scholarly journals A PCR-Based Technique to Track the Geographic Origin of Plasmodium falciparum With 23-SNP Barcode Analysis

2021 ◽  
Vol 9 ◽  
Author(s):  
Fengyue Hu ◽  
Qicheng Zou ◽  
Yinyue Li ◽  
Guoding Zhu ◽  
Huayun Zhou ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Sequence Data ◽  
Geographic Origin ◽  
Central Africa ◽  
Single Nucleotide ◽  
Organellar Genomes ◽  
Trace Back ◽  
Data Gaps ◽  
Polymerase Chain ◽  
Imported Infections

Increased population movement has increased the risk of reintroducing parasites to elimination areas and also dispersing drug-resistant parasites to new regions. Therefore, reliable and repeatable methods to trace back to the source of imported infections are essential. The recently developed 23-single-nucleotide polymorphism (SNP) barcode from organellar genomes of mitochondrion (mt) and apicoplast (apico) provides a valuable tool to locate the geographic origin of Plasmodium falciparum. This study aims to explore the feasibility of using the 23-SNP barcode for tracking P. falciparum by polymerase chain reaction and sequencing, while providing geographical haplotypes of isolates that originated from Central Africa. Based on 23-SNP barcode analysis, SNPs were found at seven loci; 27 isolates were confirmed to have originated in West Africa, and this study also showed four isolates from Central Africa (Equatorial Guinea, 3; Republic of Congo, 1) that originated in East Africa. This study provides the sequence data from Central Africa and fills 23-SNP barcode data gaps of sample origins.

scholarly journals Investigation of polymorphisms in the P. falciparum artemisinin resistance marker kelch13 in asymptomatic infections in a rural area of Cameroon

2017 ◽  
Author(s):  
Innocent Safeukui ◽  
Jerome Fru-Cho ◽  
Alassane Mbengue ◽  
Niraja Suresh ◽  
Dieudonne L. Njimoh ◽  
...  
Keyword(s):  
Plasma Levels ◽  
Central Africa ◽  
Artemisinin Resistance ◽  
Cross Sectional Study ◽  
Asymptomatic Infection ◽  
Cross Sectional ◽  
Single Nucleotide ◽  
Molecular Surveillance ◽  
Polymerase Chain ◽  
Asymptomatic Infections

AbstractBackgroundThe genetic variability of the artemisinin resistance (AR) molecular marker kelch13 (k13) has been extensively investigated in Plasmodium falciparum malaria parasites from symptomatic infections in South East (SE) Asia where AR is highly prevalent, as well as in Africa where evidence of AR has emerged only recently. However, molecular surveillance and risk of transmission of AR also require monitoring asymptomatic infection. Here, molecular analyses were used to investigate polymorphisms in k13 and their potential for transmission in asymptomatic adults in Bolifamba, Cameroon in Central Africa.MethodsUsing polymerase chain reaction (PCR), we amplified and sequenced the full length of k13 from P. falciparum infections detected in the blood of 33 asymptomatic adults (age: 18-55 years-old) collected in a cross-sectional study from July 2008 to October 2009. Risk of increased transmission was assessed by quantifying gametocytes by qPCR. Quantitative ELISA was used to detect plasma levels of PfHRP2 to establish total parasite burdens associated with asymptomatic infection.ResultsOut of 33 isolates tested, 14 (42.4%) presented at least one single nucleotide polymorphism (SNP) in k13. Five non-synonymous SNPs were detected (K189T/N, N217H, R393K and E433K). None were located in the ß-propeller domain, where AR mutations have been detected in both SE Asian and, more recently, African parasites. K189T/N and N217H have been previously reported in African strains, but R393K and E433K are new polymorphisms. Gametocytes were detected in 24.2% of infections, without significant association with detected k13 polymorphisms. Notably, polymorphisms outside of the ß-propeller domain detected in k13 were associated with a significant increase of PfHRP2 plasma levels but not circulating parasite levels detected by qPCR.ConclusionsThis study provides the baseline prevalence of k13 polymorphisms in asymptomatic infection for molecular surveillance in tracking AR. Unexpectedly, it also suggests association of k13 polymorphisms outside of the ß-propeller domain with total P. falciparum burden in asymptomatic infection, that needs to be validated in future studies.

scholarly journals Epidemiology and Genetic Variability of HHV-8/KSHV among Rural Populations and Kaposi’s Sarcoma Patients in Gabon, Central Africa. Review of the Geographical Distribution of HHV-8 K1 Genotypes in Africa

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 175
Author(s):  
Antony Idam Mamimandjiami ◽  
Augustin Mouinga-Ondémé ◽  
Jill-Léa Ramassamy ◽  
Délia Doreen Djuicy ◽  
Philippe V. Afonso ◽  
...  
Keyword(s):  
Kaposi's Sarcoma ◽  
Molecular Diversity ◽  
Central Africa ◽  
Human Herpesvirus ◽  
Kaposi’S Sarcoma ◽  
Buffy Coat ◽  
Rural Populations ◽  
Herpesvirus 8 ◽  
Nuclear Antigens ◽  
Polymerase Chain

Human herpesvirus 8 (HHV-8) is the etiological agent of all forms of Kaposi’s sarcoma (KS). K1 gene studies have identified five major molecular genotypes with geographical clustering. This study described the epidemiology of HHV-8 and its molecular diversity in Gabon among Bantu and Pygmy adult rural populations and KS patients. Plasma antibodies against latency-associated nuclear antigens (LANA) were searched by indirect immunofluorescence. Buffy coat DNA samples were subjected to polymerase chain reaction (PCR) to obtain a K1 gene fragment. We studied 1020 persons; 91% were Bantus and 9% Pygmies. HHV-8 seroprevalence was 48.3% and 36.5% at the 1:40 and 1:160 dilution thresholds, respectively, although the seroprevalence of HHV-8 is probably higher in Gabon. These seroprevalences did not differ by sex, age, ethnicity or province. The detection rate of HHV-8 K1 sequence was 2.6% by PCR. Most of the 31 HHV-8 strains belonged to the B genotype (24), while the remaining clustered within the A5 subgroup (6) and one belonged to the F genotype. Additionally, we reviewed the K1 molecular diversity of published HHV-8 strains in Africa. This study demonstrated a high seroprevalence of HHV-8 in rural adult populations in Gabon and the presence of genetically diverse strains with B, A and also F genotypes.

scholarly journals A Cotton-Fiber-Associated Cyclin-Dependent Kinase A Gene: Characterization and Chromosomal Location

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Weifan Gao ◽  
Sukumar Saha ◽  
Din-Pow Ma ◽  
Yufang Guo ◽  
Johnie N. Jenkins ◽  
...  
Keyword(s):  
Cotton Fiber ◽  
Sequence Data ◽  
Snp Markers ◽  
Pcr Analysis ◽  
Cyclin Dependent Kinase ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Gene Characterization ◽  
Protein Levels ◽  
Catalytic Domains

A cotton fiber cDNA and its genomic sequences encoding an A-type cyclin-dependent kinase (GhCDKA) were cloned and characterized. The encoded GhCDKA protein contains the conserved cyclin-binding, ATP binding, and catalytic domains. Northern blot and RT-PCR analysis revealed that the GhCDKA transcript was high in 5–10 DPA fibers, moderate in 15 and 20 DPA fibers and roots, and low in flowers and leaves. GhCDKA protein levels in fibers increased from 5–15 DPA, peaked at 15 DPA, and decreased from 15 t0 20 DPA. The differential expression of GhCDKA suggested that the gene might play an important role in fiber development. The GhCDKA sequence data was used to develop single nucleotide polymorphism (SNP) markers specific for the CDKA gene in cotton. A primer specific to one of the SNPs was used to locate the CDKA gene to chromosome 16 by deletion analysis using a series of hypoaneuploid interspecific hybrids.

Associations between varied susceptibilities of PfATP4 inhibitors and genotypes in Ugandan Plasmodium falciparum isolates

2021 ◽  
Author(s):  
Oriana Kreutzfeld ◽  
Stephanie A. Rasmussen ◽  
Aarti A. Ramanathan ◽  
Patrick K. Tumwebaze ◽  
Oswald Byaruhanga ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Single Nucleotide Polymorphisms ◽  
Ex Vivo ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Single Nucleotide ◽  
Field Isolates ◽  
Frequent Mutations ◽  
Mixed Field ◽  
P Type

Among novel compounds under recent investigation as potential new antimalarial drugs are three independently developed inhibitors of the Plasmodium falciparum P-type ATPase (PfATP4): KAE609 (cipargamin), PA92, and SJ733. We assessed ex vivo susceptibilities to these compounds of 374 fresh P. falciparum isolates collected in Tororo and Busia districts, Uganda from 2016-2019. Median IC 50 s were 65 nM for SJ733, 9.1 nM for PA92, and 0.5 nM for KAE609. Sequencing of pfatp4 for 218 of these isolates demonstrated many non-synonymous single nucleotide polymorphisms; the most frequent mutations were G1128R (69% of isolates mixed or mutant), Q1081K/R (68%), G223S (25%), N1045K (16%) and D1116G/N/Y (16%). The G223S mutation was associated with decreased susceptibility to SJ733, PA92 and KAE609. The D1116G/N/Y mutations were associated with decreased susceptibility to SJ733, and the presence of mutations at both codons 223 and 1116 was associated with decreased susceptibility to PA92 and SJ733. In all of these cases, absolute differences in susceptibilities of wild type (WT) and mutant parasites were modest. Analysis of clones separated from mixed field isolates consistently identified mutant clones as less susceptible than WT. Analysis of isolates from other sites demonstrated presence of the G223S and D1116G/N/Y mutations across Uganda. Our results indicate that malaria parasites circulating in Uganda have a number of polymorphisms in PfATP4 and that modestly decreased susceptibility to PfATP4 inhibitors is associated with some mutations now present in Ugandan parasites.

scholarly journals Prevalence of congenital non syndromic hearing loss among offspring of consanguineous marriage: a pilot study

2020 ◽  
Vol 6 (5) ◽  
pp. 874
Author(s):  
Gangadhar K. S. ◽  
Geetha Bhaktha ◽  
Manjula B. ◽  
Nageshwari P.
Keyword(s):  
Hearing Loss ◽  
Consanguineous Marriage ◽  
Gene Encoding ◽  
Single Nucleotide ◽  
Junction Protein ◽  
Study Population ◽  
Syndromic Hearing Loss ◽  
Gap Junction Protein ◽  
Polymerase Chain ◽  
Recessive Defect

<p class="abstract"><strong>Background:</strong> Mutations in the gene encoding the gap-junction protein connexin-26, is understood to be the most important cause of non-syndromic hearing loss (NSHL). An attempt to identify the single nucleotide polymorphism (SNP) for W24X mutation was done.  Consanguineous marriage was seen among the NSHL subjects.</p><p class="abstract"><strong>Methods:</strong> SNP was identified using restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR).  Forty-five subjects were screened for congenital hearing loss. Twenty subjects matched the inclusion criteria and were included in the study.</p><p class="abstract"><strong>Results:</strong> 5 out of 20 subjects were found to have mutation i.e., 25%. Though consanguinity is known to cause autosomal recessive defect, the same could not be depicted in this study.</p><p class="abstract"><strong>Conclusions:</strong> 25% of the study population had a mutation in their gene and the rest though had consanguineous marriage had not been affected genotypically.</p>

scholarly journals Sequence variability ofChrysanthemum stunt viroidin different chrysanthemum cultivars

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2933 ◽  
Author(s):  
Hoseong Choi ◽  
Yeonhwa Jo ◽  
Ju-Yeon Yoon ◽  
Seung-Kook Choi ◽  
Won Kyong Cho
Keyword(s):  
Infectious Agents ◽  
Sequence Variability ◽  
Rt Pcr ◽  
Genome Sequences ◽  
Single Nucleotide ◽  
Genomic Variations ◽  
The Family ◽  
Chrysanthemum Plant ◽  
Single Nucleotide Variations ◽  
Polymerase Chain

Viroids are the smallest infectious agents, and their genomes consist of a short single strand of RNA that does not encode any protein.Chrysanthemum stunt viroid(CSVd), a member of the familyPospiviroidae, causes chrysanthemum stunt disease. Here, we report the genomic variations of CSVd to understand the sequence variability of CSVd in different chrysanthemum cultivars. We randomly sampled 36 different chrysanthemum cultivars and examined the infection of CSVd in each cultivar by reverse transcription polymerase chain reaction (RT-PCR). Eleven cultivars were infected by CSVd. Cloning followed by Sanger sequencing successfully identified a total of 271 CSVd genomes derived from 12 plants from 11 cultivars. They were further classified into 105 CSVd variants. Each single chrysanthemum plant had a different set of CSVd variants. Moreover, different single plants from the same cultivar had different sets of CSVd variants but identical consensus genome sequences. A phylogenetic tree using 12 consensus genome sequences revealed three groups of CSVd genomes, while six different groups were defined by the phylogenetic analysis using 105 variants. Based on the consensus CSVd genome, by combining all variant sequences, we identified 99 single-nucleotide variations (SNVs) as well as three nucleotide positions showing high mutation rates. Although 99 SNVs were identified, most CSVd genomes in this study were derived from variant 1, which is identical to known CSVd SK1 showing pathogenicity.

scholarly journals Prevalence of Mutations in the pfcoronin Gene and Association with Ex Vivo Susceptibility to Common Quinoline Drugs against Plasmodium falciparum

Pharmaceutics ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1273
Author(s):  
Océane Delandre ◽  
Mathieu Gendrot ◽  
Isabelle Fonta ◽  
Joel Mosnier ◽  
Nicolas Benoit ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Sanger Sequencing ◽  
Ex Vivo ◽  
Central Africa ◽  
Artemisinin Resistance ◽  
Current Data ◽  
Artemisinin Derivative ◽  
African Countries ◽  
Low Prevalence

Background: Artemisinin-based combination therapy (ACT) was recommended to treat uncomplicated falciparum malaria. Unlike the situation in Asia where resistance to ACT has been reported, artemisinin resistance has not yet emerged in Africa. However, some rare failures with ACT or patients continuing to be parasitaemic on day 3 after ACT treatment have been reported in Africa or in travellers returning from Africa. Three mutations (G50E, R100K, and E107V) in the pfcoronin gene could be responsible for artemisinin resistance in Africa. Methods: The aims of this study were first to determine the prevalence of mutations in the pfcoronin gene in African P. falciparum isolates by Sanger sequencing, by targeting the 874 samples collected from patients hospitalised in France after returning from endemic areas in Africa between 2018 and 2019, and secondly to evaluate their association with in vitro reduced susceptibility to standard quinoline antimalarial drugs, including chloroquine, quinine, mefloquine, desethylamodiaquine, lumefantrine, piperaquine, and pyronaridine. Results: The three mutations in the pfcoronin gene (50E, 100K, and 107V) were not detected in the 874 P. falciparum isolates. Current data show that another polymorphism (P76S) is present in many countries of West Africa (mean prevalence of 20.7%) and Central Africa (11.9%) and, rarely, in East Africa (4.2%). This mutation does not appear to be predictive of in vitro reduced susceptibility to quinolines, including artemisinin derivative partners in ACT such as amodiaquine, lumefantrine, piperaquine, pyronaridine, and mefloquine. Another mutation (V62M) was identified at low prevalence (overall prevalence of 1%). Conclusions: The 76S mutation is present in many African countries with a prevalence above 10%. It is reassuring that this mutation does not confer in vitro resistance to ACT partners.

scholarly journals Avaliação das Variantes Genéticas dos Genes AMELX e ENAM na Cárie Dentária em Adolescentes

2021 ◽  
Vol 24 (5-esp.) ◽  
pp. 650-654
Author(s):  
Gabriela Paschoalini Romagni ◽  
Paula Marino Costa ◽  
Sandra Mara Maciel ◽  
Maria Paula Jacobucci ◽  
Regina Célia Poli-Frederico
Keyword(s):  
Genetic Component ◽  
World Health ◽  
Caries Experience ◽  
Nucleotide Polymorphisms ◽  
Chi Square ◽  
Single Nucleotide ◽  
Significance Level ◽  
Exact Test ◽  
Polymerase Chain ◽  
Health Organization

A doença cárie é considerada, atualmente, como biofilme sacarose dependente, entretanto, estudos recentes apontam que fatores genéticos também podem influenciar seu desenvolvimento. Variantes nos gene amelogenina (AMELX) e enamelina (ENAM), responsáveis pela formação do esmalte, têm sido propostas como potencialmente envolvidos na doença. O objetivo deste estudo foi avaliar se a ocorrência de cárie dentária em adolescentes está relacionado às variantes nos genes AMELX e ENAM. Para a avaliação da prevalência de cárie foi utilizado o índice de dentes cariados, perdidos e obturados (CPO-D), segundo critérios da Organização Mundial de Saúde. As amostras de DNA foram extraídas das células da mucosa oral. Para a análise dos polimorfismos de nucleotídeo único (SNPs) dos genes AMELX (rs17878486) e ENAM (rs7671281) foi utilizada  a técnica de amplificação de fragmentos de DNA pela reação em cadeia da polimerase foi realizada (PCR) em tempo real pelo sistema TaqMan (Applied Biosystems, Foster City, EUA). Para a análise estatística, foi utilizado o teste exato de Fisher e qui-quadrado com nível de significância de 5%. Apenas os fatores socioeconômicos influenciaram a experiência de cárie. Concluiu-se que o componente genético, na população deste estudo, não influenciou o desenvolvimento da cárie.   Palavras-chave: Polimorfismo genético. Adolescentes. Esmalte.   Abstract Caries disease is currently considered a sucrose-dependent biofilm, however recent studies indicate that a genetic component can also influence its development. Variants in the amelogenin (AMELX) and enamelin (ENAM) genes, responsible for the enamel formation, have been proposed as potentially involved in the disease. The purpose of this study was to evaluate whether the occurrence of dental caries in adolescents is related to variants in the AMELX and ENAM genes. To assess the caries prevalence, the index of decayed, missing and filled teeth (DMFT) were used, according to World Health Organization criteria. DNA samples were extracted from oral mucosa cells. For the analysis of single nucleotide polymorphisms (SNPs) of the AMELX (rs17878486) and ENAM (rs7671281) genes, the amplifying DNA fragments technique  by the polymerase chain reaction was performed (PCR) in real time by the TaqMan system (Applied Biosystems, Foster City, USA). For the statistical analysis, Fisher's exact test and chi-square were used with a 5% significance level. Only socioeconomic factors influenced the caries experience. It was concluded that the genetic component in the population of this study, did not influence the development of caries.   Keywords: Genetic polymorphism. Adolescents. Enamel.

scholarly journals Efficacy of Artemisinin Base Combination Therapy and Genetic Diversity of Plasmodium falciparum from Uncomplicated Ma-laria Falciparum Patient in District of Pesawaran, Province of Lampung, Indonesia

2019 ◽  
Author(s):  
Jhons Fatriyadi SUWANDI ◽  
Widya ASMARA ◽  
Hari KUSNANTO ◽  
Din SYAFRUDDIN ◽  
Supargiyono SUPARGIYONO
Keyword(s):  
Plasmodium Falciparum ◽  
Genetic Variation ◽  
Falciparum Malaria ◽  
Health Centre ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Pfmdr1 Gene ◽  
Pcr Product ◽  
Nucleotide Mutation ◽  
Reverse Primer

Background: Malaria is an infectious disease caused by Plasmodium sp., that still prevalence in some part of Indonesia. District of Pesawaran is one of malaria endemic area in the Province of Lampung. The purpose of this study was to evaluate the efficacy of the ACT treatment in the District of Pesawaran Province of Lampung, Indonesia from Dec 2012 to Jul 2013 and the genetic variation of the Plasmodium falciparum also studied. Methods: This study was observational analytic study of falciparum malaria patients treated with ACT and primaquine (DHP-PQ and AAQ-PQ) at Hanura Primary Health Centre (Puskesmas). DNA isolation was done with QIAmp DNA Mini Kit. Amplification of PfMDR1, MSP1, and MSP2 genes was done with appropriate forward and reverse primer and procedures optimized first. PCR Product of PfMDR1 gene was prepared for sequencing. Data analysis was done with MEGA 6 software. Results: The results of this research are DHP-PQ effectiveness was still wellness among falciparum malaria patients in District of Pesawaran, Province of Lampung, Indonesia. There is Single-nucleotide mutation of N86Y of PfMDR1 gene. The dominant alleles found are MAD20 and 3D7 alleles with Multiplicity of Infection (MOI) are low. Conclusion: Therapy of DHP-PQ as an antimalarial falciparum in Pesawaran District, Lampung, Indonesia is still good. The genetic variation found was the SNP on the N86Y PfMDR1 gene, with dominant allele MAD20 and 3D7.

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