scholarly journals Genetic diversity and population structure of the human malaria parasite Plasmodium falciparum surface protein Pfs47 in isolates from the lowlands in Western Kenya

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260434
Author(s):  
Shirley A. Onyango ◽  
Kevin O. Ochwedo ◽  
Maxwell G. Machani ◽  
Collince J. Omondi ◽  
Isaiah Debrah ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Population Structure ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Surface Protein ◽  
Dried Blood Spots ◽  
Cross Sectional ◽  
Western Kenya ◽  
Study Sites

Plasmodium falciparum parasites have evolved genetic adaptations to overcome immune responses mounted by diverse Anopheles vectors hindering malaria control efforts. Plasmodium falciparum surface protein Pfs47 is critical in the parasite’s survival by manipulating the vector’s immune system hence a promising target for blocking transmission in the mosquito. This study aimed to examine the genetic diversity, haplotype distribution, and population structure of Pfs47 and its implications on malaria infections in endemic lowlands in Western Kenya. Cross-sectional mass blood screening was conducted in malaria endemic regions in the lowlands of Western Kenya: Homa Bay, Kombewa, and Chulaimbo. Dried blood spots and slide smears were simultaneously collected in 2018 and 2019. DNA was extracted using Chelex method from microscopic Plasmodium falciparum positive samples and used to genotype Pfs47 using polymerase chain reaction (PCR) and DNA sequencing. Thirteen observed haplotypes of the Pfs47 gene were circulating in Western Kenya. Population-wise, haplotype diversity ranged from 0.69 to 0.77 and the nucleotide diversity 0.10 to 0.12 across all sites. All the study sites displayed negative Tajima’s D values although not significant. However, the negative and significant Fu’s Fs statistical values were observed across all the study sites, suggesting population expansion or positive selection. Overall genetic differentiation index was not significant (FST = -0.00891, P > 0.05) among parasite populations. All Nm values revealed a considerable gene flow in these populations. These results could have important implications for the persistence of high levels of malaria transmission and should be considered when designing potential targeted control interventions.

scholarly journals Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

2016 ◽  
Vol 24 (2) ◽  
pp. 85-97 ◽  
Author(s):  
Sylvanus A. Nwafili ◽  
Tian-Xiang Gao
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Control Region ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Recent Population Expansion ◽  
Base Pair Fragment ◽  
Population Structures ◽  
High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

scholarly journals Molecular epidemiology of Plasmodium falciparum by multiplexed amplicon deep sequencing in Senegal

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Tolla Ndiaye ◽  
Mouhamad Sy ◽  
Amy Gaye ◽  
Katherine J. Siddle ◽  
Daniel J. Park ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Molecular Epidemiology ◽  
Deep Sequencing ◽  
Haplotype Diversity ◽  
Surface Protein ◽  
Merozoite Surface Protein ◽  
The South ◽  
The North ◽  
Significant Difference

Abstract Background Molecular epidemiology can provide important information regarding the genetic diversity and transmission of Plasmodium falciparum, which can assist in designing and monitoring elimination efforts. However, malaria molecular epidemiology including understanding the genetic diversity of the parasite and performing molecular surveillance of transmission has been poorly documented in Senegal. Next Generation Sequencing (NGS) offers a practical, fast and high-throughput approach to understand malaria population genetics. This study aims to unravel the population structure of P. falciparum and to estimate the allelic diversity, multiplicity of infection (MOI), and evolutionary patterns of the malaria parasite using the NGS platform. Methods Multiplex amplicon deep sequencing of merozoite surface protein 1 (PfMSP1) and merozoite surface protein 2 (PfMSP2) in fifty-three P. falciparum isolates from two epidemiologically different areas in the South and North of Senegal, was carried out. Results A total of 76 Pfmsp1 and 116 Pfmsp2 clones were identified and 135 different alleles were found, 56 and 79 belonged to the pfmsp1 and pfmsp2 genes, respectively. K1 and IC3D7 allelic families were most predominant in both sites. The local haplotype diversity (Hd) and nucleotide diversity (π) were higher in the South than in the North for both genes. For pfmsp1, a high positive Tajima’s D (TD) value was observed in the South (D = 2.0453) while negative TD value was recorded in the North (D = − 1.46045) and F-Statistic (Fst) was 0.19505. For pfmsp2, non-directional selection was found with a highly positive TD test in both areas and Fst was 0.02111. The mean MOI for both genes was 3.07 and 1.76 for the South and the North, respectively, with a statistically significant difference between areas (p = 0.001). Conclusion This study revealed a high genetic diversity of pfmsp1 and pfmsp2 genes and low genetic differentiation in P. falciparum population in Senegal. The MOI means were significantly different between the Southern and Northern areas. Findings also showed that multiplexed amplicon deep sequencing is a useful technique to investigate genetic diversity and molecular epidemiology of P. falciparum infections.

scholarly journals Molecular epidemiology of Plasmodium falciparum by multiplexed amplicon deep sequencing in Senegal

2020 ◽  
Author(s):  
Tolla NDIAYE ◽  
Mouhamad Sy ◽  
Amy Gaye ◽  
Katherine J. Siddle ◽  
Daniel J. Park ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Molecular Epidemiology ◽  
Deep Sequencing ◽  
Haplotype Diversity ◽  
Surface Protein ◽  
Merozoite Surface Protein ◽  
The South ◽  
The North ◽  
Significant Difference

Abstract Background Molecular epidemiology can provide important information regarding the genetic diversity and transmission of Plasmodium falciparum , which can assist in designing and monitoring elimination efforts. However, malaria molecular epidemiology including understanding the genetic diversity of the parasite and performing molecular surveillance of transmission has been poorly documented in Senegal. Next Generation Sequencing (NGS) offers a practical, fast and high-throughput approach to understand malaria population genetics. This study aims to unravel the population structure of P. falciparum and to estimate the allelic diversity, multiplicity of infection (MOI), and evolutionary patterns of the malaria parasite using the NGS platform. Methods Multiplex amplicon deep sequencing of merozoite surface protein 1 (PfMSP1) and merozoite surface protein 2 (PfMSP2) genes in fifty-three P. falciparum isolates from two epidemiologically different areas in the South and North of Senegal, was carried out. Results A total of 76 Pfmsp1 and 116 Pfmsp2 clones were identified and 135 different alleles were found, 56 and 79 belonged to the pfmsp1 and pfmsp2 genes, respectively. K1 and IC3D7 allelic families were most predominant in both sites. The local haplotype diversity (Hd) and nucleotide diversity (π) were higher in the South than in the North for both genes. For pfmsp1 , a high positive Tajima’s D (TD) value was observed in the South (D=2.0453) while negative TD value was recorded in the North (D=-1.46045) and F-Statistic (Fst) was 0.19505. For pfmsp2 , non-directional selection was found with a highly positive TD test in both areas and Fst was 0.02111. The mean MOI for both genes was 3.07 and 1.76 for the South and the North, respectively, with a statistically significant difference between areas ( p=0.001 ). Conclusion This study revealed a high genetic diversity of pfmsp1 and pfmsp2 genes and low genetic differentiation in P. falciparum population in Senegal. The MOI means were significantly different between the Southern and Northern areas. Findings also showed that multiplexed amplicon deep sequencing is a useful technique to investigate genetic diversity and molecular epidemiology of P. falciparum infections.

scholarly journals Genetic diversity, population structure and historical demography of the two-spined yellowtail stargazer (Uranoscopus cognatus)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nur Ilham Syahadah Mohd Yusoff ◽  
Tun Nurul Aimi Mat Jaafar ◽  
Veera Vilasri ◽  
Siti Azizah Mohd Nor ◽  
Ying Giat Seah ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Resource Management ◽  
Nuclear Dna ◽  
Incomplete Lineage Sorting ◽  
Dna Recombination ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Management Program ◽  
Sampling Station

AbstractBenthic species, though ecologically important, are vulnerable to genetic loss and population size reduction due to impacts from fishing trawls. An assessment of genetic diversity and population structure is therefore needed to assist in a resource management program. To address this issue, the two-spined yellowtail stargazer (Uranoscopus cognatus) was collected within selected locations in the Indo-West Pacific (IWP). The partial mitochondrial DNA cytochrome c oxidase subunit 1 and the nuclear DNA recombination activating gene 1 were sequenced. Genetic diversity analyses revealed that the populations were moderately to highly diversified (haplotype diversity, H = 0.490–0.900, nucleotide diversity, π = 0.0010–0.0034) except sampling station (ST) 1 and 14. The low diversity level, however was apparent only in the matrilineal marker (H = 0.118–0.216; π = 0.0004–0.0008), possibly due to stochastic factors or anthropogenic stressors. Population structure analyses revealed a retention of ancestral polymorphism that was likely due to incomplete lineage sorting in U. cognatus, and prolonged vicariance by the Indo-Pacific Barrier has partitioned them into separate stock units. Population segregation was also shown by the phenotypic divergence in allopatric populations, regarding the premaxillary protrusion, which is possibly associated with the mechanism for upper jaw movement in biomechanical feeding approaches. The moderate genetic diversity estimated for each region, in addition to past population expansion events, indicated that U. cognatus within the IWP was still healthy and abundant (except in ST1 and 14), and two stock units were identified to be subjected to a specific resource management program.

scholarly journals Protein-energy malnutrition and malaria antiboby profiles in pre-school children in western Kenya: A potential diagnostic tool

2012 ◽  
Vol 12 (50) ◽  
pp. 5881-5894
Author(s):  
AM Kwena ◽  
◽  
J Wakhisi
Keyword(s):  
Plasmodium Falciparum ◽  
Protein Energy Malnutrition ◽  
Surface Protein ◽  
Merozoite Surface Protein ◽  
Diagnostic Value ◽  
Igg Antibody ◽  
Cross Sectional ◽  
Western Kenya ◽  
Protein Energy ◽  
High Prevalence

Protein-energy malnutrition is a serious clinical condition with high prevalence in areas where Plasmodium falciparum is highly endemic such as western Kenya. There is a major need to determine the relationship between PEM and malaria antibody profiles especially in an area where malaria is endemic. The objective of this work, therefore, was to determine the association between PEM and specific malaria antibodies and the potential diagnostic value of the antibodies in children aged between 5 and 59 months. Cross- sectional surveys as well as analysis of sera for specific malaria antibodies were carried out at Asembo Division, Bondo District, Kisumu County, Nyanza Province. A total of sixty villages identified through random sampling with each household as the sampling unit were used for data collection. Two thousand, one hundred and twelve (2112) Children < 5 years of age were sampled in three successive cross- sectional surveys: The first survey included children < 3 years of age while the subsequent two surveys included children < 5 years of age. Anthropometric measurements were carried out followed by finger prick blood sample for assay of antibodies in sera of the study children. Statistical variables (Odds Ratio, at 95% CI) were determined using SPSS 11 and SAS computer packages. Both Multivariate and Bivariate analyses were carried out. Epi-info 2002 package was used to determine anthropometric variables. Demographic variables and malaria parasite counts were determined for all the children sampled. Circumsporozoite Surface Protein (CSP) IgG antibody was found to be significantly associated with stunting and underweight (p<0.05) but not with wasting. Liver Stage Antigen (LSA) IgG antibody was significantly associated with wasting only (p<0.05) while Merozoite Surface Protein (MSP) IgG antibody was not significantly associated with any malnutrition state. The mean concentration of CSP IgG was elevated in stunted, wasted and underweight in comparison to controls. Liverstage antigen 1 IgG was elevated in stunted children only as compared to controls, whereas MSP IgG was low in all PEM cases as compared to controls. Specific Plasmodium falciparum antibody profiles could accurately be used to determine the association between malaria and Protein Energy Malnutrition.

scholarly journals Genetic Diversity of Merozoite Surface Protein 2 (MSP2) Plasmodium falciparum Clinical Isolate in Wamena General Hospital

2020 ◽  
Vol 12 (2) ◽  
pp. 123-132
Author(s):  
Dirk Y.P. Runtuboi ◽  
Rosye H.R. Tanjung ◽  
Yulius Sarungu ◽  
Meidy J. Imbiri ◽  
Irma A. Resmol ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
General Hospital ◽  
Surface Protein ◽  
Merozoite Surface Protein ◽  
Dominant Frequency ◽  
Asexual Parasite ◽  
Cross Sectional ◽  
Single Allele ◽  
Msp2 Gene

The genetic diversity of typical clinical isolated Plasmodium falciparum in the malaria population varies greatly, especially at the location where malaria disease were recorded at high incidence rate. MSP2 is known as glycoprotein expressed on the surface of merozoites, which is an antigenic protein and has a potential to act as vaccine candidate for malaria. The MSP2 gene has two main allelic groups called FC27 and 3D7/IC. Block 3 from MSP2 gene is the most polymorphic to describe the diversity of parasite populations. The P. falciparum parasite population is often characterized by wide genetic diversity in areas of high transmission intensity. Therefore, the study on P. falciparum diversity is useful to describe the level of malaria transmission. The study of genetic diversity focused on clinical isolated species at Wamena General Hospital was aimed to determine the presence of the MSP2 gene, variety of MSP2 gene allele  and the dominant frequency of the MSP2 gene allele. This research has been carried out from March 2018 to February 2019 using a cross sectional approach. The research sample was taken and prepared from Wamena Regional Hospital and followed by the analyzing of DNA isolation, PCR, electrophoresis of the research samples was done at the genetic science laboratory in Jakarta, Indonesia. The samples studied were patients who met the inclusion criteria, namely a single P. falciparum infection with an asexual parasite density >1000 parasites/µl or >3+ (1-10 P/Lp), and were agreed to become respondents by signing an informed consent. A total of 26 clinical isolates of P. falciparum were isolated with the MSP2 gene distribution on the FC27 allele with the highest as many as 25 samples (96.2%), 22 samples (84.6%) of the 3D7 / IC allele while the mixture of the two alleles was 22 samples (84.6%). From a total of 26 samples, there were samples with the male gender category counted for 77.3% and female 41%. The results of the identification of clinical isolated P. falciparum at Wamena Hospital with a total of 26 samples were found in productive age, between 15-34 years with a single allele (95.8%), while 23 cases and mix (both alleles 87.5%) about 21 cases, meanwhile in cases of before-productive age, in which ages were 12 and 14 years of age with a single allele 100% (FC27) 2 cases and 50% (3D7/IC) found to be 1 case, The mixture of the two alleles is 50% was only 1 case and there was no sample at non-productive age observed. Key words: Malaria; MSP-2; P. falciparum; Wamena

scholarly journals Identification of CSP Types and Genotypic Variability of Clinical and Environmental Isolates of Aspergillus fumigatus from Different Geographic Origins

2020 ◽  
Vol 8 (5) ◽  
pp. 688 ◽  
Author(s):  
Esperanza Duarte-Escalante ◽  
María Guadalupe Frías-De-León ◽  
Erick Martínez-Herrera ◽  
Gustavo Acosta-Altamirano ◽  
Emmanuel Rosas de Paz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Aspergillus Fumigatus ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Surface Protein ◽  
Cell Surface Protein ◽  
Environmental Isolates ◽  
Geographic Origins ◽  
High Discriminatory Power

The CSP (cell surface protein) microsatellite marker is useful for typing Aspergillus fumigatus isolates and determining relationships at the subpopulation level because it has shown high discriminatory power. In the present study, 90 A. fumigatus isolates from Mexico (MX), Argentina (AR), France (FR), and Peru (PE) were identified through a phylogenetic analysis using the benA gene fragment and were typed with the CSP microsatellite, and the types were identified using the nomenclature recommended in the literature. Genetic variability was analyzed through haplotype diversity, nucleotide diversity, polymorphic sites, and nucleotide differences between pairs of sequences. The population structure was evaluated using the Tajima’s D statistic. No new CSP types were recorded in the MX, FR, and PE isolates, while in the AR isolates, two new CSP types were identified (t25 and t26). The most common CSP types in the studied populations were t01, t02, t03, and t04A; these results are consistent with findings in other countries. In addition, the genetic diversity parameters we obtained revealed that the greatest genetic diversity was found in the MX population, followed by AR and FR. No population structure was identified among the isolates studied.

scholarly journals Genetic polymorphism of the N-terminal region in circumsporozoite surface protein of Plasmodium falciparum field isolates from Sudan

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Nouh S. Mohamed ◽  
Musab M. Ali Albsheer ◽  
Hanadi Abdelbagi ◽  
Emanuel E. Siddig ◽  
Mona A. Mohamed ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Balancing Selection ◽  
Pcr Amplification ◽  
Surface Protein ◽  
Merozoite Surface Protein ◽  
Molecular Study ◽  
Terminal Region ◽  
Sub Saharan Africa ◽  
Cross Sectional

Abstract Background Malaria caused by Plasmodium falciparum parasite is still known to be one of the most significant public health problems in sub-Saharan Africa. Genetic diversity of the Sudanese P. falciparum based on the diversity in the circumsporozoite surface protein (PfCSP) has not been previously studied. Therefore, this study aimed to investigate the genetic diversity of the N-terminal region of the pfcsp gene. Methods A cross-sectional molecular study was conducted; 50 blood samples have been analysed from different regions in Sudan. Patients were recruited from the health facilities of Khartoum, New Halfa, Red Sea, White Nile, Al Qadarif, Gezira, River Nile, and Ad Damazin during malaria transmission seasons between June to October and December to February 2017–2018. Microscopic and nested PCR was performed for detection of P. falciparum. Merozoite surface protein-1 was performed to differentiate single and multiple clonal infections. The N-terminal of the pfcsp gene has been sequenced using PCR-Sanger dideoxy method and analysed to sequences polymorphism including the numbers of haplotypes (H), segregating sites (S), haplotypes diversity (Hd) and the average number of nucleotide differences between two sequences (Pi) were obtained using the software DnaSP v5.10. As well as neutrality testing, Tajima’s D test, Fu and Li’s D and F statistics. Results PCR amplification resulted in 1200 bp of the pfcsp gene. Only 21 PCR products were successfully sequenced while 29 were presenting multiple clonal P. falciparum parasite were not sequenced. The analysis of the N-terminal region of the PfCSP amino acids sequence compared to the reference strains showed five different haplotypes. H1 consisted of 3D7, NF54, HB3 and 13 isolates of the Sudanese pfcsp. H2 comprised of 7G8, Dd2, MAD20, RO33, Wellcome strain, and 5 isolates of the Sudanese pfcsp. H3, H4, and H5 were found in 3 distinct isolates. Hd was 0.594 ± 0.065, and S was 12. The most common polymorphic site was A98G; other sites were D82Y, N83H, N83M, K85L, L86F, R87L, R87F, and A98S. Fu and Li’s D* test value was − 2.70818, Fu and Li’s F* test value was − 2.83907, indicating a role of negative balancing selection in the pfcsp N-terminal region. Analysis with the global pfcsp N-terminal regions showed the presence of 13 haplotypes. Haplotypes frequencies were 79.4%, 17.0%, 1.6% and 1.0% for H1, H2, H3 and H4, respectively. Remaining haplotypes frequency was 0.1% for each. Hd was 0.340 ± 0.017 with a Pi of 0.00485, S was 18 sites, and Pi was 0.00030. Amino acid polymorphisms identified in the N-terminal region of global pfcsp were present at eight positions (D82Y, N83H/M, K85L/T/N, L86F, R87L/F, A98G/V/S, D99G, and G100D). Conclusions Sudanese pfcsp N-terminal region was well-conserved with only a few polymorphic sites. Geographical distribution of genetic diversity showed high similarity to the African isolates, and this will help and contribute in the deployment of RTS,S, a PfCSP-based vaccine, in Sudan.

scholarly journals Short Communication: Intraspecific genetic diversity and population subdivision of rabbitfish (Siganidae: Siganus canaliculatus) in urbanized reefs of Jakarta Bay, Indonesia

2019 ◽  
Vol 20 (10) ◽  
Author(s):  
Hawis Madduppa ◽  
MUTIARA KRISTINA MARGARETHA ◽  
ADITYA BRAMANDITO ◽  
TRI PRARTONO ◽  
BEGINER SUBHAN ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Short Communication ◽  
Haplotype Diversity ◽  
Aquatic Organism ◽  
Population Subdivision ◽  
The North ◽  
Siganus Canaliculatus ◽  
Intraspecific Genetic Diversity ◽  
Study Sites

Abstract. Madduppa H, Margaretha MK, Bramandito A, Prartono T, Subhan B, Arafat D, Anggraini NP. 2019. Short Communication: Intraspecific genetic diversity and population subdivision of rabbitfish (Siganidae: Siganus canaliculatus) in urbanized reefs of Jakarta Bay, Indonesia. Biodiversitas 20: xxxx. Indonesian coral reefs and seagrass are heavily influenced by human activities through pollution and habitat loss, and sea-level rise or the increase of ocean temperature due to the global change. In the Jakarta Bay and Seribu Islands, marine communities have been impacted by an increase in eutrophication and sedimentation levels. As a result, these habitats became degraded and could affect their associated organisms such as rabbitfish. Genetic diversity and population structure can provide information about a long-term condition in an aquatic organism. The study was conducted to assess genetic diversity and population structure of rabbitfish (Siganus canaliculatus) across an environmental gradient in Jakarta Bay and Seribu Islands. A total of 31 individuals were collected using gillnet in study sites. A molecular marker mitochondrial Cytochrome oxidase 1 (CO1) was used to amplify DNA. The result of the phylogenetic tree formed two major clades, which generally separate northern and southern region of Seribu Islands populations. AMOVA analysis showed significant genetic differentiation between the population of Siganus canaliculatus in the north zone (National Park) and south zone Seribu Island (FST = 0.38, p<0.005). The highest haplotype diversity (Hd) of Siganus canaliculatus contained was observed in the north (Pulau Semak Daun) and south (Pulau Damar) in both as moderate (0.50). Nucleotide diversity ( ) of Siganus canaliculatus was categorized as low (0.076) to moderate (0.500). Environment and humans seem to affect the value of genetic diversity, and as the study suggests, a significant population subdivision makes this population vulnerable.  

Sign in / Sign up

Export Citation Format

Share Document