 1 (DENV-1) strain responsible for the 2022 epidemic through genome sequencing and phylogenetic analyses. We successfully sequenced 135 complete DENV-1 genomes from clinical samples using long-read amplicon sequencing. Results The DENV-1 genotype III strain circulating in Pakistan likely originated from Southeast Asia, with potential connections to China-Singapore strains. Mutation comparisons using reconstructed ancestral sequences indicated that the Pakistan clade shared characteristic nonsynonymous mutations with the 2014–2015 China epidemic strains, indicating the potential origin of the currently circulating DENV-1 strain. Considering the temporal gap between the China and Pakistan epidemics, there is likely a “missing link” in the transmission route. Conclusions To our knowledge, our findings provide critical insights into the genetic diversity and transmission patterns of DENV-1 in Pakistan and underscore the need for enhanced genomic surveillance and international collaboration to control the spread and predict outbreaks of DENV.