{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T03:05:08Z","timestamp":1760238308089,"version":"build-2065373602"},"reference-count":48,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2022,6,25]],"date-time":"2022-06-25T00:00:00Z","timestamp":1656115200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Deputyship for Research and Innovation, Ministry of Education in Saudi Arabia","award":["KKU-420"],"award-info":[{"award-number":["KKU-420"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>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 \u03c0~0.00789 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.<\/jats:p>","DOI":"10.3390\/genes13071149","type":"journal-article","created":{"date-parts":[[2022,6,26]],"date-time":"2022-06-26T09:00:13Z","timestamp":1656234013000},"page":"1149","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genetic Diversity and Population Genetic Analysis of Plasmodium falciparum Thrombospondin Related Anonymous Protein (TRAP) in Clinical Samples from Saudi Arabia"],"prefix":"10.3390","volume":"13","author":[{"given":"Saad M.","family":"Bin Dajem","sequence":"first","affiliation":[{"name":"Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3407-7220","authenticated-orcid":false,"given":"Md Atique","family":"Ahmed","sequence":"additional","affiliation":[{"name":"ICMR-Regional Medical Research Center, Dibrugarh 786010, Assam, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fatimah F.","family":"Alghnnam","sequence":"additional","affiliation":[{"name":"Department of Infection and Immunity, Research Centre, King Faisal Specialist Hospital Research Centre, Riyadh 11211, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shouq F.","family":"Alghannam","sequence":"additional","affiliation":[{"name":"Department of Infection and Immunity, Research Centre, King Faisal Specialist Hospital Research Centre, Riyadh 11211, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gauspasha Yusuf","family":"Deshmukh","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Microbiology, National College, Tiruchirapalli 620001, Tamil Nadu, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7993-3174","authenticated-orcid":false,"given":"Rehan Haider","family":"Zaidi","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Microbiology, National College, Tiruchirapalli 620001, Tamil Nadu, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1981-2327","authenticated-orcid":false,"given":"Marie Fe F.","family":"Bohol","sequence":"additional","affiliation":[{"name":"Department of Infection and Immunity, Research Centre, King Faisal Specialist Hospital Research Centre, Riyadh 11211, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Syeda Sabiha","family":"Salam","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Syeda Wasfeea","family":"Wazid","sequence":"additional","affiliation":[{"name":"Arogya Society of Health, Welfare and Support (ASHWAS), Dinsugia 785640, Assam, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammed I.","family":"Shafeai","sequence":"additional","affiliation":[{"name":"Sabya General Hospital, Sabya 85534, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fuad H.","family":"Rudiny","sequence":"additional","affiliation":[{"name":"Sabya General Hospital, Sabya 85534, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ali M.","family":"Motaen","sequence":"additional","affiliation":[{"name":"Sabya General Hospital, Sabya 85534, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0661-8605","authenticated-orcid":false,"given":"Kareem","family":"Morsy","sequence":"additional","affiliation":[{"name":"Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4584-5739","authenticated-orcid":false,"given":"Ahmed A.","family":"Al-Qahtani","sequence":"additional","affiliation":[{"name":"Department of Infection and Immunity, Research Centre, King Faisal Specialist Hospital Research Centre, Riyadh 11211, Saudi Arabia"},{"name":"Department of Microbiology and Immunology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,6,25]]},"reference":[{"key":"ref_1","unstructured":"(2022, April 28). World Health Organization. Available online: www.who.int\/malaria\/publications\/world-malaria-report-2016\/report\/en."},{"key":"ref_2","unstructured":"World Health Organization (2022, April 28). World Malaria Report 2019. Available online: https:\/\/www.who.int\/malaria\/publications\/world-malaria-report-2019\/en."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1186\/s12936-021-03664-8","article-title":"Genetic diversity and natural selection on the thrombospondin-related adhesive protein (TRAP) gene of Plasmodium falciparum on Bioko Island, Equatorial Guinea and global comparative analysis","volume":"20","author":"Lin","year":"2021","journal-title":"Malar. J."},{"key":"ref_4","unstructured":"World Health Organization (2021). World Malaria Report, WHO."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/S1473-3099(18)30068-9","article-title":"Origins of the current outbreak of multidrug-resistant malaria in southeast Asia: A retrospective genetic study","volume":"18","author":"Amato","year":"2018","journal-title":"Lancet Infect. Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/s12936-017-1680-8","article-title":"Rapid decline in the susceptibility of Plasmodium falciparum to dihydroartemisinin\u2013piperaquine in the south of Vietnam","volume":"16","author":"Thanh","year":"2017","journal-title":"Malar. J."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1186\/s12936-020-03524-x","article-title":"Increased prevalence of pfdhfr and pfdhps mutations associated with sulfadoxine\u2013pyrimethamine resistance in Plasmodium falciparum isolates from Jazan Region, Southwestern Saudi Arabia: Important implications for malaria treatment policy","volume":"19","author":"Madkhali","year":"2020","journal-title":"Malar. J."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1186\/s12936-021-03846-4","article-title":"Residual malaria in Jazan region, southwestern Saudi Arabia: The situation, challenges and climatic drivers of autochthonous malaria","volume":"20","author":"Madkhali","year":"2021","journal-title":"Malar. J."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/B978-0-12-407706-5.00003-4","article-title":"The malaria transition on the Arabian Peninsula: Progress toward a malaria-free region between 1960\u20132010","volume":"82","author":"Snow","year":"2013","journal-title":"Adv. Parasitol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1186\/s12936-015-0858-1","article-title":"Progress toward malaria elimination in Jazan province, Kingdom of Saudi Arabia: 2000\u20132014","volume":"14","author":"Sahly","year":"2015","journal-title":"Malar. J."},{"key":"ref_11","first-page":"S82","article-title":"The progress of Roll Back Malaria in the Eastern Mediterranean Region over the past decade","volume":"14","author":"Atta","year":"2008","journal-title":"EMHJ-East. Mediterr. Health J."},{"key":"ref_12","unstructured":"World Health Organization (2020). World Malaria Report 2020: 20 Years of Global Progress and Challenges, WHO."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1016\/S0140-6736(19)31096-7","article-title":"Mapping the global endemicity and clinical burden of Plasmodium vivax, 2000\u201317: A spatial and temporal modelling study","volume":"394","author":"Battle","year":"2019","journal-title":"Lancet"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1186\/s12936-016-1249-y","article-title":"High heterogeneity of malaria transmission and a large sub-patent and diverse reservoir of infection in Wusab As Safil district, Republic of Yemen","volume":"15","author":"Cook","year":"2016","journal-title":"Malar. J."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"233","DOI":"10.3347\/kjp.2019.57.3.233","article-title":"Malaria prevalence in a low transmission area, Jazan district of southwestern Saudi Arabia","volume":"57","author":"Hawash","year":"2019","journal-title":"Korean J. Parasitol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.20546\/ijcmas.2016.503.001","article-title":"Epidemiological trends over a ten-year period of malaria in a non-endemic area of Saudi Arabia","volume":"5","author":"Ferchichi","year":"2016","journal-title":"Int. J. Curr. Microbiol. Appl. Sci."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/j.jiph.2016.09.021","article-title":"Knowledge, attitude and practice about malaria in south-western Saudi Arabia: A household-based cross-sectional survey","volume":"10","author":"Khairy","year":"2017","journal-title":"J. Infect. Public Health"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"21420","DOI":"10.1073\/pnas.1218581109","article-title":"Shape change in the receptor for gliding motility in Plasmodium sporozoites","volume":"109","author":"Song","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1985","DOI":"10.1002\/pro.477","article-title":"Structure of the micronemal protein 2 A\/I domain from Toxoplasma gondii","volume":"19","author":"Tonkin","year":"2010","journal-title":"Protein Sci."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1760","DOI":"10.1110\/ps.052068506","article-title":"The layered fold of the TSR domain of P. falciparum TRAP contains a heparin binding site","volume":"15","author":"Tossavainen","year":"2006","journal-title":"Protein Sci."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1098\/rsif.2007.0229","article-title":"Patterns of antigenic diversity and the mechanisms that maintain them","volume":"4","author":"Lipsitch","year":"2007","journal-title":"J. R. Soc. Interface"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"359","DOI":"10.3389\/fimmu.2014.00359","article-title":"Strategies for designing and monitoring malaria vaccines targeting diverse antigens","volume":"5","author":"Barry","year":"2014","journal-title":"Front. Immunol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Patel, P., Bharti, P.K., Bansal, D., Raman, R.K., Mohapatra, P.K., Sehgal, R., Mahanta, J., Sultan, A.A., and Singh, N. (2017). Genetic diversity and antibody responses against Plasmodium falciparum vaccine candidate genes from Chhattisgarh, Central India: Implication for vaccine development. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0182674"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"4625","DOI":"10.1128\/IAI.00576-10","article-title":"Allelic diversity and naturally acquired allele-specific antibody responses to Plasmodium falciparum apical membrane antigen 1 in Kenya","volume":"78","author":"Osier","year":"2010","journal-title":"Infect. Immun."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"104197","DOI":"10.1016\/j.meegid.2020.104197","article-title":"Population genetic structure analysis of thrombospondin-related adhesive protein (TRAP) as a vaccine candidate antigen in worldwide Plasmodium falciparum isolates","volume":"80","author":"Mehrizi","year":"2020","journal-title":"Infect. Genet. Evol."},{"key":"ref_26","first-page":"69","article-title":"Thrombospondin related anonymous protein (TRAP) of Plasmodium falciparum in parasite-host cell interactions","volume":"35","author":"Scarselli","year":"1993","journal-title":"Parassitologia"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"7817","DOI":"10.1073\/pnas.1205737109","article-title":"Unexpected fold in the circumsporozoite protein target of malaria vaccines","volume":"109","author":"Doud","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1782","DOI":"10.1016\/S0140-6736(21)01065-5","article-title":"R21\/Matrix-M: A second malaria vaccine?","volume":"397","author":"Moorthy","year":"2021","journal-title":"Lancet"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1038\/nature21060","article-title":"Sterile protection against human malaria by chemoattenuated PfSPZ vaccine","volume":"542","author":"Mordmuller","year":"2017","journal-title":"Nature"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"397","DOI":"10.3389\/fimmu.2019.00397","article-title":"Comprehensive review of human Plasmodium falciparum-specific CD8+ T cell epitopes","volume":"10","author":"Heide","year":"2019","journal-title":"Front. Immunol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2025","DOI":"10.1056\/NEJMoa1505819","article-title":"Genetic diversity and protective efficacy of the RTS, S\/AS01 malaria vaccine","volume":"373","author":"Neafsey","year":"2015","journal-title":"N. Engl. J. Med."},{"key":"ref_32","unstructured":"World Health Organization (2020). World Malaria Report, World Health Organization."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1016\/S0092-8674(00)80511-5","article-title":"TRAP is necessary for gliding motility and infectivity of Plasmodium sporozoites","volume":"90","author":"Sultan","year":"1997","journal-title":"Cell"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.pt.2003.10.011","article-title":"Apicomplexan gliding motility and host cell invasion: Overhauling the motor model","volume":"20","author":"Kappe","year":"2004","journal-title":"Trends Parasitol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Ohashi, J., Suzuki, Y., Naka, I., Hananantachai, H., and Patarapotikul, J. (2014). Diversifying selection on the thrombospondin-related adhesive protein (TRAP) gene of Plasmodium falciparum in Thailand. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0090522"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"5195","DOI":"10.1093\/emboj\/18.19.5195","article-title":"The A-domain and the thrombospondin-related motif of Plasmodium falciparum TRAP are implicated in the invasion process of mosquito salivary glands","volume":"18","author":"Wengelnik","year":"1999","journal-title":"EMBO J."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1611","DOI":"10.1016\/j.str.2006.10.001","article-title":"Complement and the multifaceted functions of VWA and integrin I domains","volume":"14","author":"Springer","year":"2006","journal-title":"Structure"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1597","DOI":"10.1093\/emboj\/21.7.1597","article-title":"Plasmodium sporozoite invasion into insect and mammalian cells is directed by the same dual binding system","volume":"21","author":"Matuschewski","year":"2002","journal-title":"EMBO J."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1186\/s12936-018-2423-1","article-title":"Diversity and natural selection on the thrombospondin-related adhesive protein (TRAP) gene of Plasmodium knowlesi in Malaysia","volume":"17","author":"Ahmed","year":"2018","journal-title":"Malar. J."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Kosuwin, R., Putaporntip, C., Tachibana, H., and Jongwutiwes, S. (2014). Spatial variation in genetic diversity and natural selection on the thrombospondin-related adhesive protein locus of Plasmodium vivax (PvTRAP). PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0110463"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1093\/bioinformatics\/btp187","article-title":"DnaSP v5: A software for comprehensive analysis of DNA polymorphism data","volume":"25","author":"Librado","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1093\/molbev\/msr121","article-title":"MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods","volume":"28","author":"Tamura","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/s12686-011-9548-7","article-title":"STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method","volume":"4","author":"Earl","year":"2012","journal-title":"Conserv. Genet. Resour."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Moorthy, V.S., Imoukhuede, E.B., Milligan, P., Bojang, K., Keating, S., Kaye, P., Pinder, M., Gilbert, S.C., Walraven, G., and Greenwood, B.M. (2004). A randomised, double-blind, controlled vaccine efficacy trial of DNA\/MVA ME-TRAP against malaria infection in Gambian adults. PLoS Med., 1.","DOI":"10.1371\/journal.pmed.0010033"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1016\/j.ymthe.2016.11.003","article-title":"Viral vector malaria vaccines induce high-level T cell and antibody responses in West African children and infants","volume":"25","author":"Bliss","year":"2017","journal-title":"Mol. Ther."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Mensah, V.A., Gueye, A., Ndiaye, M., Edwards, N.J., Wright, D., Anagnostou, N.A., Syll, M., Ndaw, A., Abiola, A., and Bliss, C. (2016). Safety, immunogenicity and efficacy of prime-boost vaccination with ChAd63 and MVA encoding ME-TRAP against Plasmodium falciparum infection in adults in Senegal. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0167951"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1186\/s12936-016-1581-2","article-title":"The changing malaria landscape in Aseer region, Kingdom of Saudi Arabia: 2000\u20132015","volume":"15","author":"Alshahrani","year":"2016","journal-title":"Malar. J."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1186\/s12936-021-03901-0","article-title":"Significant differences in Fc\u03b3RIIa, Fc\u03b3RIIIa and Fc\u03b3RIIIb genes polymorphism and anti-malarial IgG subclass pattern are associated with severe Plasmodium falciparum malaria in Saudi children","volume":"20","author":"Nasr","year":"2021","journal-title":"Malar. J."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/13\/7\/1149\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:38:27Z","timestamp":1760139507000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/13\/7\/1149"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,25]]},"references-count":48,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2022,7]]}},"alternative-id":["genes13071149"],"URL":"https:\/\/doi.org\/10.3390\/genes13071149","relation":{},"ISSN":["2073-4425"],"issn-type":[{"type":"electronic","value":"2073-4425"}],"subject":[],"published":{"date-parts":[[2022,6,25]]}}}