Abstract
BackgroundPlasmodium knowlesi a parasite of the macaques is currently the most common cause of human malaria in Malaysia. The thrombospondin-related adhesive protein (TRAP) gene is pre-erythrocytic stage antigen. It is a well-characterized vaccine candidate in Plasmodium vivax and Plasmodium falciparum, however, no study has been done in the orthologous gene of P. knowlesi. This study investigates nucleotide diversity, haplotypes, natural selection and population differentiation of full-length pktrap genes in clinical samples from Malaysia.MethodsForty full-length pktrap sequences from clinical isolates of Malaysia along with the reference H-strain were downloaded from published databases. Genetic diversity, polymorphism, haplotype and natural selection were determined using DnaSP 5.10 software. McDonald–Kreitman test was conducted using P. vivax and Plasmodium coatneyi as ortholog sequence in DnaSP 5.10 software. Population genetic differentiation index (FST) of parasite populations was determined using Arlequin v3.5. Phylogenetic relationships between trap ortholog genes were determined using MEGA 5.0 software.ResultsComparison of 40 full-length pktrap sequences along with the H-strain identified 74 SNPs (53 non-synonymous and 21 synonymous substitutions) resulting in 29 haplotypes. Analysis of the full-length gene showed that the nucleotide diversity was lower compared to its nearest ortholog pvtrap. Domain-wise analysis indicated that the proline/asparagine rich region had higher nucleotide diversity compared to the von Willebrand factor domain and the thrombospondin-type-1 domain. McDonald–Kreitman test identified that the ratio of the number of nonsynonymous to synonymous polymorphic sites within P. knowlesi was significantly higher than that of the number of nonsynonymous to synonymous fixed sites between P. knowlesi and P. vivax. The von Willebrand factor domain also indicated balancing selection using MK test, however, it did not give significant results when tested with P. coatneyi as an outgroup. Phylogenetic analysis of full-length genes identified three distinct sub-clusters of P. knowlesi, one originating from Peninsular Malaysia and two originating from Malaysian Borneo. High population differentiation values was observed within samples from Peninsular Malaysia and Malaysian Borneo.ConclusionsThis study is the first to report on the genetic diversity and natural selection of full-length pktrap. Low level of genetic diversity was found across the full-length gene of pktrap. Balancing selection of the von Willebrand factor domain indicated that TRAP could be a target in inducing immune response against P. knowlesi infections. However, higher number of samples would be necessary to further confirm the findings.
Highlights
Plasmodium knowlesi a parasite of the macaques is currently the most common cause of human malaria in Malaysia
Among all P. knowlesi reported countries, the disease epicenter is in Malaysia with increasing number of human infections reported from Peninsular Malaysia and Malaysian Borneo [4, 7, 8], thereby highlighting the requirement of effective measures for control as well as development of effective vaccines
In order to determine the relationship between Pk thrombospondin-related adhesive protein (TRAP) from all the geographical location in the study, phylogenetic analyses was conducted using deduced amino acid sequences from 10 P. knowlesi TRAP (PkTRAP) full-length from Malaysian Borneo, 1 laboratory lines from Peninsular Malaysia; reference H-strain (PKNH_1265400) and the Malayan Strain (PKNOH_S09533500) (Additional file 1) along with other ortholog members of P. vivax Sal-1 (PVX_082735), Plasmodium cynomolgi (PcYM12211400), Plasmodium ovale curtisi (PoCGH0112027200), Plasmodium malariae (PmUG0112028900) and P. coatneyi (PCOAH_00042390) using unrooted neighbor-Joining (NJ) method described in MEGA 5.0
Summary
The thrombospondin-related adhesive protein (TRAP) gene is pre-erythrocytic stage antigen. It is a well-characterized vaccine candidate in Plasmodium vivax and Plasmodium falciparum, no study has been done in the orthologous gene of P. knowlesi. Among all P. knowlesi reported countries, the disease epicenter is in Malaysia with increasing number of human infections reported from Peninsular Malaysia and Malaysian Borneo [4, 7, 8], thereby highlighting the requirement of effective measures for control as well as development of effective vaccines. Mitochondrial and smaller subunit ribosomal rRNA genes of P. knowlesi isolates from humans and macaques identified two distinct sub-population which grouped geographically to Peninsular Malaysia and Malaysian Borneo [15]. Studies on orangutans from Sabah, Malaysian Borneo indicated that at least two sympatric parasite lineages exists and are rapidly speciating [16]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
