Population genomics identifies a distinct Plasmodium vivax population on the China-Myanmar border of Southeast Asia

Abstract

Plasmodium vivax has become the predominant malaria parasite and a major challenge for malaria elimination in the Greater Mekong Subregion (GMS). Yet, our knowledge about the evolution of P. vivax populations in the GMS is fragmental. We performed whole genome sequencing on 23 P. vivax samples from the China-Myanmar border (CMB) and used 21 high-coverage samples to compare to over 200 samples from the rest of the GMS. Using genome-wide single nucleotide polymorphisms (SNPs), we analyzed population differentiation, genetic structure, migration and potential selection using an array of methods. The CMB parasites displayed a higher proportion of monoclonal infections, and 52% shared over 90% of their genomes in identity-by-descent segments with at least one other sample from the CMB, suggesting preferential expansion of certain parasite strains in this region, likely resulting from the P. vivax outbreaks occurring during this study period. Principal component, admixture, fixation index and phylogenetic analyses all identified that parasites from the CMB were genetically distinct from parasites from eastern parts of the GMS (Cambodia, Laos, Vietnam, and Thailand), whereas the eastern GMS parasite populations were largely undifferentiated. Such a genetic differentiation pattern of the P. vivax populations from the GMS parasite was largely explainable through geographic distance. Using the genome-wide SNPs, we narrowed down to a set of 36 SNPs for differentiating parasites from different areas of the GMS. Genome-wide scans to determine selection in the genome with two statistical methods identified genes potentially under drug selection, including genes associated with antifolate resistance and genes linked to chloroquine resistance in Plasmodium falciparum. Plasmodium vivax is an understudied malaria parasite compared to P. falciparum despite that it is the most common Plasmodium species outside of Africa. In the Greater Mekong Subregion (GMS), the increased proportion of P. vivax proves its resilience to conventional malaria control measures. Within the GMS malaria incidence is highly heterogeneous, typified by more intensive malaria transmission along international borders. Understanding the transmission between countries and tracking parasite introduction are therefore essential to eliminating malaria within this region. The China-Myanmar border (CMB) presents such an example wherein China has eliminated autochthonous malaria cases, while Myanmar has high malaria incidence. Malaria on the CMB is nearly entirely due to P. vivax, yet few studies investigated the genetics and evolution of the P. vivax populations in the area. Here we used whole-genome sequencing for a holistic analysis of P. vivax from the CMB and compared them to those from other sites of the GMS. Parasites on the CMB had a significantly higher proportion (75%) of monoclonal infection than parasites from other regions. Many of the CMB parasites showed significant genetic sharing that is consistent with the result of clonal expansion, consistent with the malaria outbreak occurring during the study period. While P. vivax parasites from the entire GMS were substantially mixed with no evidence of significant gene flow barriers, those from the CMB were more genetically distinct from other populations. Genome-wide scans for selection identified genes potentially under selection, and especially notable are genes associated with sulfadoxine/pyrimethamine resistance. Genes also under selection include those potentially encoding membrane channels and transporters, which were associated with drug resistance in Plasmodium falciparum. Moreover, this population genomic study also identified a set of 36 single nucleotide polymorphisms, which could serve as a barcode for differentiating parasites from various regions of the GMS, a task that is important for the final phase of regional malaria elimination.