Evidence of a Recent Bottleneck in Plasmodium falciparum Populations on the Honduran–Nicaraguan Border

The countries of Central America and the island of Hispaniola have set the goal of eliminating malaria in less than a decade. Although efforts to reduce the malaria burden in the region have been successful, there has been an alarming increase in cases in the Nicaraguan Moskitia since 2014. The continuous decrease in cases between 2000 and 2014, followed by a rapid expansion from 2015 to the present, has generated a potential bottleneck effect in the populations of Plasmodium spp. Consequently, this study aimed to evaluate the genetic diversity of P. falciparum and the decrease in allelic richness in this population. The polymorphic regions of the pfmsp-1 and pfmsp-2 genes of patients with falciparum malaria from Honduras and Nicaragua were analyzed using nested PCR and sequencing. Most of the samples were classified into the K1 allelic subfamily of the pfmsp-1 gene and into the 3D7 subfamily of the pfmsp-2 gene. Despite the low genetic diversity found, more than half of the samples presented a polyclonal K1/RO33 haplotype. No sequence polymorphisms were found within each allelic subfamily. This study describes a notable decrease in the genetic diversity of P. falciparum in the Moskitia region after a bottleneck phenomenon. These results will be useful for future epidemiological investigations and the monitoring of malaria transmission in Central America.

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Low genetic diversity and complexity of submicroscopic Plasmodium falciparum infections among febrile patients in low transmission areas in Senegal

PLoS ONE ◽

10.1371/journal.pone.0215755 ◽

2019 ◽

Vol 14 (4) ◽

pp. e0215755

Author(s):

Rokhaya Sane ◽

Cheikh Talla ◽

Babacar Diouf ◽

Fatoumata Diene Sarr ◽

Nafissatou Diagne ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Low Transmission ◽

Low Genetic Diversity

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Is genetic diversity of Plasmodium falciparum suggestive of malaria endemic zone in West Africa? An attempt to respond by a cross-sectional comparative study between Senegal and Nigeria

10.1101/2020.08.27.20183178 ◽

2020 ◽

Author(s):

Mary Aigbiremo Oboh ◽

Tolla Ndiaye ◽

Khadim Diongue ◽

Yaye D Ndiaye ◽

Mouhamad Sy ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Holistic Approach ◽

Control Measures ◽

Allelic Polymorphism ◽

African Countries ◽

High Genetic Diversity ◽

Cross Sectional ◽

Low Genetic Diversity ◽

Infection Types

Background: Characterization of malaria parasite populations in different endemic settings (from low to high) could be helpful for ascertaining the progress of malaria interventions in endemic settings. The present study aims to compare Plasmodium falciparum parasite population structure between two West African countries with very different level of endemicity using P. falciparum allelic polymorphic markers: msp1 and msp2. Methods: Parasite genomic DNA was extracted from 187 dried blood spot collected from confirmed uncomplicated P. falciparum malaria infected patients in Senegal (94) being at the pre-elimination stage in most part of the country and Nigeria (93) which is still at the control stage. Allelic polymorphism of msp1 and msp2 genes were assessed by nested PCR. Results: In Senegal as well as in Nigeria, K1 and IC3D7 allelic families were the most represented for msp1 and msp2 genes respectively. A higher multiplicity of infection (MOI) was found in both study sites in Senegal (Thies:1.51/2.53; Kedougou:2.2/2.0 for msp 1/2) than from sites in Nigeria (Gbagada: 1.39/1.96; Oredo: 1.35/1.75]). The heterozygosity of msp 1 gene was higher in P. falciparum isolates from Senegal (Thies: 0.62; Kedougou: 0.53) than isolates from Nigeria (Gbagada: 0.55; Oredo: 0.50). In Senegal, K1 alleles were associated with heavy (28) than with moderate (18) infections, in Nigeria however, equal proportions of K1 were observed in both infection types. The IC3D7 subtype allele of the msp 2 family showed high occurrence in heavily infected individuals from both countries (Senegal- 32; Nigeria- 26) than in the moderately infected participants. Conclusion: With the unusual high genetic diversity obtained in low endemic setting in Senegal and low genetic diversity in a high endemic Nigerian setting, multiple holistic approach should be employed in evaluating the actual transmission of a place in order to effectively direct control measures.

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Already at the bottom? Demographic declines are unlikely further to undermine genetic diversity of a large Arctic ungulate: muskox, Ovibos moschatus (Artiodactyla: Bovidae)

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blz175 ◽

2019 ◽

Vol 129 (2) ◽

pp. 459-469

Author(s):

Erin Prewer ◽

Susan Kutz ◽

Lisa Marie Leclerc ◽

Christopher J Kyle

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Allelic Richness ◽

Evolutionary Potential ◽

Ovibos Moschatus ◽

Low Genetic Diversity ◽

Expected Heterozygosity ◽

Large Populations ◽

Victoria Island ◽

Demographic Patterns

Abstract Low genetic diversity is associated with low fitness and evolutionary potential, yet the demographic and life-history traits of some species contribute to low genetic diversity, without empirical evidence of negative impacts on fitness. Modelling past and future trajectories of genetic diversity under different demographic scenarios can provide insight into how genetic variation might impact population fitness. The muskox is an Arctic species that has undergone multiple population bottlenecks and, although populations have rebounded repeatedly, two large populations have recently declined by > 50%. It is unclear how these demographic patterns influence muskox genetic diversity and fitness. We compared the genetic diversity of Canadian muskox populations undergoing opposing population trends. Genotyping 84 mainland and 244 Victoria Island individuals at ten microsatellite loci revealed low genetic variation (Victoria Island, mean allelic richness 1.66, expected heterozygosity 0.16; mainland, mean allelic richness 2.58, expected heterozygosity 0.41), with no evidence of further reductions in diversity subsequent to recent demographic declines. Bayesian modelling showed that a 1900s bottleneck contributed to the lack of diversity in contemporary populations, and forward-in-time simulations suggested little effect on genetic diversity over the next 100 years. Muskoxen might have reached a genetic diversity minimum, and additional research will be needed to determine their capacity to adapt to rapid changes in selective pressures in a rapidly changing Arctic.

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Microsatellite analysis of pacu broodstocks used in the stocking program of Paranapanema River, Brazil

Scientia Agricola ◽

10.1590/s0103-90162011000300006 ◽

2011 ◽

Vol 68 (3) ◽

pp. 308-313 ◽

Cited By ~ 4

Author(s):

Jayme Aparecido Povh ◽

Ricardo Pereira Ribeiro ◽

Nelson Mauricio Lopera-Barrero ◽

Carolina Bespalhok Jacometo ◽

Lauro Vargas ◽

...

Keyword(s):

Genetic Diversity ◽

Null Allele ◽

Gene Diversity ◽

Genetic Difference ◽

Low Frequency ◽

Bottleneck Effect ◽

Reproductive Management ◽

The Mean ◽

Positive Coefficients ◽

Recent Bottleneck

Monitoring the genetic diversity has fundamental importance for fish stocking programs. This experiment aims to evaluate the genetic diversity in two hatchery stations (A and B) with pacu Piaractus mesopotamicus (Holmberg, 1887) in Andirá, state of Paraná, Brazil used in stocking programs of Paranapanema River. Six microsatellite loci were amplified using DNA extracted from 60 fin-clipping samples. The broodstock B had the average number of alleles and the mean heterozygosity (alleles: 3.7 and H O: 0.628) higher than the broodstock A (alleles: 3.5 and H O: 0.600). Alleles with low frequency levels were observed in the both broodstocks. The positive coefficients of endogamy in the locus Pme2 (broodstock A: F IS = 0.30 and broodstock B: F IS = 0.20), Pme5 (broodstock B: F IS = 0.15), Pme14 (broodstock A: F IS = 0.07) and Pme28 (broodstock A: F IS = 0.24 and broodstock B: F IS = 0.20) indicated deficiency of heterozygotes. Presence of null allele in the locus Pme2 was detected. The negative estimates in loci Pme4 (broodstock A: F IS = - 0.43 and broodstock B: F IS = - 0.37), Pme5 (broodstock A: F IS= - 0.11), Pme14 (broodstock B: F IS= - 0.15) and Pme32 (broodstock A: F IS = - 0.93 and broodstock B: F IS = - 0.60) were indicating the excess of heterozygotes. Evidence of linkage disequilibrium and lower allelic richness was found only in the broodstock A. Nei's gene diversity was high in both broodstocks. The genetic distance (0.085) and identity (0.918) showed similarity between broodstocks, which reflects a possible common origin. 6.05% of the total genetic variance was due to differences among broodstocks. Recent bottleneck effect in two broodstocks was observed. The results indicated a higher genetic diversity in the two broodstocks and they presented low genetic difference. This was caused by the reproductive management in both hatchery stations, reduction of population size and genetic exchange between the hatchery stations.

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Genetic diversity of Plasmodium falciparum populations in three malaria transmission settings in Madagascar

Malaria Journal ◽

10.1186/s12936-021-03776-1 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Fanomezantsoa Ralinoro ◽

Tovonahary Angelo Rakotomanga ◽

Rianasoambolanoro Rakotosaona ◽

Danielle A. Doll Rakoto ◽

Didier Menard ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Malaria Transmission ◽

Nested Pcr ◽

Drug Efficacy ◽

Control Measures ◽

Epidemiological Strata ◽

Allele Specific ◽

The Impact ◽

Pcr Targeting

Abstract Background Assessment of the genetic diversity of Plasmodium falciparum parasites from various malaria transmission settings could help to define tailored local strategies for malaria control and elimination. Such assessments are currently scarce in Madagascar. The study presented here aimed to bridge this gap by investigating the genetic diversity of P. falciparum populations in three epidemiological strata (Equatorial, Tropical and Fringes) in Madagascar. Methods Two-hundred and sixty-six P. falciparum isolates were obtained from patients with uncomplicated malaria enrolled in clinical drug efficacy studies conducted at health centres in Tsaratanana (Equatorial stratum), Antanimbary (Tropical stratum) and Anjoma Ramartina (Fringes) in 2013 and 2016. Parasite DNA was extracted from blood samples collected before anti-malarial treatment. Plasmodium species were identified by nested PCR targeting the 18 S rRNA gene. The genetic profiles of P. falciparum parasites were defined by allele-specific nested PCR on the polymorphic regions of the msp-1 and msp-2 genes. Results Fifty-eight alleles were detected in the P. falciparum samples tested: 18 alleles for msp-1 and 40 for msp-2. K1 (62.9%, 139/221) and FC27 (69.5%, 114/164) were the principal msp-1 and msp-2 allele families detected, although the proportions of the msp-1 and msp-2 alleles varied significantly between sites. Polyclonal infections were more frequent at sites in the Equatorial stratum (69.8%) than at sites in the Tropical stratum (60.5%) or Fringes (58.1%). Population genetics analyses showed that genetic diversity was similar between sites and that parasite flow within sites was limited. Conclusions This study provides recent information about the genetic diversity of P. falciparum populations in three transmission strata in Madagascar, and valuable baseline data for further evaluation of the impact of the control measures implemented in Madagascar.

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Mechanisms that may lead to high genetic divergence and to the invasive success of tall fleabane (Conyza sumatrensis; Asteraceae)

Weed Science ◽

10.1017/wsc.2021.59 ◽

2021 ◽

pp. 1-15

Author(s):

Maycon Rodrigo Ruiz ◽

Claudete Aparecida Mangolin ◽

Rubem Silvério de Oliveira ◽

Rafael Romero Mendes ◽

Hudson Kagueyama Takano ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Genetic Divergence ◽

Glyphosate Resistance ◽

Climatic Conditions ◽

Agricultural Fields ◽

Bottleneck Effect ◽

Low Genetic Diversity ◽

Expected Heterozygosity ◽

Different Levels

Abstract Tall fleabane [Conyza sumatrensis (Retz.) E. Walker] is commonly invasive in agricultural fields, reducing yield in various infested crops. The current study investigates the genetic diversity within and between a significant number of invasive C. sumatrensis biotypes in soybean fields in southern, southeastern, and midwestern Brazil, using microsatellites as molecular markers. High and low observed and expected heterozygosity estimated in microsatellite loci supported our hypothesis that different levels of genetic diversity may be detected within biotypes from different invaded fields. Analysis of a significant number of biotypes in several fields showed high and low genetic diversity not associated with geographic distribution, bottleneck effect, or susceptibility to glyphosate. A deficit of heterozygous plants, high genetic divergence, and moderate allelic transference were also observed. Allelic fixation was different in the different biotypes. The bottleneck effect was seen in biotypes with reduced genetic diversity and in biotypes with the highest genetic diversity. Data on genetic diversity, bottleneck effect, and glyphosate resistance showed contrasts in biotypes from nearby invaded fields. Our study showed different genetic diversity levels in biotypes from invaded areas under the same climatic conditions.

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Genetic Diversity Block 2 of Surface Protein-1 in Plasmodium Falciparum Merozoite by Nested-PCR Method in Southeastern Iran

Medical Laboratory Journal ◽

10.18869/acadpub.mlj.9.4.1 ◽

2015 ◽

Vol 9 (4) ◽

pp. 1-5

Author(s):

Adel Ebrahimzadeh ◽

Tahereh Davoodi ◽

Abbas Pashaei Naghadeh ◽

◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Nested Pcr ◽

Surface Protein ◽

Falciparum Merozoite ◽

Pcr Method

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Genetic Diversity Analysis of Surface-Related Antigen (SRA) in Plasmodium falciparum Imported From Africa to China

Frontiers in Genetics ◽

10.3389/fgene.2021.688606 ◽

2021 ◽

Vol 12 ◽

Author(s):

Bo Yang ◽

Hong Liu ◽

Qin-Wen Xu ◽

Yi-Fan Sun ◽

Sui Xu ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Amino Acid ◽

Migrant Workers ◽

Vaccine Development ◽

Vaccine Candidate ◽

Haplotype Diversity ◽

Low Genetic Diversity ◽

Neutrality Tests ◽

Unique Amino Acid

Plasmodium falciparum surface-related antigen (SRA) is located on the surfaces of gametocyte and merozoite and has the structural and functional characteristics of potential targets for multistage vaccine development. However, little information is available regarding the genetic polymorphism of pfsra. To determine the extent of genetic variation about P. falciparum by characterizing the sra sequence, 74 P. falciparum samples were collected from migrant workers who returned to China from 12 countries of Africa between 2015 and 2019. The full length of the sra gene was amplified and sequenced. The average pairwise nucleotide diversities (π) of P. falciparum sra gene was 0.00132, and the haplotype diversity (Hd) was 0.770. The average number of nucleotide differences (k) for pfsra was 3.049. The ratio of non-synonymous (dN) to synonymous (dS) substitutions across sites (dN/dS) was 1.365. Amino acid substitutions of P. falciparum SRA could be categorized into 35 unique amino acid variants. Neutrality tests showed that the polymorphism of PfSRA was maintained by positive diversifying selection, which indicated its role as a potential target of protective immune responses and a vaccine candidate. Overall, the ability of the N-terminal of PfSRA antibodies to evoke inhibition of merozoite invasion of erythrocytes and conserved amino acid at low genetic diversity suggest that the N-terminal of PfSRA could be evaluated as a vaccine candidate against P. falciparum infection.

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