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Bin Dajem SM, Ahmed MA, Alghnnam FF, Alghannam SF, Deshmukh GY, Zaidi RH, Bohol MFF, Salam SS, Wazid SW, Shafeai MI, Rudiny FH, Motaen AM, Morsy K, Al-Qahtani AA. Genetic Diversity and Population Genetic Analysis of Plasmodium falciparum Thrombospondin Related Anonymous Protein (TRAP) in Clinical Samples from Saudi Arabia. Genes (Basel) 2022; 13:genes13071149. [PMID: 35885932 PMCID: PMC9319867 DOI: 10.3390/genes13071149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 02/01/2023] Open
Abstract
The thrombospondin related anonymous protein (TRAP) is considered one of the most important pre-erythrocytic vaccine targets. Earlier population genetic studies revealed the TRAP gene to be under strong balancing natural selection. This study is the first attempt to analyze genetic diversity, natural selection, phylogeography and population structure in 199 clinical samples from Saudi Arabia using the full-length PfTRAP gene. We found the rate of nonsynonymous substitutions to be significantly higher than that of synonymous substitutions in the clinical samples, indicating a strong positive or diversifying selection for the full-length gene and the Von Willebrand factor (VWF). The nucleotide diversity was found to be π~0.00789 for the full-length gene; however, higher nucleotide diversity was observed for the VWF compared to the thrombospondin repeat region (TSP). Deduction of the amino acid sequence alignment of the PNP repeat region in the Saudi samples revealed six genotypes characterized by tripeptide repeat motifs (PNP, ANP, ENP and SNP). Haplotype network, population structure and population differentiation analyses indicated four distinct sub-populations in spite of the low geographical distance between the sampling sites. Our results suggest the likeliness of independent parasite evolution, creating opportunities for further adaptation, including host transition, and making malaria control even more challenging.
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Affiliation(s)
- Saad M. Bin Dajem
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia; (S.M.B.D.); (K.M.)
| | - Md Atique Ahmed
- ICMR-Regional Medical Research Center, Dibrugarh 786010, Assam, India;
| | - Fatimah F. Alghnnam
- Department of Infection and Immunity, Research Centre, King Faisal Specialist Hospital Research Centre, Riyadh 11211, Saudi Arabia; (F.F.A.); (S.F.A.); (M.F.F.B.)
| | - Shouq F. Alghannam
- Department of Infection and Immunity, Research Centre, King Faisal Specialist Hospital Research Centre, Riyadh 11211, Saudi Arabia; (F.F.A.); (S.F.A.); (M.F.F.B.)
| | - Gauspasha Yusuf Deshmukh
- Department of Biotechnology and Microbiology, National College, Tiruchirapalli 620001, Tamil Nadu, India; (G.Y.D.); (R.H.Z.)
| | - Rehan Haider Zaidi
- Department of Biotechnology and Microbiology, National College, Tiruchirapalli 620001, Tamil Nadu, India; (G.Y.D.); (R.H.Z.)
| | - Marie Fe F. Bohol
- Department of Infection and Immunity, Research Centre, King Faisal Specialist Hospital Research Centre, Riyadh 11211, Saudi Arabia; (F.F.A.); (S.F.A.); (M.F.F.B.)
| | - Syeda Sabiha Salam
- Department of Life Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India;
| | - Syeda Wasfeea Wazid
- Arogya Society of Health, Welfare and Support (ASHWAS), Dinsugia 785640, Assam, India;
| | - Mohammed I. Shafeai
- Sabya General Hospital, Sabya 85534, Saudi Arabia; (M.I.S.); (F.H.R.); (A.M.M.)
| | - Fuad H. Rudiny
- Sabya General Hospital, Sabya 85534, Saudi Arabia; (M.I.S.); (F.H.R.); (A.M.M.)
| | - Ali M. Motaen
- Sabya General Hospital, Sabya 85534, Saudi Arabia; (M.I.S.); (F.H.R.); (A.M.M.)
| | - Kareem Morsy
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia; (S.M.B.D.); (K.M.)
| | - Ahmed A. Al-Qahtani
- Department of Infection and Immunity, Research Centre, King Faisal Specialist Hospital Research Centre, Riyadh 11211, Saudi Arabia; (F.F.A.); (S.F.A.); (M.F.F.B.)
- Department of Microbiology and Immunology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Correspondence:
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