Genomic Investigation and Traceback of a Mysterious Malaria Case in Chongqing, 2019

In 2019, a case of Plasmodium falciparum malaria with unknown origin was detected in Chongqing, a region where had no indigenous case since 2011. Genomic sequences were obtained from a P. falciparum clinical isolate from the 2019 Chongqing malaria case, involving a patient with no overseas travel history. Additionally, we obtained another sequence from a case reported in the same hospital in Chongqing with a known travel history to the Democratic Republic of the Congo (DRC). These sequences were compared to each other and to those of reference isolates from Africa and Asia to determine the likely origin of the unknown isolate. For the first time, we included genomic data from Angola (AO), Republic of the Congo (UDR), DRC, South Sudan (SD), Central African Republic (CF), and Tanzania (TZ), countries whose P. falciparum genomes have not been previously published. Genetic relatedness was assessed using PCA and NJ-tree, while IBD analysis across the genome was performed among the Chongqing samples to evaluate evidence for transmission introduced by imported cases. The results from the NJ-tree and PCA confirmed that the unknown Chongqing strain is closely related to African reference parasites. IBD analysis further indicated that this sample was directly linked to an imported case from the Democratic Republic of the Congo. Based on these findings, we examined all cases imported from the COD and neighboring countries during that year. The IBD analysis revealed very low IBD values among all sample pairs, suggesting they were imported separately with no correlation between them.