巴基斯坦哈扎拉地区恶性疟原虫顶膜抗原 1 域 I 的种群遗传结构。
Population genetic structure of domain I of apical membrane antigen-1 in Plasmodium falciparum isolates from Hazara division of Pakistan.
机构信息
Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, 23200, Pakistan.
Center for Human Genetics, Hazara University, Mansehra, 21310, Pakistan.
出版信息
Malar J. 2018 Oct 26;17(1):389. doi: 10.1186/s12936-018-2539-3.
BACKGROUND
The Plasmodium falciparum apical membrane antigen-1 (PfAMA1) is considered as an ideal vaccine candidate for malaria control due to its high level of immunogenicity and essential role in parasite survival. Among the three domains of PfAMA1 protein, hyper-variable region (HVR) of domain I is the most immunogenic. The present study was conducted to evaluate the extent of genetic diversity across HVR domain I of the pfama1 gene in P. falciparum isolates from Hazara division of Pakistan.
METHODS
The HVR domain I of the pfama1 was amplified and sequenced from 20 P. falciparum positive cases from Hazara division of Pakistan. The sequences were analysed in context of global population data of P. falciparum from nine malaria endemic countries. The DNA sequence reads quality assessment, reads assembling, sequences alignment/phylogenetic and population genetic analyses were performed using Staden, Lasergene v. 7.1, MEGA7 and DnaSP v.5 software packages respectively.
RESULTS
Total 14 mutations were found in Pakistani isolates with 12 parsimony informative sites. During comparison with global isolates, a novel non-synonymous mutation (Y240F) was found specifically in a single Pakistani sample with 5% frequency. The less number of mutations, haplotypes, recombination and low pairwise nucleotide differences revealed tightly linked uniform genetic structure with low genetic diversity at HVR domain I of pfama1 among P. falciparum isolates from Hazara region of Pakistan. This uniform genetic structure may be shaped across Pakistani P. falciparum isolates by bottleneck or natural selection events.
CONCLUSION
The Pakistani P. falciparum isolates were found to maintain a distinct genetic pattern at HVR pfama1 with some extent of genetic relationship with geographically close Myanmar and Indian samples. However, the exact pattern of gene flow and demographic events may infer from whole genome sequence data with large sample size of P. falciparum collected from broad area of Pakistan.
背景
恶性疟原虫顶膜蛋白-1（PfAMA1）被认为是疟疾控制的理想疫苗候选物，因为它具有高度的免疫原性和在寄生虫生存中的重要作用。在 PfAMA1 蛋白的三个结构域中，I 结构域的高变区（HVR）是最具免疫原性的。本研究旨在评估巴基斯坦哈扎拉地区恶性疟原虫分离株 Pfama1 基因 I 结构域 HVR 的遗传多样性程度。
方法
从巴基斯坦哈扎拉地区 20 例疟原虫阳性病例中扩增和测序 Pfama1 的 HVR I 区。将序列与来自 9 个疟疾流行国家的全球恶性疟原虫群体数据进行分析。使用 Staden、Lasergene v. 7.1、MEGA7 和 DnaSP v.5 软件包分别进行 DNA 序列读取质量评估、读取组装、序列比对/系统发育和群体遗传分析。
结果
在巴基斯坦分离株中发现了 14 个突变，其中 12 个为简约信息位点。与全球分离株比较时，在一个巴基斯坦样本中发现了一个新的非同义突变（Y240F），频率为 5%。HVR Ⅰ区 Pfama1 的突变、单倍型、重组和核苷酸差异较少，表明巴基斯坦哈扎拉地区恶性疟原虫分离株的遗传结构紧密相连，遗传多样性较低。这种一致的遗传结构可能是由瓶颈或自然选择事件在巴基斯坦恶性疟原虫分离株中形成的。
结论
巴基斯坦恶性疟原虫分离株在 Pfama1 HVR 上保持了独特的遗传模式，与地理上相近的缅甸和印度样本有一定程度的遗传关系。然而，从广泛采集的大样本量全基因组序列数据中，可以推断出基因流动和人口动态事件的确切模式。
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