Whole-genome sequencing of a Plasmodium vivax isolate from the China-Myanmar border area

Shen, Hai-Mo; Chen, Shen-Bo; Wang, Yue; Zhou, Xiao‐Nong

doi:10.1590/0074-02760150216

Cited by 8 publications

(6 citation statements)

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“…The high level of diversity within Plasmodium antigens is a major challenge for effective malaria vaccines. Compared to merozoite surface proteins (MSPs) and circumsporozoite protein (CSP), PvDBP-II bears less polymorphism ( Shen et al, 2015 ). Hence, PvDBP-II is considered as the primary fragment of candidate antigen for vaccine against malaria.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Natural Selection of Plasmodium vivax Duffy Binding Protein-II From China-Myanmar Border of Yunnan Province, China

et al. 2021

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Malaria incidence has declined dramatically over the past decade and China was certified malaria-free in 2021. However, the presence of malaria in border areas and the importation of cases of malaria parasites are major challenges for the consolidation of the achievements made by China. Plasmodium vivax Duffy binding protein (PvDBP) performs a significant role in erythrocyte invasion, and is considered a promising P. vivax vaccine. However, the highly polymorphic region of PvDBP (PvDBP-II) impedes the development of blood-stage vaccine against P. vivax. In this study, we investigated the genetic diversity and natural selection of PvDBP-II among 124 P. vivax isolates collected from the China-Myanmar border (CMB) in Yunnan Province, China, during 2009–2011. To compare genetic diversity, natural selection, and population structure with CMB isolates, 85 pvdbp-II sequences of eastern Myanmar isolates were obtained from GenBank. In addition, global sequences of pvdbp-II were retrieved from GenBank to establish genetic differentiation relationships and networks with the CMB isolates. In total, 22 single nucleotide polymorphisms reflected in 20 non-synonymous and two synonymous mutations were identified. The overall nucleotide diversity of PvDBP-II from the 124 CMB isolates was 0.0059 with 21 haplotypes identified (Hd = 0.91). The high ratio of non-synonymous to synonymous mutations suggests that PvDBP-II had evolved under positive selection. Population structure analysis of the CMB and eastern Myanmar isolates were optimally grouped into five sub-populations (K = 5). Polymorphisms of PvDBP-II display that CMB isolates were genetically diverse. Mutation, recombination, and positive selection promote polymorphism of PvDBP-II of P. vivax population. Although low-level genetic differentiation in eastern Myanmar was identified along with the more effective malaria control measures, the complexity of population structure in malaria parasites has maintained. In conclusion, findings from this study advance knowledge of the understanding of the dynamic of P. vivax population, which will contribute to guiding the rational design of a PvDBP-II based vaccine.

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Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Natural Selection of Plasmodium vivax Duffy Binding Protein-II From China-Myanmar Border of Yunnan Province, China

et al. 2021

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“…The fragmented DNA molecules were used to construct the Illumina sequencing libraries with insert sizes of 250 bp. In our previous work, we reported an initial sequencing result of this sample [ 22 ]. Our preliminary sequencing generated 31,471,932 paired-end reads and 5.86% of the quality-evaluated reads were aligned onto 96.43% of the reference strain Sal I genome in 7.84-fold coverage.…”

Section: Methodsmentioning

confidence: 99%

“…In this research, we sequenced and annotated the first P. vivax genome sequence of a clinical isolate obtained from the China-Myanmar border area (CMB-1). Genomic DNA for CMB-1 isolate was extracted from the whole blood of P. vivax microscopically positive patient and single P. vivax infection for this area was confirmed by PCR [ 22 ]. Our mapping and de-novo assembling show that this approach has similar results conformed to the method used by the past and meets the requirements of high-sensitivity mutation detection as well.…”

Section: Introductionmentioning

confidence: 99%

Whole-genome sequencing of a Plasmodium vivax clinical isolate exhibits geographical characteristics and high genetic variation in China-Myanmar border area

et al. 2017

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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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3523-y) contains supplementary material, which is available to authorized users.

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“…Genomic DNA was extracted from each frozen blood sample using the QIAGEN DNeasy Blood & Tissue Kit (Qiagen, UK), and sheared into 500 bp fragments to construct the Illumina sequencing libraries with insert sizes of 250 bp. Previously, an initial sequencing result of sample CMB-1 and subsequent analysis was reported [ 23 ]. Using the same method, all libraries on Illumina HiSeq2000 were sequenced and generated an average of 120 M paired-end reads of 125 bp.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide scans for the identification of Plasmodium vivax genes under positive selection

Shen

Chen

Wang

et al. 2017

Malar J

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BackgroundThe current trend of Plasmodium vivax cases imported from Southeast Asia into China has sharply increased recently, especially from the China–Myanmar border (CMB) area. High recombination rates of P. vivax populations associated with varied transmission intensity might cause distinct local selective pressures. The information on the genetic variability of P. vivax in this area is scant. Hence, this study assessed the genetic diversity of P. vivax genome sequence in CMB area and aimed to provide information on the positive selection of new gene loci.ResultsThis study reports a genome-wide survey of P. vivax in CMB area, using blood samples from local patients to identify population-specific selective processes. The result showed that considerable genetic diversity and mean pair-wise divergence among the sequenced P. vivax isolates were higher in some important gene families. Using the standardized integrated haplotype score (|iHS|) for all SNPs in chromosomal regions with SNPs above the top 1% distribution, it was observed that the top score locus involved 356 genes and most of them are associated with red blood cell invasion and immune evasion. The XP-EHH test was also applied and some important genes associated with anti-malarial drug resistance were observed in high positive scores list. This result suggests that P. vivax in CMB area is facing more pressure to survive than any other region and this has led to the strong positive selection of genes that are associated with host-parasite interactions.ConclusionsThis study suggests that greater genetic diversity in P. vivax from CMB area and positive selection signals in invasion and drug resistance genes are consistent with the history of drug use during malaria elimination programme in CMB area. Furthermore, this result also demonstrates that haplotype-based detecting selection can assist the genome-wide methods to identify the determinants of P. vivax diversity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12936-017-1882-0) contains supplementary material, which is available to authorized users.

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Whole-genome sequencing of a Plasmodium vivax isolate from the China-Myanmar border area

Cited by 8 publications

References 16 publications

Genetic Diversity and Natural Selection of Plasmodium vivax Duffy Binding Protein-II From China-Myanmar Border of Yunnan Province, China

Genetic Diversity and Natural Selection of Plasmodium vivax Duffy Binding Protein-II From China-Myanmar Border of Yunnan Province, China

Whole-genome sequencing of a Plasmodium vivax clinical isolate exhibits geographical characteristics and high genetic variation in China-Myanmar border area

Genome-wide scans for the identification of Plasmodium vivax genes under positive selection

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