Sequencing genome viral. Medical search. Frequent questions

Furthermore, we developed a targeted ultra-deep sequencing approach to assess the dynamics of clinically relevant mutations in the RdRp-region and to detect insertions in the HVR-domain in the HEV genomes. (nature.com)
We are trying to place the samples collected in Western New York on more or less of a timeline, organized by the dates we collect the sample and by the type of mutations we have seen in each virus genome. (buffalo.edu)
The trunk of the tree would be the very first virus sequenced, while the branches and off-shoots are strains with different mutations over the past many months," says Bard. (buffalo.edu)
We detected a high number of mutations (range, 64-73) relatively to a 2018 Nigerian genome ( genome GenBank Accession no. (bvsalud.org)
and we detected 35 mutations relatively to genome ON563414.3 (a B.1 lineage reference genome ). (bvsalud.org)
The increasing diversity of SARS-CoV-2 variants and the potential threat of increased virulence, higher infectivity and altered epitopes of these newly evolving viral strains, underline the need to identify, trace and track mutations over the complete viral genome. (eurofinscentrallaboratory.com)
This study reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems. (elifesciences.org)
The VOC differ from the original Wuhan virus as they have mutations across the genome. (who.int)
Mutations in other regions of the genome may also be informative for known VOI/VOC detection. (who.int)
To date, WHO has designated 4 SARS CoV-2 genotypes that meet the working definition of a VOC: i) contain mutations divergent from the Wuhan strain and ii) that the mutations impact one or more of the aspects of viral infection that have public health significance. (who.int)
Overall, these assays and approaches detect specific mutations or features such as insertions, deletions and point mutations in the SARS CoV-2 genome that are characteristic of a particular VOC/VOI using PCR. (who.int)
In viral molecular epidemiology, reconstruction of consensus genomes from sequence data is critical for tracking mutations and variants of concern. (niema.net)
SARS-CoV-2 genome variation study enables a comprehensive understanding of virus transmission, rate of mutations, track evolution, development of vaccines, and treatment 5 . (medrxiv.org)
Tracking viral mutations demands sequencing all the genetic material in a virus - its genome. (skyscraperpage.com)
Once researchers have gathered the genomes from a number of virus samples, they can compare their mutations. (skyscraperpage.com)
Mutations are alterations in nucleic acid base pairs (in the viral RNA) which code for proteins so viral mutations produce slight changes to the proteins of the virus (or of the cells of other organisms). (skyscraperpage.com)
The B.1.1.7 variant contains several mutations, including several in the gene that encodes the viral spike protein. (eurekalert.org)
The SGTF pattern can occur with other SARS-CoV-2 variants that have spike gene mutations, but the researchers found by sequencing every SGTF sample they had from December through February, 662 of the 986 samples (67 percent) contained the B.1.1.7 variant. (eurekalert.org)
possibility is that the damage is not induces mutations in a mutation integrated viral genome ( Todaro and repaired at al , and when the cell rep- assay permits it to be classified as Huebner, 1972) , and alteration of im- licates, the DNA polymerase correct- mutagenic. (who.int)

Population-based Sanger sequencing has been shown to miss minor variants with a frequency below 20% 20 . (nature.com)
The large size and showed the minority viral variants in the specimen. (cdc.gov)
Whole genome SARS-CoV-2 sequencing identify mutant strains and spot emerging risks, including potentially immune and vaccine evasive variants, at an early stage. (eurofinscentrallaboratory.com)
During this period, tremendous success has been achieved in the fields of decoding of human genome, technological advancement of new era of human genome applications, toward personalized genomes and discovery of rare variants, leveraging genome sequencing to impact on cancer researches and mammalian evolution and population structure. (springer.com)
Wuhan strain will continue to arise, yet not all viral variants generated through mutation of the virus are important or have immediate public health relevance. (who.int)
A virus variant model-based clustering method, ViVaMBC, is presented that explores quality scores and second best base calls for identifying and quantifying viral variants. (biomedcentral.com)
ViVaMBC is the first method to call viral variants directly at the codon level. (biomedcentral.com)
Standard genotyping such as direct PCR sequencing methods, however, only provides information on the most abundant sequence variants. (biomedcentral.com)
Emergence of resistant variants detected by ultra-deep sequencing after asunaprevir and daclatasvir combination therapy in patients infected with hepatitis C virus genotype 1. (genomeweb.com)

Through collaboration with Dr. Jennifer Surtees in the Department of Biochemistry and the Erie County Health Laboratory, COVID-19 viral genomes isolated from patients in Western New York were sequenced at the Genomics and Bioinformatics Core (GBC), located in the CBLS, using an illumina MiSeq sequencing platform," says Jonathan Bard, senior programmer and bioinformatics analyst at the GBC. (buffalo.edu)
Here, we performed DNA metagenomics using next-generation sequencing with Illumina or Nanopore technologies for clinical samples from MPXV-infected patients diagnosed between June and July 2022. (bvsalud.org)
To ease future molecular studies, this study compares first- (partial sequencing via Sanger), second- (Illumina), and third-generation (MinION Nanopore) sequencing platforms for USUV. (frontiersin.org)
We concluded that depending on the focus of a research project, amplicon-based MinION Nanopore sequencing can be an ideal cost- and time-effective alternative to Illumina in producing optimal genome coverage. (frontiersin.org)
Each bacterial and fungal genome is sequenced on both Illumina and Oxford Nanopore platforms, resulting in a "hybrid-assembly" incorporating both sequencing technologies. (atcc.org)
To date, viral genomes have been produced using only Illumina sequencing. (atcc.org)
Fortunately, base calls are complemented with quality scores which are derived from a quadruplet of intensities, one channel for each nucleotide type for Illumina sequencing. (biomedcentral.com)
Moreover, the incorporation of quality scores is most appropriate for Illumina sequencing data. (biomedcentral.com)

First, a DNA fragment can be converted into a new sequence in which each original nucleotide is encoded by a specific 8-nt sequence (A8, T8, G8 and C8) and then ligated to a hairpin. (wikipedia.org)
This manageable size together with the current advances in nucleotide sequencing technology means that partial and whole virus genome sequencing will become an essential component in epidemiologic investigations of disease outbreaks. (msdmanuals.com)
Although the Entrez Genome Project database does not include viral genome sequencing projects, data from those projects are submitted to GenBank and are available in the Entrez Nucleotide and Entrez Genome databases. (lu.se)
Även om databasen Entrez Genome Project inte inkluderar virala genomsekvenseringsprojekt, skickas data från dessa projekt till GenBank och är tillgängliga i databaserna Entrez Nucleotide och Entrez Genome. (lu.se)
8%) such as sub-Saharan Africa, and one complete HBV genomes and according consequence is the possible introduction to the criterion of 8% differences in into our country of genotype non-D HBV the complete nucleotide sequence of the infections. (who.int)

In November 2022, Broad's Genomics Platform sequenced its 500,000th whole human genome, a mere four years after sequencing its 100,000th. (broadinstitute.org)
Méthodologie: Entre septembre 2021 et février 2022, des écouvillonnages oropharyngés et/ou nasopharyngés de travailleurs symptomatiques COVID-19 et apparemment en bonne santé sélectionnés consécutivement du site minier de Wahgnion dans le sud-ouest du Burkina Faso qui ont consenti à l'étude ont été prélevés selon les deux programme de quart de semaines et testé pour le SRAS-CoV-2 à l'aide d'un test RT-PCR. (bvsalud.org)

These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. (nih.gov)
Current diagnostic PCR assays target a variety of SARS CoV-2 genes and the vast majority target sequences in regions of the SARS CoV-2 genome that are highly conserved. (who.int)
In some countries laws specifically provide that isolated genetic material, such as gene sequences, may be considered patentable inventions (as long as they meet the other criteria for the granting of a patent) even if corresponding genes occur in nature. (who.int)

Eurofins Genomics launches an optimized, cost-effective, SARS-CoV-2, next-generation sequencing service providing full length viral genome sequences. (eurofinscentrallaboratory.com)
Eurofins Genomics optimized the formulation of the oligo pool achieving highest performance and best-in-class uniformity of coverage for the full-length viral genome. (eurofinscentrallaboratory.com)
Eurofins Genomics' sophisticated bioinformatic pipeline assembles and compares the resulting contiguous full-length SARS-CoV-2 isolate sequences and delivers a report for conclusive interpretation. (eurofinscentrallaboratory.com)
The new service exploits Eurofins Genomics scalable, automated, standardized laboratory information management system (LIMS) controlled high throughput next generation sequencing facility. (eurofinscentrallaboratory.com)
The full coronavirus product range offered by Eurofins Genomics Europe, including SARS-CoV-2 qPCR assays or SARS-CoV-2 plasmid controls, can be found on https://www.eurofinsgenomics.eu/en/covid-19/ . (eurofinscentrallaboratory.com)
The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. (springer.com)
The leading genome research centers and scientists have publicly recognized that these are the core enabling goals for the next decade genomics research. (springer.com)
The National Human Genome Research Institute (NHGRI) has echoed this need through its vision for genomics research (Collins et al. (springer.com)
The GCID has led many technical, analytical, and translational advances that have revolutionized the application of genomics to viral human disease. (broadinstitute.org)
GCID scientists conduct additional work on viral genomics through the Broad Institute's Infectious Disease and Microbiome Program . (broadinstitute.org)
Broad Genomics Platform sequences a whole human genome every four minutes. (broadinstitute.org)

Understanding the viral genome and its function will lead to answers sought by many of the world's top COVID-19 scientists and clinicians, such as how quickly the virus is mutating, how many strains exist and whether or not the virus is becoming more lethal or slowing down. (buffalo.edu)
The ATCC Genome Portal was created to reestablish the trustworthiness, reliability, and accuracy of genome assemblies associated with ATCC microbial strains . (atcc.org)
Modern massive parallel sequencing (MPS) technologies, on the contrary, have the opportunity to allow in-depth characterization of sequence variation in more complex populations, including low-frequency viral strains. (biomedcentral.com)
However, one of the challenges in the detection of low-frequency viral strains concerns the errors introduced during the sequencing process. (biomedcentral.com)
According to the research report, the virus "could be a direct progenitor of modern viral strains or a member of an ancient lineage that did not cause outbreaks in the 20th century. (latimes.com)

Viral tests (nucleic acid or antigen detection tests) are used to assess acute infection, whereas antibody tests provide evidence of prior infection with SARS-CoV-2. (medscape.com)
Hepatitis B is a viral liver infection that can lead to acute or chronic conditions. (pasteur.fr)
The viral S gene is important as it codes for the Spike protein which is the molecule that makes contact with, and allows entry of the virus into susceptible host cells, causing infection. (who.int)
The 5' terminus genome encodes nonstructural proteins (nsps) that are involved in the process of the virus infection cycle. (medrxiv.org)
Vaccines, which induce the production of antibodies that recognize and binding to very specific viral surface molecules, are an unlikely player in fighting HIV, because throughout infection, HIV surface molecules are continually changing. (cellsalive.com)
The latest cycle threshold (Ct) values of coronavirus (COVID-19) positive tests, as well as latest analysis of the genetic lineages of COVID-19 seen in the samples we sequence, are provided in our Coronavirus (COVID-19) Infection Survey dataset . (ons.gov.uk)
Studying tissue-specific and single-cell characterizations of host response and viral dynamics during viral hemorrhagic fever infection. (broadinstitute.org)
The aim of this study was to determine the prevalence of SARSCoV-2 infection in Burkina Faso and to use the initial cycle threshold (Ct) values of RT-PCR as a tool to monitor the dynamics of the viral load. (bvsalud.org)
The more typical form of hepatocellular carcinoma is often associated with active hepatic inflammation, hepatitis B or C viral infection, alcohol-related liver disease, nonalcoholic fatty liver disease (NAFLD), cirrhosis from any other cause, or dietary aflatoxin B1. (medscape.com)

Previously known single-molecule sequencing technologies include Nanopore sequencing (Oxford Nanopore),SMRT sequencing (Pacific Biosciences), and Heliscope single molecule sequencing (Helicos Biosciences). (wikipedia.org)
Using long sequencing reads from the Oxford Nanopore Technologies platform, we phased SNVs within large gene copy arrays for the first time. (elifesciences.org)
With emphasis on MinION Nanopore sequencing, cDNA-direct and target-enrichment (amplicon-based) sequencing approaches were validated in parallel. (frontiersin.org)
Our study implemented an amplicon-based sequencing approach using the Oxford Nanopore Technology (ONT) portable device. (medrxiv.org)

As announced on 23 December 2020, Eurofins is offering part of its sequencing capacity for free to public healthcare authorities who do not have emergency budgets available to detect the VUI2020-12/01 strain reported to be currently fast-spreading in the UK in their positive samples so they can evaluate local prevalence of this new strain. (eurofinscentrallaboratory.com)
Since the publication of the first sequence at the beginning of 2020, viral genome sequencing has become a powerful tool to study the SARS-CoV-2 genome 1 , 4 . (medrxiv.org)
The researchers' family tree-type analysis of the detected B.1.1.7 sequences show the variant has been introduced to the U.S. multiple times since at least late November 2020, especially in California and Florida, and in periods coinciding with increased travel, including Thanksgiving week. (eurekalert.org)

RHDV has a polyadenylated positive-sense single-stranded RNA genome of about 7.5 kb, comprising two open reading frames (ORFs) [ 6 ]. (biomedcentral.com)
Positive-sense RNA viruses possess a single-stranded RNA genome that can serve as messenger RNA (mRNA) that can be directly translated to produce an amino acid sequence. (msdmanuals.com)

Sequencing of monkeypox virus from infected patients reveals viral genomes with APOBEC3-like editing, gene inactivation, and bacterial agents of skin superinfection. (bvsalud.org)

We dissected the reaction promoted by CHYSEL sequences using yeast genetics and in vitro translation systems. (portlandpress.com)

Therefore, to capture the heterogeneity of the HEV quasispecies, including recombination events and SNP that occur with very low frequencies, we developed new sequencing approaches for HEV genotype 3 based on the amplification of the near full-length genome of HEV by long-range PCR (lrPCR) followed by subsequent next-generation sequencing (NGS) and third-generation sequencing. (nature.com)
However, the majority of the sequencing technologies rely on PCR-based clonal amplification of the DNA molecule in order to bring the signal to a detectable range. (wikipedia.org)
Therefore, there is an increased interest in developing single-molecule sequencing technologies, where no amplification is required. (wikipedia.org)
The ARTIC approach utilises an oligo pool for multiplexed PCR amplification of the complete viral genome. (eurofinscentrallaboratory.com)
Virus detection often utilizes nucleic acid amplification to identify the presence of specific sequences in SARS-CoV-2 viral RNA. (neb.com)

The more researchers know about the virus at the genome level, the better prepared they are for developing drugs and treatment protocols. (buffalo.edu)
The same group of researchers initially published both sequences, but there is a qualitative difference between the papers. (news-medical.net)
The researchers found that using the available data, they were unable to detect any contiguous sequences larger than 17 kb, using several different settings. (news-medical.net)
Working with Addgene, Broad Institute has shared CRISPR genome-editing reagents with researchers at more than 3,200 institutions in 76 countries. (broadinstitute.org)
In response to the demand for information in a quickly changing clinical environment when treating viral diseases, researchers at the Connected Health Branch created the Antimicrobial Stewardship application to provide up-to-date guidelines for infectious diseases, including COVID-19. (health.mil)
The 662 instances of B.1.1.7 sequenced in the study were from samples gathered in 10 U.S. states, although the researchers note that other testing labs covering a total of 33 U.S. states and territories have by now reported to the CDC at least one B.1.1.7 case. (eurekalert.org)
Researchers have identified and shared hundreds of viral genome sequences. (franchising.com)

We use a combination of cell-based and in vitro assays to show that the interface of the FluPol A dimer is required for vRNA synthesis during replication of the viral genome. (nature.com)
Our study provides high-resolution structures of medically relevant FluPol A , as well as insights into the replication mechanisms of the viral RNA genome. (nature.com)
Some viruses have an outer envelope consisting of protein and lipid, surrounding a protein capsid complex with genomic RNA or DNA and sometimes enzymes needed for the first steps of viral replication. (msdmanuals.com)
Classification of viruses is principally according to their genome sequence taking into consideration nature and structure of their genome and their method of replication, but not according to the diseases they cause (see International Committee on Taxonomy of Viruses (ICTV), 2021 release ). (msdmanuals.com)

Once the provirus is integrated into the host cell DNA, it is transcribed using typical cellular mechanisms to produce viral proteins and genetic material. (msdmanuals.com)

Currently, there are three basic types of tests to determine if an individual has been infected with SARS-CoV-2: viral nucleic acid (RNA) detection, viral antigen detection, and detection of antibodies to the virus. (medscape.com)
An enzyme (protein) that's part of the human immunodeficiency virus reads the sequence of viral RNA nucleic acids (yellow in graphic) that have entered the host cell and transcribes the sequence into a complementary DNA sequence (shown in blue). (cellsalive.com)

Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). (nih.gov)

Initial direct viral detection is typically performed using an upper respiratory tract (URT) specimen. (medscape.com)
The objective of this document is to outline the available methods and tools for screening and sequencing patient specimens for the detection of VOC or VOI, with a focus on those that offer a rapid turn-around time so as to support rapid implementation of public health actions for COVID 19 control. (who.int)
CoV-2 genome and can be targeted as a region for detection of VOC/VOI. (who.int)
Extraction of RNA is often the first step in viral detection assays and has become an increasingly important laboratory technique in the midst of this global pandemic. (neb.com)
Traditionally used for cleanup applications, these kits have now been validated for extraction, expanding its utility to support viral detection. (neb.com)
The genomic detection and epidemiology of emerging viral threats in humans and vectors. (broadinstitute.org)
Tests included viral isolation in cell culture from peripheral blood leukocytes (PBL) and detection of serum BAV-7 antibodies by use of microtitration viral neutralization. (avma.org)

Lassa fever, a viral hemorrhagic fever caused by the Lassa virus (LASV), is endemic in West Africa and is associated with high morbidity and mortality. (bvsalud.org)

One of the viruses, EMC/2012, has been sequenced, and es (melting temperature 58°C-60°C, guanine plus cytosine content 35%-60%) yielding 357,198 potential primers. (cdc.gov)
Conclusions and Clinical Relevance -Results of our study indicate that BAV-7 infections can be found in postweaning commingled calves and may develop more commonly in calves with concurrent infections with viruses such as bovine viral diarrhea virus (BVDV). (avma.org)
Negative-sense RNA viruses possess a single-stranded negative-sense genome that first must synthesize a complementary positive-sense antigenome, which is then used to make genomic negative-sense RNA. (msdmanuals.com)
the genome of RNA viruses ranges from 3.5 kilobases (some retroviruses) to 27 kilobases (some reoviruses), and the genome of DNA viruses ranges from 5 kilobases (some parvoviruses) to 280 kilobases (some poxviruses). (msdmanuals.com)

Full experimental details backed up the published genomic sequence of SARS-CoV-2, but not so that of the RaTG13. (news-medical.net)

The DNA sequences are determined by measuring the changes in the hairpin length following successful hybridization of complementary nucleotides. (wikipedia.org)
After applying a magnetic force, in the unzipped state of the hairpin, a small number of discriminating nucleotides can hybridize to the new individual complementary sequences on the hairpin which can transiently block the refolding of the hairpin. (wikipedia.org)
SARS-CoV-2 has a genome of 29,903 nucleotides, with 5'-cap structure and 3' poly(A) tail 9 , 10 . (medrxiv.org)
A mutation is defined as a sing of the DNA damage by the cel by replicating past the unrepaired change in the sequence or number (the DNA damage response), and DNA damage, thereby introducing a of nucleotides in the DNA. (who.int)

The completion of the first human genome drafts (Yamey 2000 ) was just a start of the modern DNA sequencing era which resulted in further invention, improved development toward new advanced strategies of high-throughput DNA sequencing, so called the " high-throughput next generation sequencing " (HT-NGS). (springer.com)
Hull , R , Harper , G , Lockhart , B ( 2000 ) Viral sequences integrated into plant genomes. (cambridge.org)

Hepatitis E virus (HEV) is one of the main causes of acute viral hepatitis worldwide. (nature.com)
It is a hepatotropic, approximately 7.2 kb single-stranded positive-sense RNA virus whose genome contains three open reading frames (ORF1, ORF2, and ORF3), 5′ and 3′ untranslated regions (UTRs), and a poly(A) tract at the 3′ end. (nature.com)
Additional genome sequenc- the deep genome sequencing of the virus directly from a es from this virus are needed to aid diagnostics, moni- patient's sputum sample. (cdc.gov)
EMC/2012) and September 2012 (England/Qatar/2012) nome determination of the novel CoV directly from patient share a common virus ancestor most likely considerably be- sputum using next-generation short-read sequencing. (cdc.gov)
Next-generation sequencing allows us to place a spotlight on each and every part of the virus genome, allowing us to look for the smallest of changes, which helps us better understand how the virus is changing over time. (buffalo.edu)
Scientists at the Institut Pasteur working in collaboration with the CNRS have demonstrated that a cellular protein is capable of acting as a restriction factor for the hepatitis B virus by degrading the viral DNA. (pasteur.fr)
During our research, we demonstrated that a cellular protein capable of degrading DNA could be incorporated into the viral particle and induce degradation of the hepatitis B virus genome," explains Jean-Pierre Vartanian from the Institut Pasteur's Molecular Retrovirology Unit. (pasteur.fr)
The first SARS-CoV-2 genome sequence confirmed the virus as part of the betacoronavirus genus, belonging to the Coronaviridae family, consisting of single-strand positive-sense RNA 1 , 3 . (medrxiv.org)
I've been working on a lineage typing tool called pangolin (phylogenetic assignment of named global outbreak lineages) that will allow any research group to type their virus genome. (ed.ac.uk)
The genome data provides insight into how the virus is moving within the community, and helps inform decisions on the most effective control measures to limit virus spread. (ed.ac.uk)
Many scientists mention the genome sequence of this bat CoVs, RaTG13, as being part of the ancestral descent of the current virus. (news-medical.net)
This is documented by several papers that have shown up the holes in the dataset underlying the published genome of the bat virus. (news-medical.net)
Concurrent bovine viral diarrhea virus infections were detected in most calves from which BAV-7 was isolated. (avma.org)
Objective -To evaluate economic effects and health and performance of the general cattle population after exposure to cattle persistently infected (PI) with bovine viral diarrhea virus (BVDV) in a feedlot. (avma.org)

[ 4 ] Swabs are typically placed in 1.5-3 mL of viral transport media (VTM) prior to transport to the laboratory. (medscape.com)
This was integrated alongside an existing RT-qPCR diagnostic laboratory to provide a sample-to-sequence turnaround time of approximately 30 hours with significant scope for optimisation. (medrxiv.org)
Here, we describe our laboratory and bioinformatics methods, the diversity of the current contents of the ATCC Genome Portal , it's current capabilities, and new features for use by the research community. (atcc.org)

Our high-throughput sequencing tor population dynamics, identify the animal source, and yielded a substantial depth of genome sequence assembly characterize mechanisms of pathogenesis. (cdc.gov)
With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. (springer.com)
And for most viral threats, our ability to respond is hampered by a lack of systematic, high-throughput methods that evaluate and inform the development of therapeutics and vaccines. (broadinstitute.org)

Along with colleagues at the Wellcome Sanger Institute in Cambridge and a number of other UK universities, the project is now processing about 1000 samples each week and sequencing them on the MinION sequencing platform. (ed.ac.uk)

Clinical activity of FOLFIRI plus cetuximab according to extended gene mutation status by next generation sequencing: findings from the CAPRI-GOIM trial. (genomeweb.com)

For instance, the largest contig contains genetic material with 98% similarity to the full-length mitochondrial sequence of the Chinese rufous horseshoe bat ( Rhinolophus sinicus ), an unlikely event since a complete assembly of such a sequence is typically interrupted by stop codons. (news-medical.net)

However, storage of the raw sequence data can become prohibitively large, and computing consensus genome from sequence data can be slow and requires bioinformatics expertise. (niema.net)
Áine has been setting up the bioinformatics system to allow the automated and efficient analysis of the huge amounts sequence data generated by the project. (ed.ac.uk)
Dr. Jonathan Jacobs leads ATCC's Sequencing & Bioinformatics Center and the development of the ATCC Genome Portal. (atcc.org)

From the results of Southern blot hybridization, it appeared that HPV-16 DNA had been integrated into the genome of the host cell in cervical cancer. (nih.gov)

This link shows a sample mRNA sequence from the Mammalian Genome Collection. (nih.gov)

Abstract Targeted metagenomics using strand-specific libraries with target enrichment is a sensitive, generalized approach to pathogen sequencing and transcriptome profiling. (ox.ac.uk)

In the background, whiteheads are unique viral particles of HBV that together look like hundreds of stars. (pasteur.fr)
The aim of our research is to use this protein to produce viral particles containing the nuclease so that we can pursue a "Trojan horse" approach," continues Jean-Pierre Vartanian. (pasteur.fr)
These particles will target infected liver cells, inducing degradation of the viral and cellular DNA found in them. (pasteur.fr)
Four tested doses, negligible (10 − 1 viral genome copies), low (10 4 ), high (10 7 ) and very high (10 11 ) were quantified using a method combining density gradient centrifugation of the viral particles and an RT-qPCR technique developed to quantify genomic RNA (gRNA). (biomedcentral.com)
Determining the minimum dose of viral particles required to cause mortality in rabbits is an important input for in vivo studies. (biomedcentral.com)
Genetic analysis also showed that only snippets of DNA from the new strain, called PoxSib, remained and that no intact viral particles had survived. (latimes.com)

Each genome entry is provided with sequencing and assembly quality metrics, annotation metrics, and additional metadata for each strain such as antibiotic susceptibility, geographical origins, and phenotypic data. (atcc.org)
The NCBI Entrez Genome Project database is intended to be a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. (lu.se)

To investigate how LINE-1s influence human glioma, we will generate a transcriptomic and epigenomic atlas of LINE-1s in glioma resections at single-cell resolution, by combining multi-omics and long-read sequencing with unique bioinformatic tools. (lu.se)

Gastroenteritis Branch in the Division of Viral Diseases at the Centers for Disease Control and Prevention. (cdc.gov)
For the future direction, we need the in-depth genome sequence information and analysis for most of the mammals, including human to fully understand genome variation of economic traits, genetic susceptibility to diseases, and pharmacogenomics of drug response. (springer.com)
The experience, resources, and innovative capacity of this group will all be necessary to fully address the significant gaps that remain in our understanding and ability to respond to the ongoing threat posed by viral diseases. (broadinstitute.org)

Possible roles of endogenous plant viral sequences. (cambridge.org)
Staginnus C, Richert-Pöggeler KR (2006) Endogenous pararetroviruses: two-faced travelers in the plant genome. (cambridge.org)
The sequencing of the human genome revealed that at least 1% of the human genome consists of endogenous retroviral sequences, representing past encounters with retroviruses during the course of human evolution. (msdmanuals.com)

The ATCC Genome Portal and the data contained therein is freely available for research-use and is accessible online ( https://genomes.atcc.org ) or via an authenticated REST-API. (atcc.org)
The scientists assembled the viral genome from scratch, performed a metagenomic analysis, and looked at data quality. (news-medical.net)
They concluded that the RaTG13 genome had serious issues and all data related to it required a full review. (news-medical.net)
The focus of the current paper is on the accuracy of the data on these sequences. (news-medical.net)
creating public data sets to enable the design of new interventions for viral disease. (broadinstitute.org)

Thus, this molecular approach will add incrementally to our current knowledge of the HEV-genome organization and pathogenesis in chronic hepatitis E. (nature.com)

It can be implemented for an array of lab- or field-based objectives, including among others: phylodynamic studies and the analysis of viral quasispecies. (frontiersin.org)
In a virology research environment, the study of viral quasispecies in infected patients is essential for understanding pathways to resistance and can substantially improve treatment. (biomedcentral.com)

To gain in-depth insights into the viral population and to perform detailed characterization of viral genomes, we used a new approach combining long-range PCR with next-generation and third-generation sequencing which allowed near full-length sequencing of HEV-3 genomes. (nature.com)
Deep-sequencing allows for an in-depth characterization of sequence variation in complex populations. (biomedcentral.com)

Using this new approach, we not only identified several insertions of human (AHNAK, RPL18) and viral origin (RdRp-derived) in the HVR-region isolated from an exemplary sample but detected a variant containing two different insertions simultaneously (AHNAK- and RdRp-derived). (nature.com)
Full fore early 2012, suggesting the human diversity is the result genomes from 2 epidemiologically unlinked novel CoV in- of multiple zoonotic events. (cdc.gov)
Year 2011 is celebrated as the 10th anniversary since the human genome was first sequenced ( www.nature.com/natureconferences/hg10years/index.html ). (springer.com)
For example, you will find all information regarding the human genome project on this project page. (lu.se)
A large portion of our genetic information is stored in TEs, viral-like sequences that make up around 50% of the human genome. (lu.se)

Classification of the MPXV genomes and determination of their mutational patterns were performed using Nextclade. (bvsalud.org)
Genome-wide mutational landscape of mucinous carcinomatosis peritonei of appendiceal origin. (genomeweb.com)

With the development of various next-generation sequencing platforms, there has been a substantial reduction in costs, and increase in throughput of DNA sequencing. (wikipedia.org)

SARS-CoV-2 has spread with the evolution of its viral genome since its emergence in late 2019. (medrxiv.org)

When the DNA hairpin is unzipped into single-strand, oligonucleotides complementary to the hairpin sequence are allowed to hybridize. (wikipedia.org)

Though NEB does not offer a kit specifically designed for viral RNA extraction, both the Monarch Total RNA Miniprep Kit and the Monarch RNA Cleanup Kits have been used successfully to extract total RNA, including viral RNA, from clinically-relevant samples. (neb.com)

2003 ). The NHGRI has categorized new sequencing approaches into those that offer near-term and revolutionary benefits with a 100-fold cost reduction per base pair (bp) within the next five years. (springer.com)

Following duplication events, the resulting stretches of homologous sequence can promote recombination between gene copies. (elifesciences.org)
Turturo C, Friscina A, Gaubert S, Jacquemond M, Thompson JR, Tepfer M (in press) Evaluation of the potential risks associated with recombination in transgenic plants expressing viral sequences. (cambridge.org)

From a dataset of 1 million trimmed mapped SARS-CoV-2 reads, it is able to compute the base counts and the consensus genome in 16 minutes, store the reads alongside the base counts and consensus in 50 MB, and optionally store just the base counts and consensus (without the reads) in 300 KB. (niema.net)
Secondly, non-adapter-related repetitive sequences were found in most reads, often at the same end of the read, comprising one G-quadruplex sequence and its reverse complement. (news-medical.net)

With increased sequencing cycle, the signal of the lagging molecules will eventually overwhelm the true signal. (wikipedia.org)
This not only shortens the preparation time for the sequencing libraries, it also has the potential to achieve much longer read lengths, as the lagging molecules with failed extensions can be ignored or considered separately. (wikipedia.org)

Retroviruses use reverse transcription to create a double-stranded DNA copy (a provirus) of their RNA genome, which is inserted into the genome of their host cell. (msdmanuals.com)

One UB research team is aiding this objective by sequencing the viral genome from patient samples in Western New York. (buffalo.edu)

Anatomy11

Organisms21

Diseases4

Chemicals and Drugs43

Analytical, Diagnostic and Therapeutic Techniques and Equipment41

Phenomena and Processes140

Disciplines and Occupations5

Technology, Industry, Agriculture3

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Health Care7

Mutations19

Variants9

Illumina8

Nucleotide5

20222

Genes3

Genomics11

Strains5

Infection9

Nanopore4

20203

Single-stranded RNA genome2

Bacterial1

Genetics1

Amplification5

Researchers7

Replication4

Proteins1

Nucleic2

CDNA libraries1

Detection7

Hemorrhagic fever1

Viruses4

Genomic Sequence1

Nucleotides4

20002

Virus14

Laboratory3

High throughput3

Sanger1

Clinical1

Mitochondrial1

Bioinformatics3

Cervical cancer1

MRNA1

Transcriptome1

Particles6

Annotation2

Bioinformatic1

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Endogenous3

Data5

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Human5

Mutational2

Platforms1

Emergence1

Complementary1

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Approaches1

Recombination2

Reads2

Molecules2

Double-stranded1

RESEARCH1