First isolation and whole genome characterization of Porcine Deltacoronavirus from pigs in Peru

Porcine Deltacoronavirus is a newly emergent enteric pathogen affecting swine farms worldwide. It has been detected in several countries in Europe, Asia and North America; yet, it has not been reported in South America. In November 2019, an enteric disease outbreak in a pig farm located in San Martin, Peru; was reported along with submission of three intestinal samples from pigs who succumbed to the disease. Samples were processed for molecular detection by qRT-PCR, viral isolation and further sequencing analysis. A taqman-based RT-PCR was performed to differentiate among the most relevant swine enteric coronaviruses described to date. All samples were positive to Porcine Deltacoronavirus with a cycle threshold (Ct) value between 9-14, revealing a high viral load, while testing negative to Porcine Epidemic diarrhea and Transmissible Gastroenteritis viruses. Following detection, viral isolation was performed using PK-15 and Vero cell lines. After 5 days of inoculation, no cytopathic effect was observed. A second blind passage allowed the observation of cytopathic effect on PK-15 cells, while it remained absent in Vero cells. A fluorescence test using an anti-N monoclonal antibody confirmed viral replication. One sample was processed for whole genome sequencing (NGS). In short, raw reads were imported into CLC genomics and assembled de novo. Out of 479k reads generated from the sample, 436k assembled into a 25501 bp contig which was 99.5% identical to a reference Porcine Deltacoronavirus strain from US within the North American phylogroup. Yet, there are relevant differences at the nucleotide and amino acid levels compared to previously described Porcine Deltacoronavirus strains. Altogether, our findings represent the first report of Porcine Deltacoronavirus in South America, its genomic characterization, which provides information of its evolutionary origin. Thus, this study offers new insights into the molecular epidemiology of Porcine Deltacoronavirus infections in the swine industry.

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Sequencing Analysis and Phylogenetic Tree of HPV Isolated from Breast Cancer Patients at Thi-Qar Province/Iraq

10.32792/utq/utjsci/vol7/2/10 ◽

2020 ◽

pp. 37-40

Keyword(s):

Nucleotide Sequence ◽

Phylogenetic Tree ◽

Evolutionary Relationship ◽

Nucleotide Sequencing ◽

Sequencing Analysis ◽

Breast Cancer Patients ◽

The North ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

History Of

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.

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A Synopsis of Dicliptera (Acanthaceae) in Brazil, with the Description of Two New Species

Systematic Botany ◽

10.1600/036364420x15862837791186 ◽

2020 ◽

Vol 45 (2) ◽

pp. 340-348

Author(s):

James Lucas da Costa-Lima ◽

Earl Celestino de Oliveira Chagas

Keyword(s):

New Species ◽

South America ◽

The State ◽

Northeastern Brazil ◽

Mato Grosso ◽

The North ◽

New Synonyms ◽

Two New Species ◽

Mato Grosso Do Sul ◽

A New Species

Abstract—A synopsis of Dicliptera (Acanthaceae) for Brazil is presented. Six species are recognized: Dicliptera ciliaris, D. sexangularis, and D. squarrosa, widely distributed in South America; D. purpurascens, which ranges from the North Region of Brazil (in the state of Acre) to eastern Bolivia; D. gracilirama, a new species from the Atlantic Forest of northeastern Brazil; and D. granchaquenha, a new species recorded in dry and semideciduous forests in Bolivia and western Brazil, in the state of Mato Grosso do Sul. Furthermore, we propose new synonyms and designate lectotypes for eleven names. An identification key to the six accepted Dicliptera species in Brazil is provided.

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1722-P: Colocalization of TOPMed Whole Genome Sequencing Analysis and Tissue-Specific eQTL Signals Detects Target Genes for Type 2 Diabetes Risk

Diabetes ◽

10.2337/db19-1722-p ◽

2019 ◽

Vol 68 (Supplement 1) ◽

pp. 1722-P

Author(s):

MINDY D. SZETO ◽

HEATHER M. HIGHLAND ◽

ALISA MANNING ◽

Keyword(s):

Type 2 Diabetes ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Target Genes ◽

Diabetes Risk ◽

Whole Genome ◽

Sequencing Analysis ◽

Tissue Specific

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Whole-exome sequencing with targeted analysis and epilepsy after acute symptomatic neonatal seizures

Pediatric Research ◽

10.1038/s41390-021-01509-3 ◽

2021 ◽

Author(s):

Adam L. Numis ◽

Gilberto da Gente ◽

Elliott H. Sherr ◽

Hannah C. Glass

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

De Novo ◽

List Type ◽

Sequencing Analysis ◽

Neonatal Seizures ◽

Pathogenic Variants ◽

Targeted Analysis ◽

Whole Exome ◽

Epilepsy Gene

Abstract Background The contribution of pathogenic gene variants with development of epilepsy after acute symptomatic neonatal seizures is not known. Methods Case–control study of 20 trios in children with a history of acute symptomatic neonatal seizures: 10 with and 10 without post-neonatal epilepsy. We performed whole-exome sequencing (WES) and identified pathogenic de novo, transmitted, and non-transmitted variants from established and candidate epilepsy association genes and correlated prevalence of these variants with epilepsy outcomes. We performed a sensitivity analysis with genes associated with coronary artery disease (CAD). We analyzed variants throughout the exome to evaluate for differential enrichment of functional properties using exploratory KEGG searches. Results Querying 200 established and candidate epilepsy genes, pathogenic variants were identified in 5 children with post-neonatal epilepsy yet in only 1 child without subsequent epilepsy. There was no difference in the number of trios with non-transmitted pathogenic variants in epilepsy or CAD genes. An exploratory KEGG analysis demonstrated a relative enrichment in cell death pathways in children without subsequent epilepsy. Conclusions In this pilot study, children with epilepsy after acute symptomatic neonatal seizures had a higher prevalence of coding variants with a targeted epilepsy gene sequencing analysis compared to those patients without subsequent epilepsy. Impact We performed whole-exome sequencing (WES) in 20 trios, including 10 children with epilepsy and 10 without epilepsy, both after acute symptomatic neonatal seizures. Children with post-neonatal epilepsy had a higher burden of pathogenic variants in epilepsy-associated genes compared to those without post-neonatal epilepsy. Future studies evaluating this association may lead to a better understanding of the risk of epilepsy after acute symptomatic neonatal seizures and elucidate molecular pathways that are dysregulated after brain injury and implicated in epileptogenesis.

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Steller’s sea cow genome suggests this species began going extinct before the arrival of Paleolithic humans

Nature Communications ◽

10.1038/s41467-021-22567-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Fedor S. Sharko ◽

Eugenia S. Boulygina ◽

Svetlana V. Tsygankova ◽

Natalia V. Slobodova ◽

Dmitry A. Alekseev ◽

...

Keyword(s):

Bering Sea ◽

De Novo ◽

Anthropogenic Activity ◽

Commander Islands ◽

The North ◽

Extinction Process ◽

Sea Cow ◽

The North Pacific ◽

The Bering Sea ◽

Woolly Mammoth

AbstractAnthropogenic activity is the top factor directly related to the extinction of several animal species. The last Steller’s sea cow (Hydrodamalis gigas) population on the Commander Islands (Russia) was wiped out in the second half of the 18th century due to sailors and fur traders hunting it for the meat and fat. However, new data suggests that the extinction process of this species began much earlier. Here, we present a nuclear de novo assembled genome of H. gigas with a 25.4× depth coverage. Our results demonstrate that the heterozygosity of the last population of this animal is low and comparable to the last woolly mammoth population that inhabited Wrangel Island 4000 years ago. Besides, as a matter of consideration, our findings also demonstrate that the extinction of this marine mammal starts along the North Pacific coastal line much earlier than the first Paleolithic humans arrived in the Bering sea region.

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Effective variant filtering and expected candidate variant yield in studies of rare human disease

npj Genomic Medicine ◽

10.1038/s41525-021-00227-3 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Brent S. Pedersen ◽

Joe M. Brown ◽

Harriet Dashnow ◽

Amelia D. Wallace ◽

Matt Velinder ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Rare Disease ◽

Genome Sequencing ◽

Autosomal Dominant ◽

De Novo ◽

Autosomal Dominant Inheritance ◽

Compound Heterozygous ◽

Whole Genome ◽

Dominant Inheritance ◽

Family Based

AbstractIn studies of families with rare disease, it is common to screen for de novo mutations, as well as recessive or dominant variants that explain the phenotype. However, the filtering strategies and software used to prioritize high-confidence variants vary from study to study. In an effort to establish recommendations for rare disease research, we explore effective guidelines for variant (SNP and INDEL) filtering and report the expected number of candidates for de novo dominant, recessive, and autosomal dominant modes of inheritance. We derived these guidelines using two large family-based cohorts that underwent whole-genome sequencing, as well as two family cohorts with whole-exome sequencing. The filters are applied to common attributes, including genotype-quality, sequencing depth, allele balance, and population allele frequency. The resulting guidelines yield ~10 candidate SNP and INDEL variants per exome, and 18 per genome for recessive and de novo dominant modes of inheritance, with substantially more candidates for autosomal dominant inheritance. For family-based, whole-genome sequencing studies, this number includes an average of three de novo, ten compound heterozygous, one autosomal recessive, four X-linked variants, and roughly 100 candidate variants following autosomal dominant inheritance. The slivar software we developed to establish and rapidly apply these filters to VCF files is available at https://github.com/brentp/slivar under an MIT license, and includes documentation and recommendations for best practices for rare disease analysis.

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A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome

Experimental & Molecular Medicine ◽

10.1038/s12276-021-00586-y ◽

2021 ◽

Author(s):

Seyoung Mun ◽

Songmi Kim ◽

Wooseok Lee ◽

Keunsoo Kang ◽

Thomas J. Meyer ◽

...

Keyword(s):

Genome Sequencing ◽

Genome Assembly ◽

De Novo ◽

Personal Genome ◽

Human Populations ◽

Whole Genome ◽

Structural Variations ◽

Insert Size ◽

Human Genomes ◽

Next Generation Sequencing Ngs

AbstractAdvances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have now been sequenced. Comparisons of these individual genomes have revealed substantial genomic differences between human populations as well as between individuals from closely related ethnic groups. Transposable elements (TEs) are known to be one of the major sources of these variations and act through various mechanisms, including de novo insertion, insertion-mediated deletion, and TE–TE recombination-mediated deletion. In this study, we carried out de novo whole-genome sequencing of one Korean individual (KPGP9) via multiple insert-size libraries. The de novo whole-genome assembly resulted in 31,305 scaffolds with a scaffold N50 size of 13.23 Mb. Furthermore, through computational data analysis and experimental verification, we revealed that 182 TE-associated structural variation (TASV) insertions and 89 TASV deletions contributed 64,232 bp in sequence gain and 82,772 bp in sequence loss, respectively, in the KPGP9 genome relative to the hg19 reference genome. We also verified structural differences associated with TASVs by comparative analysis with TASVs in recent genomes (AK1 and TCGA genomes) and reported their details. Here, we constructed a new Korean de novo whole-genome assembly and provide the first study, to our knowledge, focused on the identification of TASVs in an individual Korean genome. Our findings again highlight the role of TEs as a major driver of structural variations in human individual genomes.

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Whole-Genome DNA Methylation Analysis in Hydrogen Peroxide Overproducing Transgenic Tobacco Resistant to Biotic and Abiotic Stresses

Plants ◽

10.3390/plants10010178 ◽

2021 ◽

Vol 10 (1) ◽

pp. 178

Author(s):

Ana L. Villagómez-Aranda ◽

Luis F. García-Ortega ◽

Irineo Torres-Pacheco ◽

Ramón G. Guevara-González

Keyword(s):

Hydrogen Peroxide ◽

Dna Methylation ◽

Transgenic Tobacco ◽

Stress Responses ◽

Abiotic Stresses ◽

Methylation Status ◽

Physiological Adaptation ◽

Whole Genome ◽

Sequencing Analysis ◽

Biotic And Abiotic Stresses

Epigenetic regulation is a key component of stress responses, acclimatization and adaptation processes in plants. DNA methylation is a stable mark plausible for the inheritance of epigenetic traits, such that it is a potential scheme for plant breeding. However, the effect of modulators of stress responses, as hydrogen peroxide (H2O2), in the methylome status has not been elucidated. A transgenic tobacco model to the CchGLP gene displayed high H2O2 endogen levels correlated with biotic and abiotic stresses resistance. The present study aimed to determine the DNA methylation status changes in the transgenic model to obtain more information about the molecular mechanism involved in resistance phenotypes. The Whole-genome bisulfite sequencing analysis revealed a minimal impact of overall levels and distribution of methylation. A total of 9432 differential methylated sites were identified in distinct genome regions, most of them in CHG context, with a trend to hypomethylation. Of these, 1117 sites corresponded to genes, from which 83 were also differentially expressed in the plants. Several genes were associated with respiration, energy, and calcium signaling. The data obtained highlighted the relevance of the H2O2 in the homeostasis of the system in stress conditions, affecting at methylation level and suggesting an association of the H2O2 in the physiological adaptation to stress functional linkages may be regulated in part by DNA methylation.

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Genomic evolution of antimicrobial resistance in Escherichia coli

Scientific Reports ◽

10.1038/s41598-021-93970-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Pimlapas Leekitcharoenphon ◽

Markus Hans Kristofer Johansson ◽

Patrick Munk ◽

Burkhard Malorny ◽

Magdalena Skarżyńska ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Virulence Genes ◽

Mobile Genetic Elements ◽

Whole Genome ◽

Sequencing Analysis ◽

Metagenomic Sequencing ◽

Fecal Samples ◽

E Coli ◽

Genetic Elements

AbstractThe emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

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