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    Home > Active Ingredient News > Infection > Scientific Reports: The use of a new generation of base sequence analysis method "long read sequencing" for the new coronavirus will greatly reduce time and cost

    Scientific Reports: The use of a new generation of base sequence analysis method "long read sequencing" for the new coronavirus will greatly reduce time and cost

    • Last Update: 2021-07-29
    • Source: Internet
    • Author: User
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    Recently, the research team of the University of Southern California (USC) School of Medicine SungYong Park and others have developed a faster and more accurate new coronavirus pneumonia ( COVID-19 ) gene analysis (sequence) technology
    .
    This result was published in "Scientific Reports".
    The article introduced the new generation of base sequence analysis method "long-read sequencing" as a whole to analyze the
    new coronavirus pneumonia virus, which has attracted the attention of the academic community
    .

    COVID-19 New Coronary Pneumonia

    Amino acid mutations, clades and lineage NP/OP specimens of 25 whole-genome sequences from COVID-19 remnants

    Amino acid mutations, clades and lineage NP/OP specimens of 25 whole-genome sequences from COVID-19 remnants

    The study, using this technology, successfully analyzed the base sequences of the viral genes of 25 people infected with the new coronavirus in Los Angeles, California, the United States from April to June last year
    .
    Previously, "short-read sequencing" was used to subdivide the new coronavirus gene into about 100 and analyze it, and then grasp the true face of the virus and whether it has mutated or not
    .
    On the contrary, the research team divided the gene into three parts for analysis, which greatly reduced the time and cost

    .
    There are expectations that it will shorten the sequencing time, which previously took about 10 days, to within a few days

    .

    Before


    infection , “short-read sequencing” is used to subdivide the new coronavirus genes into about 100 and analyze them, and then grasp the true face of the virus and whether it has mutated or not .
    On the contrary, the research team divided the gene into three parts for analysis, which greatly reduced the time and cost .
    There are expectations that it will shorten the sequencing time, which previously took about 10 days, to within a few days .
    Previously, "short-read sequencing" was used to subdivide the new coronavirus gene into about 100 and analyze it, and then grasp the true face of the virus and whether it has mutated or not
    .
    On the contrary, the research team divided the gene into three parts for analysis, which greatly reduced the time and cost

    .
    There are expectations that it will shorten the sequencing time, which previously took about 10 days, to within a few days

    .

    The estimated low sequencing cost shows a cost advantage compared with the current SARS-CoV-2 whole-genome sequencing method based on short read lengths
    .
    For samples, the time required for CorvGenSurv is approximately 15 hours for library preparation and 30 hours for sequencing
    .
    Therefore, our cost-effective workflow may enhance the implementation of real-time large-scale genomic SARS-CoV-2 monitoring
    .

    For samples, the time required for CorvGenSurv is approximately 15 hours for library preparation and 30 hours for sequencing
    .
    For samples, the time required for CorvGenSurv is approximately 15 hours for library preparation and 30 hours for sequencing
    .

    The team developed this high-precision, cost-effective SARS-CoV-2 whole-genome sequencing platform for COVID-19 genome monitoring, called CorvGenSurv (coronavirus genome monitoring)
    .
    CorvGenSurv directly amplifies nasopharyngeal/oropharyngeal (NP/OP) swab specimens from patients with viral RNA from COVID-19 and sequenced SARS-CoV-2.
    Through long-read, high-throughput sequencing, the entire gene component is divided into three Fragments

    .
    Sequencing the three-segment whole genome significantly reduces the waste of sequencing data, thereby preventing the decline in genome coverage

    .
    We verified the accuracy of RNA sequencing and Sanger sequencing of our pipeline by controlling the genome

    .
    Research on these samples found that these sequences are highly diversified in the G clade, with nine new amino acid mutations including NSP12-M755I and ORF8-V117F

    .
    With its easily adaptable design, CorvGenSurv

    grants a wide range of genomic monitoring opportunities, allowing immediate response to threats of public health emergencies
    .


    After the outbreak of the new crown pneumonia virus, the World Health Organization (WHO) has been urging countries to speed up the sequencing of the new crown virus
    .
    However, judging from existing methods, the average global sequencing rate is only over 1%, which has limitations in dealing with unprecedented pandemics

    .
    Some observations believe that with this in mind, this research will make a huge contribution to the end of the new coronavirus

    .
    In particular, among the genes analyzed by the research team, there are delta mutations and beta mutations that have recently spread rapidly, so the research on mutant viruses will also play a considerable role

    .




     

    Reference materials: Park, SY, Faraci, G.
    , Ward, PM 
    et al.
     High-precision and cost-efficient sequencing for real-time COVID-19 surveillance.
     
    Sci Rep 11,  13669 (2021).
    https://doi.
    org/10.
    1038/s41598-021-93145-4
     

    Park, SY, Faraci, G.
    , Ward, PM 
    et al.
     High-precision and cost-efficient sequencing for real-time COVID-19 surveillance.
     
    Sci Rep 11,  13669 (2021).
    https://doi.
    org/10.
    1038 /s41598-021-93145-4
    https://doi.
    org/10.
    1038/s41598-021-93145-4
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