Spatiotemporal Changes in Plasmodium vivax msp142 Haplotypes in Southern Mexico: From the Control to the Pre-Elimination Phase

For 20 years, Plasmodium vivax has been the only prevalent malaria species in Mexico, and cases have declined significantly and continuously. Spatiotemporal genetic studies can be helpful for understanding parasite dynamics and developing strategies to weaken malaria transmission, thus facilitating the elimination of the parasite. The aim of the current contribution was to analyze P. vivax-infected blood samples from patients in southern Mexico during the control (1993–2007) and pre-elimination phases (2008–2011). Nucleotide and haplotype changes in the pvmsp142 fragment were evaluated over time. The majority of multiple genotype infections occurred in the 1990s, when the 198 single nucleotide sequences exhibited 57 segregating sites, 64 mutations, and 17 haplotypes. Nucleotide and genetic diversity parameters showed subtle fluctuations from across time, in contrast to the reduced haplotype diversity and the increase in the R2 index and Tajima’s D value from 2008 to 2011. The haplotype network consisted of four haplogroups, the geographical distribution of which varied slightly over time. Haplogroup-specific B-cell epitopes were predicted. Since only high-frequency and divergent haplotypes persisted, there was a contraction of the parasite population. Given that 84% of haplotypes were exclusive to Mesoamerica, P. vivax flow is likely circumscribed to this region, representing important information for parasite surveillance.

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Real-Time PCR for Dihydrofolate Reductase Gene Single-Nucleotide Polymorphisms in Plasmodium vivax Isolates

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.48.7.2581-2587.2004 ◽

2004 ◽

Vol 48 (7) ◽

pp. 2581-2587 ◽

Cited By ~ 33

Author(s):

Sara Brega ◽

Frédérique de Monbrison ◽

Carlo Severini ◽

Rachanee Udomsangpetch ◽

Inge Sutanto ◽

...

Keyword(s):

Plasmodium Vivax ◽

World Health ◽

Nucleotide Polymorphisms ◽

Hybridization Probe ◽

Mutant Type ◽

Single Nucleotide ◽

Infected Blood ◽

Reductase Gene ◽

Health Organization ◽

National Programs

ABSTRACT Mutations in the dhfr gene of Plasmodium vivax (pvdhfr) are associated with resistance to the antifolate antimalarial drugs. Polymorphisms in the pvdhfr gene were assessed by hybridization probe technology on the LightCycler instrument with 134 P. vivax-infected blood samples from Turkey (n = 24), Azerbaijan (n = 39), Thailand (n = 16), Indonesia (n = 53), and travelers (n = 19). Double mutations (S58R and S117N) or quadruple mutations (F57L/I, S58R, T61M, and S117N) in the pvdhfr genes were found in all Thai samples (100%). pvdhfr mutant-type alleles were significantly more common in samples from travelers (42%) than in those from patients from Indonesia (5%). Surprisingly, the pvdhfr single-mutation allele (S117N) was identified at a high frequency in parasites from Turkey and Azerbaijan (71 and 36%, respectively), where sulfadoxine-pyrimethamine is not recommended for the treatment of P. vivax malaria by the World Health Organization and the Malaria National Programs.

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Differential Susceptibilities of Anopheles albimanus and Anopheles pseudopunctipennis to Infections with Coindigenous Plasmodium vivaxVariants VK210 and VK247 in Southern Mexico

Infection and Immunity ◽

10.1128/iai.67.1.410-412.1999 ◽

1999 ◽

Vol 67 (1) ◽

pp. 410-412 ◽

Cited By ~ 57

Author(s):

Lilia Gonzalez-Ceron ◽

Mario H. Rodriguez ◽

Jose C. Nettel ◽

Cuauhtemoc Villarreal ◽

Kevin C. Kain ◽

...

Keyword(s):

Plasmodium Vivax ◽

Oligonucleotide Probe ◽

Circumsporozoite Protein ◽

Anopheles Albimanus ◽

Protein Variant ◽

Southern Mexico ◽

Infected Blood ◽

Blood Samples ◽

Genes Encoding ◽

Probe Hybridization

ABSTRACT The susceptibilities to coindigenous Plasmodium vivaxof colonized Anopheles albimanus and Anopheles pseudopunctipennis from southern Mexico were investigated by simultaneous feeding with infected blood obtained from patients. The genes encoding circumsporozoite protein variant types (VK210 and VK247) in blood samples were determined by PCR and oligonucleotide probe hybridization. A. albimanus was more susceptible to VK210, and A. pseudopunctipennis was more susceptible to VK247.

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Plasmodium vivax Cysteine-Rich Protective Antigen Polymorphism at Exon-1 Shows Recombination and Signatures of Balancing Selection

Genes ◽

10.3390/genes12010029 ◽

2020 ◽

Vol 12 (1) ◽

pp. 29

Author(s):

Lilia González-Cerón ◽

José Cebrián-Carmona ◽

Concepción M. Mesa-Valle ◽

Federico García-Maroto ◽

Frida Santillán-Valenzuela ◽

...

Keyword(s):

Amino Acid ◽

B Cell ◽

Plasmodium Vivax ◽

Nucleotide Diversity ◽

Protective Antigen ◽

Balancing Selection ◽

Southern Mexico ◽

Exon 2 ◽

Exon 1 ◽

Tajima’S D

Plasmodium vivax Cysteine-Rich Protective Antigen (CyRPA) is a merozoite protein participating in the parasite invasion of human reticulocytes. During natural P. vivax infection, antibody responses against PvCyRPA have been detected. In children, low anti-CyRPA antibody titers correlated with clinical protection, which suggests this protein as a potential vaccine candidate. This work analyzed the genetic and amino acid diversity of pvcyrpa in Mexican and global parasites. Consensus coding sequences of pvcyrpa were obtained from seven isolates. Other sequences were extracted from a repository. Maximum likelihood phylogenetic trees, genetic diversity parameters, linkage disequilibrium (LD), and neutrality tests were analyzed, and the potential amino acid polymorphism participation in B-cell epitopes was investigated. In 22 sequences from Southern Mexico, two synonymous and 21 nonsynonymous mutations defined nine private haplotypes. These parasites had the highest LD-R2 index and the lowest nucleotide diversity compared to isolates from South America or Asia. The nucleotide diversity and Tajima’s D values varied across the coding gene. The exon-1 sequence had greater diversity and Rm values than those of exon-2. Exon-1 had significant positive values for Tajima’s D, β-α values, and for the Z (HA: dN > dS) and MK tests. These patterns were similar for parasites of different origin. The polymorphic amino acid residues at PvCyRPA resembled the conformational B-cell peptides reported in PfCyRPA. Diversity at pvcyrpa exon-1 is caused by mutation and recombination. This seems to be maintained by balancing selection, likely due to selective immune pressure, all of which merit further study.

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New resources for genetic studies in maize ( Zea mays L.): a genome‐wide Maize6H‐60K single nucleotide polymorphism array and its application

The Plant Journal ◽

10.1111/tpj.15089 ◽

2020 ◽

Author(s):

Hongli Tian ◽

Yang Yang ◽

Hongmei Yi ◽

Liwen Xu ◽

Hang He ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Zea Mays ◽

Zea Mays L ◽

Single Nucleotide Polymorphism Array ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Genetic Studies ◽

Genome Wide ◽

A Genome

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Sequence variation of ookinete surface proteins Pvs25 and Pvs28 of Plasmodium vivax isolates from Southern Mexico and their association to local anophelines infectivity

Infection Genetics and Evolution ◽

10.1016/j.meegid.2010.03.014 ◽

2010 ◽

Vol 10 (5) ◽

pp. 645-654 ◽

Cited By ~ 15

Author(s):

Lilia González-Cerón ◽

Alejandro Alvarado-Delgado ◽

Jesus Martínez-Barnetche ◽

Mario H. Rodríguez ◽

Marbella Ovilla-Muñoz ◽

...

Keyword(s):

Plasmodium Vivax ◽

Sequence Variation ◽

Surface Proteins ◽

Southern Mexico

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Genetic variability and demographic history of Heliothis virescens (Lepidoptera: Noctuidae) populations from Brazil inferred by mtDNA sequences

Bulletin of Entomological Research ◽

10.1017/s0007485311000678 ◽

2011 ◽

Vol 102 (3) ◽

pp. 333-343 ◽

Cited By ~ 16

Author(s):

K.C. Albernaz ◽

K.L. Silva-Brandão ◽

P. Fresia ◽

F.L. Cônsoli ◽

C. Omoto

Keyword(s):

Genetic Structure ◽

Genetic Variability ◽

Heliothis Virescens ◽

Demographic History ◽

Haplotype Diversity ◽

Low Frequency ◽

Haplotype Network ◽

Demographic Expansion ◽

Significant Genetic Structure ◽

History Of

AbstractIntra- and inter-population genetic variability and the demographic history of Heliothis virescens (F.) populations were evaluated by using mtDNA markers (coxI, coxII and nad6) with samples from the major cotton- and soybean-producing regions in Brazil in the growing seasons 2007/08, 2008/09 and 2009/10. AMOVA indicated low and non-significant genetic structure, regardless of geographical scale, growing season or crop, with most of genetic variation occurring within populations. Clustering analyzes also indicated low genetic differentiation. The haplotype network obtained with combined datasets resulted in 35 haplotypes, with 28 exclusive occurrences, four of them sampled only from soybean fields. The minimum spanning network showed star-shaped structures typical of populations that underwent a recent demographic expansion. The recent expansion was supported by other demographic analyzes, such as the Bayesian skyline plot, the unimodal distribution of paired differences among mitochondrial sequences, and negative and significant values of neutrality tests for the Tajima's D and Fu's FS parameters. In addition, high values of haplotype diversity (Ĥ) and low values of nucleotide diversity (π), combined with a high number of low frequency haplotypes and values of θπ<θW, suggested a recent demographic expansion of H. virescens populations in Brazil. This demographic event could be responsible for the low genetic structure currently found; however, haplotypes present uniquely at the same geographic regions and from one specific host plant suggest an initial differentiation among H. virescens populations within Brazil.

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Detecting Genetic Associations betweenATG5and Lupus Nephritis bytrans-eQTL

Journal of Immunology Research ◽

10.1155/2015/153132 ◽

2015 ◽

Vol 2015 ◽

pp. 1-7 ◽

Cited By ~ 8

Author(s):

Yue-miao Zhang ◽

Fa-juan Cheng ◽

Xu-jie Zhou ◽

Yuan-yuan Qi ◽

Ping Hou ◽

...

Keyword(s):

Lupus Nephritis ◽

Lupus Erythematosus ◽

Clinical Information ◽

Nucleotide Polymorphisms ◽

Genetic Associations ◽

Single Nucleotide ◽

Genetic Studies ◽

Genome Wide ◽

Custom Made ◽

Regulatory Effects

Objectives. Numerous loci were identified to perturb gene expression intrans. As elevatedATG5expression was observed in systemic lupus erythematosus (SLE), the study was conducted to analyze the genome-wide genetic regulatory mechanisms associated withATG5expression in a Chinese population with lupus nephritis (LN).Methods. The online expression quantitative trait loci database was searched fortrans-expression single nucleotide polymorphisms (trans-eSNPs) ofATG5. Taggingtrans-eSNPs were genotyped by a custom-made genotyping chip in 280 patients and 199 controls. For positive findings, clinical information and bioinformation analyses were performed.Results. Fourtrans-eSNPs were observed to be associated with susceptibility to LN (P< 0.05), including ANKRD50 rs17008504, AGA rs2271100, PAK7 rs6056923, and TET2 rs1391441, while seven othertrans-eSNPs showed marginal significant associations (0.05 <P< 0.1). Correlations between thetrans-eSNPs andATG5expression and different expression levels ofATG5in SLE patients and controls were validated, and their regulatory effects were annotated. However, no significant associations were observed between different genotypes oftrans-eSNPs and severity or outcome of the patients.Conclusion. Using the new systemic genetics approach, we identified 10 loci associated with susceptibility to LN potentially, which may be complementary to future pathway based genetic studies.

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DGAT1 GENE POLYMORPHISM AND ITS RELATIONSHIPS WITH CATTLE MILK YIELD AND CHEMICAL COMPOSITION

Periódico Tchê Química ◽

10.52571/ptq.v17.n35.2020.16_faraj_pgs_174_180.pdf ◽

2020 ◽

Vol 17 (35) ◽

pp. 174-180

Author(s):

Salah H. FARAJ ◽

Asaad Y. AYIED ◽

D. K. SEGER

Keyword(s):

Single Nucleotide Polymorphism ◽

Chemical Composition ◽

Milk Yield ◽

Haplotype Diversity ◽

Genotypic Frequency ◽

Production Traits ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Dgat1 Gene ◽

Fat Yield

Several polymorphisms in different gene loci have been noted to affect production traits such as milk yield and milk composition. The present study aimed to determine the allelic and genotypic frequency of the DGAT1 gene and evaluate the associations between DGAT1 genetic variants and milk yield and its chemical composition of local Iraqi cattle. Blood samples from 100 cows were obtained for DNA isolation. The primer used in this study amplified 411-bp fragments at exon 8 of the DGAT1 gene. DNA sequencing methods were applied to detect single nucleotide polymorphism of the DGAT1 gene in 100 cows. The nucleotide sequences of exon 8 of the DGAT1 gene were registered for local Iraqi cattle in the National Center for Biotechnology Information (NCBI), DNA Data Bank of Japan (DDBJ), and the European Nucleotide Archive (ENA) under the following accession numbers (LC492073 and LC492074). The results showed the presence of two polymorphic sites leading to the construction of 2 different haplotypes in the cow. Haplotype diversity was 0.536, while nucleotide diversity was 0.0031. Two single-nucleotide polymorphism (SNP) loci of the DGAT1 gene were detected, namely A10433G (A/G) and A10434C (A/C). The resulting of this mutation changes lysine to alanine substitution at position 232 (A232K mutation) of amino acid sequence. Geneious software V. 2020.0.4 was used to detect genotypes of the DGAT1 gene, as the sequence alignment showed the presence of three genotypes. The genotypic frequencies of KK, KA, and AA were 0.40, 0.30, and 0.30, respectively. Frequencies of K and A alleles were 0.60 and 0.40, respectively. The KK genotype was significantly (P 0.05) associated with higher fat yield. Therefore, the DGAT1 gene could serve as a genetic marker for the selection of fat yield in cows.

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Haplotype Network Analysis and Phylogenetic Tree Construction of Hepatitis C Virus (HCV) Isolated from Tuban, Indonesia

Research Journal of Pharmacy and Technology ◽

10.52711/0974-360x.2021.00734 ◽

2021 ◽

pp. 4231-4235

Author(s):

Supiana Dian Nurtjahyani ◽

Rasyadan Taufiq Probojati ◽

Arif Nur Muhammad Ansori ◽

Mochammad Amin ◽

Retno Handajani

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Phylogenetic Tree ◽

Haplotype Diversity ◽

Haplotype Network ◽

Likelihood Method ◽

Tree Construction ◽

Transfusion Center ◽

Genealogical Relationship ◽

Blood Transfusion Center

This study aimed to analyzed the haplotype network and constructed the phylogenetic tree topology of hepatitis C virus (HCV) in Tuban, Indonesia and those from other countries, to determine the visualize genealogical relationship and inference about gene connected. The HCV isolates were collected from blood transfusion center of Tuban, East Java, Indonesia in 2015 and as a comparison, also the sequences of HCV isolates were retrieved from the GenBank®, National Center of Biotechnology Information (NCBI), USA database. To constructed of distribution map was performed through median joining analysis using Haplotype Network v4.6, whereas to constructed and phylogenetic model analyses were constructed based on the NS5B and 5’UTR regions using MEGA X, maximum-likelihood method based on the Tamura-Nei model. In the HCV NS5B region haplotype network showed high haplotype diversity (Hd=1.00) in 22 haplotypes. Based on phylogenetic analysis 3 sample isolates Tuban (BDT-55-p23, BDT-79-p23 and BDT-112-p23) were identified one group and closely related to isolates from Indonesia. However, isolates Tuban also have the same sequence characters as the isolates from Thailand. It was also confirmed in haplotype network that the three isolates are connected to each other. The identification of HCV genotypes circulating in blood donors in the Tuban of East Java confirmed were closely related to HCV isolates from Indonesia and Thailand. Therefore, this result might contribute in a better medical management towards HCV.

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