Genetic diversity of  Plasmodium falciparum  in Grande Comore Island

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Background

Despite several control interventions resulting in a considerable decrease in malaria prevalence in the Union of the Comoros, the disease remains a public health problem with high transmission in Grande Comore compared to neighbouring islands. In this country, only a few studies investigating the genetic diversity of Plasmodium falciparum have been performed so far. For this reason, this study aims to examine the genetic diversity of P. falciparum by studying samples collected in Grande Comore in 2012 and 2013, using merozoite surface protein 1 ( msp1), merozoite surface protein 2 ( msp2) and single nucleotide polymorphism (SNP) genetic markers.

Methods

A total of 162 positive rapid diagnostic test (RDT) samples from Grande Comore were used to extract parasite DNA. Allelic families K1, Mad20 and RO33 of the msp1 gene as well as allelic families IC3D7 and FC37 of the msp2 gene were determined by using nested PCR. Additionally, 50 out of 151 samples were genotyped to study 24 SNPs by using high resolution melting (HRM).

Results

Two allelic families were predominant, the K1 family of msp1 gene (55%) and the FC27 family of msp2 gene (47.4%). Among 50 samples genotyped for 24 SNPs, 42 (84%) yielded interpretable results. Out of these isolates, 36 (85%) were genetically unique and 6 (15%) grouped into two clusters. The genetic diversity of P. falciparum calculated from msp1 and msp2 genes and SNPs was 0.82 and 0.61, respectively.

Conclusion

In summary, a large genetic diversity of P. falciparum was observed in Grande Comore. This may favour persistence of malaria and might be one of the reasons for the high malaria transmission compared to neighbouring islands. Further surveillance of P. falciparum isolates, mainly through environmental management and vector control, is warranted until complete elimination is attained.

Related collections

Most cited references 23

Record: found
Abstract: found
Article: not found

Estimation of average heterozygosity and genetic distance from a small number of individuals.

M Nei (1978)

The magnitudes of the systematic biases involved in sample heterozygosity and sample genetic distances are evaluated, and formulae for obtaining unbiased estimates of average heterozygosity and genetic distance are developed. It is also shown that the number of individuals to be used for estimating average heterozygosity can be very small if a large number of loci are studied and the average heterozygosity is low. The number of individuals to be used for estimating genetic distance can also be very small if the genetic distance is large and the average heterozygosity of the two species compared is low.

0 comments Cited 1216 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum.

T. J. Anderson, B Haubold, J T Williams … (2000)

Multilocus genotyping of microbial pathogens has revealed a range of population structures, with some bacteria showing extensive recombination and others showing almost complete clonality. The population structure of the protozoan parasite Plasmodium falciparum has been harder to evaluate, since most studies have used a limited number of antigen-encoding loci that are known to be under strong selection. We describe length variation at 12 microsatellite loci in 465 infections collected from 9 locations worldwide. These data reveal dramatic differences in parasite population structure in different locations. Strong linkage disequilibrium (LD) was observed in six of nine populations. Significant LD occurred in all locations with prevalence <1% and in only two of five of the populations from regions with higher transmission intensities. Where present, LD results largely from the presence of identical multilocus genotypes within populations, suggesting high levels of self-fertilization in populations with low levels of transmission. We also observed dramatic variation in diversity and geographical differentiation in different regions. Mean heterozygosities in South American countries (0.3-0.4) were less than half those observed in African locations (0. 76-0.8), with intermediate heterozygosities in the Southeast Asia/Pacific samples (0.51-0.65). Furthermore, variation was distributed among locations in South America (F:(ST) = 0.364) and within locations in Africa (F:(ST) = 0.007). The intraspecific patterns of diversity and genetic differentiation observed in P. falciparum are strikingly similar to those seen in interspecific comparisons of plants and animals with differing levels of outcrossing, suggesting that similar processes may be involved. The differences observed may also reflect the recent colonization of non-African populations from an African source, and the relative influences of epidemiology and population history are difficult to disentangle. These data reveal a range of population structures within a single pathogen species and suggest intimate links between patterns of epidemiology and genetic structure in this organism.

0 comments Cited 307 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking

Caroline Daniels, Sarah K Volkman, Danny A. Milner … (2008)

Background Single nucleotide polymorphism (SNP) genotyping provides the means to develop a practical, rapid, inexpensive assay that will uniquely identify any Plasmodium falciparum parasite using a small amount of DNA. Such an assay could be used to distinguish recrudescence from re-infection in drug trials, to monitor the frequency and distribution of specific parasites in a patient population undergoing drug treatment or vaccine challenge, or for tracking samples and determining purity of isolates in the laboratory during culture adaptation and sub-cloning, as well as routine passage. Methods A panel of twenty-four SNP markers has been identified that exhibit a high minor allele frequency (average MAF > 35%), for which robust TaqMan genotyping assays were constructed. All SNPs were identified through whole genome sequencing and MAF was estimated through Affymetrix array-based genotyping of a worldwide collection of parasites. These assays create a "molecular barcode" to uniquely identify a parasite genome. Results Using 24 such markers no two parasites known to be of independent origin have yet been found to have the same allele signature. The TaqMan genotyping assays can be performed on a variety of samples including cultured parasites, frozen whole blood, or whole blood spotted onto filter paper with a success rate > 99%. Less than 5 ng of parasite DNA is needed to complete a panel of 24 markers. The ability of this SNP panel to detect and identify parasites was compared to the standard molecular methods, MSP-1 and MSP-2 typing. Conclusion This work provides a facile field-deployable genotyping tool that can be used without special skills with standard lab equipment, and at reasonable cost that will unambiguously identify and track P. falciparum parasites both from patient samples and in the laboratory.

0 comments Cited 124 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

Nasserdine Papa Mze:

ORCID: http://orcid.org/0000-0002-1415-4882

npapamze@gmail.com

Ambroise D. Ahouidi: aahouidi@gmail.com

Journal

Journal ID (nlm-ta): Malar J

Journal ID (iso-abbrev): Malar. J

Title: Malaria Journal

Publisher: BioMed Central (London )

ISSN (Electronic): 1475-2875

Publication date (Electronic): 3 September 2020

Publication date PMC-release: 3 September 2020

Publication date Collection: 2020

Volume: 19

Electronic Location Identifier: 320

Affiliations

[1 ]GRID grid.413774.2, ISNI 0000 0004 0622 016X, Laboratory of Bacteriology-Virology, , Hospital Aristide Le Dantec, ; BP 7325 Dakar, Senegal

[2 ]Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formations, Arrondissement 4 Rue 2D1 Pôle Urbain de Diamniadio, Dakar, Senegal

[3 ]Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France

[4 ]GRID grid.483853.1, ISNI 0000 0004 0519 5986, IHU-Méditerranée Infection, ; Marseille, France

[5 ]Laboratory of National Malaria Control Program, Moroni, Comoros

[6 ]GRID grid.418221.c, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, , Unité Parasitologie et Entomologie, ; Marseille, France

[7 ]Centre National de Référence du Paludisme, Marseille, France

[8 ]GRID grid.4714.6, ISNI 0000 0004 1937 0626, Karolinska Institutet, ; Berzelius väg 3, 17177 Stockholm, Sweden

[9 ]GRID grid.47100.32, ISNI 0000000419368710, Department of Epidemiology of Microbial Diseases, , Yale School of Public Health, ; New Haven, CT 06510 USA

[10 ]GRID grid.66859.34, Broad Institute: The Broad Institute of MIT and Harvard, ; Cambridge, MA 02142 USA

Author information

Nasserdine Papa Mze http://orcid.org/0000-0002-1415-4882

Article

Publisher ID: 3384

DOI: 10.1186/s12936-020-03384-5

PMC ID: 7469287

PubMed ID: 32883282

SO-VID: d65b0ac1-5d00-408e-a390-29f1a5bf7bbd

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.