scholarly journals The Plasmodium knowlesi Pk41 surface protein diversity, natural selection, sub population and geographical clustering: a 6-cysteine protein family member

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6141 ◽  
Author(s):  
Md Atique Ahmed ◽  
Ki-Back Chu ◽  
Fu-Shi Quan
Keyword(s):  
Natural Selection ◽  
Plasmodium Knowlesi ◽  
Surface Protein ◽  
Purifying Selection ◽  
Full Length ◽  
Clinical Isolates ◽  
Rich Region ◽  
Vaccine Target ◽  
Geographical Clustering ◽  
Selection Of

Introduction The zoonotic malaria parasite Plasmodium knowlesi has currently become the most dominant form of infection in humans in Malaysia and is an emerging infectious disease in most Southeast Asian countries. The P41 is a merozoite surface protein belonging to the 6-cysteine family and is a well-characterized vaccine candidate in P. vivax and P. falciparum; however, no study has been done in the orthologous gene of P. knowlesi. This study investigates the level of polymorphism, haplotypes and natural selection of pk41 genes in clinical isolates from Malaysia. Method Thirty-five full-length pk41 sequences from clinical isolates of Malaysia along with four laboratory lines (along with H-strain) were downloaded from public databases. For comparative analysis between species, orthologous P41 genes from P. falciparum, P. vivax, P. coatneyi and P. cynomolgi were also downloaded. Genetic diversity, polymorphism, haplotype and natural selection were determined using DnaSP 5.10 software. Phylogenetic relationships between Pk41 genes were determined using MEGA 5.0 software. Results Analysis of 39 full-length pk41 sequences along with the H-strain identified 36 SNPs (20 non-synonymous and 16 synonymous substitutions) resulting in 31 haplotypes. Nucleotide diversity across the full-length gene was low and was similar to its ortholog in P. vivax; pv41. Domain-wise amino acid analysis of the two s48/45 domains indicated low level of polymorphisms for both the domains, and the glutamic acid rich region had extensive size variations. In the central domain, upstream to the glutamate rich region, a unique two to six (K-E)n repeat region was identified within the clinical isolates. Overall, the pk41 genes were indicative of negative/purifying selection due to functional constraints. Domain-wise analysis of the s48/45 domains also indicated purifying selection. However, analysis of Tajima’s D across the genes identified non-synonymous SNPs in the s48/45 domain II with high positive values indicating possible epitope binding regions. All the 6-cysteine residues within the s48/45 domains were conserved within the clinical isolates indicating functional conservation of these regions. Phylogenetic analysis of full-length pk41 genes indicated geographical clustering and identified three subpopulations of P. knowlesi; one originating in the laboratory lines and two originating from Sarawak, Malaysian Borneo. Conclusion This is the first study to report on the polymorphism and natural selection of pk41 genes from clinical isolates of Malaysia. The results reveal that there is low level of polymorphism in both s48/45 domains, indicating that this antigen could be a potential vaccine target. However, genetic and molecular immunology studies involving higher number of samples from various parts of Malaysia would be necessary to validate this antigen’s candidacy as a vaccine target for P. knowlesi.

scholarly journals Plasmodium knowlesi clinical isolates from Malaysia show extensive diversity and strong differential selection pressure at the merozoite surface protein 7D (MSP7D)

2019 ◽  
Author(s):  
Md Atique Ahmed ◽  
Fu-Shi Quan
Keyword(s):  
Natural Selection ◽  
Central Region ◽  
Nucleotide Diversity ◽  
Plasmodium Knowlesi ◽  
Surface Protein ◽  
Merozoite Surface Protein ◽  
Full Length ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Geographical Clustering

AbstractBackgroundHigh proportion of human cases due to the simian malaria parasite Plasmodium knowlesi in Malaysia has been a cause of concern, as it can be severe and fatal. Merozoite surface protein 7 (MSP7) is a multigene family which forms a non-covalent complex with MSP-1 prior to receptor-ligand recognition in Plasmodium falciparum and thus an important antigen for vaccine development. However, no study has been done in any of the ortholog family members in Plasmodium knowlesi from clinical samples. Thus in this study we investigated the level of polymorphism, haplotypes, and natural selection acting at the pkmsp-7D gene in clinical samples from Malaysia.MethodsWe analyzed 36 full-length pkmsp7D gene sequences (along with the reference H-strain: PKNH_1266000) which were orthologous to pvmsp7H (PVX_082680) from clinical isolates of Malaysia available from public databases. Population genetic, evolutionary and phylogenetic analyses were performed to determine the level of genetic diversity, polymorphism, recombination and natural selection.ResultsAnalysis of 36 full-length pkmsp7D sequences identified 147 SNPs (91 non-synonymous and 56 synonymous substitutions). Nucleotide diversity across the full-length gene was higher than its ortholog in P. vivax (msp7H). Region-wise analysis of the gene indicated that the nucleotide diversity at the central region was very high (π = 0.14) compared to the 5’ and 3’ regions. Most hyper-variable SNPs were detected at the central domain. Multiple test for natural selection indicated the central region was under strong positive natural selection however, the 5’ and 3’ regions were under negative/purifying selection. Evidence of intragenic recombination were detected at the central region of the gene. Phylogenetic analysis using full-length msp7D genes indicated there was no geographical clustering of parasite population.ConclusionsHigh genetic diversity with hyper-variable SNPs and strong evidence of positive natural selection at the central region of MSP7D indicated exposure of the region to host immune pressure. Negative selection at the 5’ and the 3’ regions of MSP7D might be because of functional constraints at the unexposed regions during the merozoite invasion process of P. knowlesi. No evidence of geographical clustering among the clinical isolates from Malaysia indicated uniform selection pressure in all populations. These findings highlight the further evaluation of the regions and functional characterization of the protein as a potential blood stage vaccine candidate for P. knowlesi.

scholarly journals Genetic polymorphism and natural selection of circumsporozoite protein in Myanmar Plasmodium vivax

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Tuấn Cường Võ ◽  
Hương Giang Lê ◽  
Jung-Mi Kang ◽  
Mya Moe ◽  
Haung Naw ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Plasmodium Vivax ◽  
Surface Protein ◽  
Genetic Profile ◽  
Repeat Region ◽  
Polymorphic Pattern ◽  
High Level ◽  
Global Population ◽  
Selection Of

Abstract Background Circumsporozoite surface protein (CSP) of malaria parasites has been recognized as one of the leading vaccine candidates. Clinical trials of vaccines for vivax malaria incorporating Plasmodium vivax CSP (PvCSP) have demonstrated their effectiveness in preventing malaria, at least in part. However, genetic diversity of pvcsp in the natural population remains a major concern. Methods A total of 171 blood samples collected from patients infected with Plasmodium vivax in Myanmar were analysed in this study. The pvcsp was amplified by polymerase chain reaction, followed by cloning and sequencing. Polymorphic characteristics and natural selection of pvcsp population in Myanmar were analysed using DNASTAR, MEGA6 and DnaSP programs. The polymorphic pattern and natural selection of publicly accessible global pvcsp sequences were also comparatively analysed. Results Myanmar pvcsp sequences were divided into two subtypes VK210 and VK247 comprising 143 and 28 sequences, respectively. The VK210 subtypes showed higher levels of genetic diversity and polymorphism than the VK247 subtypes. The N-terminal non-repeat region of pvcsp displayed limited genetic variations in the global population. Different patterns of octapeptide insertion (ANKKAEDA in VK210 and ANKKAGDA in VK247) and tetrapeptide repeat motif (GGNA) were identified in the C-terminal region of global pvcsp population. Meanwhile, the central repeat region (CRR) of Myanmar and global pvcsp, both in VK210 and VK247 variants, was highly polymorphic. The high level of genetic diversity in the CRR has been attributed to the different numbers, types and combinations of peptide repeat motifs (PRMs). Interestingly, 27 and 5 novel PRMs were found in Myanmar VK210 and VK247 variants, respectively. Conclusion Comparative analysis of the global pvcsp population suggests a complex genetic profile of pvcsp in the global population. These results widen understanding of the genetic make-up of pvcsp in the global P. vivax population and provide valuable information for the development of a vaccine based on PvCSP.

scholarly journals Genetic polymorphism and natural selection of circumsporozoite protein in Myanmar Plasmodium vivax

2020 ◽  
Author(s):  
Tuấn Cường Võ ◽  
Hương Giang Lê ◽  
Jung-Mi Kang ◽  
Mya Moe ◽  
Haung Naw ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Plasmodium Vivax ◽  
Surface Protein ◽  
Genetic Profile ◽  
Repeat Region ◽  
Vivax Population ◽  
High Level ◽  
Global Population ◽  
Selection Of

Abstract Background: Circumsporozoite surface protein (CSP) of malaria parasites has been recognized as one of the leading vaccine candidates. Clinical trials of vaccines for vivax malaria incorporating Plasmodium vivax CSP (PvCSP) have demonstrated their effectiveness in preventing malaria, at least in part. However, genetic diversity of PvCSP in the natural population is still a major concern. Methods: A total of 171 blood samples collected from patients infected with Plasmodium vivax in Myanmar analysed in this study. The gene for PvCSP was amplified by polymerase chain reaction, followed by T&A cloning and sequencing. Polymorphic characteristics and natural selection of Myanmar PvCSP population in Myanmar were analysed using DNASTAR, MEGA6 and DnaSP programs. The polymorphic pattern and natural selection of publicly accessible global PvCSP sequences were also comparatively analysed. Results: Myanmar PvCSP sequences were divided into two subtypes VK210 and VK247 comprising 143 and 28 sequences, respectively. The VK210 subtypes showed higher levels of genetic diversity and polymorphism than the VK247 subtypes. The N-terminal non-repeat region of PvCSP displayed limited genetic variations in the global population. Different patterns of octapeptide insertion (ANKKAEDA in VK210 and ANKKAGDA in VK247) and tetrapeptide repeat motif (GGNA) were identified in the C-terminal region of global PvCSP population. Meanwhile, the central repeat region (CRR) of Myanmar and global PvCSP, both in VK210 and VK247 variants, was highly polymorphic. The high level of genetic diversity in the CRR has been attributed to the different numbers, types and combinations of peptide repeat motifs (PRMs). Interestingly, 27 and 5 novel PRMs were found in Myanmar VK210 and VK247 variants, respectively. Conclusion: Comparative analysis of the global PvCSP population suggests a complex genetic profile of PvCSP in the global population. These results widen understanding of the genetic make-up of PvCSP in the global P. vivax population and provide valuable information for the development of a vaccine based on PvCSP.

scholarly journals Genetic polymorphism and natural selection of circumsporozoite protein in Myanmar Plasmodium vivax

2020 ◽  
Author(s):  
Tuấn Cường Võ ◽  
Hương Giang Lê ◽  
Jung-Mi Kang ◽  
Mya Moe ◽  
Haung Naw ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Plasmodium Vivax ◽  
Surface Protein ◽  
Genetic Profile ◽  
Repeat Region ◽  
Vivax Population ◽  
High Level ◽  
Global Population ◽  
Selection Of

Abstract Background: Circumsporozoite surface protein (CSP) of malaria parasites has been recognized as one of the leading vaccine candidates. Clinical trials of vaccines for vivax malaria incorporating Plasmodium vivax CSP (PvCSP) have demonstrated their effectiveness in preventing malaria, at least in part. However, genetic diversity of PvCSP in the natural population is still a major concern.Methods: A total of 171 blood samples collected from patients infected with Plasmodium vivax in Myanmar analysed in this study. The gene for PvCSP was amplified by polymerase chain reaction, followed by T&A cloning and sequencing. Polymorphic characteristics and natural selection of Myanmar PvCSP population in Myanmar were analysed using DNASTAR, MEGA6 and DnaSP programs. The polymorphic pattern and natural selection of publicly accessible global PvCSP sequences were also comparatively analysed.Results: Myanmar PvCSP sequences were divided into two subtypes VK210 and VK247 comprising 143 and 28 sequences, respectively. The VK210 subtypes showed higher levels of genetic diversity and polymorphism than the VK247 subtypes. The N-terminal non-repeat region of PvCSP displayed limited genetic variations in the global population. Different patterns of octapeptide insertion (ANKKAEDA in VK210 and ANKKAGDA in VK247) and tetrapeptide repeat motif (GGNA) were identified in the C-terminal region of global PvCSP population. Meanwhile, the central repeat region (CRR) of Myanmar and global PvCSP, both in VK210 and VK247 variants, was highly polymorphic. The high level of genetic diversity in the CRR has been attributed to the different numbers, types and combinations of peptide repeat motifs (PRMs). Interestingly, 27 and 5 novel PRMs were found in Myanmar VK210 and VK247 variants, respectively.Conclusion: Comparative analysis of the global PvCSP population suggests a complex genetic profile of PvCSP in the global population. These results widen understanding of the genetic make-up of PvCSP in the global P. vivax population and provide valuable information for the development of a vaccine based on PvCSP.

Sign in / Sign up

Export Citation Format

Share Document