schliessen

Filtern

 

Bibliotheken

Within-population genetic diversity and population structure of Plasmodium knowlesi merozoite surface protein 1 gene from geographically distinct regions of Malaysia and Thailand

Background The C-terminal 42 kDa domain of Plasmodium knowlesi merozoite surface protein 1 (PkMSP1) is a potential asexual blood-stage vaccine candidate, however, only a limited number of clinical isolates have been analysed from Malaysia and no inter-country comparative diversity study has been con... Full description

Journal Title: Malaria Journal 2018, Vol.17
Main Author: Vythilingam, Indra
Other Authors: Fu-Shi, Quan
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 14752875 ; DOI: 10.1186/s12936-018-2583-z
Zum Text:
SendSend as email Add to Book BagAdd to Book Bag
Staff View
recordid: proquest2158103961
title: Within-population genetic diversity and population structure of Plasmodium knowlesi merozoite surface protein 1 gene from geographically distinct regions of Malaysia and Thailand
format: Article
creator:
  • Vythilingam, Indra
  • Fu-Shi, Quan
subjects:
  • Malaysia
  • Indonesia
  • Sarawak Malaysia
  • Plasmodium Knowlesi
  • Thailand
  • Borneo
  • Databases
  • Analysis
  • Evaluation
  • Vaccines
  • Population Differentiation
  • Strain
  • Disease Control
  • Identification
  • Data Bases
  • Haplotypes
  • Parasites
  • Negative Selection
  • Genetic Diversity
  • Proteins
  • Samples
  • Proteins
  • Merozoite Surface Protein 1
  • Population Genetics
  • Studies
  • Parasites
  • Population Studies
  • Regions
  • Infections
  • Clinical Isolates
  • Genes
  • Population
  • Parasites
  • Gene Polymorphism
  • Population Differentiation
  • Length
  • Vaccines
  • Genetic Diversity
  • Genes
  • Population Structure
  • Natural Selection
  • Genetic Diversity
  • Countries
  • Population Growth
  • Population Structure
  • Malaria
  • Natural Selection
  • Computer Programs
  • Haplotypes
  • Parasites
  • Population Structure
  • Antigens
  • Haplotypes
  • Nucleotides
  • Polymorphism
  • Genetic Diversity
  • Merozoite Surface Protein 1
  • Natural Selection
  • Vaccine
  • Genetic Diversity
  • Sub-Populations
  • Plasmodium Knowlesi
ispartof: Malaria Journal, 2018, Vol.17
description: Background The C-terminal 42 kDa domain of Plasmodium knowlesi merozoite surface protein 1 (PkMSP1) is a potential asexual blood-stage vaccine candidate, however, only a limited number of clinical isolates have been analysed from Malaysia and no inter-country comparative diversity study has been conducted. In the present study, nucleotide diversity, haplotypes and natural selection levels of pkmsp1 in clinical samples from geographically distinct regions of Malaysia and Thailand were investigated. The overall population structure of the parasite from the region was determined. Methods Eleven full-length pkmsp1 sequences obtained from clinical isolates of Malaysia along with the H-strain were downloaded from the database for domain wise characterization of pkmsp1 gene. Additionally, 76 pkmsp-142 sequences from Thailand and Malaysia were downloaded from the database for intra and inter-population analysis. DnaSP 5.10 and MEGA 5.0 software were used to determine genetic diversity, polymorphism, haplotypes and natural selection. Genealogical relationships were determined using haplotype network tree in NETWORK software v5.0. Population genetic differentiation index (FST) of parasites were analysed using Arlequin v3.5. Results Sequence analysis of 11 full-length pkmsp1 sequences along with the H-strain identified 477 (8.4%) polymorphic sites, of which 107 were singleton sites. The overall diversity observed in the full-length genes were high in comparison to its ortholog pvmsp1 and the 4 variable domains showed extensive size variations. The nucleotide diversity was low towards the pkmsp1-42 compared to the conserved domains. The 19 kDa domain was less diverse and completely conserved among isolates from Malaysian Borneo. The nucleotide diversity of isolates from Peninsular Malaysia and Thailand were higher than Malaysian Borneo. Network analysis of pkmsp1-42 haplotypes showed geographical clustering of the isolates from Malaysian Borneo and grouping of isolates from Peninsular Malaysia and Thailand. Population differentiation analysis indicated high FST values between parasite populations originating from Malaysian Borneo, Peninsular Malaysia and Thailand attributing to geographical distance. Moderate genetic differentiation was observed for parasite populations from Thailand and Peninsular Malaysia. Evidence of population expansion and purifying selection were observed in all conserved domains with strongest selection within the pkmsp1-42 domain. Conclusions
language: eng
source:
identifier: E-ISSN: 14752875 ; DOI: 10.1186/s12936-018-2583-z
fulltext: fulltext_linktorsrc
issn:
  • 14752875
  • 1475-2875
url: Link


@attributes
ID1532888306
RANK0.07
NO1
SEARCH_ENGINEprimo_central_multiple_fe
SEARCH_ENGINE_TYPEPrimo Central Search Engine
LOCALfalse
PrimoNMBib
record
control
sourcerecordid2158103961
sourceidproquest
recordidTN_proquest2158103961
sourcesystemOther
pqid2158103961
galeid568306666
display
typearticle
titleWithin-population genetic diversity and population structure of Plasmodium knowlesi merozoite surface protein 1 gene from geographically distinct regions of Malaysia and Thailand
creatorVythilingam, Indra ; Fu-Shi, Quan
ispartofMalaria Journal, 2018, Vol.17
identifierE-ISSN: 14752875 ; DOI: 10.1186/s12936-018-2583-z
subjectMalaysia ; Indonesia ; Sarawak Malaysia ; Plasmodium Knowlesi ; Thailand ; Borneo ; Databases ; Analysis ; Evaluation ; Vaccines ; Population Differentiation ; Strain ; Disease Control ; Identification ; Data Bases ; Haplotypes ; Parasites ; Negative Selection ; Genetic Diversity ; Proteins ; Samples ; Proteins ; Merozoite Surface Protein 1 ; Population Genetics ; Studies ; Parasites ; Population Studies ; Regions ; Infections ; Clinical Isolates ; Genes ; Population ; Parasites ; Gene Polymorphism ; Population Differentiation ; Length ; Vaccines ; Genetic Diversity ; Genes ; Population Structure ; Natural Selection ; Genetic Diversity ; Countries ; Population Growth ; Population Structure ; Malaria ; Natural Selection ; Computer Programs ; Haplotypes ; Parasites ; Population Structure ; Antigens ; Haplotypes ; Nucleotides ; Polymorphism ; Genetic Diversity ; Merozoite Surface Protein 1 ; Natural Selection ; Vaccine ; Genetic Diversity ; Sub-Populations ; Plasmodium Knowlesi
descriptionBackground The C-terminal 42 kDa domain of Plasmodium knowlesi merozoite surface protein 1 (PkMSP1) is a potential asexual blood-stage vaccine candidate, however, only a limited number of clinical isolates have been analysed from Malaysia and no inter-country comparative diversity study has been conducted. In the present study, nucleotide diversity, haplotypes and natural selection levels of pkmsp1 in clinical samples from geographically distinct regions of Malaysia and Thailand were investigated. The overall population structure of the parasite from the region was determined. Methods Eleven full-length pkmsp1 sequences obtained from clinical isolates of Malaysia along with the H-strain were downloaded from the database for domain wise characterization of pkmsp1 gene. Additionally, 76 pkmsp-142 sequences from Thailand and Malaysia were downloaded from the database for intra and inter-population analysis. DnaSP 5.10 and MEGA 5.0 software were used to determine genetic diversity, polymorphism, haplotypes and natural selection. Genealogical relationships were determined using haplotype network tree in NETWORK software v5.0. Population genetic differentiation index (FST) of parasites were analysed using Arlequin v3.5. Results Sequence analysis of 11 full-length pkmsp1 sequences along with the H-strain identified 477 (8.4%) polymorphic sites, of which 107 were singleton sites. The overall diversity observed in the full-length genes were high in comparison to its ortholog pvmsp1 and the 4 variable domains showed extensive size variations. The nucleotide diversity was low towards the pkmsp1-42 compared to the conserved domains. The 19 kDa domain was less diverse and completely conserved among isolates from Malaysian Borneo. The nucleotide diversity of isolates from Peninsular Malaysia and Thailand were higher than Malaysian Borneo. Network analysis of pkmsp1-42 haplotypes showed geographical clustering of the isolates from Malaysian Borneo and grouping of isolates from Peninsular Malaysia and Thailand. Population differentiation analysis indicated high FST values between parasite populations originating from Malaysian Borneo, Peninsular Malaysia and Thailand attributing to geographical distance. Moderate genetic differentiation was observed for parasite populations from Thailand and Peninsular Malaysia. Evidence of population expansion and purifying selection were observed in all conserved domains with strongest selection within the pkmsp1-42 domain. Conclusions This study is the first to report on inter country genetic diversity and population structure of P. knowlesi based on msp1. Strong evidence of negative selection was observed in the 42 kDa domain, indicating functional constrains. Geographical clustering of P. knowlesi and moderate to high genetic differentiation values between populations identified in this study highlights the importance of further evaluation using larger number of clinical samples from Southeast Asian countries.
languageeng
source
version7
oafree_for_read
lds50peer_reviewed
links
openurl$$Topenurl_article
openurlfulltext$$Topenurlfull_article
linktorsrc$$Uhttp://search.proquest.com/docview/2158103961/?pq-origsite=primo$$EView_record_in_ProQuest_(subscribers_only)
search
creatorcontrib
0Vythilingam, Indra
1Fu-Shi, Quan
titleWithin-population genetic diversity and population structure of Plasmodium knowlesi merozoite surface protein 1 gene from geographically distinct regions of Malaysia and Thailand
descriptionBackground The C-terminal 42 kDa domain of Plasmodium knowlesi merozoite surface protein 1 (PkMSP1) is a potential asexual blood-stage vaccine candidate, however, only a limited number of clinical isolates have been analysed from Malaysia and no inter-country comparative diversity study has been conducted. In the present study, nucleotide diversity, haplotypes and natural selection levels of pkmsp1 in clinical samples from geographically distinct regions of Malaysia and Thailand were investigated. The overall population structure of the parasite from the region was determined. Methods Eleven full-length pkmsp1 sequences obtained from clinical isolates of Malaysia along with the H-strain were downloaded from the database for domain wise characterization of pkmsp1 gene. Additionally, 76 pkmsp-142 sequences from Thailand and Malaysia were downloaded from the database for intra and inter-population analysis. DnaSP 5.10 and MEGA 5.0 software were used to determine genetic diversity, polymorphism, haplotypes and natural selection. Genealogical relationships were determined using haplotype network tree in NETWORK software v5.0. Population genetic differentiation index (FST) of parasites were analysed using Arlequin v3.5. Results Sequence analysis of 11 full-length pkmsp1 sequences along with the H-strain identified 477 (8.4%) polymorphic sites, of which 107 were singleton sites. The overall diversity observed in the full-length genes were high in comparison to its ortholog pvmsp1 and the 4 variable domains showed extensive size variations. The nucleotide diversity was low towards the pkmsp1-42 compared to the conserved domains. The 19 kDa domain was less diverse and completely conserved among isolates from Malaysian Borneo. The nucleotide diversity of isolates from Peninsular Malaysia and Thailand were higher than Malaysian Borneo. Network analysis of pkmsp1-42 haplotypes showed geographical clustering of the isolates from Malaysian Borneo and grouping of isolates from Peninsular Malaysia and Thailand. Population differentiation analysis indicated high FST values between parasite populations originating from Malaysian Borneo, Peninsular Malaysia and Thailand attributing to geographical distance. Moderate genetic differentiation was observed for parasite populations from Thailand and Peninsular Malaysia. Evidence of population expansion and purifying selection were observed in all conserved domains with strongest selection within the pkmsp1-42 domain. Conclusions This study is the first to report on inter country genetic diversity and population structure of P. knowlesi based on msp1. Strong evidence of negative selection was observed in the 42 kDa domain, indicating functional constrains. Geographical clustering of P. knowlesi and moderate to high genetic differentiation values between populations identified in this study highlights the importance of further evaluation using larger number of clinical samples from Southeast Asian countries.
subject
0Malaysia
1Indonesia
2Sarawak Malaysia
3Plasmodium Knowlesi
4Thailand
5Borneo
6Databases
7Analysis
8Evaluation
9Vaccines
10Population Differentiation
11Strain
12Disease Control
13Identification
14Data Bases
15Haplotypes
16Parasites
17Negative Selection
18Genetic Diversity
19Proteins
20Samples
21Merozoite Surface Protein 1
22Population Genetics
23Studies
24Population Studies
25Regions
26Infections
27Clinical Isolates
28Genes
29Population
30Gene Polymorphism
31Length
32Population Structure
33Natural Selection
34Countries
35Population Growth
36Malaria
37Computer Programs
38Antigens
39Nucleotides
40Polymorphism
41Vaccine
42Sub-Populations
43Merozoite surface protein 1
44Natural selection
45Genetic diversity
46Sub-populations
47Plasmodium knowlesi
general
0English
1BioMed Central
210.1186/s12936-018-2583-z
3Medical Database
4Health & Medical Collection (Alumni edition)
5Medical Database (Alumni edition)
6Health & Medical Collection
7Entomology Abstracts
8ProQuest Public Health
9Publicly Available Content Database
10ASFA: Aquatic Sciences and Fisheries Abstracts
11ProQuest Aquatic Science Collection
12ProQuest Biological Science Collection
13ProQuest Central
14ProQuest Environmental Science Collection
15ProQuest Hospital Collection
16ProQuest Natural Science Collection
17Hospital Premium Collection (Alumni edition)
18ProQuest SciTech Collection
19ProQuest Health & Medical Complete
20ProQuest Medical Library
21Biological Science Database
22Earth, Atmospheric & Aquatic Science Database
23Natural Science Collection
24ProQuest Central (new)
25ProQuest Central Korea
26SciTech Premium Collection
27Health Research Premium Collection
28Health Research Premium Collection (Alumni edition)
29ProQuest Central Essentials
30ProQuest Central China
31Biological Science Index (ProQuest)
sourceidproquest
recordidproquest2158103961
issn
014752875
11475-2875
rsrctypearticle
creationdate2018
addtitleMalaria Journal
searchscope
01000273
11006761
21006762
31007067
41007396
51007426
61007428
71007490
81007531
91007617
101007945
111008886
121009127
131009240
141009386
1510000002
1610000003
1710000004
1810000006
1910000036
2010000038
2110000039
2210000043
2310000047
2410000050
2510000118
2610000119
2710000120
2810000155
2910000156
3010000157
3110000158
3210000197
3310000198
3410000200
3510000209
3610000217
3710000238
3810000244
3910000253
4010000255
4110000256
4210000258
4310000260
4410000270
4510000271
4610000281
4710000300
4810000302
4910000348
5010000350
51proquest
scope
01000273
11006761
21006762
31007067
41007396
51007426
61007428
71007490
81007531
91007617
101007945
111008886
121009127
131009240
141009386
1510000002
1610000003
1710000004
1810000006
1910000036
2010000038
2110000039
2210000043
2310000047
2410000050
2510000118
2610000119
2710000120
2810000155
2910000156
3010000157
3110000158
3210000197
3310000198
3410000200
3510000209
3610000217
3710000238
3810000244
3910000253
4010000255
4110000256
4210000258
4310000260
4410000270
4510000271
4610000281
4710000300
4810000302
4910000348
5010000350
51proquest
lsr43
01000273true
11006761true
21006762true
31007067true
41007396false
51007426false
61007428false
71007490false
81007531false
91007617true
101007945true
111008886true
121009127true
131009240true
141009386true
1510000002false
1610000003false
1710000004false
1810000006false
1910000036false
2010000038false
2110000039true
2210000043false
2310000047true
2410000050false
2510000118true
2610000119true
2710000120false
2810000155true
2910000156true
3010000157true
3110000158true
3210000197false
3310000198false
3410000200false
3510000209false
3610000217false
3710000238false
3810000244false
3910000253false
4010000255true
4110000256true
4210000258true
4310000260false
4410000270true
4510000271true
4610000281true
4710000300true
4810000302true
4910000348true
5010000350false
startdate20180101
enddate20180101
citationvol 17
lsr30VSR-Enriched:[galeid, pqid, pages, date, issue]
sort
titleWithin-population genetic diversity and population structure of Plasmodium knowlesi merozoite surface protein 1 gene from geographically distinct regions of Malaysia and Thailand
authorVythilingam, Indra ; Fu-Shi, Quan
creationdate20180101
lso0120180101
facets
frbrgroupid6937302519218280937
frbrtype5
newrecords20181225
languageeng
creationdate2018
topic
0Malaysia
1Indonesia
2Sarawak Malaysia
3Plasmodium Knowlesi
4Thailand
5Borneo
6Databases
7Analysis
8Evaluation
9Vaccines
10Population Differentiation
11Strain
12Disease Control
13Identification
14Data Bases
15Haplotypes
16Parasites
17Negative Selection
18Genetic Diversity
19Proteins
20Samples
21Merozoite Surface Protein 1
22Population Genetics
23Studies
24Population Studies
25Regions
26Infections
27Clinical Isolates
28Genes
29Population
30Gene Polymorphism
31Length
32Population Structure
33Natural Selection
34Countries
35Population Growth
36Malaria
37Computer Programs
38Antigens
39Nucleotides
40Polymorphism
41Vaccine
42Sub-Populations
collection
0Medical Database
1Health & Medical Collection (Alumni edition)
2Medical Database (Alumni edition)
3Health & Medical Collection
4Entomology Abstracts
5ProQuest Public Health
6Publicly Available Content Database
7ASFA: Aquatic Sciences and Fisheries Abstracts
8ProQuest Aquatic Science Collection
9ProQuest Biological Science Collection
10ProQuest Central
11ProQuest Environmental Science Collection
12ProQuest Hospital Collection
13ProQuest Natural Science Collection
14Hospital Premium Collection (Alumni edition)
15ProQuest SciTech Collection
16ProQuest Health & Medical Complete
17ProQuest Medical Library
18Biological Science Database
19Earth, Atmospheric & Aquatic Science Database
20Natural Science Collection
21ProQuest Central (new)
22ProQuest Central Korea
23SciTech Premium Collection
24Health Research Premium Collection
25Health Research Premium Collection (Alumni edition)
26ProQuest Central Essentials
27ProQuest Central China
28Biological Science Index (ProQuest)
prefilterarticles
rsrctypearticles
creatorcontrib
0Vythilingam, Indra
1Fu-Shi, Quan
jtitleMalaria Journal
toplevelpeer_reviewed
delivery
delcategoryRemote Search Resource
fulltextfulltext_linktorsrc
addata
aulast
0Vythilingam
1Fu-Shi
aufirst
0Indra
1Quan
au
0Vythilingam, Indra
1Fu-Shi, Quan
atitleWithin-population genetic diversity and population structure of Plasmodium knowlesi merozoite surface protein 1 gene from geographically distinct regions of Malaysia and Thailand
jtitleMalaria Journal
risdate20180101
volume17
eissn14752875
formatjournal
genrearticle
ristypeJOUR
abstractBackground The C-terminal 42 kDa domain of Plasmodium knowlesi merozoite surface protein 1 (PkMSP1) is a potential asexual blood-stage vaccine candidate, however, only a limited number of clinical isolates have been analysed from Malaysia and no inter-country comparative diversity study has been conducted. In the present study, nucleotide diversity, haplotypes and natural selection levels of pkmsp1 in clinical samples from geographically distinct regions of Malaysia and Thailand were investigated. The overall population structure of the parasite from the region was determined. Methods Eleven full-length pkmsp1 sequences obtained from clinical isolates of Malaysia along with the H-strain were downloaded from the database for domain wise characterization of pkmsp1 gene. Additionally, 76 pkmsp-142 sequences from Thailand and Malaysia were downloaded from the database for intra and inter-population analysis. DnaSP 5.10 and MEGA 5.0 software were used to determine genetic diversity, polymorphism, haplotypes and natural selection. Genealogical relationships were determined using haplotype network tree in NETWORK software v5.0. Population genetic differentiation index (FST) of parasites were analysed using Arlequin v3.5. Results Sequence analysis of 11 full-length pkmsp1 sequences along with the H-strain identified 477 (8.4%) polymorphic sites, of which 107 were singleton sites. The overall diversity observed in the full-length genes were high in comparison to its ortholog pvmsp1 and the 4 variable domains showed extensive size variations. The nucleotide diversity was low towards the pkmsp1-42 compared to the conserved domains. The 19 kDa domain was less diverse and completely conserved among isolates from Malaysian Borneo. The nucleotide diversity of isolates from Peninsular Malaysia and Thailand were higher than Malaysian Borneo. Network analysis of pkmsp1-42 haplotypes showed geographical clustering of the isolates from Malaysian Borneo and grouping of isolates from Peninsular Malaysia and Thailand. Population differentiation analysis indicated high FST values between parasite populations originating from Malaysian Borneo, Peninsular Malaysia and Thailand attributing to geographical distance. Moderate genetic differentiation was observed for parasite populations from Thailand and Peninsular Malaysia. Evidence of population expansion and purifying selection were observed in all conserved domains with strongest selection within the pkmsp1-42 domain. Conclusions This study is the first to report on inter country genetic diversity and population structure of P. knowlesi based on msp1. Strong evidence of negative selection was observed in the 42 kDa domain, indicating functional constrains. Geographical clustering of P. knowlesi and moderate to high genetic differentiation values between populations identified in this study highlights the importance of further evaluation using larger number of clinical samples from Southeast Asian countries.
copLondon
pubBioMed Central
doi10.1186/s12936-018-2583-z
urlhttp://search.proquest.com/docview/2158103961/
pages1-12
issue1
oafree_for_read
date2018-11-29