scholarly journals Mitochondrial DNA from the eradicated European Plasmodium vivax and P. falciparum from 70-year-old slides from the Ebro Delta in Spain

2016 ◽  
Vol 113 (41) ◽  
pp. 11495-11500 ◽  
Author(s):  
Pere Gelabert ◽  
Marcela Sandoval-Velasco ◽  
Iñigo Olalde ◽  
Rosa Fregel ◽  
Adrien Rieux ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Plasmodium Vivax ◽  
Dried Blood Spots ◽  
Ebro Delta ◽  
American Continent ◽  
European Isolate ◽  
Dna Yield ◽  
Human Genomic ◽  
Outstanding Question ◽  
Historical Accounts

Phylogenetic analysis of Plasmodium parasites has indicated that their modern-day distribution is a result of a series of human-mediated dispersals involving transport between Africa, Europe, America, and Asia. A major outstanding question is the phylogenetic affinity of the malaria causing parasites Plasmodium vivax and falciparum in historic southern Europe—where it was endemic until the mid-20th century, after which it was eradicated across the region. Resolving the identity of these parasites will be critical for answering several hypotheses on the malaria dispersal. Recently, a set of slides with blood stains of malaria-affected people from the Ebro Delta (Spain), dated between 1942 and 1944, have been found in a local medical collection. We extracted DNA from three slides, two of them stained with Giemsa (on which Plasmodium parasites could still be seen under the microscope) and another one consisting of dried blood spots. We generated the data using Illumina sequencing after using several strategies aimed at increasing the Plasmodium DNA yield: depletion of the human genomic (g)DNA content through hybridization with human gDNA baits, and capture-enrichment using gDNA derived from P. falciparum. Plasmodium mitochondrial genome sequences were subsequently reconstructed from the resulting data. Phylogenetic analysis of the eradicated European P. vivax mtDNA genome indicates that the European isolate is closely related to the most common present-day American haplotype and likely entered the American continent post-Columbian contact. Furthermore, the European P. falciparum mtDNA indicates a link with current Indian strains that is in agreement with historical accounts.

scholarly journals Assessing Quality and Functionality of DNA from Fresh and Archival Dried Blood Spots and Recommendations for Quality Control Guidelines

2007 ◽  
Vol 53 (8) ◽  
pp. 1401-1407 ◽  
Author(s):  
Malin Ida Linnea Sjöholm ◽  
Joakim Dillner ◽  
Joyce Carlson
Keyword(s):  
Dna Extraction ◽  
Multiple Displacement Amplification ◽  
Dried Blood Spots ◽  
Extraction Methods ◽  
Population Based ◽  
Alkaline Lysis ◽  
Screening Programs ◽  
Blood Spots ◽  
Dna Yield ◽  
Chelex 100

Abstract Background: Dried blood spots (DBS) are a convenient and inexpensive method for biobanking. Although many countries have established population-based DBS biobanks from neonatal screening programs, the quality and usefulness of DNA from DBS have not been extensively assessed. Methods: We compared 4 common DNA extraction methods (Qiagen, EZNA, Chelex 100, and alkaline lysis) in a pilot study using fresh DBS with known lymphocyte count. We assessed suitability for multiple displacement amplification (MDA) and subsequent single-nucleotide polymorphism (SNP) analyses. We selected the EZNA method for DNA extraction from archival samples up to 27 years old, stored at room temperature or −20 °C, and SNP analyses were performed after MDA. Results: Extraction using alkaline lysis failed in most tests, and Chelex 100 was unsuccessful in real-time PCR, whereas the EZNA and Qiagen methods were successful by all evaluated quality indices. DNA extraction by EZNA, MDA, and SNP analyses were successful for the archival samples stored at −20 °C. Conclusion: Routine protocols for evaluation of the quality and functional integrity of DNA based on DNA yield, DNA size, and quantification of amplifiable DNA allow use of sufficient template for MDA and successful SNP analyses from both primary DBS extract and MDA product. A single 3-mm disc can yield sufficient DNA for several thousand SNP analyses. DNA from DBS is thus suitable for genetic epidemiology studies.

scholarly journals Missed Plasmodium falciparum and Plasmodium vivax Mixed Infections in Ethiopia Threaten Malaria Elimination

2021 ◽  
Author(s):  
Colleen M. Leonard ◽  
Hussein Mohammed ◽  
Mekonnen Tadesse ◽  
Jessica N. McCaffery ◽  
Doug Nace ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Plasmodium Falciparum ◽  
Lactate Dehydrogenase ◽  
Plasmodium Vivax ◽  
Therapeutic Efficacy ◽  
Dried Blood Spots ◽  
Mixed Infections ◽  
Efficacy Study ◽  
Chain Reaction ◽  
Polymerase Chain

Plasmodium falciparum and Plasmodium vivax are co-endemic in Ethiopia. This study investigated whether mixed infections were missed by microscopy from a 2017 therapeutic efficacy study at two health facilities in Ethiopia. All patients (N = 304) were initially classified as having single-species P. falciparum (n = 148 samples) or P. vivax infections (n = 156). Dried blood spots were tested for Plasmodium antigens by bead-based multiplex assay for pan-Plasmodium aldolase, pan-Plasmodium lactate dehydrogenase, P. vivax lactate dehydrogenase, and histidine-rich protein 2. Of 304 blood samples, 13 (4.3%) contained both P. falciparum and P. vivax antigens and were analyzed by polymerase chain reaction for species-specific DNA. Of these 13 samples, five were confirmed by polymerase chain reaction for P. falciparum/P. vivax co-infection. One sample, initially classified as P. vivax by microscopy, was found to only have Plasmodium ovale DNA. Plasmodium falciparum/P. vivax mixed infections can be missed by microscopy even in the context of a therapeutic efficacy study with multiple trained readers.

Assessment of DNA contamination from dried blood spots and determination of DNA yield and function using archival newborn dried blood spots

2009 ◽  
Vol 402 (1-2) ◽  
pp. 107-113 ◽  
Author(s):  
Suzanne K. Cordovado ◽  
Marie C. Earley ◽  
Miyono Hendrix ◽  
Rena Driscoll-Dunn ◽  
Michael Glass ◽  
...  
Keyword(s):  
Dried Blood Spots ◽  
Blood Spots ◽  
Dna Yield ◽  
Dna Contamination ◽  
And Function

scholarly journals Ancient Yersinia pestis genomes provide no evidence for the origins or spread of the Justinianic Plague

2019 ◽  
Author(s):  
Marcel Keller ◽  
Maria A. Spyrou ◽  
Michael McCormick ◽  
Kirsten I. Bos ◽  
Alexander Herbig ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Yersinia Pestis ◽  
Red Sea ◽  
Historical Context ◽  
Black Death ◽  
Archaeological Remains ◽  
Eurasian Steppe ◽  
Human Genomes ◽  
Historical Accounts ◽  
The Silk Road

AbstractAlong with the publication of 137 ancient human genomes retrieved from archaeological remains of the Eurasian steppe, Damgaard et al., 2018 identified two individuals infected with Yersinia pestis, yielding one genome with 0.24x average coverage (DA147, 6th–9th c. AD) and another with 8.7x (DA101, 2nd–3rd c. AD). A phylogenetic analysis performed on the latter placed it in a position ancestral to a 6th-century Justinianic genome from Aschheim, Germany. These results are used to fuel an argument that the Justinianic Plague (541–544 AD) “was brought to Europe towards the end of the Hunnic period through the Silk Road along the southern fringes of the steppes” in contrast to the leading hypothesis of introduction via the Red Sea that is supported by historical accounts. In our reanalysis, we question the contested historical context of the presented genomes with the Justinianic Plague and show that the lower coverage genome might be rather related to the Black Death (1346–1353 AD).

Bluetongue virus in South America: current status based on phylogenetic analysis

2021 ◽  
Author(s):  
Danilo Legisa ◽  
Maria José Dus Santos
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
South America ◽  
Bluetongue Virus ◽  
Phylogenetic Analyses ◽  
Current Status ◽  
Accurate Information ◽  
South American ◽  
American Continent ◽  
Genetic Continuity

Bluetongue (BT) is an insect-borne disease affecting domestic and wild ruminants. Bluetongue virus (BTV) is the causative agent of the BT disease. BT outbreaks have been widely recorded worldwide. However, in the South American subcontinent, accurate information about the disease and molecular epidemiology is still lacking because little effort has been made to cover the region. This study comprises an exhaustive phylogenetic analysis including all BTV sequences available in databases and reports new Argentinean sequences for Seg 8 and Seg 9. Maximum-likelihood phylogenetic analyses were conducted for Seg 2, Seg 3, Seg 6, Seg 7, Seg 8, Seg 9 and Seg 10. Throughout the study, wide circulation and genetic continuity along the American continent were detected. Also, reassortment events are reported, and the historical virus introduction path into and through South America is suggested.

scholarly journals An Efficiency Human Genomic DNA Extraction from Dried Blood Spots

2011 ◽  
Vol 8 ◽  
pp. 179-185 ◽  
Author(s):  
Nguyen Thi Hue ◽  
Phan Tuan Phong ◽  
Nguyen Dieu Hoai Chan ◽  
Nguyen Khac Han Hoan ◽  
Huynh Thi Thu Thuy
Keyword(s):  
Dna Extraction ◽  
Genomic Dna ◽  
Dried Blood Spots ◽  
Genomic Dna Extraction ◽  
Blood Spots ◽  
Human Genomic ◽  
Human Genomic Dna

scholarly journals High frequency of the Duffy-negative genotype and absence of Plasmodium vivax infections in Ghana

2020 ◽  
Author(s):  
Charles Brown ◽  
Prince Pappoe-Ashong ◽  
Nancy Duah ◽  
Anita Ghansah ◽  
Harry Asmah ◽  
...  
Keyword(s):  
Plasmodium Vivax ◽  
High Frequency ◽  
Dried Blood Spots ◽  
Small Subunit ◽  
Host Susceptibility ◽  
Rrna Genes ◽  
Pcr Analysis ◽  
Small Subunit Rrna ◽  
Nested Polymerase Chain Reaction ◽  
Duffy Negative

Abstract Background The Duffy-negative phenotype is a condition which is thought to confer complete resistance against blood infection with Plasmodium vivax. However, recent studies from different malaria-endemic regions including western Africa have now shown that P. vivax can infect red blood cells (RBCs) and cause clinical disease in Duffy-negative people. The actual prevalence of P. vivax in local populations in Ghana is unknown. In addition, little information is available about the distribution of Duffy genotypes in Ghana. We determined the prevalence of P. vivax and the distribution of Duffy genotypes in Ghana. Methods DNA was extracted from dried blood spots (DBS) collected from 952 subjects (845 malaria patients and 107 asymptomatic persons) from nine locations in Ghana. Plasmodium species identification was carried out by nested polymerase chain reaction (PCR) amplification of the small-subunit rRNA genes; P. vivax was further characterized by PCR analysis of the central region of the Pvcsp gene. Duffy blood group genotyping was performed by PCR with sequence-specific primers (PCR-SSP) to detect the presence of the FYES allele. Results No cases of P. vivax were detected in any of the samples by both PCR methods used. Majority of infections (542, 94.8%) in the malaria patient samples were due to P. falciparum with only 1 infection (0.0017%) and 2 infections (0.0034%) due to P. malariae and P. ovale, respectively. No case of mixed infection was identified. Of the samples tested for the FYES allele from all the sites, 90.5% (862/952) had the FYES allele. All positive samples were genotyped as FY*B-33/FY*B-33 (Duffy-negative homozygous) and therefore classified as Fy(a-b-). Conclusions No cases of P. vivax were detected by both PCRs and 90.5% of the subjects tested carried the FYES allele. The lack of P. vivax infections observed can be attributed to the high frequency of the FYES allele that silences erythroid expression of the Duffy. These results provide insights on the host susceptibility for P. vivax infections that has before not been investigated in Ghana.

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