Abstract
BackgroundCurrently in China, the trend of Plasmodium vivax cases imported from Southeast Asia was increased especially in the China-Myanmar border area. Driven by the increase in P. vivax cases and stronger need for vaccine and drug development, several P. vivax isolates genome sequencing projects are underway. However, little is known about the genetic variability in this area until now.ResultsThe sequencing of the first P. vivax isolate from China-Myanmar border area (CMB-1) generated 120 million paired-end reads. A percentage of 10.6 of the quality-evaluated reads were aligned onto 99.9% of the reference strain Sal I genome in 62-fold coverage with an average of 4.8 SNPs per kb. We present a 539-SNP marker data set for P. vivax that can identify different parasites from different geographic origins with high sensitivity. We also identified exceptionally high levels of genetic variability in members of multigene families such as RBP, SERA, vir, MSP3 and AP2. The de-novo assembly yielded a database composed of 8,409 contigs with N50 lengths of 6.6 kb and revealed 661 novel predicted genes including 78 vir genes, suggesting a greater functional variation in P. vivax from this area.ConclusionOur result contributes to a better understanding of P. vivax genetic variation, and provides a fundamental basis for the geographic differentiation of vivax malaria from China-Myanmar border area using a direct sequencing approach without leukocyte depletion. This novel sequencing method can be used as an essential tool for the genomic research of P. vivax in the near future.
Highlights
In China, the trend of Plasmodium vivax cases imported from Southeast Asia was increased especially in the China-Myanmar border area
We identified 108,846 nucleotide variants in at least half of the sequenced P. vivax strains or isolates with an average of 4.84 single nucleotide polymorphism (SNP) per kb distributed throughout the genome (Additional file 1: Table S1)
Just like in a recent study [41], we found that most of these highly polymorphic genes are associated with red blood cell invasion and immune evasion such as Merozoite surface protein 7 (MSP7) (PVX_082665), Pv-fam-e (PVX_089875), RBP2c, MSP1, serine-repeat antigen (SERA) (PVX_003840), Pv-fam-b (PVX_002525), as well as variable surface protein (VIR), such as Vir22 (PVX_097530) and Vir12 (PVX_083590)
Summary
In China, the trend of Plasmodium vivax cases imported from Southeast Asia was increased especially in the China-Myanmar border area. Plasmodium vivax is the most widely distributed human malaria species and causes more illness than P. falciparum in many regions [1]. Half of the world’s population is estimated to be at risk for malaria caused by P. vivax [2, 3]. Previous research in P. vivax showed that members of multigene families are genetically variable [5]. Some mutations may help the parasite evade drug and human immune response, or stabilize the protein's structure and function [6]. This pattern was observed by sequencing P
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