scholarly journals Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals

2020 ◽  
Author(s):  
harshavardhan doddapaneni ◽  
Sara Javornik Cregeen ◽  
Richard Sucgang ◽  
Qingchang Meng ◽  
Xiang Qin ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Oligonucleotide Probe ◽  
Threshold Value ◽  
Open Reading Frames ◽  
Clinical Samples ◽  
Viral Loads ◽  
Full Length Genome ◽  
Probe Set ◽  
Reading Frames ◽  
Capture Sequencing

The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.

scholarly journals Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals

2020 ◽  
Author(s):  
Harsha Doddapaneni ◽  
Sara Javornik Cregeen ◽  
Richard Sucgang ◽  
Qingchang Meng ◽  
Xiang Qin ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Oligonucleotide Probe ◽  
Threshold Value ◽  
Open Reading Frames ◽  
Clinical Samples ◽  
Viral Loads ◽  
Full Length Genome ◽  
Probe Set ◽  
Reading Frames ◽  
Capture Sequencing

AbstractThe newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.

scholarly journals Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0244468
Author(s):  
Harsha Doddapaneni ◽  
Sara Javornik Cregeen ◽  
Richard Sucgang ◽  
Qingchang Meng ◽  
Xiang Qin ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Oligonucleotide Probe ◽  
Threshold Value ◽  
Open Reading Frames ◽  
Clinical Samples ◽  
Viral Loads ◽  
Full Length Genome ◽  
Probe Set ◽  
Reading Frames ◽  
Capture Sequencing

The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.

scholarly journals Genome Sequence of “ Candidatus Carsonella ruddii” Strain BT from the Psyllid Bactericera trigonica

2018 ◽  
Vol 6 (4) ◽  
Author(s):  
Leron Katsir ◽  
Ruan Zhepu ◽  
Alon Piasezky ◽  
Jiandong Jiang ◽  
Noa Sela ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Full Length ◽  
Open Reading Frames ◽  
Full Length Genome ◽  
Reading Frames

ABSTRACT The genome of “ Candidatus Carsonella ruddii” strain BT from Bactericera trigonica in Israel was sequenced. The full-length genome is 173,904 bp long and has a G+C content of 14.6%, with 224 predicted open reading frames (ORFs) and 30 RNAs.

scholarly journals Complete Genome Sequence of a Rhabdovirus Strain from Culex Mosquitos Collected in Southern Switzerland

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Jakub Kubacki ◽  
Isabelle Hardmeier ◽  
Weihong Qi ◽  
Eleonora Flacio ◽  
Mauro Tonolla ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Culex Pipiens ◽  
Full Length ◽  
Open Reading Frames ◽  
Content Type ◽  
Full Length Genome ◽  
Reading Frames

ABSTRACT We report here the full-length genome sequence of a rhabdovirus strain detected in a pool of 21 Culex pipiens and Culex torrentium mosquitos collected in southern Switzerland. The genome has a length of 11,914 nucleotides and encodes five major putative open reading frames.

scholarly journals Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes

2021 ◽  
Author(s):  
Camilla Borges Gazolla ◽  
Adriana Ludwig ◽  
Joana de Moura Gama ◽  
Daniel Pacheco Bruschi
Keyword(s):  
Molecular Structure ◽  
Xenopus Laevis ◽  
Transposable Elements ◽  
Phylogenetic Relationships ◽  
Transcriptional Activity ◽  
Evolutionary Dynamics ◽  
Open Reading Frames ◽  
Xenopus Tropicalis ◽  
Molecular Signatures ◽  
Reading Frames

Abstract Anuran genomes have a large number and diversity of transposable elements, but are little explored, mainly in relation to their molecular structure and evolutionary dynamics. Here, we investigated the retrotransposons containing tyrosine recombinase (YR) (order DIRS) in the genome of Xenopus tropicalis and Xenopus laevis. These anurans show 2n = 20 and the 2n = 36 karyotypes, respectively. They diverged about 48 million years ago (mya) and X. laevis had an allotetraploid origin (around 17-18 mya). Our investigation is based on the analysis of the molecular structure and the phylogenetic relationships of 95 DIRS families of Xenopus belonging to DIRS-like and Ngaro-like superfamilies. We were able to identify molecular signatures in the 5' and 3' non-coding terminal regions, preserved open reading frames (ORFs) and conserved domains that are specific to distinguish each superfamily. We recognize two ancient amplification waves of DIRS-like elements that occurred in the ancestor of both species and a higher density of the old/degenerate copies detected in both subgenomes of X. laevis. More recent amplification waves are seen in X. tropicalis (less than 3.2 mya) and X. laevis (around 10 mya) corroborating with transcriptional activity evidence. All DIRS-like families were found in both X. laevis subgenomes, while a few were most represented in the L subgenome. Ngaro-like elements presented less diversity and quantity in X. tropicalis and X. laevis genomes, although potentially active copies were found in both species and this is consistent with a recent amplification wave seen in the evolutionary landscape. Our findings highlight a differential diversity-level and evolutionary dynamics of the YR retrotransposons in X. tropicalis and X. laevis species expanding our comprehension of the behavior of these elements in both genomes during the diversification process.

scholarly journals Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes

2021 ◽  
Author(s):  
Camilla Borges Gazolla ◽  
Adriana Ludwig ◽  
Joana Gama Moura ◽  
Daniel Pacheco Bruschi
Keyword(s):  
Molecular Structure ◽  
Xenopus Laevis ◽  
Phylogenetic Relationships ◽  
Transcriptional Activity ◽  
Evolutionary Dynamics ◽  
Open Reading Frames ◽  
Xenopus Tropicalis ◽  
Molecular Signatures ◽  
Reading Frames ◽  
High Diversity

Anuran genomes have a large number and diversity of transposable elements, but are little explored, mainly in relation to their molecular structure and evolutionary dynamics. Here, we investigated the retrotransposons containing tyrosine recombinase (YR) (order DIRS) in the genome of Xenopus tropicalis and Xenopus laevis. These anurans show 2n = 20 and the 2n = 36 karyotypes, respectively. They diverged about 48 million years ago (mya) and X. laevis had an allotetraploid origin (around 17-18 mya). Our investigation is based on the analysis of the molecular structure and the phylogenetic relationships of 95 DIRS families of Xenopus belonging to DIRS-like and Ngaro-like superfamilies. We were able to identify molecular signatures in the 5' and 3' non-coding terminal regions, preserved open reading frames (ORFs) and conserved domains that are specific to distinguish each superfamily. We recognize two ancient amplification waves of DIRS-like elements that occurred in the ancestor of both species and a higher density of the old/degenerate copies detected in the X. laevis. X. tropicalis showed more recent amplification waves estimated around 16 mya and 3.2 mya and corroborate with high diversity-level of families in this species and with transcriptional activity evidence. Ngaro-like elements presented less diversity and quantity in the genomes, although potentially active copies were also found. Our findings highlight a differential diversity-level and evolutionary dynamics of the YR retrotransposons in the diploid X. tropicalis and X. laevis species expanding our comprehension of the behavior of these elements in both genomes during the diversification process

scholarly journals Complete Genome Sequence of Feline Leukemia Virus Kawakami-Theilen Strain KT-FeLV-UCD-1

2020 ◽  
Vol 9 (20) ◽  
Author(s):  
Pei-Ju Chin ◽  
Fabio La Neve ◽  
Valeria Zanda ◽  
Arifa S. Khan
Keyword(s):  
Genome Sequence ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Genomic Organization ◽  
Leukemia Virus ◽  
Open Reading Frames ◽  
Feline Leukemia Virus ◽  
Long Terminal Repeats ◽  
Full Length Genome ◽  
Reading Frames

This full-length genome sequence of a feline leukemia virus Kawakami-Theilen strain (designated KT-FeLV-UCD-1), produced from the chronically infected FL74-UCD-1 cell line, was obtained using high-throughput sequencing. It consisted of 8,464 bp and had a genomic organization similar to that of other gammaretroviruses, containing long terminal repeats and open reading frames for Gag, Pol, and Env.

scholarly journals Molecular Analysis of the Enterobacter sakazakii O-Antigen Gene Locus

2008 ◽  
Vol 74 (12) ◽  
pp. 3783-3794 ◽  
Author(s):  
N. Mullane ◽  
P. O'Gaora ◽  
J. E. Nally ◽  
C. Iversen ◽  
P. Whyte ◽  
...  
Keyword(s):  
Proximal Region ◽  
Open Reading Frames ◽  
Clinical Samples ◽  
Polymorphism Analysis ◽  
Enterobacter Sakazakii ◽  
Pcr Assay ◽  
Banding Patterns ◽  
O Antigen ◽  
Dna Profiles ◽  
Reading Frames

ABSTRACT Nucleotide polymorphism associated with the O-antigen-encoding locus, rfb, in Enterobacter sakazakii was determined by PCR-restriction fragment length polymorphism analysis. Based on the analysis of these DNA profiles, 12 unique banding patterns were detected among a collection of 62 strains from diverse origins. Two common profiles were identified and were designated serotypes O:1 and O:2. DNA sequencing of the 12,500-bp region flanked by galF and gnd identified 11 open reading frames, all with the same transcriptional direction. Analysis of the proximal region of both sequences demonstrated remarkable heterogeneity. A PCR assay targeting genes specific for the two prominent serotypes was developed and applied for the identification of these strains recovered from food, environmental, and clinical samples.

scholarly journals Host mitochondrial transcriptome response to SARS-CoV-2 in multiple cell models and clinical samples

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Brendan Miller ◽  
Ana Silverstein ◽  
Melanie Flores ◽  
Kevin Cao ◽  
Hiroshi Kumagai ◽  
...  
Keyword(s):  
Mitochondrial Dynamics ◽  
Open Reading Frames ◽  
Cellular Respiration ◽  
Clinical Samples ◽  
Protein Signaling ◽  
Rnaseq Data ◽  
Multiple Cell ◽  
Transcriptome Response ◽  
Mitochondrial Antiviral Signaling ◽  
Reading Frames

AbstractSARS-CoV-2 induces a muted innate immune response compared to other respiratory viruses. Mitochondrial dynamics might partially mediate this effect of SARS-CoV-2 on innate immunity. Polypeptides encoded by open reading frames of SARS-CoV and SARS-CoV-2 have been shown to localize to mitochondria and disrupt Mitochondrial Antiviral Signaling (MAVS) protein signaling. Therefore, we hypothesized that SARS-CoV-2 would distinctly regulate the mitochondrial transcriptome. We analyzed multiple publicly available RNASeq data derived from primary cells, cell lines, and clinical samples (i.e., BALF and lung). We report that SARS-CoV-2 did not dramatically regulate (1) mtDNA-encoded gene expression or (2) MAVS expression, and (3) SARS-CoV-2 downregulated nuclear-encoded mitochondrial (NEM) genes related to cellular respiration and Complex I.

Sign in / Sign up

Export Citation Format

Share Document