☆ 4.4 Article

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

MALARIA JOURNAL (2017)

Journal

MALARIA JOURNAL

Volume 16, Issue -, Pages -

Publisher

BMC

DOI: 10.1186/s12936-017-1882-0

Keywords

Plasmodium vivax; Haplotype-based detecting; Positive selection; Invasion; Immune evasion; Drug resistance

Funding

National Research and Development Plan of China [2016YFC1200500, 2016YFC1202000]
fourth round of Three-Year Public Health Action Plan [GWTD2015S06, GWIV-29]
National Natural Science Foundation of China [81101266]

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Abstract

Background: The 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. Results: This 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. Conclusions: This 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.

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Retrospective analysis of Plasmodium vivax genomes from a pre-elimination China inland population in the 2010s

Ying Liu, Tao Zhang, Shen-Bo Chen, Yan-Bing Cui, Shu-Qi Wang, Hong-Wei Zhang, Hai-Mo Shen, Jun-Hu Chen

Summary: This study retrospectively reported the whole-genome sequence variation of 10 Plasmodium vivax isolates from inland China, aiming to investigate the molecular epidemiology during the pre-elimination stage. The results showed that China's inland population was highly structured with a single potential ancestor. Furthermore, selective signatures of drug resistance genes were identified, and an increase in the proportion of wild-type dhps and dhfr-ts after the prohibition of specific drugs was observed.

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